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Bhattarai P, Gunasekaran TI, Belloy ME, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Turgutalp B, Sukumar G, Alba C, McGrath EM, Hupalo DN, Bacikova D, Le Guen Y, Lantigua R, Medrano M, Rivera D, Recio P, Nuriel T, Ertekin-Taner N, Teich AF, Dickson DW, Holley S, Greicius M, Dalgard CL, Zody M, Mayeux R, Kizil C, Vardarajan BN. Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease. Acta Neuropathol 2024; 147:70. [PMID: 38598053 PMCID: PMC11006751 DOI: 10.1007/s00401-024-02721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEε4 allele. Elderly cognitively healthy individuals with APOEε4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEε4; however, these mechanisms are unknown. We hypothesized that APOEε4 carriers without dementia might carry genetic variations that could protect them from developing APOEε4-mediated AD pathology. To test this, we leveraged whole-genome sequencing (WGS) data in the National Institute on Aging Alzheimer's Disease Family Based Study (NIA-AD FBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEε4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain (COL6A2) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. An independent analysis in a large cohort of 7185 APOEε4 homozygous carriers found that rs140926439 variant in FN1 was protective of AD (OR = 0.29; 95% CI [0.11, 0.78], P = 0.014) and delayed age at onset of disease by 3.37 years (95% CI [0.42, 6.32], P = 0.025). The FN1 and COL6A2 protein levels were increased at the BBB in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4-mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b-the ortholog for human FN1. We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling, and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEε4, and LOF variants in FN1 may reduce APOEε4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.
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Affiliation(s)
- Prabesh Bhattarai
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Tamil Iniyan Gunasekaran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Dolly Reyes-Dumeyer
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Dörthe Jülich
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Hüseyin Tayran
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Elanur Yilmaz
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Delaney Flaherty
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Bengisu Turgutalp
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Camille Alba
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Elisa Martinez McGrath
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Daniel N Hupalo
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Dagmar Bacikova
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rafael Lantigua
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University New York, New York, USA
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | - Diones Rivera
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
- School of Medicine, Universidad Pedro Henriquez Urena (UNPHU), Santo Domingo, Dominican Republic
| | - Patricia Recio
- Department of Neurology, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
| | - Tal Nuriel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Andrew F Teich
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA
| | - Scott Holley
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Michael Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The American Genome Center, Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael Zody
- New York Genome Center, New York, NY, 10013, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, NY, 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 W 168th St., New York, NY, 10032, USA
| | - Caghan Kizil
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Badri N Vardarajan
- Department of Neurology, Columbia University Irving Medical Center, Columbia University New York, New York, NY, USA.
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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2
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. Cell Genom 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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3
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Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:68. [PMID: 38480868 PMCID: PMC10937683 DOI: 10.1038/s41698-024-00519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024] Open
Abstract
We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.
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Grants
- HU0001-16-2-0006 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-19-2-0031 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-20-2-0033 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-18-2-0032 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-18-2-0032 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- 1092856, 1117044, 2008781, and 1186505 Department of Health | National Health and Medical Research Council (NHMRC)
- 1092856, 1117044 and 2008781 Department of Health | National Health and Medical Research Council (NHMRC)
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
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4
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Schobel SA, Gann ER, Unselt D, Grey SF, Lisboa FA, Upadhyay MM, Rouse M, Tallowin S, Be NA, Zhang X, Dalgard CL, Wilkerson MD, Hauskrecht M, Badylak SF, Zamora R, Vodovotz Y, Potter BK, Davis TA, Elster EA. The influence of microbial colonization on inflammatory versus pro-healing trajectories in combat extremity wounds. Sci Rep 2024; 14:5006. [PMID: 38438404 PMCID: PMC10912443 DOI: 10.1038/s41598-024-52479-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/19/2024] [Indexed: 03/06/2024] Open
Abstract
A combination of improved body armor, medical transportation, and treatment has led to the increased survival of warfighters from combat extremity injuries predominantly caused by blasts in modern conflicts. Despite advances, a high rate of complications such as wound infections, wound failure, amputations, and a decreased quality of life exist. To study the molecular underpinnings of wound failure, wound tissue biopsies from combat extremity injuries had RNA extracted and sequenced. Wounds were classified by colonization (colonized vs. non-colonized) and outcome (healed vs. failed) status. Differences in gene expression were investigated between timepoints at a gene level, and longitudinally by multi-gene networks, inferred proportions of immune cells, and expression of healing-related functions. Differences between wound outcomes in colonized wounds were more apparent than in non-colonized wounds. Colonized/healed wounds appeared able to mount an adaptive immune response to infection and progress beyond the inflammatory stage of healing, while colonized/failed wounds did not. Although, both colonized and non-colonized failed wounds showed increasing inferred immune and inflammatory programs, non-colonized/failed wounds progressed beyond the inflammatory stage, suggesting different mechanisms of failure dependent on colonization status. Overall, these data reveal gene expression profile differences in healing wounds that may be utilized to improve clinical treatment paradigms.
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Affiliation(s)
- Seth A Schobel
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Eric R Gann
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Desiree Unselt
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Q2 Solutions, Durham, NC, USA
| | - Scott F Grey
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Felipe A Lisboa
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Meenu M Upadhyay
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
| | - Michael Rouse
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Simon Tallowin
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Academic Department of Military Surgery and Trauma, Royal Centre for Defence Medicine, Birmingham, UK
| | - Nicholas A Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Xijun Zhang
- Uniformed Services University (USU) The American Genome Center (TAGC), Bethesda, MD, USA
| | - Clifton L Dalgard
- Uniformed Services University (USU) The American Genome Center (TAGC), Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- Uniformed Services University (USU) The American Genome Center (TAGC), Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Milos Hauskrecht
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen F Badylak
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ruben Zamora
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Benjamin K Potter
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Thomas A Davis
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Eric A Elster
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Uniformed Services University (USU) Surgical Critical Care Initiative (SC2i), Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
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5
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Bayram E, Reho P, Litvan I, Ding J, Gibbs JR, Dalgard CL, Traynor BJ, Scholz SW, Chia R. Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci. NPJ Parkinsons Dis 2024; 10:39. [PMID: 38378815 PMCID: PMC10879525 DOI: 10.1038/s41531-024-00649-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Sex influences the prevalence and symptoms of Lewy body dementia (LBD). However, genome-wide association studies typically focus on autosomal variants and exclude sex-specific risk factors. We addressed this gap by performing an X chromosome-wide association study using whole-genome sequence data from 2591 LBD cases and 4391 controls. We identified a significant risk locus within intron 1 of MAP3K15 (rs141773145, odds ratio = 2.42, 95% confidence interval = 1.65-3.56, p-value = 7.0 × 10-6) in female LBD cases conditioned for APOE ε4 dosage. The locus includes an enhancer region that regulates MAP3K15 expression in ganglionic eminence cells derived from primary cultured neurospheres. Rare variant burden testing showed differential enrichment of missense mutations in TEX13A in female LBD cases, that did not reach significance (p-value = 1.34 × 10-4). These findings support the sex-specific effects of genetic factors and a potential role of Alzheimer's-related risk for females with LBD.
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Affiliation(s)
- Ece Bayram
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Irene Litvan
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Therapeutics Development Laboratory, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA.
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6
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Liu D, Billington CJ, Raja N, Wong ZC, Levin MD, Resch W, Alba C, Hupalo DN, Biamino E, Bedeschi MF, Digilio MC, Squeo GM, Villa R, Parrish PCR, Knutsen RH, Osgood S, Freeman JA, Dalgard CL, Merla G, Pober BR, Mervis CB, Roberts AE, Morris CA, Osborne LR, Kozel BA. Matrisome and Immune Pathways Contribute to Extreme Vascular Outcomes in Williams-Beuren Syndrome. J Am Heart Assoc 2024; 13:e031377. [PMID: 38293922 DOI: 10.1161/jaha.123.031377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/28/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND Supravalvar aortic stenosis (SVAS) is a characteristic feature of Williams-Beuren syndrome (WBS). Its severity varies: ~20% of people with Williams-Beuren syndrome have SVAS requiring surgical intervention, whereas ~35% have no appreciable SVAS. The remaining individuals have SVAS of intermediate severity. Little is known about genetic modifiers that contribute to this variability. METHODS AND RESULTS We performed genome sequencing on 473 individuals with Williams-Beuren syndrome and developed strategies for modifier discovery in this rare disease population. Approaches include extreme phenotyping and nonsynonymous variant prioritization, followed by gene set enrichment and pathway-level association tests. We next used GTEx v8 and proteomic data sets to verify expression of candidate modifiers in relevant tissues. Finally, we evaluated overlap between the genes/pathways identified here and those ascertained through larger aortic disease/trait genome-wide association studies. We show that SVAS severity in Williams-Beuren syndrome is associated with increased frequency of common and rarer variants in matrisome and immune pathways. Two implicated matrisome genes (ACAN and LTBP4) were uniquely expressed in the aorta. Many genes in the identified pathways were previously reported in genome-wide association studies for aneurysm, bicuspid aortic valve, or aortic size. CONCLUSIONS Smaller sample sizes in rare disease studies necessitate new approaches to detect modifiers. Our strategies identified variation in matrisome and immune pathways that are associated with SVAS severity. These findings suggest that, like other aortopathies, SVAS may be influenced by the balance of synthesis and degradation of matrisome proteins. Leveraging multiomic data and results from larger aorta-focused genome-wide association studies may accelerate modifier discovery for rare aortopathies like SVAS.
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Affiliation(s)
- Delong Liu
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Charles J Billington
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
- Department of Pediatrics University of Minnesota Minneapolis MN
| | - Neelam Raja
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Zoe C Wong
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Mark D Levin
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Wulfgang Resch
- The High Performance Computing Facility Center for Information Technology, National Institutes of Health Bethesda MD
| | - Camille Alba
- Henry M Jackson Foundation for the Advancement of Military Medicine Bethesda MD
| | - Daniel N Hupalo
- Henry M Jackson Foundation for the Advancement of Military Medicine Bethesda MD
| | | | | | | | - Gabriella Maria Squeo
- Laboratory of Regulatory and Functional Genomics Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo (Foggia) Italy
| | - Roberta Villa
- Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico Medical Genetic Unit Milan Italy
| | - Pheobe C R Parrish
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
- Department of Genome Sciences University of Washington Seattle WA
| | - Russell H Knutsen
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Sharon Osgood
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Joy A Freeman
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, School of Medicine the Uniformed Services University of the Health Sciences Bethesda MD
| | - Giuseppe Merla
- Laboratory of Regulatory and Functional Genomics Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo (Foggia) Italy
- Department of Molecular Medicine and Medical Biotechnology University of Naples Federico II Naples Italy
| | - Barbara R Pober
- Section of Genetics, Department of Pediatrics Massachusetts General Hospital Boston MA
| | - Carolyn B Mervis
- Department of Psychological and Brain Sciences University of Louisville Louisville KY
| | - Amy E Roberts
- Department of Cardiology and Division of Genetics and Genomics, Department of Pediatrics Boston Children's Hospital Boston MA
| | - Colleen A Morris
- Department of Pediatrics Kirk Kerkorian School of Medicine at UNLV Las Vegas NV
| | - Lucy R Osborne
- Departments of Medicine and Molecular Genetics University of Toronto Canada
| | - Beth A Kozel
- National Heart, Lung, and Blood Institute National Institutes of Health Bethesda MD
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7
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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, Zein LE, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Correction: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2024; 16:6. [PMID: 38184654 PMCID: PMC10771638 DOI: 10.1186/s13073-023-01278-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024] Open
Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Anesthesiology and Critical Care Medicine Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, School of Microbiology, University of Antioquia UdeA, Medellin, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- MNM Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Département d'immunologie, INSERM Centre d'Immunologie Et Des Maladies Infectieuses CIMI-Paris, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Florence Tubach
- Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Institut Pierre Louis d'Epidémiologie Et de Santé Publique, INSERM, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1166, IHU ICAN, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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8
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Delmonte OM, Oguz C, Dobbs K, Myint-Hpu K, Palterer B, Abers MS, Draper D, Truong M, Kaplan IM, Gittelman RM, Zhang Y, Rosen LB, Snow AL, Dalgard CL, Burbelo PD, Imberti L, Sottini A, Quiros-Roldan E, Castelli F, Rossi C, Brugnoni D, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Anderson MV, Saracino A, Chironna M, Di Stefano M, Fiore JR, Santantonio T, Castagnoli R, Marseglia GL, Magliocco M, Bosticardo M, Pala F, Shaw E, Matthews H, Weber SE, Xirasagar S, Barnett J, Oler AJ, Dimitrova D, Bergerson JRE, McDermott DH, Rao VK, Murphy PM, Holland SM, Lisco A, Su HC, Lionakis MS, Cohen JI, Freeman AF, Snyder TM, Lack J, Notarangelo LD. Perturbations of the T-cell receptor repertoire in response to SARS-CoV-2 in immunocompetent and immunocompromised individuals. J Allergy Clin Immunol 2023:S0091-6749(23)02544-7. [PMID: 38154666 DOI: 10.1016/j.jaci.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Functional T-cell responses are essential for virus clearance and long-term protection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas certain clinical factors, such as older age and immunocompromise, are associated with worse outcome. OBJECTIVE We sought to study the breadth and magnitude of T-cell responses in patients with coronavirus disease 2019 (COVID-19) and in individuals with inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine. METHODS Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. RESULTS Our analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. CONCLUSIONS Elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
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Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Boaz Palterer
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew L Snow
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md; Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Md; The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Peter D Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Md
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Alessandra Sottini
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili, Brescia, Italy
| | - Duilio Brugnoni
- Laboratorio Analisi Chimico-Cliniche, ASST Spedali Civili, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Megan V Anderson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari, Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Mariantonietta Di Stefano
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Jose Ramon Fiore
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Teresa Santantonio
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Riccardo Castagnoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sarah E Weber
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jason Barnett
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dimana Dimitrova
- Center for Immuno-Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | - Justin Lack
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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9
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Scholz SW, Moroz BE, Saez-Atienzar S, Chia R, Cahoon EK, Dalgard CL, Freedman DM, Pfeiffer RM. Association of cardiovascular disease management drugs with Lewy body dementia: a case-control study. Brain Commun 2023; 6:fcad346. [PMID: 38162907 PMCID: PMC10754316 DOI: 10.1093/braincomms/fcad346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/04/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Lewy body dementia is the second most common neurodegenerative dementia after Alzheimer's disease. Disease-modifying therapies for this disabling neuropsychiatric condition are critically needed. To identify drugs associated with the risk of developing Lewy body dementia, we performed a population-based case-control study of 148 170 US Medicare participants diagnosed with Lewy body dementia between 1 January 2008 and 31 December 2014 and of 1 253 043 frequency-matched controls. We estimated odds ratios and 95% confidence intervals for the association of Lewy body dementia risk with 1017 prescription drugs overall and separately for the three major racial groups (Black, Hispanic and White Americans). We identified significantly reduced Lewy body dementia risk associated with drugs used to treat cardiovascular diseases (anti-hypertensives: odds ratio = 0.72, 95% confidence interval = 0.70-0.74, P-value = 0; cholesterol-lowering agents: odds ratio = 0.85, 95% confidence interval = 0.83-0.87, P-value = 0; anti-diabetics: odds ratio = 0.83, 95% confidence interval = 0.62-0.72, P-value = 0). Notably, anti-diabetic medications were associated with a larger risk reduction among Black Lewy body dementia patients compared with other racial groups (Black: odds ratio = 0.67, 95% confidence interval = 0.62-0.72, P-value = 0; Hispanic: odds ratio = 0.86, 95% = 0.80-0.92, P-value = 5.16 × 10-5; White: odds ratio = 0.85, 95% confidence interval = 0.82-0.88, P-value = 0). To independently confirm the epidemiological findings, we looked for evidence of genetic overlap between Lewy body dementia and cardiovascular traits using whole-genome sequence data generated for 2591 Lewy body dementia patients and 4027 controls. Bivariate mixed modelling identified shared genetic risk between Lewy body dementia and low-density lipoprotein cholesterol levels, Type 2 diabetes and hypertension. By combining epidemiological and genomic data, we demonstrated that drugs treating cardiovascular diseases are associated with reduced Lewy body dementia risk, and these associations varied across racial groups. Future randomized clinical trials need to confirm our findings, but our data suggest that assiduous management of cardiovascular diseases may be beneficial in this understudied form of dementia.
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Affiliation(s)
- Sonja W Scholz
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian E Moroz
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sara Saez-Atienzar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Elizabeth K Cahoon
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Daryl Michal Freedman
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between HLA and asymptomatic SARS-CoV-2 infection. medRxiv 2023:2023.12.06.23299623. [PMID: 38168184 PMCID: PMC10760282 DOI: 10.1101/2023.12.06.23299623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ryan S. Thwaites
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | | | | | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands, EU
| | - Justin B. Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France, EU
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- Epidémiologie clinique du Centre d’Investigation Clinique (CIC-EP), INSERM CIC 1425, Hôpital Bichat, 75018 Paris, France, EU
- Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France, EU
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d’immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France, EU
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Paris, France, EU
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France, EU
- GRC-14 BIOFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France, EU
| | | | | | | | | | | | | | | | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J. Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
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11
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Chen G, Calcaterra F, Ma Y, Ping X, Pontarini E, Yang D, Oriolo F, Yu Z, Cancellara A, Mikulak J, Huang Y, Della Bella S, Liu Y, Biesecker LG, Harper RL, Dalgard CL, Boehm M, Mavilio D. Derived myeloid lineage induced pluripotent stem as a platform to study human C-C chemokine receptor type 5Δ32 homozygotes. iScience 2023; 26:108331. [PMID: 38026202 PMCID: PMC10663745 DOI: 10.1016/j.isci.2023.108331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
The C-C chemokine receptor type 5 (CCR5) expressed on immune cells supports inflammatory responses by directing cells to the inflammation site. CCR5 is also a major coreceptor for macrophage tropic human immunodeficiency viruses (R5-HIV-1) and its variants can confer protection from HIV infection, making it an ideal candidate to target for therapy. We developed a stepwise protocol that differentiates induced pluripotent stem cells (iPSCs) from individuals homozygous for the CCR5Δ32 variant and healthy volunteers into myeloid lineage induced monocytes (iMono) and macrophages (iMac). By characterizing iMono and iMac against their primary counterparts, we demonstrated that CCR5Δ32 homozygous cells are endowed with similar pluripotent potential for self-renewal and differentiation as iPSC lines generated from non-variant individuals while also showing resistance to HIV infection. In conclusion, these cells are a platform to investigate CCR5 pathophysiology in HIV-positive and negative individuals and to help develop novel therapies.
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Affiliation(s)
- Guibin Chen
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Calcaterra
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Yuchi Ma
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xianfeng Ping
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Elena Pontarini
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, London, England, UK
| | - Dan Yang
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ferdinando Oriolo
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Zhen Yu
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Assunta Cancellara
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Joanna Mikulak
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Yuting Huang
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Silvia Della Bella
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
| | - Yangtengyu Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Leslie G. Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca L. Harper
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA
| | - Manfred Boehm
- Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
- Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, 20054 Segrate, Italy
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12
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Makarious MB, Lake J, Pitz V, Ye Fu A, Guidubaldi JL, Solsberg CW, Bandres-Ciga S, Leonard HL, Kim JJ, Billingsley KJ, Grenn FP, Jerez PA, Alvarado CX, Iwaki H, Ta M, Vitale D, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Real R, Morris HR, Ding J, Gibbs JR, Singleton AB, Nalls MA, Bhangale T, Blauwendraat C. Large-scale rare variant burden testing in Parkinson's disease. Brain 2023; 146:4622-4632. [PMID: 37348876 PMCID: PMC10629770 DOI: 10.1093/brain/awad214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson's disease. To address this gap, we investigated the rare genetic component of Parkinson's disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson's disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson's disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson's disease. To date, this is the largest analysis of rare genetic variants in Parkinson's disease.
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Affiliation(s)
- Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Vanessa Pitz
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Allen Ye Fu
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph L Guidubaldi
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Caroline Warly Solsberg
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
- Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Jonggeol Jeffrey Kim
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Michael Ta
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dan Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Debra J Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
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13
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André MR, Ikeda P, Lee DAB, do Amaral RB, Carvalho LAL, Pinheiro DG, Torres JM, de Mello VVC, Rice GK, Cer RZ, Lourenço EC, Oliveira CE, Herrera HM, Barros-Battesti DM, Machado RZ, Bishop-Lilly KA, Dalgard CL, Dumler JS. Characterization of the bacterial microbiome of non-hematophagous bats and associated ectoparasites from Brazil. Front Microbiol 2023; 14:1261156. [PMID: 37928691 PMCID: PMC10620512 DOI: 10.3389/fmicb.2023.1261156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil. Methods Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n = 9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing. Results The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella). Discussion and conclusion Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.
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Affiliation(s)
- Marcos Rogério André
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Priscila Ikeda
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Antônio Braga Lee
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Renan Bressianini do Amaral
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Lucas Amoroso Lopes Carvalho
- Departamento de Biotecnologia Ambiental e Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Guariz Pinheiro
- Departamento de Biotecnologia Ambiental e Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Jaire Marinho Torres
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Victória Valente Califre de Mello
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Gregory K. Rice
- Leidos, Inc., Reston, VA, United States
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | - Regina Z. Cer
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | | | - Carisa Elisei Oliveira
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Heitor Miraglia Herrera
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Darci Moraes Barros-Battesti
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Rosangela Zacarias Machado
- Vector-Borne Bioagents Laboratory (VBBL), Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brazil
| | - Kimberly A. Bishop-Lilly
- Department of Genomics and Bioinformatics, Naval Medical Research Command, Fort Detrick, Frederick, MD, United States
| | - Clifton L. Dalgard
- The American Genome Center, Center for Military Precision Health and Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - J. Stephen Dumler
- Department of Pathology, University of the Health Sciences, Bethesda, MD, United States
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14
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Bauman BM, Dorjbal B, Pittaluga S, Zhang Y, Niemela JE, Stoddard JL, Rosenzweig SD, Anderson R, Guilcher GMT, Auer I, Perrier R, Campbell M, Bhandal SK, Alba C, Sukumar G, Dalgard CL, Schelotto M, Wright NAM, Su HC, Snow AL. Subcutaneous panniculitis-like T-cell lymphoma in two unrelated individuals with BENTA disease. Clin Immunol 2023; 255:109732. [PMID: 37562721 PMCID: PMC10551883 DOI: 10.1016/j.clim.2023.109732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/12/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare primary cutaneous non-Hodgkin lymphoma involving CD8+ T cells, the genetic underpinnings of which remain incompletely understood. Here we report two unrelated patients with B cell Expansion with NF-κB and T cell Anergy (BENTA) disease and a novel presentation of SPTCL. Patient 1 presented early in life with recurrent infections and B cell lymphocytosis, linked to a novel gain-of-function (GOF) CARD11 mutation (p.Lys238del). He developed SPTCL-like lesions and membranoproliferative glomerulonephritis by age 2, treated successfully with cyclosporine. Patient 2 presented at 13 months with splenomegaly, lymphadenopathy, and SPTCL with evidence of hemophagocytic lymphohistiocytosis. Genetic analysis revealed two in cis germline GOF CARD11 variants (p.Glu121Asp/p.Gly126Ser). Autologous bone marrow transplant resulted in SPTCL remission despite persistent B cell lymphocytosis. These cases illuminate an unusual pathological manifestation for BENTA disease, suggesting that CARD11 GOF mutations can manifest in cutaneous CD4+and CD8+ T cell malignancies.
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Affiliation(s)
- Bradly M Bauman
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Batsukh Dorjbal
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; NIAID Clinical Genomics Program, National Institutes of Health, Bethesda, MD, USA
| | - Julie E Niemela
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Jennifer L Stoddard
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Ronald Anderson
- Department of Pediatrics, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Gregory M T Guilcher
- Department of Pediatrics, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Iwona Auer
- Alberta Precision Laboratories, University of Calgary, Calgary, AB, Canada
| | - Renee Perrier
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | | | | | - Camille Alba
- The American Genome Center, Precision Medicine Initiative for Military Medical Education and Research (PRIMER), Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gauthaman Sukumar
- The American Genome Center, Precision Medicine Initiative for Military Medical Education and Research (PRIMER), Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Precision Medicine Initiative for Military Medical Education and Research (PRIMER), Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Magdalena Schelotto
- Department of Pediatric Hematology and Oncology, Fundación Pérez Scremini, Hospital Pereira Rossell, Montevideo, Uruguay
| | - Nicola A M Wright
- Department of Pediatrics, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Helen C Su
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; NIAID Clinical Genomics Program, National Institutes of Health, Bethesda, MD, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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15
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Ao W, Kim HI, Tommarello D, Conrads KA, Hood BL, Litzi T, Abulez T, Teng PN, Dalgard CL, Zhang X, Wilkerson MD, Darcy KM, Tarney CM, Phippen NT, Bakkenist CJ, Maxwell GL, Conrads TP, Risinger JI, Bateman NW. Metronomic dosing of ovarian cancer cells with the ATR inhibitor AZD6738 leads to loss of CDC25A expression and resistance to ATRi treatment. Gynecol Oncol 2023; 177:60-71. [PMID: 37639904 DOI: 10.1016/j.ygyno.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/07/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE ATR kinase inhibitors promote cell killing by inducing replication stress and through potentiation of genotoxic agents in gynecologic cancer cells. To explore mechanisms of acquired resistance to ATRi in ovarian cancer, we characterized ATRi-resistant ovarian cancer cells generated by metronomic dosing with the clinical ATR inhibitor AZD6738. METHODS ATRi-resistant ovarian cancer cells (OVCAR3 and OV90) were generated by dosing with AZD6738 and assessed for sensitivity to Chk1i (LY2603618), PARPi (Olaparib) and combination with cisplatin or a CDK4/6 inhibitor (Palbociclib). Models were characterized by diverse methods including silencing CDC25A in OV90 cells and assessing impact on ATRi response. Serum proteomic analysis of ATRi-resistant OV90 xenografts was performed to identify circulating biomarker candidates of ATRi-resistance. RESULTS AZD6738-resistant cell lines are refractory to LY2603618, but not to Olaparib or combinations with cisplatin. Cell cycle analyses showed ATRi-resistant cells exhibit G1/S arrest following AZD6738 treatment. Accordingly, combination with Palbociclib confers resistance to AZD6738. AZD6738-resistant cells exhibit altered abundances of G1/S phase regulatory proteins, including loss of CDC25A in AZD6738-resistant OV90 cells. Silencing of CDC25A in OV90 cells confers resistance to AZD6738. Serum proteomics from AZD6738-resistant OV90 xenografts identified Vitamin D-Binding Protein (GC), Apolipoprotein E (APOE) and A1 (APOA1) as significantly elevated in AZD6738-resistant backgrounds. CONCLUSIONS We show that metronomic dosing of ovarian cancer cells with AZD6738 results in resistance to ATR/ Chk1 inhibitors, that loss of CDC25A expression represents a mechanism of resistance to ATRi treatment in ovarian cancer cells and identify several circulating biomarker candidates of CDC25A low, AZD6738-resistant ovarian cancer cells.
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Affiliation(s)
- Wei Ao
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Hong Im Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University Grand Rapids, MI, USA
| | - Domenic Tommarello
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Tracy Litzi
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Clifton L Dalgard
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xijun Zhang
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D Wilkerson
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Christopher J Bakkenist
- Departments of Radiation Biology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd. Falls Church, VA 22042, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd. Falls Church, VA 22042, USA
| | - John I Risinger
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University Grand Rapids, MI, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA.
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16
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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. bioRxiv 2023:2023.04.13.536694. [PMID: 37214860 PMCID: PMC10197727 DOI: 10.1101/2023.04.13.536694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics; The American Genome Center, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center For Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC Groningen, The Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
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17
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Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM. Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. Alzheimers Dement 2023; 19:3902-3915. [PMID: 37037656 PMCID: PMC10529851 DOI: 10.1002/alz.13075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in AD brains from APOE ε4/ε4 carriers. Chromatin accessibility differences could contribute to these expression changes. METHODS We performed single nuclei assays for transposase accessible chromatin sequencing from the frontal cortex of six ALA and six ELA AD brains, homozygous for local ancestry and APOE ε4. RESULTS Our results showed an increased chromatin accessibility at the APOE ε4 promoter area in ELA versus ALA astrocytes. This increased accessibility in ELA astrocytes extended genome wide. Genes with increased accessibility in ELA in astrocytes were enriched for synapsis, cholesterol processing, and astrocyte reactivity. DISCUSSION Our results suggest that increased chromatin accessibility of APOE ε4 in ELA astrocytes contributes to the observed elevated APOE ε4 expression, corresponding to the increased AD risk in ELA versus ALA APOE ε4/ε4 carriers.
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Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Maria DM. Muniz Moreno
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Margaret Flanagan
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Sandra Weintraub
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Changiz Geula
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Marla Gearing
- Goizueta Alzheimer’s Disease Research Center, Emory University, Atlanta, GA, USA, 15213
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA, 20814
- Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, MD, USA, 20817
- Department of Anatomy Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA, 20814
| | - Fulai Jin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA, 44106
| | - David A. Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA, 60612
| | - Theresa Schuck
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,19104
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Juan I. Young
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
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18
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Ray NR, Ayodele T, Jean-Francois M, Baez P, Fernandez V, Bradley J, Crane PK, Dalgard CL, Kuzma A, Nicaretta H, Sims R, Williams J, Cuccaro ML, Pericak-Vance MA, Mayeux R, Wang LS, Schellenberg GD, Cruchaga C, Beecham GW, Reitz C. The Early-Onset Alzheimer's Disease Whole-Genome Sequencing Project: Study design and methodology. Alzheimers Dement 2023; 19:4187-4195. [PMID: 37390458 PMCID: PMC10527497 DOI: 10.1002/alz.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
INTRODUCTION Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations, resulting in a lack of understanding of its molecular etiology. METHODS Whole-genome sequencing and harmonization of clinical, neuropathological, and biomarker data of over 5000 EOAD cases of diverse ancestries. RESULTS A publicly available genomics resource for EOAD with extensive harmonized phenotypes. Primary analysis will (1) identify novel EOAD risk loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. DISCUSSION This novel resource complements over 50,000 control and late-onset AD samples generated through the Alzheimer's Disease Sequencing Project (ADSP). The harmonized EOAD/ADSP joint call will be available through upcoming ADSP data releases and will allow for additional analyses across the full onset range. HIGHLIGHTS Sequencing efforts to identify genetic variants and pathways underlying Alzheimer's disease (AD) have largely focused on late-onset AD although early-onset AD (EOAD), accounting for ∼10% of cases, is largely unexplained by known mutations. This results in a significant lack of understanding of the molecular etiology of this devastating form of the disease. The Early-Onset Alzheimer's Disease Whole-genome Sequencing Project is a collaborative initiative to generate a large-scale genomics resource for early-onset Alzheimer's disease with extensive harmonized phenotype data. Primary analyses are designed to (1) identify novel EOAD risk and protective loci and druggable targets; (2) assess local-ancestry effects; (3) create EOAD prediction models; and (4) assess genetic overlap with cardiovascular and other traits. The harmonized genomic and phenotypic data from this initiative will be available through NIAGADS.
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Affiliation(s)
- Nicholas R. Ray
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Temitope Ayodele
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Penelope Baez
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
| | - Victoria Fernandez
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Joseph Bradley
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Paul K. Crane
- Division of General Internal Medicine, University of
Washington, Seattle, WA 98195, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics,
Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- The American Genome Center, Uniformed Services University
of the Health Sciences, Bethesda, MD 20814, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Heather Nicaretta
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Rebecca Sims
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Julie Williams
- UK Dementia Research Institute, Cardiff University,
Cardiff CF10 3AT, UK
- Division of Psychological Medicine and Clinical
Neurosciences, School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Richard Mayeux
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of
Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of
Medicine, Philadelphia, PA 19104, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Neurology and Genetics,
Washington University School of Medicine, St. Louis, MO 63130, USA
- Neurogenomics and Informatic (NGI) Center, Washington
University School of Medicine, St. Louis, MO 63130, USA
| | - Gary W. Beecham
- The John P. Hussman Institute for Human Genomics,
University of Miami, Miami, FL 33136, USA
- Dr. John T. MacDonald Foundation Department of Human
Genetics, University of Miami, Coral Gables, FL 33146, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New
York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY
10032, USA
- Department of Epidemiology, Columbia University, New York,
NY 10032, USA
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19
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Vazzana KM, Musolf AM, Bailey-Wilson JE, Hiraki LT, Silverman ED, Scott C, Dalgard CL, Hasni S, Deng Z, Kaplan MJ, Lewandowski LB. Transmission disequilibrium analysis of whole genome data in childhood-onset systemic lupus erythematosus. Genes Immun 2023; 24:200-206. [PMID: 37488248 PMCID: PMC10529982 DOI: 10.1038/s41435-023-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Childhood-onset systemic lupus erythematosus (cSLE) patients are unique, with hallmarks of Mendelian disorders (early-onset and severe disease) and thus are an ideal population for genetic investigation of SLE. In this study, we use the transmission disequilibrium test (TDT), a family-based genetic association analysis that employs robust methodology, to analyze whole genome sequencing data. We aim to identify novel genetic associations in an ancestrally diverse, international cSLE cohort. Forty-two cSLE patients and 84 unaffected parents from 3 countries underwent whole genome sequencing. First, we performed TDT with single nucleotide variant (SNV)-based (common variants) using PLINK 1.9, and gene-based (rare variants) analyses using Efficient and Parallelizable Association Container Toolbox (EPACTS) and rare variant TDT (rvTDT), which applies multiple gene-based burden tests adapted for TDT, including the burden of rare variants test. Applying the GWAS standard threshold (5.0 × 10-8) to common variants, our SNV-based analysis did not return any genome-wide significant SNVs. The rare variant gene-based TDT analysis identified many novel genes significantly enriched in cSLE patients, including HNRNPUL2, a DNA repair protein, and DNAH11, a ciliary movement protein, among others. Our approach identifies several novel SLE susceptibility genes in an ancestrally diverse childhood-onset lupus cohort.
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Affiliation(s)
- Kathleen M Vazzana
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Linda T Hiraki
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Earl D Silverman
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Christiaan Scott
- Paediatric Rheumatology, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa
| | - Clifton L Dalgard
- The American Genome Center, Department of Anatomy, Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Sarfaraz Hasni
- Clinical Program, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zuoming Deng
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura B Lewandowski
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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20
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Fiore JR, Di Stefano M, Oler A, Zhang Y, Gu J, Dalgard CL, Faleo G, Epling B, Notarangelo L, Lisco A, Santantonio TA. Lack of Evidence for a Role of ACE-2 Polymorphisms as a Bedside Clinical Prognostic Marker of COVID-19. Viruses 2023; 15:1448. [PMID: 37515136 PMCID: PMC10383962 DOI: 10.3390/v15071448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/03/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The novel SARS-CoV-2 coronavirus causes a severe respiratory syndrome referred to as coronavirus disease (COVID-19). The angiotensin-converting enzyme 2 (ACE-2) plays an important role as a cellular receptor for SARS-CoV-2 and is largely expressed in lungs, kidneys, heart and the gastrointestinal tract along with being shed in plasma. The ACE-2 gene and protein show a high level of genetic polymorphism, including simple nucleotide variation, transcriptional variation, post-transcriptional changes, and putative protein mutations that could interfere with the binding or entry of SARS-CoV-2 and affect tissue damage in lungs or other organs. Genetic polymorphisms can impact SARS-CoV-2 viral entry and COVID-19 severity. This single-center study evaluated the possible role of the main ACE-2 polymorphisms (rs143936283, rs2285666, rs41303171, rs35803318, and rs2106809) as potential prognostic markers in SARS-CoV-2-infected individuals. Frozen whole blood was used for DNA isolation and genomic DNA samples were sheared using the Covaris LE220 Focused-ultrasonicator for targeting a peak size of 410 bp. Whole-genome sequencing libraries were generated from fragmented DNA using the Illumina TruSeq DNA PCR-Free HT Library Preparation Kit and sequenced on an Illumina NovaSeq 6000. We did not identify any correlation between ACE-2 polymorphisms and COVID-19 prognosis, suggesting that the interpretation and clinical use of ACE-2 genetic polymorphisms in real-world clinical settings requires further experimental and clinical validation.
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Affiliation(s)
- Josè R Fiore
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Mariantonietta Di Stefano
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Andrew Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - Yu Zhang
- Immune Deficiency Genetics Disease Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease (NIAID), Division of Intramural Research (DIR), National Institutes of Health, Bethesda, MD 20892, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - Clifton L Dalgard
- Collaborative Health Initiative Research Program, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20892, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20892, USA
| | - Giuseppina Faleo
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Brian Epling
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - Luigi Notarangelo
- Immune Deficiency Genetics Disease Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease (NIAID), Division of Intramural Research (DIR), National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Lisco
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD 20892, USA
| | - Teresa A Santantonio
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
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21
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Kaivola K, Chia R, Ding J, Rasheed M, Fujita M, Menon V, Walton RL, Collins RL, Billingsley K, Brand H, Talkowski M, Zhao X, Dewan R, Stark A, Ray A, Solaiman S, Alvarez Jerez P, Malik L, Dawson TM, Rosenthal LS, Albert MS, Pletnikova O, Troncoso JC, Masellis M, Keith J, Black SE, Ferrucci L, Resnick SM, Tanaka T, Topol E, Torkamani A, Tienari P, Foroud TM, Ghetti B, Landers JE, Ryten M, Morris HR, Hardy JA, Mazzini L, D'Alfonso S, Moglia C, Calvo A, Serrano GE, Beach TG, Ferman T, Graff-Radford NR, Boeve BF, Wszolek ZK, Dickson DW, Chiò A, Bennett DA, De Jager PL, Ross OA, Dalgard CL, Gibbs JR, Traynor BJ, Scholz SW. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias. Cell Genom 2023; 3:100316. [PMID: 37388914 PMCID: PMC10300553 DOI: 10.1016/j.xgen.2023.100316] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 07/01/2023]
Abstract
We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.
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Affiliation(s)
- Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Memoona Rasheed
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Masashi Fujita
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Ronald L. Walton
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Ryan L. Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
| | - Ramita Dewan
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Ali Stark
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Anindita Ray
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sultana Solaiman
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Laksh Malik
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | - Ted M. Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan C. Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Mario Masellis
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
| | - Julia Keith
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Sandra E. Black
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Toshiko Tanaka
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
| | - PROSPECT Consortium
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T.), Cambridge, MA, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Centre for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pharmacology and Molecular Science, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, USA
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
- Cognitive & Movement Disorders Clinic, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- LC Campbell Cognitive Neurology Research Unit, Sunnybrook Research Institute, University of Toronto, 2075 Bayview Avenue, Toronto, ON, Canada
- Department of Anatomical Pathology, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Heart and Stroke Foundation Canadian Partnership for Stroke Recovery, Sunnybrook Health Sciences Centre, University of Toronto, 1 King’s College Circle, Room 2374, Toronto, ON, Canada
- Longitudinal Studies Section, National Institute on Aging, Baltimore, MD, USA
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Maggiore della Carita University Hospital, Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
- Center for Sleep Medicine, Mayo Clinic, Rochester, MN, USA
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Eric Topol
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Ali Torkamani
- Scripps Research Translational Institute, Scripps Research, La Jolla, CA, USA
| | - Pentti Tienari
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - John A. Hardy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- UK Dementia Research Institute, Department of Neurogenerative Disease and Reta Lila Weston Institute, London, UK
- Institute of Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Cristina Moglia
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Andrea Calvo
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
| | - Geidy E. Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G. Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Tanis Ferman
- Department of Psychiatry and Psychology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | | | | | - Zbigniew K. Wszolek
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, University of Turin, Turin, Italy
- Azienda Ospedaliero Universitaria Città, della Salute e della Scienza, Corso Bramante, 88, Turin, Italy
- Institute of Cognitive Sciences and Technologies, C.N.R., Via S. Martino della Battaglia, 44, Rome, Italy
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, New York, NY, USA
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- RNA Therapeutics Laboratory, Therapeutics Development Branch, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
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22
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Billingsley KJ, Ding J, Jerez PA, Illarionova A, Levine K, Grenn FP, Makarious MB, Moore A, Vitale D, Reed X, Hernandez D, Torkamani A, Ryten M, Hardy J, Chia R, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach T, Serrano GE, Quinn JP, Bubb VJ, Collins RL, Zhao X, Walker M, Pierce-Hoffman E, Brand H, Talkowski ME, Casey B, Cookson MR, Markham A, Nalls MA, Mahmoud M, Sedlazeck FJ, Blauwendraat C, Gibbs JR, Singleton AB. Genome-Wide Analysis of Structural Variants in Parkinson Disease. Ann Neurol 2023; 93:1012-1022. [PMID: 36695634 PMCID: PMC10192042 DOI: 10.1002/ana.26608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/03/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Identification of genetic risk factors for Parkinson disease (PD) has to date been primarily limited to the study of single nucleotide variants, which only represent a small fraction of the genetic variation in the human genome. Consequently, causal variants for most PD risk are not known. Here we focused on structural variants (SVs), which represent a major source of genetic variation in the human genome. We aimed to discover SVs associated with PD risk by performing the first large-scale characterization of SVs in PD. METHODS We leveraged a recently developed computational pipeline to detect and genotype SVs from 7,772 Illumina short-read whole genome sequencing samples. Using this set of SV variants, we performed a genome-wide association study using 2,585 cases and 2,779 controls and identified SVs associated with PD risk. Furthermore, to validate the presence of these variants, we generated a subset of matched whole-genome long-read sequencing data. RESULTS We genotyped and tested 3,154 common SVs, representing over 412 million nucleotides of previously uncatalogued genetic variation. Using long-read sequencing data, we validated the presence of three novel deletion SVs that are associated with risk of PD from our initial association analysis, including a 2 kb intronic deletion within the gene LRRN4. INTERPRETATION We identified three SVs associated with genetic risk of PD. This study represents the most comprehensive assessment of the contribution of SVs to the genetic risk of PD to date. ANN NEUROL 2023;93:1012-1022.
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Affiliation(s)
- Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | | | | | - Francis P. Grenn
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Anni Moore
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Daniel Vitale
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
- Data Tecnica International, Washington, DC, USA
| | - Xylena Reed
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Ali Torkamani
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Bryan J. Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK
| | - Clifton L. Dalgard
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Debra J. Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas.G. Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ
| | - Geidy E. Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Mark Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Data Sciences Platform, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Emma Pierce-Hoffman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Data Sciences Platform, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Bradford Casey
- The Michael J. Fox Foundation for Parkinson’s Research, New York, NY 10001
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | | | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
- Data Tecnica International, Washington, DC, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, US
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
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23
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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2023; 15:22. [PMID: 37020259 PMCID: PMC10074346 DOI: 10.1186/s13073-023-01173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. METHODS We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. RESULTS No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5). CONCLUSIONS Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias; Health Research Institute of Principality of Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Intensive Care Unit Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- Gordion Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX , CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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Zhang X, Dalgard CL, Wilkerson MD. Abstract 3168: DE-meta: Revealing tumor gene expression by meta-analysis of RNASeq and proteomics datasets. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Detecting differentially expressed genes under different biological conditions is crucial to characterize mechanisms of cancer development and identifying determinants of patient outcome. High throughput technologies such as RNA sequencing and mass spectrometry-based proteomics have been widely used to identify differentially expressed genes (DEG), on a transcript and on a peptide basis, respectively. However, both transcription and translation of genes provide information about gene expression. Thus, leveraging both RNA and protein expression data could potentially produce more accurate results. Various statistical tools have been developed to tackle the differential expression problem for a single platform, such as edgeR, DESeq2, etc. However, a tool that integrates both transcriptome and proteomics data for differential expression analysis has not yet been developed. Meta-analysis can potentially increase statistical power and generate a more consensus conclusion by combining multiple datasets. Here we present DE-Meta, a new tool developed using R, which performs combined meta-analysis of RNA-seq and MS-based proteomics on matched tumor specimens. To characterize the performance of our method using real world data, we utilized a published lung cancer dataset and set a truth standard of DEG between known two expression subtypes: terminal respiratory unit (TRU) and proximal proliferative (PP). Briefly, we restricted to 7,458 common genes detected by RNA-seq and MS-based proteomics. We then, randomly selected tumors as the truth sample set, n=20 TRU and n=20 PP tumors. With this truth sample set, DEGs were calculated separately by RNA or by protein, using DESeq2 and regression models. The union of these DEGs defined the truth DEG set. Using independent tumors (n=10 TRU and n=10 PP), we applied DE-meta to detect DEGs by RNA, by protein or joint RNA and protein data. Through receiver operating characteristic curve analysis, we show that the DE-meta joint model performed better than the single platform models (joint AUC=0.651, RNA AUC=0.610, protein AUC=0.623). Focusing genes relevant to tumor biology, we found that the DE-meta joint model called an 169 cancer-relevant DEGs, such as MSH2, CD4, WDR3, PIK3R1, and RPS6KA3. which were not detected by the RNA or protein models, at the same false discovery rate threshold of 0.05 (Benjamini-Hochberg procedure). In summary, our new DE-meta tool, by joint analysis of RNA-seq and MS-based proteomics datasets, yields more accurate and biologically-relevant results.
The views expressed in this abstract are solely of the authors and do not reflect the official policy of the Departments of Army/Navy/Air Force, Department of Defense, USUHS, HJF, or U.S. Government.
Citation Format: Xijun Zhang, Clifton L. Dalgard, Matthew D. Wilkerson. DE-meta: Revealing tumor gene expression by meta-analysis of RNASeq and proteomics datasets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3168.
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Affiliation(s)
- Xijun Zhang
- 1Uniformed Services University, Bethesda, MD
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25
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Condello C, Ayers JI, Dalgard CL, Garcia Garcia MM, Rivera BM, Seeley WW, Perl DP, Prusiner SB. Guam ALS-PDC is a distinct double-prion disorder featuring both tau and Aβ prions. Proc Natl Acad Sci U S A 2023; 120:e2220984120. [PMID: 36952379 PMCID: PMC10068802 DOI: 10.1073/pnas.2220984120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
The amyotrophic lateral sclerosis-parkinsonism dementia complex (ALS-PDC) of Guam is an endemic neurodegenerative disease that features widespread tau tangles, occasional α-synuclein Lewy bodies, and sparse β-amyloid (Aβ) plaques distributed in the central nervous system. Extensive studies of genetic or environmental factors have failed to identify a cause of ALS-PDC. Building on prior work describing the detection of tau and Aβ prions in Alzheimer's disease (AD) and Down syndrome brains, we investigated ALS-PDC brain samples for the presence of prions. We obtained postmortem frozen brain tissue from 26 donors from Guam with ALS-PDC or no neurological impairment and 71 non-Guamanian donors with AD or no neurological impairment. We employed cellular bioassays to detect the prion conformers of tau, α-synuclein, and Aβ proteins in brain extracts. In ALS-PDC brain samples, we detected high titers of tau and Aβ prions, but we did not detect α-synuclein prions in either cohort. The specific activity of tau and Aβ prions was increased in Guam ALS-PDC compared with sporadic AD. Applying partial least squares regression to all biochemical and prion infectivity measurements, we demonstrated that the ALS-PDC cohort has a unique molecular signature distinguishable from AD. Our findings argue that Guam ALS-PDC is a distinct double-prion disorder featuring both tau and Aβ prions.
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Affiliation(s)
- Carlo Condello
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Jacob I Ayers
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Clifton L Dalgard
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - M Madhy Garcia Garcia
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Brianna M Rivera
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - William W Seeley
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
- Department of Pathology, University of California, San Francisco, CA 94143
| | - Daniel P Perl
- Department of Pathology (Neuropathology), Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD 20814
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
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26
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Bressan E, Reed X, Bansal V, Hutchins E, Cobb MM, Webb MG, Alsop E, Grenn FP, Illarionova A, Savytska N, Violich I, Broeer S, Fernandes N, Sivakumar R, Beilina A, Billingsley KJ, Berghausen J, Pantazis CB, Pitz V, Patel D, Daida K, Meechoovet B, Reiman R, Courtright-Lim A, Logemann A, Antone J, Barch M, Kitchen R, Li Y, Dalgard CL, Rizzu P, Hernandez DG, Hjelm BE, Nalls M, Gibbs JR, Finkbeiner S, Cookson MR, Van Keuren-Jensen K, Craig DW, Singleton AB, Heutink P, Blauwendraat C. The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism. Cell Genom 2023; 3:100261. [PMID: 36950378 PMCID: PMC10025424 DOI: 10.1016/j.xgen.2023.100261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/22/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The Foundational Data Initiative for Parkinson Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources for Parkinson disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in a cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, a major affected cell type in PD. The lines were derived from the Parkinson's Progression Markers Initiative study, which included participants with PD carrying monogenic PD variants, variants with intermediate effects, and variants identified by genome-wide association studies and unaffected individuals. We generated genetic, epigenetic, regulatory, transcriptomic, and longitudinal cellular imaging data from iPSC-derived DA neurons to understand molecular relationships between disease-associated genetic variation and proximate molecular events. These data reveal that iPSC-derived DA neurons provide a valuable cellular context and foundational atlas for modeling PD genetic risk. We have integrated these data into a FOUNDIN-PD data browser as a resource for understanding the molecular pathogenesis of PD.
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Affiliation(s)
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Corresponding author
| | - Elizabeth Hutchins
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Melanie M. Cobb
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Michelle G. Webb
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Francis P. Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Natalia Savytska
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ivo Violich
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Stefanie Broeer
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Noémia Fernandes
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ramiyapriya Sivakumar
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Alexandra Beilina
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Joos Berghausen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline B. Pantazis
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Vanessa Pitz
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Dhairya Patel
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bessie Meechoovet
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amanda Courtright-Lim
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amber Logemann
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mariya Barch
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Robert Kitchen
- Massachusetts General Hospital, Cardiovascular Research Center, Charlestown, MA, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Brooke E. Hjelm
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
- Corresponding author
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Corresponding author
| | - Kendall Van Keuren-Jensen
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Corresponding author
| | - David W. Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
- Corresponding author
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Corresponding author
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Corresponding author
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Corresponding author
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Braunstein EM, Imada E, Pasca S, Wang S, Chen H, Alba C, Hupalo DN, Wilkerson M, Dalgard CL, Ghannam J, Liu Y, Marchionni L, Moliterno A, Hourigan CS, Gondek LP. Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia 2023; 37:627-635. [PMID: 36543879 DOI: 10.1038/s41375-022-01797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Genetic predisposition (familial risk) in the myeloproliferative neoplasms (MPNs) is more common than the risk observed in most other cancers, including breast, prostate, and colon. Up to 10% of MPNs are considered to be familial. Recent genome-wide association studies have identified genomic loci associated with an MPN diagnosis. However, the identification of variants with functional contributions to the development of MPN remains limited. In this study, we have included 630 MPN patients and whole genome sequencing was performed in 64 individuals with familial MPN to uncover recurrent germline predisposition variants. Both targeted and unbiased filtering of single nucleotide variants (SNVs) was performed, with a comparison to 218 individuals with MPN unselected for familial status. This approach identified an ATM L2307F SNV occurring in nearly 8% of individuals with familial MPN. Structural protein modeling of this variant suggested stabilization of inactive ATM dimer, and alteration of the endogenous ATM locus in a human myeloid cell line resulted in decreased phosphorylation of the downstream tumor suppressor CHEK2. These results implicate ATM, and the DNA-damage response pathway, in predisposition to MPN.
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Affiliation(s)
- Evan M Braunstein
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Eddie Imada
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hang Chen
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA.,Committee on Genetics, Genomics and Systems Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Camille Alba
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dan N Hupalo
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew Wilkerson
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujia Liu
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Luigi Marchionni
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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28
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Wong KK, Bateman NW, Ng CW, Tsang YTM, Sun CS, Celestino J, Nguyen TV, Malpica A, Hillman RT, Zhang J, Futreal PA, Rojas C, Conrads KA, Hood BL, Dalgard CL, Wilkerson MD, Phippen NT, Conrads TP, Maxwell GL, Sood AK, Gershenson DM. Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors. J Transl Med 2022; 20:606. [PMID: 36528667 PMCID: PMC9758924 DOI: 10.1186/s12967-022-03820-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we compared the proteogenomic analyses of LGSOCs from short- and long-term survivors (defined as < 40 and > 60 months, respectively). Our goal was to identify novel mutations, proteins, and mRNA transcripts that are dysregulated in LGSOC, particularly in short-term survivors. METHODS Initially, targeted sequencing of 409 cancer-related genes was performed on 22 LGSOC and 6 serous borderline ovarian tumor samples. Subsequently, whole-genome sequencing analysis was performed on 14 LGSOC samples (7 long-term survivors and 7 short-term survivors) with matched normal tissue samples. RNA sequencing (RNA-seq), quantitative proteomics, and phosphoproteomic analyses were also performed. RESULTS We identified single-nucleotide variants (SNVs) (range: 5688-14,833 per sample), insertion and deletion variants (indels) (range: 880-1065), and regions with copy number variants (CNVs) (range: 62-335) among the 14 LGSOC samples. Among all SNVs and indels, 2637 mutation sites were found in the exonic regions. The allele frequencies of the detected variants were low (median12%). The identified recurrent nonsynonymous missense mutations included KRAS, NRAS, EIF1AX, UBR5, and DNM3 mutations. Mutations in DNM3 and UBR5 have not previously been reported in LGSOC. For the two samples, somatic DNM3 nonsynonymous missense mutations in the exonic region were validated using Sanger sequencing. The third sample contained two missense mutations in the intronic region of DNM3, leading to a frameshift mutation detected in RNA transcripts in the RNA-seq data. Among the 14 LGSOC samples, 7754 proteins and 9733 phosphosites were detected by global proteomic analysis. Some of these proteins and signaling pathways, such as BST1, TBXAS1, MPEG1, HBA1, and phosphorylated ASAP1, are potential therapeutic targets. CONCLUSIONS This is the first study to use whole-genome sequencing to detect somatic mutations in LGSOCs with matched normal tissues. We detected and validated novel mutations in DNM3, which were present in 3 of the 14 samples analyzed. Additionally, we identified novel indels, regions with CNVs, dysregulated mRNA, dysregulated proteins, and phosphosites that are more prevalent in short-term survivors. This integrated proteogenomic analysis can guide research into the pathogenesis and treatment of LGSOC.
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Affiliation(s)
- Kwong-Kwok Wong
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Nicholas W. Bateman
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Chun Wai Ng
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Yvonne T. M. Tsang
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Charlotte S. Sun
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Joseph Celestino
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Tri V. Nguyen
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Anais Malpica
- grid.240145.60000 0001 2291 4776Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - R. Tyler Hillman
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christine Rojas
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Kelly A. Conrads
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Brian L. Hood
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Clifton L. Dalgard
- grid.265436.00000 0001 0421 5525Department of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Matthew D. Wilkerson
- grid.265436.00000 0001 0421 5525Department of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Neil T. Phippen
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Thomas P. Conrads
- grid.414629.c0000 0004 0401 0871Women’s Health Integrated Research Center at Inova Health System, Women’s Service Line, Inova Fairfax Medical Campus, Falls Church, VA USA ,grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - George L. Maxwell
- grid.414629.c0000 0004 0401 0871Women’s Health Integrated Research Center at Inova Health System, Women’s Service Line, Inova Fairfax Medical Campus, Falls Church, VA USA ,grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Anil K. Sood
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - David M. Gershenson
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
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Sambo D, Gohel C, Yuan Q, Sukumar G, Alba C, Dalgard CL, Goldman D. Cell type-specific changes in Wnt signaling and neuronal differentiation in the developing mouse cortex after prenatal alcohol exposure during neurogenesis. Front Cell Dev Biol 2022; 10:1011974. [PMID: 36544903 PMCID: PMC9761331 DOI: 10.3389/fcell.2022.1011974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/26/2022] [Indexed: 12/11/2022] Open
Abstract
Fetal Alcohol Spectrum Disorder (FASD) encompasses an array of effects of prenatal alcohol exposure (PAE), including physical abnormalities and cognitive and behavioral deficits. Disruptions of cortical development have been implicated in multiple PAE studies, with deficits including decreased progenitor proliferation, disrupted neuronal differentiation, aberrant radial migration of pyramidal neurons, and decreased cortical thickness. While several mechanisms of alcohol teratogenicity have been explored, how specific cell types in the brain at different developmental time points may be differentially affected by PAE is still poorly understood. In this study, we used single nucleus RNA sequencing (snRNAseq) to investigate whether moderate PAE from neurulation through peak cortical neurogenesis induces cell type-specific transcriptomic changes in the developing murine brain. Cluster analysis identified 25 neuronal cell types, including subtypes of radial glial cells (RGCs), intermediate progenitor cells (IPCs), projection neurons, and interneurons. Only Wnt-expressing cortical hem RGCs showed a significant decrease in the percentage of cells after PAE, with no cell types showing PAE-induced apoptosis as measured by caspase expression. Cell cycle analysis revealed only a subtype of RGCs expressing the downstream Wnt signaling transcription factor Tcf7l2 had a decreased percentage of cells in the G2/M phase of the cell cycle, suggesting decreased proliferation in this RGC subtype and further implicating disrupted Wnt signaling after PAE at this early developmental timepoint. An increased pseudotime score in IPC and projection neuron cell types indicated that PAE led to increased or premature differentiation of these cells. Biological processes affected by PAE included the upregulation of pathways related to synaptic activity and neuronal differentiation and downregulation of pathways related to chromosome structure and the cell cycle. Several cell types showed a decrease in Wnt signaling pathways, with several genes related to Wnt signaling altered by PAE in multiple cell types. As Wnt has been shown to promote proliferation and inhibit differentiation at earlier stages in development, the downregulation of Wnt signaling may have resulted in premature neuronal maturation of projection neurons and their intermediate progenitors. Overall, these findings provide further insight into the cell type-specific effects of PAE during early corticogenesis.
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Affiliation(s)
- Danielle Sambo
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, United States
| | - Chiraag Gohel
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, United States
| | - Qiaoping Yuan
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, United States
| | - Gauthaman Sukumar
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, United States,*Correspondence: David Goldman,
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30
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Chang T, Wang H, Lee W, Kumar U, Leung YY, Dickson DW, Dalgard CL, Wang L, Schellenberg GD, Geschwind DH. Rare Genetic Risk in Progressive Supranuclear Palsy. Alzheimers Dement 2022. [DOI: 10.1002/alz.062971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Timothy Chang
- David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
| | - Hui Wang
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Wan‐Ping Lee
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Urvashi Kumar
- David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
| | - Yuk Yee Leung
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | | | | | - Li‐San Wang
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | | | - Daniel H. Geschwind
- David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
- School of Biological Sciences, University of California, Irvine Irvine CA USA
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31
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Mena PR, Kunkle BW, Faber KM, Adams LD, Inciute JD, Whitehead PL, Foroud TM, Reyes‐Dumeyer D, Kuzma AB, Leung YY, Naj AC, Martin ER, Dalgard CL, Schellenberg GD, Wang L, Mayeux R, Vardarajan BN, Vance JM, Cuccaro ML, Pericak‐Vance MA. The Alzheimer’s Disease Sequencing Project Follow Up Study (ADSP‐FUS): increasing ethnic diversity in Alzheimer’s disease (AD) genetics research. Alzheimers Dement 2022. [DOI: 10.1002/alz.068083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Kelley M. Faber
- Indiana University School of Medicine Indianapolis IN USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD) Indianapolis IN USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jovita D. Inciute
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Tatiana M. Foroud
- Indiana University School of Medicine Indianapolis IN USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD) Indianapolis IN USA
| | | | - Amanda B Kuzma
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Yuk Yee Leung
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Adam C. Naj
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics and Epidemiology/Center for Clinical Epidemiology and Biostatistics Philadelphia PA USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | - Gerard D. Schellenberg
- University of Pennsylvania, Perelman School of Medicine, Path & Lab Med, Stellar Chance Philadelphia PA USA
| | - Li‐San Wang
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Richard Mayeux
- Columbia University Irving Medical Center New York NY USA
| | - Badri N. Vardarajan
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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32
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Cornejo‐Olivas M, Rajabli F, Kushch NA, Mena PR, Illanes‐Manrique M, Adams LD, Whitehead PL, Hamilton‐Nelson KL, Milla‐Neyra K, Marca V, Sarapura‐Castro E, Manrique‐Enciso C, Mejía KK, Isasi R, Castro‐Suarez S, Araujo‐Aliaga I, Custodio N, Montesinos R, Griswold AJ, Dalgard CL, Beecham GW, Cuccaro ML, Vance JM, Pericak‐Vance MA. Exploring effect of known Alzheimer disease genetic loci in the Peruvian population. Alzheimers Dement 2022. [DOI: 10.1002/alz.068028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mario Cornejo‐Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia Lima Peru
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | | | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Karina Milla‐Neyra
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | - Victoria Marca
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | | | - Carla Manrique‐Enciso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | - Koni K. Mejía
- Daniel Alcides Carrion National Hospital Callao Peru
| | - Rosario Isasi
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Sheila Castro‐Suarez
- CBI en Demencias y Enfermedades Desmielinizantes del Sistema Nervioso, Instituto Nacional de Ciencias Neurológicas Lima Peru
- Atlantic Senior Fellow for Equity in Brain Health at University of California San Francisco. San Francisco CA USA
| | - Ismael Araujo‐Aliaga
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas Lima Peru
| | | | | | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
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33
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Vasquez ML, Rajabli F, Beecham GW, Hendrie HC, Baiyewu O, Ogunniyi A, Gao S, Kushch NA, Hamilton‐Nelson KL, Young JJ, Dykxhoorn DM, Nuytemans K, Kunkle BW, Wang L, Jin F, Liu X, Feliciano‐Astacio BE, Dalgard CL, Griswold AJ, Byrd GS, Reitz C, Haines JL, Pericak‐Vance MA, Vance JM. A Novel Protective locus significantly reduces the
ApoEε4
risk for Alzheimer’s Disease in individuals of African Ancestry. Alzheimers Dement 2022. [DOI: 10.1002/alz.067279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marina Lipkin Vasquez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Hugh C Hendrie
- Department of Psychiatry, Indiana University School of Medicine Indianapolis IN USA
| | | | | | - Sujuan Gao
- Department of Biostatistics, Indiana University School of Medicine Indianapolis IN USA
| | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Juan J Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Brian W. Kunkle
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
| | | | | | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston‐Salem NC USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University New York NY USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
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Cubas‐Montecino D, Rajabli F, Illanes‐Manrique M, Kushch NA, Mena PR, Whitehead PL, Hamilton‐Nelson KL, Milla‐Neyra K, Marca V, Sarapura‐Castro E, Manrique‐Enciso C, Mejía KK, Isasi R, Castro‐Suarez S, Araujo‐Aliaga I, Custodio N, Montesinos R, Griswold AJ, Dalgard CL, Beecham GW, Cuccaro ML, Vance JM, Cornejo‐Olivas M, Pericak‐Vance MA. Admixed ancestral composition with Amerindian predominance at the Peruvian Alzheimer Disease Initiative (PeADI). Alzheimers Dement 2022. [DOI: 10.1002/alz.068155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Diana Cubas‐Montecino
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | | | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Karina Milla‐Neyra
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | - Victoria Marca
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | | | - Carla Manrique‐Enciso
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | - Koni K. Mejía
- Daniel Alcides Carrion National Hospital Callao Peru
| | - Rosario Isasi
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Sheila Castro‐Suarez
- CBI en Demencias y Enfermedades Desmielinizantes del Sistema Nervioso, Instituto Nacional de Ciencias Neurológicas Lima Peru
- Atlantic Senior Fellow for Equity in Brain Health at University of California San Francisco San Francisco CA USA
| | - Ismael Araujo‐Aliaga
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
| | | | | | - Anthony J. Griswold
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Mario Cornejo‐Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas Lima Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia Lima Peru
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
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Celis K, Rajabli F, Simon SA, Wang L, Hamilton‐Nelson KL, Adams LD, Mena PR, Whitehead PL, Van Booven D, Feliciano‐Astacio BE, Chinea A, Feliciano NI, Acosta H, Dalgard CL, Haines JL, Vance JM, Cuccaro ML, Beecham GW, Dykxhoorn DM, Griswold AJ, Pericak‐Vance MA. Fine‐mapping of chromosome 9p21 linkage in Puerto Rican Alzheimer disease families. Alzheimers Dement 2022. [DOI: 10.1002/alz.067835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Shaina A Simon
- Dr. John T. MacDonald Foundation Department of Human Genetics Miami FL USA
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | | | | | | | | | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Gary W. Beecham
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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Matuozzo D, Talouarn E, Marchal A, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Zhang P, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, Pérez de Diego R, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. medRxiv 2022:2022.10.22.22281221. [PMID: 36324795 PMCID: PMC9628204 DOI: 10.1101/2022.10.22.22281221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background We previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and auto-antibodies against type I IFN in another 15-20% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7 , with an OR of 27.68 (95%CI:1.5-528.7, P= 1.1×10 -4 ), in analyses restricted to biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70 [95%CI:1.3-8.2], P= 2.1×10 -4 ). Adding the recently reported TYK2 COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4]; P= 3.4×10 -3 ). When these 14 loci and TLR7 were considered, all individuals hemizygous ( n =20) or homozygous ( n =5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0], P =4.7×10 -7 ), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9], P =0.02). Finally, the patients with pLOF or bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P= 1.68×10 -5 ). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Ford MKB, Hari A, Rodriguez O, Xu J, Lack J, Oguz C, Zhang Y, Weber S, Magliocco M, Barnett J, Xirasagar S, Samuel S, Imberti L, Bonfanti P, Biondi A, Dalgard CL, Chanock S, Rosen L, Holland S, Su H, Notarangelo L, Vishkin U, Watson CT, Sahinalp SC. ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data. Cell Syst 2022; 13:808-816.e5. [PMID: 36265467 PMCID: PMC10084889 DOI: 10.1016/j.cels.2022.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/20/2022] [Accepted: 08/22/2022] [Indexed: 01/26/2023]
Abstract
Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which are critical for the structure of antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype when using standard short-read sequencing technologies. Here, we introduce ImmunoTyper-SR, an algorithmic tool for the genotyping and CNV analysis of the germline IGHV genes on Illumina whole-genome sequencing (WGS) data using a combinatorial optimization formulation that resolves ambiguous read mappings. We have validated ImmunoTyper-SR on 12 individuals, whose IGHV allele composition had been independently validated, as well as concordance between WGS replicates from nine individuals. We then applied ImmunoTyper-SR on 585 COVID patients to investigate the associations between IGHV alleles and anti-type I IFN autoantibodies, which were previously associated with COVID-19 severity.
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Affiliation(s)
| | - Ananth Hari
- National Cancer Institute, NIH, Bethesda, MD, USA; Department of Electrical Engineering, University of Maryland, College Park, MD, USA
| | - Oscar Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Junyan Xu
- National Cancer Institute, NIH, Bethesda, MD, USA
| | - Justin Lack
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Cihan Oguz
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Yu Zhang
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Sarah Weber
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Mary Magliocco
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jason Barnett
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Sandhya Xirasagar
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Smilee Samuel
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Luisa Imberti
- Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Paolo Bonfanti
- University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - Andrea Biondi
- University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Lindsey Rosen
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Steven Holland
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Helen Su
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Luigi Notarangelo
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Uzi Vishkin
- Department of Electrical Engineering, University of Maryland, College Park, MD, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
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38
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Zhou Y, Shalhoub R, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Shin TH, Diangson A, Deng W, Anand S, Lu W, Cullen M, Godfrey AL, Preller J, Hadjadj J, Jouanguy E, Cobat A, Abel L, Rieux-Laucat F, Terrier B, Fischer A, Novik L, Gordon IJ, Strom L, Gaudinski MR, Lisco A, Sereti I, Gniadek TJ, Biondi A, Bonfanti P, Imberti L, Dalgard CL, Zhang Y, Dobbs K, Su HC, Notarangelo LD, Wu CO, Openshaw PJ, Semple MG, Mallat Z, Baillie K, Dunbar CE, Vassiliou GS. Clonal hematopoiesis is not significantly associated with COVID-19 disease severity. Blood 2022; 140:1650-1655. [PMID: 35839449 PMCID: PMC9293387 DOI: 10.1182/blood.2022015721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yifan Zhou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Stephanie N. Rogers
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shiqin Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A. Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pedro M. Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Arch Diangson
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhan Deng
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhua Lu
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matthew Cullen
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Anna L. Godfrey
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacobus Preller
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
| | - Jerome Hadjadj
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Frederic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Alain Fischer
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
| | - Lara Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Larisa Strom
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Thomas J. Gniadek
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Clifton L. Dalgard
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - COVID-STORM Clinicians
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - NIAID Immune Response to COVID Group
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - The ISARIC4C Investigators
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Peter J.M. Openshaw
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Billingsley KJ, Alvarez Jerez P, Grenn FP, Bandres-Ciga S, Malik L, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Ding J, Gibbs JR, Blauwendraat C, Singleton AB. Profiling the NOTCH2NLC GGC Repeat Expansion in Parkinson's Disease in the European Population. Mov Disord 2022; 37:2161-2162. [PMID: 35866887 DOI: 10.1002/mds.29155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Ali Torkamani
- The Scripps Research Institute, La Jolla, California, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London, United Kingdom
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Clifton L Dalgard
- Department of Anatomy Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Debra J Ehrlich
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Thomas G Beach
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
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40
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Reho P, Koga S, Shah Z, Chia R, Rademakers R, Dalgard CL, Boeve BF, Beach TG, Dickson DW, Ross OA, Scholz SW. GRN Mutations Are Associated with Lewy Body Dementia. Mov Disord 2022; 37:1943-1948. [PMID: 35810449 PMCID: PMC9474656 DOI: 10.1002/mds.29144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Loss-of-function mutations in GRN are a cause of familial frontotemporal dementia, and common variants within the gene have been associated with an increased risk of developing Alzheimer's disease and Parkinson's disease. Although TDP-43-positive inclusions are characteristic of GRN-related neurodegeneration, Lewy body copathology has also been observed in many GRN mutation carriers. OBJECTIVE The objective of this study was to assess a Lewy body dementia (LBD) case-control cohort for pathogenic variants in GRN and to test whether there is an enrichment of damaging mutations among patients with LBD. METHODS We analyzed whole-genome sequencing data generated for 2591 European-ancestry LBD cases and 4032 neurologically healthy control subjects to identify disease-causing mutations in GRN. RESULTS We identified six heterozygous exonic GRN mutations in seven study participants (cases: n = 6; control subjects: n = 1). Each variant was predicted to be pathogenic or likely pathogenic. We found significant enrichment of GRN loss-of-function mutations in patients with LBD compared with control subjects (Optimized Sequence Kernel Association Test P = 0.0162). Immunohistochemistry in three definite LBD cases demonstrated Lewy body pathology and TDP-43-positive neuronal inclusions. CONCLUSIONS Our findings suggest that deleterious GRN mutations are a rare cause of familial LBD. © 2022 International Parkinson Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Shunsuke Koga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Zalak Shah
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
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41
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Zhang Q, Matuozzo D, Le Pen J, Lee D, Moens L, Asano T, Bohlen J, Liu Z, Moncada-Velez M, Kendir-Demirkol Y, Jing H, Bizien L, Marchal A, Abolhassani H, Delafontaine S, Bucciol G, Bayhan GI, Keles S, Kiykim A, Hancerli S, Haerynck F, Florkin B, Hatipoglu N, Ozcelik T, Morelle G, Zatz M, Ng LF, Lye DC, Young BE, Leo YS, Dalgard CL, Lifton RP, Renia L, Meyts I, Jouanguy E, Hammarström L, Pan-Hammarström Q, Boisson B, Bastard P, Su HC, Boisson-Dupuis S, Abel L, Rice CM, Zhang SY, Cobat A, Casanova JL. Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia. J Exp Med 2022; 219:213287. [PMID: 35708626 PMCID: PMC9206114 DOI: 10.1084/jem.20220131] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/01/2022] [Accepted: 05/24/2022] [Indexed: 12/16/2022] Open
Abstract
Recessive or dominant inborn errors of type I interferon (IFN) immunity can underlie critical COVID-19 pneumonia in unvaccinated adults. The risk of COVID-19 pneumonia in unvaccinated children, which is much lower than in unvaccinated adults, remains unexplained. In an international cohort of 112 children (<16 yr old) hospitalized for COVID-19 pneumonia, we report 12 children (10.7%) aged 1.5-13 yr with critical (7 children), severe (3), and moderate (2) pneumonia and 4 of the 15 known clinically recessive and biochemically complete inborn errors of type I IFN immunity: X-linked recessive TLR7 deficiency (7 children) and autosomal recessive IFNAR1 (1), STAT2 (1), or TYK2 (3) deficiencies. Fibroblasts deficient for IFNAR1, STAT2, or TYK2 are highly vulnerable to SARS-CoV-2. These 15 deficiencies were not found in 1,224 children and adults with benign SARS-CoV-2 infection without pneumonia (P = 1.2 × 10-11) and with overlapping age, sex, consanguinity, and ethnicity characteristics. Recessive complete deficiencies of type I IFN immunity may underlie ∼10% of hospitalizations for COVID-19 pneumonia in children.
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Affiliation(s)
- Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Leen Moens
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Yasemin Kendir-Demirkol
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Huie Jing
- Laboratory of Clinical Immunology and Microbiology, Intramural Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Selket Delafontaine
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Giorgia Bucciol
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | | | | | - Sevgi Keles
- Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey
| | - Ayca Kiykim
- Istanbul University-Cerrahpasa, Pediatric Allergy and Immunology, Istanbul, Turkey
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Filomeen Haerynck
- Department of Pediatric Immunology and Pulmonology, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, PID Research Laboratory, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium
| | - Benoit Florkin
- Department of Pediatrics, Hôpital de la Citadelle, Liége, Belgium
| | - Nevin Hatipoglu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Bilkent-Ankara, Turkey
| | - Guillaume Morelle
- Department of General Pediatrics, Bicêtre Hospital, Assistance Publique – Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Lisa F.P. Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Richard P. Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY
- Department of Genetics, Yale University School of Medicine, New Haven, CT
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Isabelle Meyts
- Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | | | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Intramural Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Charles M. Rice
- Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY
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42
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Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Brahier MS, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chisholm RL, Colli LM, Dalgard CL, Dude CM, Edberg J, Erdmann N, Feigelson HS, Fonseca BA, Firestein GS, Gehring AJ, Guo C, Ho M, Holland S, Hutchinson AA, Im H, Irby L, Ison MG, Joseph NT, Kim HB, Kreitman RJ, Korf BR, Lipkin SM, Mahgoub SM, Mohammed I, Paschoalini GL, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenblum B, Ross ME, Anna HPS, Savage SA, Sharma S, Siouti E, Smith AK, Triantafyllia V, Vargas JM, Vargas JD, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries. Nat Genet 2022; 54:1103-1116. [PMID: 35835913 PMCID: PMC9355882 DOI: 10.1038/s41588-022-01113-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/26/2022] [Indexed: 12/22/2022]
Abstract
The chr12q24.13 locus encoding OAS1-OAS3 antiviral proteins has been associated with coronavirus disease 2019 (COVID-19) susceptibility. Here, we report genetic, functional and clinical insights into this locus in relation to COVID-19 severity. In our analysis of patients of European (n = 2,249) and African (n = 835) ancestries with hospitalized versus nonhospitalized COVID-19, the risk of hospitalized disease was associated with a common OAS1 haplotype, which was also associated with reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance in a clinical trial with pegIFN-λ1. Bioinformatic analyses and in vitro studies reveal the functional contribution of two associated OAS1 exonic variants comprising the risk haplotype. Derived human-specific alleles rs10774671-A and rs1131454 -A decrease OAS1 protein abundance through allele-specific regulation of splicing and nonsense-mediated decay (NMD). We conclude that decreased OAS1 expression due to a common haplotype contributes to COVID-19 severity. Our results provide insight into molecular mechanisms through which early treatment with interferons could accelerate SARS-CoV-2 clearance and mitigate against severe COVID-19.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Brenen W Papenberg
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Muhammad A Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Timothy J Ring
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Chia-Han Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Paul S Albert
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evgeny Arons
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - David L Boyle
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Mark S Brahier
- Georgetown University School of Medicine, Washington, DC, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leandro M Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Carolynn M Dude
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeff Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Benedito A Fonseca
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary S Firestein
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Adam J Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cuncai Guo
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Ho
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Steven Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hogune Im
- Genome Opinion, Inc., Seoul, Republic of Korea
| | - Les'Shon Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Naima T Joseph
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Lipkin
- Department of Medicine and Program in Mendelian Genetics, Weill Cornell Medicine, New York, NY, USA
| | - Siham M Mahgoub
- Department of Medicine, Infectious Diseases Division, Howard University Hospital, Howard University College of Medicine, Washington, DC, USA
| | - Iman Mohammed
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Guilherme L Paschoalini
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brooke Rosenblum
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hanaisa P Sant Anna
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jose D Vargas
- Veterans Affairs Medical Center, Washington, DC, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan J Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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Carmona-Rivera C, Zhang Y, Dobbs K, Markowitz TE, Dalgard CL, Oler AJ, Claybaugh DR, Draper D, Truong M, Delmonte OM, Licciardi F, Ramenghi U, Crescenzio N, Imberti L, Sottini A, Quaresima V, Fiorini C, Discepolo V, Lo Vecchio A, Guarino A, Pierri L, Catzola A, Biondi A, Bonfanti P, Poli Harlowe MC, Espinosa Y, Astudillo C, Rey-Jurado E, Vial C, de la Cruz J, Gonzalez R, Pinera C, Mays JW, Ng A, Platt A, Drolet B, Moon J, Cowen EW, Kenney H, Weber SE, Castagnoli R, Magliocco M, Stack MA, Montealegre G, Barron K, Fink DL, Kuhns DB, Hewitt SM, Arkin LM, Chertow DS, Su HC, Notarangelo LD, Kaplan MJ. Multicenter analysis of neutrophil extracellular trap dysregulation in adult and pediatric COVID-19. JCI Insight 2022; 7:160332. [PMID: 35852866 PMCID: PMC9534551 DOI: 10.1172/jci.insight.160332] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Dysregulation in neutrophil extracellular trap (NET) formation and degradation may play a role in the pathogenesis and severity of COVID-19; however, its role in the pediatric manifestations of this disease, including multisystem inflammatory syndrome in children (MIS-C) and chilblain-like lesions (CLLs), otherwise known as “COVID toes,” remains unclear. Studying multinational cohorts, we found that, in CLLs, NETs were significantly increased in serum and skin. There was geographic variability in the prevalence of increased NETs in MIS-C, in association with disease severity. MIS-C and CLL serum samples displayed decreased NET degradation ability, in association with C1q and G-actin or anti-NET antibodies, respectively, but not with genetic variants of DNases. In adult COVID-19, persistent elevations in NETs after disease diagnosis were detected but did not occur in asymptomatic infection. COVID-19–affected adults displayed significant prevalence of impaired NET degradation, in association with anti-DNase1L3, G-actin, and specific disease manifestations, but not with genetic variants of DNases. NETs were detected in many organs of adult patients who died from COVID-19 complications. Infection with the Omicron variant was associated with decreased NET levels when compared with other SARS-CoV-2 strains. These data support a role for NETs in the pathogenesis and severity of COVID-19 in pediatric and adult patients.
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Affiliation(s)
- Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID); and
| | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, School of Medicine, and the American Genome Center, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, USA
| | - Andrew J. Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, Maryland, USA
| | - Dillon R. Claybaugh
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
| | | | | | | | | | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences and
| | - Nicoletta Crescenzio
- Pediatric Hematology, “Regina Margherita” Children Hospital, University of Turin, Turin, Italy
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Virginia Quaresima
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Chiara Fiorini
- Centro di Ricerca Emato-oncologica AIL, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Luca Pierri
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Catzola
- Department of Translational Medical Sciences, Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Andrea Biondi
- Department of Pediatrics, University of Milano-Bicocca, European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital–University of Milano-Bicocca, Monza, Italy
| | - Maria C. Poli Harlowe
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Hospital Roberto del Rio, Santiago, Chile
| | | | | | - Emma Rey-Jurado
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Javiera de la Cruz
- Programa de Inmunogenética e Inmunología Traslacional, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Ricardo Gonzalez
- Pediatric Intensive Care Unit, Hospital Exequiel Gonzalez Cortés, Santiago, Chile
| | - Cecilia Pinera
- Infectious Diseases Unit, Hospital Dr. Exequiel González Cortés, Región Metropolitana, Chile
- Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jacqueline W. Mays
- National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, Maryland, USA
| | - Ashley Ng
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Andrew Platt
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland, USA
| | | | | | - Beth Drolet
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - John Moon
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | | | | | | | | | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID; and
| | - Michael A. Stack
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID; and
| | - Gina Montealegre
- Division of Clinical Research, NIAID, NIH, Bethesda, Maryland, USA
| | - Karyl Barron
- Division of Clinical Research, NIAID, NIH, Bethesda, Maryland, USA
| | - Danielle L. Fink
- Applied/Developmental Research Directorate, Frederick and National Laboratory for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Douglas B. Kuhns
- Applied/Developmental Research Directorate, Frederick and National Laboratory for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Lisa M. Arkin
- Department of Dermatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, and Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland, USA
| | - Helen C. Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID); and
| | | | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
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Lippa SM, Lange RT, Dalgard CL, Soltis AR, Guedes VA, Brickell TA, French LM, Gill J. APOE Is Associated With Serum Tau Following Uncomplicated Mild Traumatic Brain Injury. Front Neurol 2022; 13:816625. [PMID: 35911887 PMCID: PMC9329522 DOI: 10.3389/fneur.2022.816625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Objectives APOE e4 has been linked to poor outcome following traumatic brain injury (TBI); however, the mechanisms behind this relationship are unclear. Few studies have investigated the relationship between the APOE genotype and established brain related protein biomarkers following TBI. The purpose of this study was to examine this relationship in service members and veterans (SMVs) following TBI. Methods Participants were 209 SMVs [124 uncomplicated mild TBI (mTBI); 85 complicated mild, moderate, severe, or penetrating TBI (mod-sev TBI)] prospectively enrolled in the DVBIC-TBICoE 15-Year Longitudinal TBI Study. APOE genotyping was undertaken using non-fasting blood serum samples. Participants were divided into three groups: APOE e2+, APOE e3/e3, and APOE e4+. Results In participants with mTBI, those with the APOE e2 allele had significantly lower levels of tau than those with APOE e4 (p = 0.005, r = 0.43, medium-large effect size). Those with APOE e3/e3 trended toward having higher tau than those APOE e2+ (p = 0.076, r = 0.20, small-medium effect size) and lower tau than those with APOE e4+ (p = 0.062, r = 0.21, small-medium effect size). There were no significant differences in biomarkers based on APOE in the mod-sev TBI group. Discussion This study is the first to demonstrate APOE genotype is related to serum tau levels following a mTBI, extending prior findings to human serum following mTBI. In addition to higher serum tau levels in APOE e4 carriers, lower tau levels were observed in APOE e2 carriers, suggesting a possible protective effect.
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Affiliation(s)
- Sara M. Lippa
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Rael T. Lange
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Centre of Excellence on Post-traumatic Stress Disorder, Ottawa, ON, Canada
- General Dynamics Information Technology, Falls Church, VA, United States
| | - Clifton L. Dalgard
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The American Genome Center, Bethesda, MD, United States
| | - Anthony R. Soltis
- Henry M. Jackson Foundation, Bethesda, MD, United States
- PRIMER, Bethesda, MD, United States
| | | | - Tracey A. Brickell
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Centre of Excellence on Post-traumatic Stress Disorder, Ottawa, ON, Canada
- General Dynamics Information Technology, Falls Church, VA, United States
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Louis M. French
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jessica Gill
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
- School of Nursing, Johns Hopkins University, Baltimore, MD, United States
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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45
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Rajabli F, Beecham GW, Hendrie HC, Baiyewu O, Ogunniyi A, Gao S, Kushch NA, Lipkin-Vasquez M, Hamilton-Nelson KL, Young JI, Dykxhoorn DM, Nuytemans K, Kunkle BW, Wang L, Jin F, Liu X, Feliciano-Astacio BE, Schellenberg GD, Dalgard CL, Griswold AJ, Byrd GS, Reitz C, Cuccaro ML, Haines JL, Pericak-Vance MA, Vance JM. A locus at 19q13.31 significantly reduces the ApoE ε4 risk for Alzheimer's Disease in African Ancestry. PLoS Genet 2022; 18:e1009977. [PMID: 35788729 PMCID: PMC9286282 DOI: 10.1371/journal.pgen.1009977] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 07/15/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
African descent populations have a lower Alzheimer disease risk from ApoE ε4 compared to other populations. Ancestry analysis showed that the difference in risk between African and European populations lies in the ancestral genomic background surrounding the ApoE locus (local ancestry). Identifying the mechanism(s) of this protection could lead to greater insight into the etiology of Alzheimer disease and more personalized therapeutic intervention. Our objective is to follow up the local ancestry finding and identify the genetic variants that drive this risk difference and result in a lower risk for developing Alzheimer disease in African ancestry populations. We performed association analyses using a logistic regression model with the ApoE ε4 allele as an interaction term and adjusted for genome-wide ancestry, age, and sex. Discovery analysis included imputed SNP data of 1,850 Alzheimer disease and 4,331 cognitively intact African American individuals. We performed replication analyses on 63 whole genome sequenced Alzheimer disease and 648 cognitively intact Ibadan individuals. Additionally, we reproduced results using whole-genome sequencing of 273 Alzheimer disease and 275 cognitively intact admixed Puerto Rican individuals. A further comparison was done with SNP imputation from an additional 8,463 Alzheimer disease and 11,365 cognitively intact non-Hispanic White individuals. We identified a significant interaction between the ApoE ε4 allele and the SNP rs10423769_A allele, (β = -0.54,SE = 0.12,p-value = 7.50x10-6) in the discovery data set, and replicated this finding in Ibadan (β = -1.32,SE = 0.52,p-value = 1.15x10-2) and Puerto Rican (β = -1.27,SE = 0.64,p-value = 4.91x10-2) individuals. The non-Hispanic Whites analyses showed an interaction trending in the "protective" direction but failing to pass a 0.05 significance threshold (β = -1.51,SE = 0.84,p-value = 7.26x10-2). The presence of the rs10423769_A allele reduces the odds ratio for Alzheimer disease risk from 7.2 for ApoE ε4/ε4 carriers lacking the A allele to 2.1 for ApoE ε4/ε4 carriers with at least one A allele. This locus is located approximately 2 mB upstream of the ApoE locus, in a large cluster of pregnancy specific beta-1 glycoproteins on chromosome 19 and lies within a long noncoding RNA, ENSG00000282943. This study identified a new African-ancestry specific locus that reduces the risk effect of ApoE ε4 for developing Alzheimer disease. The mechanism of the interaction with ApoEε4 is not known but suggests a novel mechanism for reducing the risk for ε4 carriers opening the possibility for potential ancestry-specific therapeutic intervention.
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Affiliation(s)
- Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Hugh C. Hendrie
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | | | | | - Sujuan Gao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Marina Lipkin-Vasquez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Kara L. Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Juan I. Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Fulai Jin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | | | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York State, United States of America
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
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46
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Dewan R, Jaunmuktane Z, Garcia‐Segura ME, Strand C, Wild E, Villar J, Dalgard CL, Tabrizi SJ, Traynor BJ, Proukakis C. CAG Somatic Instability in a Huntington Disease Expansion Carrier Presenting with a Progressive Supranuclear Palsy-like Phenotype. Mov Disord 2022; 37:1555-1557. [PMID: 35510647 PMCID: PMC9308656 DOI: 10.1002/mds.29035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/15/2022] [Accepted: 04/08/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Ramita Dewan
- Neuromuscular Disease Research Section, Laboratory of NeurogeneticsNational Institute on AgingBethesdaMarylandUSA
| | - Zane Jaunmuktane
- Department of Clinical and Movement NeurosciencesQueen Square Institute of Neurology, UCLLondonUnited Kingdom
- Queen Square Brain Bank, UCLLondonUnited Kingdom
| | - Monica Emili Garcia‐Segura
- Department of Clinical and Movement NeurosciencesQueen Square Institute of Neurology, UCLLondonUnited Kingdom
| | | | - Edward Wild
- Huntington's Disease Centre, Queen Square Institute of Neurology, UCLLondonUnited Kingdom
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCLLondonUnited Kingdom
| | - Joaquin Villar
- Center for Military Precision MedicineUniformed Services University of the Health SciencesBethesdaMarylandUSA
- Henry M Jackson Foundation for the Advancement of Military MedicineBethesdaMarylandUSA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health SciencesBethesdaMarylandUSA
- The American Genome CenterUniformed Services University of the Health SciencesBethesdaMarylandUSA
| | - Sarah J. Tabrizi
- Huntington's Disease Centre, Queen Square Institute of Neurology, UCLLondonUnited Kingdom
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCLLondonUnited Kingdom
- UK Dementia Research Institute, UCLLondonUnited Kingdom
| | - Bryan J. Traynor
- Neuromuscular Disease Research Section, Laboratory of NeurogeneticsNational Institute on AgingBethesdaMarylandUSA
| | - Christos Proukakis
- Department of Clinical and Movement NeurosciencesQueen Square Institute of Neurology, UCLLondonUnited Kingdom
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47
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Khayrullina G, Alipio‐Gloria ZA, Deguise M, Gagnon S, Chehade L, Stinson M, Belous N, Bergman EM, Lischka FW, Rotty J, Dalgard CL, Kothary R, Johnson KA, Burnett BG. Survival motor neuron protein deficiency alters microglia reactivity. Glia 2022; 70:1337-1358. [PMID: 35373853 PMCID: PMC9081169 DOI: 10.1002/glia.24177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022]
Abstract
Survival motor neuron (SMN) protein deficiency results in loss of alpha motor neurons and subsequent muscle atrophy in patients with spinal muscular atrophy (SMA). Reactive microglia have been reported in SMA mice and depleting microglia rescues the number of proprioceptive synapses, suggesting a role in SMA pathology. Here, we explore the contribution of lymphocytes on microglia reactivity in SMA mice and investigate how SMN deficiency alters the reactive profile of human induced pluripotent stem cell (iPSC)-derived microglia. We show that microglia adopt a reactive morphology in spinal cords of SMA mice. Ablating lymphocytes did not alter the reactive morphology of SMA microglia and did not improve the survival or motor function of SMA mice, indicating limited impact of peripheral immune cells on the SMA phenotype. We found iPSC-derived SMA microglia adopted an amoeboid morphology and displayed a reactive transcriptome profile, increased cell migration, and enhanced phagocytic activity. Importantly, cell morphology and electrophysiological properties of motor neurons were altered when they were incubated with conditioned media from SMA microglia. Together, these data reveal that SMN-deficient microglia adopt a reactive profile and exhibit an exaggerated inflammatory response with potential impact on SMA neuropathology.
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Affiliation(s)
- Guzal Khayrullina
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | | | - Marc‐Olivier Deguise
- Regenerative Medicine ProgramOttawa Hospital Research InstituteOttawaOntarioCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
- Centre for Neuromuscular DiseaseUniversity of OttawaOttawaOntarioCanada
- Department of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada
| | - Sabrina Gagnon
- Regenerative Medicine ProgramOttawa Hospital Research InstituteOttawaOntarioCanada
| | - Lucia Chehade
- Regenerative Medicine ProgramOttawa Hospital Research InstituteOttawaOntarioCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
- Centre for Neuromuscular DiseaseUniversity of OttawaOttawaOntarioCanada
| | - Matthew Stinson
- Department of BiochemistryUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | - Natalya Belous
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | - Elizabeth M. Bergman
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | - Fritz W. Lischka
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | - Jeremy Rotty
- Department of BiochemistryUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
- The American Genome CenterUniformed Services University of the Health SciencesBethesdaMarylandUSA
| | - Rashmi Kothary
- Regenerative Medicine ProgramOttawa Hospital Research InstituteOttawaOntarioCanada
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
- Centre for Neuromuscular DiseaseUniversity of OttawaOttawaOntarioCanada
- Department of MedicineUniversity of OttawaOttawaOntarioCanada
| | | | - Barrington G. Burnett
- Department of Anatomy, Physiology, and GeneticsUniformed Services University of the Health Sciences, F. Edward Hebert School of MedicineBethesdaMarylandUSA
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48
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Wang X, Gardner K, Tegegn MB, Dalgard CL, Alba C, Menzel S, Patel H, Pirooznia M, Fu YP, Seifuddin FT, Thein SL. Genetic variants of PKLR are associated with acute pain in sickle cell disease. Blood Adv 2022; 6:3535-3540. [PMID: 35271708 PMCID: PMC9198922 DOI: 10.1182/bloodadvances.2021006668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Acute pain, the most prominent complication of sickle cell disease (SCD), results from vaso-occlusion triggered by sickling of deoxygenated red blood cells (RBCs). Concentration of 2,3-diphosphoglycerate (2,3-DPG) in RBCs promotes deoxygenation by preferentially binding to the low-affinity T conformation of HbS. 2,3-DPG is an intermediate substrate in the glycolytic pathway in which pyruvate kinase (gene PKLR, protein PKR) is a rate-limiting enzyme; variants in PKLR may affect PKR activity, 2,3-DPG levels in RBCs, RBC sickling, and acute pain episodes (APEs). We performed a candidate gene association study using 2 cohorts: 242 adult SCD-HbSS patients and 977 children with SCD-HbSS or SCD-HbSβ0 thalassemia. Seven of 47 PKLR variants evaluated in the adult cohort were associated with hospitalization: intron 4, rs2071053; intron 2, rs8177970, rs116244351, rs114455416, rs12741350, rs3020781, and rs8177964. All 7 variants showed consistent effect directions in both cohorts and remained significant in weighted Fisher's meta-analyses of the adult and pediatric cohorts using P < .0071 as threshold to correct for multiple testing. Allele-specific expression analyses in an independent cohort of 52 SCD adults showed that the intronic variants are likely to influence APE by affecting expression of PKLR, although the causal variant and mechanism are not defined.
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Affiliation(s)
- Xunde Wang
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Kate Gardner
- School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Department of Haematology, Guy and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Mickias B. Tegegn
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, and
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
| | - Stephan Menzel
- School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Hamel Patel
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | | | - Yi-Ping Fu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | | | - Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
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49
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Zhu Q, Wang J, Yu H, Hu Q, Bateman NW, Long M, Rosario S, Schultz E, Dalgard CL, Wilkerson MD, Sukumar G, Huang RY, Kaur J, Lele SB, Zsiros E, Villella J, Lugade A, Moysich K, Conrads TP, Maxwell GL, Odunsi K. Whole-Genome Sequencing Identifies PPARGC1A as a Putative Modifier of Cancer Risk in BRCA1/2 Mutation Carriers. Cancers (Basel) 2022; 14:2350. [PMID: 35625955 PMCID: PMC9139302 DOI: 10.3390/cancers14102350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
While BRCA1 and BRCA2 mutations are known to confer the largest risk of breast cancer and ovarian cancer, the incomplete penetrance of the mutations and the substantial variability in age at cancer onset among carriers suggest additional factors modifying the risk of cancer in BRCA1/2 mutation carriers. To identify genetic modifiers of BRCA1/2, we carried out a whole-genome sequencing study of 66 ovarian cancer patients that were enriched with BRCA carriers, followed by validation using data from the Pan-Cancer Analysis of Whole Genomes Consortium. We found PPARGC1A, a master regulator of mitochondrial biogenesis and function, to be highly mutated in BRCA carriers, and patients with both PPARGC1A and BRCA1/2 mutations were diagnosed with breast or ovarian cancer at significantly younger ages, while the mutation status of each gene alone did not significantly associate with age of onset. Our study suggests PPARGC1A as a possible BRCA modifier gene. Upon further validation, this finding can help improve cancer risk prediction and provide personalized preventive care for BRCA carriers.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Han Yu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
| | - Mark Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Spencer Rosario
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Emily Schultz
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Ruea-Yea Huang
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Jasmine Kaur
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Shashikant B. Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Emese Zsiros
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Jeannine Villella
- Division of Gynecologic Oncology, Lenox Hill Hospital/Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY 11549, USA;
| | - Amit Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL 60637, USA
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50
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Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S, Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, Pala F, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, Montealegre Sanchez GA, Barron K, Rey-Jurado E, Vial C, Poli MC, Licari A, Montagna D, Marseglia GL, Licciardi F, Ramenghi U, Discepolo V, Lo Vecchio A, Guarino A, Eisenstein EM, Imberti L, Sottini A, Biondi A, Mató S, Gerstbacher D, Truong M, Stack MA, Magliocco M, Bosticardo M, Kawai T, Danielson JJ, Hulett T, Askenazi M, Hu S, Cohen JI, Su HC, Kuhns DB, Lionakis MS, Snyder TM, Holland SM, Goldbach-Mansky R, Tsang JS, Notarangelo LD. Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19. Nat Med 2022; 28:1050-1062. [PMID: 35177862 PMCID: PMC9119950 DOI: 10.1038/s41591-022-01724-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022]
Abstract
Pediatric Coronavirus Disease 2019 (pCOVID-19) is rarely severe; however, a minority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might develop multisystem inflammatory syndrome in children (MIS-C), with substantial morbidity. In this longitudinal multi-institutional study, we applied multi-omics (analysis of soluble biomarkers, proteomics, single-cell gene expression and immune repertoire analysis) to profile children with COVID-19 (n = 110) and MIS-C (n = 76), along with pediatric healthy controls (pHCs; n = 76). pCOVID-19 was characterized by robust type I interferon (IFN) responses, whereas prominent type II IFN-dependent and NF-κB-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission. Transient expansion of TRBV11-2 T cell clonotypes in MIS-C was associated with signatures of inflammation and T cell activation. The association of MIS-C with the combination of HLA A*02, B*35 and C*04 alleles suggests genetic susceptibility. MIS-C B cells showed higher mutation load than pCOVID-19 and pHC. These results identify distinct immunopathological signatures in pCOVID-19 and MIS-C that might help better define the pathophysiology of these disorders and guide therapy.
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Affiliation(s)
- Keith Sacco
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Svetlana Vakkilainen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cihan Oguz
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | | | - Sara Alehashemi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Farzana Bhuyan
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana A de Jesus
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aristine Cheng
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Lack
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danielle L Fink
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vasileios Oikonomou
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jinguo Chen
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Gina A Montealegre Sanchez
- Intramural Clinical Management and Operation Branch (ICMOB), Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karyl Barron
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Rey-Jurado
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Maria Cecilia Poli
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Unidad de Inmunología y Reumatología, Hospital de niños Dr. Roberto del Río, Santiago, Chile
| | - Amelia Licari
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Daniela Montagna
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
- Laboratory of Immunology and Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Francesco Licciardi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Eli M Eisenstein
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Mount Scopus, Jerusalem, Israel
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN, University of Milano Bicocca, Fondazione MBBM, Ospedale San Gerardo, Monza, Italy
| | - Sayonara Mató
- Randall Children's Hospital at Legacy Emanuel, Portland, OR, USA
| | - Dana Gerstbacher
- Division of Pediatric Rheumatology, Stanford Children's Hospital, Stanford, CA, USA
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tomoki Kawai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey J Danielson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Hulett
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | | | - Shaohui Hu
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Douglas B Kuhns
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raphaela Goldbach-Mansky
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIH Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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