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Zheng T, Roda G, Zabana Y, Escudero-Hernández C, Liu X, Chen Y, Camargo Tavares L, Bonfiglio F, Mellander MR, Janczewska I, Vigren L, Sjöberg K, Ohlsson B, Almer S, Halfvarson J, Miehlke S, Madisch A, Lieb W, Kupčinskas J, Weersma RK, Bujanda L, Julià A, Marsal S, Esteve M, Guagnozzi D, Fernández-Bañares F, Ferrer C, Peter I, Ludvigsson JF, Pardi D, Verhaegh B, Jonkers D, Pierik M, Münch A, Franke A, Bresso F, Khalili H, Colombel JF, D'Amato M. Human Leukocyte Antigen Signatures as Pathophysiological Discriminants of Microscopic Colitis Subtypes. J Crohns Colitis 2024; 18:349-359. [PMID: 37768647 DOI: 10.1093/ecco-jcc/jjad165] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND AND AIMS Microscopic colitis [MC] is currently regarded as an inflammatory bowel disease that manifests as two subtypes: collagenous colitis [CC] and lymphocytic colitis [LC]. Whether these represent a clinical continuum or distinct entities is, however, an open question. Genetic investigations may contribute important insight into their respective pathophysiologies. METHODS We conducted a genome-wide association study [GWAS] meta-analysis in 1498 CC, 373 LC patients, and 13 487 controls from Europe and the USA, combined with publicly available MC GWAS data from UK Biobank and FinnGen [2599 MC cases and 552 343 controls in total]. Human leukocyte antigen [HLA] alleles and polymorphic residues were imputed and tested for association, including conditional analyses for the identification of key causative variants and residues. Genetic correlations with other traits and diagnoses were also studied. RESULTS We detected strong HLA association with CC, and conditional analyses highlighted the DRB1*03:01 allele and its residues Y26, N77, and R74 as key to this association (best p = 1.4 × 10-23, odds ratio [OR] = 1.96). Nominally significant genetic correlations were detected between CC and pneumonia [rg = 0.77; p = 0.048] and oesophageal diseases [rg = 0.45, p = 0.023]. An additional locus was identified in MC GWAS analyses near the CLEC16A and RMI2 genes on chromosome 16 [rs35099084, p = 2.0 × 10-8, OR = 1.31]. No significant association was detected for LC. CONCLUSION Our results suggest CC and LC have distinct pathophysiological underpinnings, characterised by an HLA predisposing role only in CC. This challenges existing classifications, eventually calling for a re-evaluation of the utility of MC umbrella definitions.
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Affiliation(s)
- Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giulia Roda
- Biostructures and Biosystems National Institute, Rome, Italy
| | - Yamile Zabana
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Celia Escudero-Hernández
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Xingrong Liu
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ye Chen
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Ferdinando Bonfiglio
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Lina Vigren
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Klas Sjöberg
- Department of Clinical Sciences, Lund University, Skane University Hospital, Malmo, Sweden
| | - Bodil Ohlsson
- Department of Clinical Sciences, Lund University, Skane University Hospital, Malmo, Sweden
| | - Sven Almer
- Division of Gastroenterology, Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Orebro University Hospital, Örebro, Sweden
| | - Stephan Miehlke
- Centre for Digestive Diseases, Internal Medicine Centre Eppendorf, and Centre for Oesophageal Disorders, University Hospital Eppendorf, Hamburg, Germany
| | - Ahmed Madisch
- Department of Gastroenterology, CRH Clinic Siloah, Hannover, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Juozas Kupčinskas
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, Universidad del País Vasco, San Sebastian, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d' Hebron Research Institute, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d' Hebron Research Institute, Barcelona, Spain
| | - Maria Esteve
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Danila Guagnozzi
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
- Department of Gastroenterology, Vall d'Hebron University Hospital, Neuro-Immuno-Gastroenterology Group, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Fernando Fernández-Bañares
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | - Carmen Ferrer
- Pathology Department, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Darrell Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Bas Verhaegh
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daisy Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Marieke Pierik
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Andreas Münch
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Gastroenterology and Hepatology, Linköping University, Linköping, Sweden
- Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Francesca Bresso
- Division of Gastroenterology, Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jean-Frederic Colombel
- Dr Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mauro D'Amato
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Medicine and Surgery, LUM University, Casamassima, Italy
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Crane HM, Nance RM, Ruderman SA, Haidar L, Tenforde MW, Heckbert SR, Budoff MJ, Hahn AW, Drumright LN, Ma J, Mixson LS, Lober WB, Barnes GS, McReynolds J, Attia EF, Peter I, Moges T, Bamford L, Cachay E, Mathews WC, Christopolous K, Hunt PW, Napravnik S, Keruly J, Moore RD, Burkholder G, Willig AL, Lindstrom S, Whitney BM, Saag MS, Kitahata MM, Crothers KA, Delaney JAC. Venous Thromboembolism Among People With HIV: Design, Implementation, and Findings of a Centralized Adjudication System in Clinical Care Sites Across the United States. J Acquir Immune Defic Syndr 2024; 95:207-214. [PMID: 37988634 DOI: 10.1097/qai.0000000000003339] [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: 02/09/2023] [Accepted: 08/30/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND People with HIV (PWH) are at increased risk for venous thromboembolism (VTE). We conducted this study to characterize VTE including provoking factors among PWH in the current treatment era. METHODS We included PWH with VTE between 2010 and 2020 at 6 sites in the CFAR Network of Integrated Clinical Systems cohort. We ascertained for possible VTE using diagnosis, VTE-related imaging, and VTE-related procedure codes, followed by centralized adjudication of primary data by expert physician reviewers. We evaluated sensitivity and positive predictive value of VTE ascertainment approaches. VTEs were classified by type and anatomic location. Reviewers identified provoking factors such as hospitalizations, infections, and other potential predisposing factors such as smoking. RESULTS We identified 557 PWH with adjudicated VTE: 239 (43%) had pulmonary embolism with or without deep venous thrombosis, and 318 (57%) had deep venous thrombosis alone. Ascertainment with clinical diagnoses alone missed 6% of VTEs identified with multiple ascertainment approaches. DVTs not associated with intravenous lines were most often in the proximal lower extremities. Among PWH with VTE, common provoking factors included recent hospitalization (n = 134, 42%), infection (n = 133, 42%), and immobilization/bed rest (n = 78, 25%). Only 57 (10%) PWH had no provoking factor identified. Smoking (46%), HIV viremia (27%), and injection drug use (22%) were also common. CONCLUSIONS We conducted a robust adjudication process that demonstrated the benefits of multiple ascertainment approaches followed by adjudication. Provoked VTEs were more common than unprovoked events. Nontraditional and modifiable potential predisposing factors such as viremia and smoking were common.
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Affiliation(s)
- Heidi M Crane
- Department of Medicine, University of Washington, Seattle, WA
| | - Robin M Nance
- Department of Medicine, University of Washington, Seattle, WA
| | | | - Lara Haidar
- Department of Pharmacy, University of Manitoba, Manitoba, CA
| | - Mark W Tenforde
- Department of Medicine, University of Washington, Seattle, WA
| | | | - Matthew J Budoff
- Department of Medicine, Lundquist Institute at Harbor-UCLA, Torrance, CA
| | - Andrew W Hahn
- Department of Medicine, University of Washington, Seattle, WA
| | | | - Jimmy Ma
- Department of Medicine, University of Washington, Seattle, WA
| | - L S Mixson
- Department of Medicine, University of Washington, Seattle, WA
| | - William B Lober
- Department of Medicine and Clinical Informatics Research Group, University of Washington, Seattle, WA
| | - Gregory S Barnes
- Clinical Informatics Research Group, University of Washington, Seattle, WA
| | - Justin McReynolds
- Clinical Informatics Research Group, University of Washington, Seattle, WA
| | - Engi F Attia
- Department of Medicine, University of Washington, Seattle, WA
| | - Inga Peter
- Department of Genetics, Mount Sinai University, New York NY
| | - Tesfaye Moges
- Department of Medicine, University of California, San Diego, CA
| | - Laura Bamford
- Department of Medicine, University of California, San Diego, CA
| | - Edward Cachay
- Department of Medicine, University of California, San Diego, CA
| | | | | | - Peter W Hunt
- Department of Medicine, University of California, San Francisco, CA
| | - Sonia Napravnik
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Jeanne Keruly
- Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Greer Burkholder
- Department of Medicine, University of Alabama Birmingham, Birmingham, AL
| | - Amanda L Willig
- Department of Medicine, University of Alabama Birmingham, Birmingham, AL
| | - Sara Lindstrom
- Department of Genetics, University of Washington, Seattle, WA; and
| | | | - Michael S Saag
- Department of Medicine, University of North Carolina, Chapel Hill, NC
| | - Mari M Kitahata
- Department of Medicine, University of Washington, Seattle, WA
| | | | - Joseph A C Delaney
- Department of Medicine, University of Washington, Seattle, WA
- Department of Medicine, University of Manitoba, Manitoba, CA
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3
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Sabino J, Tarassishin L, Eisele C, Hawkins K, Barré A, Nair N, Rendon A, Debebe A, Picker M, Agrawal M, Stone J, George J, Legnani P, Maser E, Chen CL, Thjømøe A, Mørk E, Dubinsky M, Hu J, Colombel JF, Peter I, Torres J. Influence of Early Life Factors, including breast milk Composition, on the Microbiome of Infants Born to Mothers with and without Inflammatory Bowel Disease. J Crohns Colitis 2023; 17:1723-1732. [PMID: 37279927 PMCID: PMC10673817 DOI: 10.1093/ecco-jcc/jjad096] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Herein we analysed the influence of early life factors, including breast milk composition, on the development of the intestinal microbiota of infants born to mothers with and without IBD. METHODS The MECONIUM [Exploring MEChanisms Of disease traNsmission In Utero through the Microbiome] study is a prospective cohort study consisting of pregnant women with or without IBD and their infants. Longitudinal stool samples were collected from babies and analysed using 16s rRNA sequencing and faecal calprotectin. Breast milk proteomics was profiled using Olink inflammation panel. RESULTS We analysed gut microbiota of 1034 faecal samples from 294 infants [80 born to mothers with and 214 to mothers without IBD]. Alpha diversity was driven by maternal IBD status and time point. The major influencers of the overall composition of the microbiota were mode of delivery, feeding, and maternal IBD status. Specific taxa were associated with these exposures, and maternal IBD was associated with a reduction in Bifidobacterium. In 312 breast milk samples [91 from mothers with IBD], mothers with IBD displayed lower abundance of proteins involved in immune regulation, such as thymic stromal lymphopoietin, interleukin-12 subunit beta, tumour necrosis factor-beta, and C-C motif chemokine 20, as compared with control mothers [adjusted p = 0.0016, 0.049, 0.049, and 0.049, respectively], with negative correlations with baby´s calprotectin, and microbiome at different time points. CONCLUSION Maternal IBD diagnosis influences microbiota in their offspring during early life. The proteomic profile of breast milk of women with IBD differs from that of women without IBD, with distinct time-dependent associations with baby's gut microbiome and feacal calprotectin.
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Affiliation(s)
- João Sabino
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
- Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Leonid Tarassishin
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Caroline Eisele
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
- College of Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Kelly Hawkins
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Amelie Barré
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Nile Nair
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Alexa Rendon
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Anketse Debebe
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Mellissa Picker
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Manasi Agrawal
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
- Center for Molecular Prediction of IBD [PREDICT], Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Joanne Stone
- Gastroenterology Division, Icahn School of Medicine at Mount Sinai, Department of Obstetrics, Gynecology and Reproductive Sciences, New York, NY, USA
| | - James George
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
| | - Peter Legnani
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
| | - Elana Maser
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
| | - Ching-Lynn Chen
- Gastroenterology Division, Icahn School of Medicine at Mount Sinai, Department of Obstetrics, Gynecology and Reproductive Sciences, New York, NY, USA
| | | | | | - Marla Dubinsky
- Icahn School of Medicine at Mount Sinai, Division of Pediatric Gastroenterology and Hepatology, New York, NY, USA
| | - Jianzhong Hu
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Jean-Frederic Colombel
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Joanna Torres
- Icahn School of Medicine at Mount Sinai, Division of Gastroenterology, Department of Medicine, New York, NY, USA
- Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
- Gastroenterology Division, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Portugal
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4
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Haas CB, Jordahl KM, Nance RM, Whitney BM, Wang L, Delaney JAC, Ruderman S, Jia T, Mathews WC, Saag MS, Lee SA, Napravnik S, Jacobson JM, Chander G, McCall EM, Moore RD, Mayer KH, Mukherjee S, Lee WJ, Crane PK, Crane H, Peter I, Lindström S. Assessing the associations between known genetic variants and substance use in people with HIV in the United States. PLoS One 2023; 18:e0292068. [PMID: 37796845 PMCID: PMC10553320 DOI: 10.1371/journal.pone.0292068] [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: 05/11/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND The prevalence of substance use in people with HIV (PWH) in the United States is higher than in the general population and is an important driver of HIV-related outcomes. We sought to assess if previously identified genetic associations that contribute to substance use are also observed in a population of PWH. METHODS We performed genome-wide association studies (GWAS) of alcohol, smoking, and cannabis use phenotypes in a multi-ancestry population of 7,542 PWH from the Center for AIDS Research Network of Integrated Clinical Systems (CNICS). We conducted multi-ancestry GWAS for individuals of African (n = 3,748), Admixed American (n = 1,334), and European (n = 2,460) ancestry. Phenotype data were self-reported and collected using patient reported outcomes (PROs) and three questions from AUDIT-C, an alcohol screening tool. We analyzed nine phenotypes: 1) frequency of alcohol consumption, 2) typical number of drinks on a day when drinking alcohol, 3) frequency of five or more alcoholic drinks in a 30-day period, 4) smoking initiation, 5) smoking cessation, 6) cigarettes per day, 7) cannabis use initiation, 8) cannabis use cessation, 9) frequency of cannabis use during the previous 30 days. For each phenotype we considered a) variants previously identified as associated with a substance use trait and b) novel associations. RESULTS We observed evidence for effects of previously reported single nucleotide polymorphisms (SNPs) related to alcohol (rs1229984, p = 0.001), tobacco (rs11783093, p = 2.22E-4), and cannabis use (rs2875907, p = 0.005). We also report two novel loci (19p13.2, p = 1.3E-8; and 20p11.21, p = 2.1E-8) associated with cannabis use cessation. CONCLUSIONS Our analyses contribute to understanding the genetic bases of substance use in a population with relatively higher rates of use compared to the general population.
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Affiliation(s)
- Cameron B. Haas
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Kristina M. Jordahl
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Robin M. Nance
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Bridget M. Whitney
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States of America
| | | | - Stephanie Ruderman
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Tongqiu Jia
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Wm. Christopher Mathews
- Department of Medicine, University of California at San Diego, San Diego, CA, United States of America
| | - Michael S. Saag
- Department of Medicine at the School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Sulggi A. Lee
- Department of Medicine, University of California at San Francisco, San Francisco, CA, United States of America
| | - Sonia Napravnik
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jeffrey M. Jacobson
- Center for AIDS Research, Case Western Reserve University/University Hospitals Case Medical Center, Cleveland, OH, United States of America
| | - Geetanjali Chander
- Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Elizabeth M. McCall
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Kenneth H. Mayer
- Harvard Medical School, Beth Israel Deaconess Medical Center, Fenway Health, Boston, MA, United States of America
| | - Shubhabrata Mukherjee
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Won Jun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Heidi Crane
- Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
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5
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Michaely P, Bielinski SJ, Campbell K, D’Alessio F, Dean D, Earley YF, Paine R, Salama G, Peter I. Guide to assembling a successful K99/R00 application. J Clin Transl Sci 2023; 7:e215. [PMID: 37900348 PMCID: PMC10603388 DOI: 10.1017/cts.2023.639] [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: 07/24/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
The National Institutes of Health's (NIH) K99/R00 Pathway to Independence Award offers promising postdoctoral researchers and clinician-scientists an opportunity to receive research support at both the mentored and the independent levels with the goal of facilitating a timely transition to a tenure-track faculty position. This transitional program has been generally successful, with most K99/R00 awardees successfully securing R01-equivalent funding by the end of the R00 period. However, often highly promising proposals fail because of poor grantsmanship. This overview provides guidance from the perspective of long-standing members of the National Heart, Lung, and Blood Institute's Mentored Transition to Independence study section for the purpose of helping mentors and trainees regarding how best to assemble competitive K99/R00 applications.
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Affiliation(s)
- Peter Michaely
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Suzette J. Bielinski
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Kenneth Campbell
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY, USA
| | - Franco D’Alessio
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Delphine Dean
- Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Yumei Feng Earley
- Department of Pharmacology, Center for Molecular and Cellular Signaling in the Cardiovascular System, University of Nevada, Reno, NV, USA
| | - Robert Paine
- Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, University of Utah, Salt Lake City, UT, USA
| | - Guy Salama
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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6
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Taymans JM, Fell M, Greenamyre T, Hirst WD, Mamais A, Padmanabhan S, Peter I, Rideout H, Thaler A. Perspective on the current state of the LRRK2 field. NPJ Parkinsons Dis 2023; 9:104. [PMID: 37393318 PMCID: PMC10314919 DOI: 10.1038/s41531-023-00544-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/05/2023] [Indexed: 07/03/2023] Open
Abstract
Almost 2 decades after linking LRRK2 to Parkinson's disease, a vibrant research field has developed around the study of this gene and its protein product. Recent studies have begun to elucidate molecular structures of LRRK2 and its complexes, and our understanding of LRRK2 has continued to grow, affirming decisions made years ago to therapeutically target this enzyme for PD. Markers of LRRK2 activity, with potential to monitor disease progression or treatment efficacy, are also under development. Interestingly, there is a growing understanding of the role of LRRK2 outside of the central nervous system in peripheral tissues such as gut and immune cells that may also contribute to LRRK2 mediated pathology. In this perspective, our goal is to take stock of LRRK2 research by discussing the current state of knowledge and critical open questions in the field.
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Affiliation(s)
- Jean-Marc Taymans
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172-LilNCog-Lille Neuroscience & Cognition, F-59000, Lille, France.
| | - Matt Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Tim Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh, 3501 Fifth Avenue, Suite 7039, Pittsburgh, PA, 15260, USA
| | - Warren D Hirst
- Neurodegenerative Diseases Research Unit, Biogen, 115 Broadway, Cambridge, MA, 02142, USA
| | - Adamantios Mamais
- Center for Translational Research in Neurodegenerative Disease, Department of Neurology, University of Florida, Gainesville, FL, USA
| | - Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson's Research, Grand Central Station, P.O. Box 4777, New York, NY, 10120, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Hardy Rideout
- Centre for Clinical, Experimental Surgery, and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Avner Thaler
- Movement Disorders Unit and Laboratory of Early Markers of Neurodegeneration, Neurological Institute, Tel-Aviv Medical Center, Faculty of medicine, Tel-Aviv University, Tel-Aviv, Israel
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7
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Olendzki BC, Hsiao BS, Weinstein K, Chen R, Frisard C, Madziar C, Picker M, Pauplis C, Maldonado-Contreras A, Peter I. Dietary Intake of Pregnant Women with and without Inflammatory Bowel Disease in the United States. Nutrients 2023; 15:nu15112464. [PMID: 37299427 DOI: 10.3390/nu15112464] [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: 05/02/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Pregnancy is a vulnerable time where the lives of mother and baby are affected by diet, especially high-risk pregnancies in women with inflammatory bowel disease (IBD). Limited research has examined diet during pregnancy with IBD. AIMS Describe and compare the diet quality of pregnant women with and without IBD, and examine associations between dietary intake and guidelines during pregnancy. METHODS Three 24 h recalls were utilized to assess the diets of pregnant women with IBD (n = 88) and without IBD (n = 82) during 27-29 weeks of gestation. A customized frequency questionnaire was also administered to measure pre- and probiotic foods. RESULTS Zinc intake (p = 0.02), animal protein (g) (p = 0.03), and ounce equivalents of whole grains (p = 0.03) were significantly higher in the healthy control (HC) group than the IBD group. Nutrients of concern with no significant differences between groups included iron (3% IBD and 2% HC met the goals), saturated fat (only 1% of both groups met the goals), choline (23% IBD and 21% HC met the goals), magnesium (38% IBD and 35% HC met the goals), calcium (48% IBD and 60% HC met the goals), and water intake (49% IBD and 48% HC met the goals). CONCLUSIONS Most pregnant women in this cohort fell short of the dietary nutrients recommended in pregnancy, especially concerning for women with IBD.
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Affiliation(s)
- Barbara C Olendzki
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Bi-Sek Hsiao
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Kaitlyn Weinstein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rosemary Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christine Frisard
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Camilla Madziar
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Mellissa Picker
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Connor Pauplis
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ana Maldonado-Contreras
- Department of Microbiology and Physiology Systems, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Lee WJ, Cheng H, Whitney BM, Nance RM, Britton SR, Jordahl K, Lindstrom S, Ruderman SA, Kitahata MM, Saag MS, Willig AL, Burkholder G, Eron JJ, Kovacic JC, Björkegren JLM, Mathews WC, Cachay E, Feinstein MJ, Budoff M, Hunt PW, Moore RD, Keruly J, McCaul ME, Chander G, Webel A, Mayer KH, Delaney JA, Crane PK, Martinez C, Crane HM, Hao K, Peter I. Polygenic risk scores point toward potential genetic mechanisms of type 2 myocardial infarction in people with HIV. Int J Cardiol 2023:S0167-5273(23)00648-4. [PMID: 37149004 DOI: 10.1016/j.ijcard.2023.04.058] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/03/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND People with human immunodeficiency virus (HIV) infection (PWH) are at higher risk of myocardial infarction (MI) than those without HIV. About half of MIs in PWH are type 2 (T2MI), resulting from mismatch between myocardial oxygen supply and demand, in contrast to type 1 MI (T1MI), which is due to primary plaque rupture or coronary thrombosis. Despite worse survival and rising incidence in the general population, evidence-based treatment recommendations for T2MI are lacking. We used polygenic risk scores (PRS) to explore genetic mechanisms of T2MI compared to T1MI in PWH. METHODS We derived 115 PRS for MI-related traits in 9541 PWH enrolled in the Centers for AIDS Research Network of Integrated Clinical Systems cohort with adjudicated T1MI and T2MI. We applied multivariate logistic regression analyses to determine the association with T1MI and T2MI. Based on initial findings, we performed gene set enrichment analysis of the top variants composing PRS associated with T2MI. RESULTS We found that T1MI was strongly associated with PRS for cardiovascular disease, lipid profiles, and metabolic traits. In contrast, PRS for alcohol dependence and cholecystitis, significantly enriched in energy metabolism pathways, were predictive of T2MI risk. The association remained after the adjustment for actual alcohol consumption. CONCLUSIONS We demonstrate distinct genetic traits associated with T1MI and T2MI among PWH further highlighting their etiological differences and supporting the role of energy regulation in T2MI pathogenesis.
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Affiliation(s)
- Won Jun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Bridget M Whitney
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA
| | - Robin M Nance
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA
| | - Sierra R Britton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA; Department of Population Health Sciences, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Kristina Jordahl
- Department of Epidemiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephanie A Ruderman
- Department of Epidemiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Mari M Kitahata
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amanda L Willig
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Greer Burkholder
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joseph J Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA; Victor Chang Cardiac Research Institute, Darlinghurst, Australia; St Vincent's Clinical School, University of NSW, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA; Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | | | - Edward Cachay
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Matthew J Feinstein
- Department of Medicine, Northwestern University Feinberg School of Medicine, Evanston, IL, USA
| | - Mathew Budoff
- Deparment of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Peter W Hunt
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jeanne Keruly
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mary E McCaul
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Geetanjali Chander
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA; Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Allison Webel
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, University of Washington, Seattle, WA, USA
| | | | - Joseph A Delaney
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA; College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Canada
| | - Paul K Crane
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA
| | - Claudia Martinez
- Department of Medicine, Division of Cardiology, University of Miami Miller School of Medicine, Florida, USA
| | - Heidi M Crane
- Department of Medicine, University of Washington School of Public Health, Seattle, WA, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York, USA.
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Peter I, Strober W. Immunological Features of LRRK2 Function and Its Role in the Gut-Brain Axis Governing Parkinson's Disease. J Parkinsons Dis 2023; 13:279-296. [PMID: 37066923 DOI: 10.3233/jpd-230021] [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] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Emerging evidence implicates intestinal involvement in the onset and/or progression on the selective degeneration of dopaminergic neurons characterizing Parkinson's disease (PD). On the one hand, there are studies supporting the Braak hypothesis that holds that pathologic α-synuclein, a hallmark of PD, is secreted by enteric nerves into intestinal tissue and finds its way to the central nervous system (CNS) via retrograde movement in the vagus nerve. On the other hand, there is data showing that cells bearing leucine-rich repeat kinase 2 (LRRK2), a signaling molecule with genetic variants associated with both PD and with inflammatory bowel disease, can be activated in intestinal tissue and contribute locally to intestinal inflammation, or peripherally to PD pathogenesis via cell trafficking to the CNS. Importantly, these gut-centered factors affecting PD development are not necessarily independent of one another: they may interact and enhance their respective pathologic functions. In this review, we discuss this possibility by analysis of studies conducted in recent years focusing on the ability of LRRK2 to shape immunologic responses and the role of α-synuclein in influencing this ability.
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Affiliation(s)
- Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Shah SC, Tarassishin L, Eisele C, Rendon A, Debebe A, Hawkins K, Hillenbrand C, Agrawal M, Torres J, Peek RM, Stone J, Dubinsky M, Colombel JF, Peter I, Hu J. Breastfeeding Is Associated with Lower Likelihood of Helicobacter Pylori Colonization in Babies, Based on a Prospective USA Maternal-Infant Cohort. Dig Dis Sci 2022; 67:5149-5157. [PMID: 35119598 PMCID: PMC9349469 DOI: 10.1007/s10620-021-07371-x] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mother-to-child transmission of Helicobacter pylori (H. pylori) is the primary source of intrafamilial spread in early childhood in regions of high H. pylori prevalence. However, early-in-life H. pylori colonization and associated protective or risk factors have not been fully evaluated in lower prevalence regions, such as the USA. AIMS Therefore, from a well-characterized prospective US cohort, we selected women who provided fecal samples during pregnancy and had paired fecal samples from their babies up to 24 months postpartum. We evaluated maternal and baby factors associated with likelihood of H. pylori colonization in the babies. Fecal antigen testing was used to determine H. pylori status. We also evaluated the association between maternal breastmilk cytokines and H. pylori colonization in breastfed babies. RESULTS Among included mother-baby pairs (n = 66), H. pylori prevalence was 31.8% in mothers and 19.7% in their babies. Dominant breastfeeding (adjusted odds ratio [aOR] 0.17, 95% CI 0.03-0.98) and maternal IBD (aOR 0.05, 95% CI 0.01-0.27) were associated with significantly lower likelihood of H. pylori colonization among babies; no other clinical factors were associated with H. pylori colonization in the babies. Matrix metalloproteinase-10 (MMP-10) and tumor necrosis factor-related activation-induced cytokine expression were significantly higher in breastmilk of mothers with H. pylori positive vs negative babies. CONCLUSIONS Consistent with data from high H. pylori prevalence regions, our findings suggest dominant breastfeeding may protect against early H. pylori colonization. Downregulation of pro-inflammatory cytokines such as MMP-10 may be relevant in mediating this protection among breastfed babies, but more data are needed.
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Affiliation(s)
- Shailja C Shah
- Section of Gastroenterology, Veterans Affairs San Diego Health System, 3350 La Jolla Villa Drive, San Diego VA, GI Section 3, rdFl, San Diego, CA, 92161, USA
- Division of Gastroenterology, University of California, San Diego, CA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leonid Tarassishin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Caroline Eisele
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Alexa Rendon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Anketse Debebe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Kelly Hawkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Christen Hillenbrand
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Manasi Agrawal
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joana Torres
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Gastroenterology, Surgical Department, Hospital Beatriz Ângelo, Loures, Portugal
| | - Richard M Peek
- Section of Gastroenterology, Veterans Affairs San Diego Health System, 3350 La Jolla Villa Drive, San Diego VA, GI Section 3, rdFl, San Diego, CA, 92161, USA
| | - Joanne Stone
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Science,, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- Department of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., 1402F, New York, NY, 10029, USA.
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Luu B, Ruderman S, Nance R, Delaney JAC, Ma J, Hahn A, Heckbert SR, Budoff MJ, Crothers K, Mathews WC, Christopolous K, Hunt PW, Eron J, Moore R, Keruly J, Lober WB, Burkholder GA, Willig A, Chander G, McCaul ME, Cropsey K, O'Cleirigh C, Peter I, Feinstein M, Tsui JI, Lindstroem S, Saag M, Kitahata MM, Crane HM, Drumright LN, Whitney BM. Tobacco smoking and binge alcohol use are associated with incident venous thromboembolism in an HIV cohort. HIV Med 2022; 23:1051-1060. [PMID: 35343038 PMCID: PMC9515244 DOI: 10.1111/hiv.13309] [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: 06/22/2021] [Revised: 01/27/2022] [Accepted: 03/14/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND People with HIV (PWH) are at increased risk of cardiovascular comorbidities and substance use is a potential predisposing factor. We evaluated associations of tobacco smoking and alcohol use with venous thromboembolism (VTE) in PWH. METHODS We assessed incident, centrally adjudicated VTE among 12 957 PWH within the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) cohort between January 2009 and December 2018. Using separate Cox proportional hazards models, we evaluated associations of time-updated alcohol and cigarette use with VTE, adjusting for demographic and clinical characteristics. Smoking was evaluated as pack-years and never, former, or current use with current cigarettes per day. Alcohol use was parameterized using categorical and continuous alcohol use score, frequency of use, and binge frequency. RESULTS During a median of 3.6 years of follow-up, 213 PWH developed a VTE. One-third of PWH reported binge drinking and 40% reported currently smoking. In adjusted analyses, risk of VTE was increased among both current (HR: 1.44, 95% CI: 1.02-2.03) and former (HR: 1.44, 95% CI: 0.99-2.07) smokers compared to PWH who never smoked. Additionally, total pack-years among ever-smokers (HR: 1.10 per 5 pack-years; 95% CI: 1.03-1.18) was associated with incident VTE in a dose-dependent manner. Frequency of binge drinking was associated with incident VTE (HR: 1.30 per 7 days/month, 95% CI: 1.11-1.52); however, alcohol use frequency was not. Severity of alcohol use was not significantly associated with VTE. CONCLUSIONS Current smoking and pack-year smoking history were dose-dependently associated with incident VTE among PWH in CNICS. Binge drinking was also associated with VTE. Interventions for smoking and binge drinking may decrease VTE risk among PWH.
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Affiliation(s)
- Brandon Luu
- Northern Ontario School of Medicine, Thunder Bay, Ontario, Canada
| | | | - Robin Nance
- University of Washington, Seattle, Washington, USA
| | - Joseph A C Delaney
- University of Washington, Seattle, Washington, USA
- University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jimmy Ma
- University of Washington, Seattle, Washington, USA
| | - Andrew Hahn
- University of Washington, Seattle, Washington, USA
| | | | | | | | | | | | - Peter W Hunt
- University of California, San Francisco, California, USA
| | - Joseph Eron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Amanda Willig
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | - Karen Cropsey
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Inga Peter
- Mount Sinai Hospital, New York, New York, USA
| | | | | | | | - Michael Saag
- University of Alabama at Birmingham, Birmingham, Alabama, USA
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Shelton BA, Sawinski D, MacLennan PA, Lee W, Wyatt C, Nadkarni G, Fatima H, Mehta S, Crane HM, Porrett P, Julian B, Moore RD, Christopoulos K, Jacobson JM, Muller E, Eron JJ, Saag M, Peter I, Locke JE. Associations between female birth sex and risk of chronic kidney disease development among people with HIV in the USA: A longitudinal, multicentre, cohort study. EClinicalMedicine 2022; 53:101653. [PMID: 36159042 PMCID: PMC9489495 DOI: 10.1016/j.eclinm.2022.101653] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/19/2022] [Accepted: 08/30/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Women represent a meaningful proportion of new HIV diagnoses, with Black women comprising 58% of new diagnoses among women. As HIV infection also increases risk of chronic kidney disease (CKD), understanding CKD risk among women with HIV (WWH), particularly Black women, is critical. METHODS In this longitudinal cohort study of people with HIV (PWH) enrolled in CFAR Network of Integrated Clinical Systems (CNICS), a multicentre study comprised of eight academic medical centres across the United States from Jan 01, 1996 and Nov 01, 2019, adult PWH were excluded if they had ≤2 serum creatinine measurements, developed CKD prior to enrollment, or identified as intersex or transgendered, leaving a final cohort of 33,998 PWH. The outcome was CKD development, defined as estimated glomerular filtration rate (eGFR) <60 mL/min/1·73 m2 calculated using the CKD-EPI equation, for ≥90 days with no intervening higher values. FINDINGS Adjusting for demographic and clinical characteristics, WWH were 61% more likely to develop CKD than men (adjusted hazard ratio [aHR]: 1·61, 95% CI: 1·46-1·78, p<0·001). This difference persisted after further adjustment for APOL1 risk variants (aHR female sex: 1·92, 95% CI: 1·63-2·26, p<0·001) and substance abuse (aHR female sex: 1·70, 95% CI: 1·54-1·87, p<0·001). INTERPRETATION WWH experienced increased risk of CKD. Given disparities in care among patients with end-stage kidney disease, efforts to engage WWH in nephrology care to improve chronic disease management are critical. FUNDING US National Institutes of Health.
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Affiliation(s)
- Brittany A. Shelton
- Department of Public Health, University of Tennessee, Knoxville, TN, United States
| | | | - Paul A. MacLennan
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | - Wonjun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Girish Nadkarni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huma Fatima
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | - Shikha Mehta
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | - Heidi M. Crane
- University of Washington School of Medicine, United States
| | - Paige Porrett
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | - Bruce Julian
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | | | | | | | - Elmi Muller
- Stellenbosch University, Medicine and Health Sciences, South Africa
| | - Joseph J. Eron
- University of North Carolina at Chapel Hill School of Medicine, United States
| | - Michael Saag
- University of Alabama at Birmingham Heersink School of Medicine, United States
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jayme E. Locke
- University of Alabama at Birmingham Heersink School of Medicine, United States
- Corresponding author at: Arnold G. Diethelm MD Endowed Chair in Transplantation Surgery, Department of Surgery, Division of Transplantation, 701 19th Street South, LHRB 780, Birmingham, AL 35294, United States.
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13
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Velosa M, Hochner H, Yerushalmi B, Harel S, Friss C, Calderon-Margalit R, Paltiel O, Manor O, Balicer RD, Greenfeld S, Kariv R, Ledderman N, Matz E, Peter I, Friedlander Y, Turner D. Pre- and Perinatal Factors Predicting Inflammatory Bowel Disease: A Population-Based Study with Fifty Years of Follow-Up. J Crohns Colitis 2022; 16:1397-1404. [PMID: 35299254 DOI: 10.1093/ecco-jcc/jjac043] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 12/29/2021] [Accepted: 03/14/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Pre- and perinatal events may be associated with an increased risk of inflammatory bowel disease [IBD]. We aimed to investigate the role of pre- and perinatal factors as potential risk factors for the development of IBD in a population with a follow-up of 50 years. METHODS We conducted a nested case-control study, reporting IBD incidence among individuals born in 1964-76, for whom pre- and perinatal exposures were reported as part of the Jerusalem Perinatal Study [JPS], by linking them to the database of the epidemiology group of the Israeli IBD Research Nucleus [epi-IIRN], including all IBD patients in Israel since 2005 and their matched controls. RESULTS We identified 2789 individuals within the epi-IIRN cohort who were also included in the JPS cohort [n = 90 079]: 746 IBD patients (405 with Crohn's disease [CD] and 341 with ulcerative colitis [UC]) and 2043 non-IBD controls. Those with a 'Non-western' family origin had decreased odds of developing CD and UC. High socioeconomic status was associated with CD but not UC. Low birth weight [≤2500 g] occurred less frequently in IBD cases compared to controls, especially in UC patients, showing a protective effect. Being the first born was associated with CD, and having older siblings lowered the odds of developing CD, decreasing 7% with each additional sibling. Smoking and breastfeeding data were available for a subset of individuals, but neither was associated with IBD development. CONCLUSION This population-based study identifies several pre- and perinatal variables as predictors of IBD development. This information may be helpful to facilitate implementation of early diagnosis interventions and family follow-up protocols.
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Affiliation(s)
- Monica Velosa
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Baruch Yerushalmi
- Department of Gastroenterology and Hepatology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sasha Harel
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Chagit Friss
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | | | - Ora Paltiel
- Hadassah, Hebrew University Braun School of Public Health, Jerusalem, Israel
| | - Orly Manor
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ran D Balicer
- Clalit Research Institute, Chief's Office, Clalit Health Services, Tel Aviv, Israel
| | | | | | | | - Eran Matz
- Leumit Health Services, Tel Aviv, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
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14
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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet 2022; 54:1275-1283. [PMID: 36038634 PMCID: PMC9700438 DOI: 10.1038/s41588-022-01156-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.
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Affiliation(s)
- Aleksejs Sazonovs
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christine R Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kai Yuan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandon Avila
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Abreu
- Crohn's and Colitis Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Matthieu Allez
- Hopital Saint-Louis, APHP, Universite de Paris, INSERM U1160, Paris, France
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Crohn's and Colitis Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gil Atzmon
- Department for Human Biology, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- The Institute for Aging Research, The Nathan Shock Center of Excellence in the Basic Biology of Aging and the Paul F. Glenn Center for the Biology of Human Aging Research at Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Laurent Beaugerie
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Alain Bitton
- McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Bernd Bokemeyer
- Department of Internal Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Jacques Cosnes
- Professeur Chef de Service chez APHP and Universite Paris-6, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Allan Daly
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noor Dawany
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
- University of Rome Sapienza, Rome, Italy
- IRGB - CNR, Cagliari, Italy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eva Ellinghaus
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Laura Fachal
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kyle Gettler
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Philippe Goyette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Daniel Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marc Hoeppner
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Peter Irving
- Department of Gastroenterology, Guys and Saint Thomas Hospital, London, UK
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Vivek Iyer
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Chaim Jalas
- Director of Genetic Resources and Services, Center for Rare Jewish Genetic Disorders, Bonei Olam, Brooklyn, NY, USA
| | - Judith Kelsen
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Barbara S Kirschner
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Kimmo Kontula
- Department of Medicine, Helsinki University Hospital, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Subra Kugathasan
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Chloé Lévesque
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - James D Lewis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Crohn's and Colitis Foundation, New York, NY, USA
| | | | - Britt-Sabina Loescher
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - John Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra May
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Myriam Mni
- University of Liège, ULG, Liège, Belgium
| | | | | | | | | | - David T Okou
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
- Institut National de Sante Publique (INSP), Abidjan, Côte d'Ivoire
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jean Paquette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Joel Pekow
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Natalie Prescott
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel L Rice
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Bruce Sands
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Stefan Schreiber
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Philippe Seksik
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Rasha Shawky
- IBD BioResource, NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Alison Simmons
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skeiceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Matthew Solomonson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hari Somineni
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Turner
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
- Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Andrea E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Séverine Vermeire
- University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Andre Franke
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Crohn's Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Kurt Isselbacher Professor of Medicine at Harvard Medical School, Cambridge, MA, USA
- Core Institute Member, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Immunology Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John D Rioux
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Mark J Daly
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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15
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Bowles KR, Pugh DA, Liu Y, Patel T, Renton AE, Bandres-Ciga S, Gan-Or Z, Heutink P, Siitonen A, Bertelsen S, Cherry JD, Karch CM, Frucht SJ, Kopell BH, Peter I, Park YJ, Charney A, Raj T, Crary JF, Goate AM. 17q21.31 sub-haplotypes underlying H1-associated risk for Parkinson's disease are associated with LRRC37A/2 expression in astrocytes. Mol Neurodegener 2022; 17:48. [PMID: 35841044 PMCID: PMC9284779 DOI: 10.1186/s13024-022-00551-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 09/23/2021] [Accepted: 06/21/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is genetically associated with the H1 haplotype of the MAPT 17q.21.31 locus, although the causal gene and variants underlying this association have not been identified. METHODS To better understand the genetic contribution of this region to PD and to identify novel mechanisms conferring risk for the disease, we fine-mapped the 17q21.31 locus by constructing discrete haplotype blocks from genetic data. We used digital PCR to assess copy number variation associated with PD-associated blocks, and used human brain postmortem RNA-seq data to identify candidate genes that were then further investigated using in vitro models and human brain tissue. RESULTS We identified three novel H1 sub-haplotype blocks across the 17q21.31 locus associated with PD risk. Protective sub-haplotypes were associated with increased LRRC37A/2 copy number and expression in human brain tissue. We found that LRRC37A/2 is a membrane-associated protein that plays a role in cellular migration, chemotaxis and astroglial inflammation. In human substantia nigra, LRRC37A/2 was primarily expressed in astrocytes, interacted directly with soluble α-synuclein, and co-localized with Lewy bodies in PD brain tissue. CONCLUSION These data indicate that a novel candidate gene, LRRC37A/2, contributes to the association between the 17q21.31 locus and PD via its interaction with α-synuclein and its effects on astrocytic function and inflammatory response. These data are the first to associate the genetic association at the 17q21.31 locus with PD pathology, and highlight the importance of variation at the 17q21.31 locus in the regulation of multiple genes other than MAPT and KANSL1, as well as its relevance to non-neuronal cell types.
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Affiliation(s)
- Kathryn R. Bowles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Derian A. Pugh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Yiyuan Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Tulsi Patel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alan E. Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute On Aging, National Institutes of Health, Bethesda, MD USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Québec Canada
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, Québec Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, Québec Canada
| | - Peter Heutink
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ari Siitonen
- Institute of Clinical Medicine, Department of Neurology, University of Oulu, Oulu, Finland
- Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Sarah Bertelsen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Jonathan D. Cherry
- Alzheimer’s Disease and CTE Center, Boston University, Boston University School of Medicine, Boston, MA USA
- Department of Neurology, Boston University School of Medicine, Boston, MA USA
- VA Boston Healthcare System, 150 S. Huntington Avenue, Boston, MA USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA USA
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St Louis, St. Louis, MO USA
| | - Steven J. Frucht
- Department of Neurology, Fresco Institute for Parkinson’s and Movement Disorders, New York University Langone, New York, NY USA
| | - Brian H. Kopell
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Center for Neuromodulation, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Inga Peter
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Y. J. Park
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Alexander Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John F. Crary
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - A. M. Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY USA
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16
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Peter I, Dubinsky M, Xuan S, Chen N, Wang A. Letter to the Editor: Re-Revisiting the Association Between Inflammatory Bowel Disease and Parkinson's Disease. Inflamm Bowel Dis 2022; 28:e72. [PMID: 35267013 DOI: 10.1093/ibd/izac049] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla Dubinsky
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Si Xuan
- AbbVie, North Chicago, IL, USA
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17
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Deloer S, Fuss I, Suebsuwong C, Kumar K, Devita RJ, Peter I, Strober W. Inhibition of LRRK2 Kinase Activity in the Treatment of Crohn’s Disease. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.163.06] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The leucine-rich repeat kinase 2 (LRRK2) gene is a genetic hotspot for gain-of-function mutations associated with various diseases such as Crohn’s and Parkinson’s disease. These mutations enhance LRRK2 kinase activity and, consequently, various inhibitors of this activity are currently being tested as treatment modalities. Here, we report studies of two novel kinase inhibitors (Termed CS-190 and CS-82) with LRRK2 inhibition activity. In vitro studies disclosed that the two inhibitors suppress LRRK2 phosphorylation as well as its ability to phosphorylate the LRRK2 targets, Rab 10 and 12; in addition, they suppress human dendritic cell production of TNFa stimulated by several known LRRK2 activators including the Dectin-1-ligand, zymosan-depleted S. cerevisiae extract. Finally, the inhibitors exhibited powerful suppression of the ability of LRRK2 to mediate NLRC4 inflammasome production of IL-1beta. These in vitro finding correlated with in vivo studies showing that IP administration of one of the kinase inhibitors (CS-82) ameliorates colitis in the DSS-colitis model as evaluated by weight loss and inflammation scores. These findings suggest that these newly developed inhibitors are potential agents for treatment of Crohn’s disease.
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Affiliation(s)
- Sharmina Deloer
- 11Mucosal Immunology Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
| | - Ivan Fuss
- 11Mucosal Immunology Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
| | - Chalada Suebsuwong
- 2Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai
| | - Kunal Kumar
- 2Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai
| | - Robert J Devita
- 2Department of Pharmacological Sciences, Drug Discovery Institute, Icahn School of Medicine at Mount Sinai
| | - Inga Peter
- 3Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
| | - Warren Strober
- 11Mucosal Immunology Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH
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18
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Kontorovich AR, Tang Y, Patel N, Georgievskaya Z, Shadrina M, Williams N, Moscati A, Peter I, Itan Y, Sampson B, Gelb BD. Burden of Cardiomyopathic Genetic Variation in Lethal Pediatric Myocarditis. Circ Genom Precis Med 2021; 14:e003426. [PMID: 34228484 DOI: 10.1161/circgen.121.003426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Acute myocarditis (AM) is a well-known cause of sudden death and heart failure, often caused by prevalent viruses. We previously showed that some pediatric AM correlates with putatively damaging variants in genes related to cardiomyocyte structure and function. We sought to evaluate whether deleterious cardiomyopathic variants were enriched among fatal pediatric AM cases in New York City compared with ancestry-matched controls. METHODS Twenty-four children (aged 3 weeks to 20 years) with death due to AM were identified through autopsy records; histologies were reviewed to confirm that all cases met Dallas criteria for AM and targeted panel sequencing of 57 cardiomyopathic genes was performed. Controls without cardiovascular disease were identified from a pediatric database and matched by genetic ancestry to cases using principal components from exome sequencing. Rates of putative deleterious variations (DV) were compared between cases and controls. Where available, AM tissues underwent viral analysis by polymerase chain reaction. RESULTS DV were identified in 4 of 24 AM cases (16.7%), compared with 2 of 96 age and ancestry-matched controls (2.1%, P=0.014). Viral causes were proven for 6 of 8 AM cases (75%), including the one DV+ case where tissue was available for testing. DV+ cases were more likely to be female, have no evidence of chronic inflammation, and associate with sudden cardiac death than DV- cases. CONCLUSIONS Deleterious variants in genes related to cardiomyocyte integrity are more common in children with fatal AM than controls, likely conferring susceptibility. Additionally, genetically mediated AM may progress more rapidly and be more severe.
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Affiliation(s)
- Amy R Kontorovich
- Zena and Michael A. Weiner Cardiovascular Institute (A.R.K.), Icahn School of Medicine at Mount Sinai, New York.,Institute for Genomic Health (A.R.K.), Icahn School of Medicine at Mount Sinai, New York.,The Mindich Child Health and Development Institute (A.R.K., N.P., M.S., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Yingying Tang
- Office of the Chief Medical Examiner of New York, New York, NY (Y.T., Z.G., N.W., B.S.)
| | - Nihir Patel
- The Mindich Child Health and Development Institute (A.R.K., N.P., M.S., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Zhanna Georgievskaya
- Office of the Chief Medical Examiner of New York, New York, NY (Y.T., Z.G., N.W., B.S.)
| | - Mariya Shadrina
- The Mindich Child Health and Development Institute (A.R.K., N.P., M.S., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Nori Williams
- Office of the Chief Medical Examiner of New York, New York, NY (Y.T., Z.G., N.W., B.S.)
| | - Arden Moscati
- Department of Genetics & Genomic Sciences (A.M., I.P., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Inga Peter
- Department of Genetics & Genomic Sciences (A.M., I.P., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Yuval Itan
- The Mindich Child Health and Development Institute (A.R.K., N.P., M.S., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York.,Department of Genetics & Genomic Sciences (A.M., I.P., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York
| | - Barbara Sampson
- Office of the Chief Medical Examiner of New York, New York, NY (Y.T., Z.G., N.W., B.S.)
| | - Bruce D Gelb
- The Mindich Child Health and Development Institute (A.R.K., N.P., M.S., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York.,Department of Genetics & Genomic Sciences (A.M., I.P., Y.I., B.D.G.), Icahn School of Medicine at Mount Sinai, New York.,Department of Pediatrics (B.D.G.), Icahn School of Medicine at Mount Sinai, New York
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19
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Kontorovich AR, Patel N, Moscati A, Richter F, Peter I, Purevjav E, Selejan SR, Kindermann I, Towbin JA, Bohm M, Klingel K, Gelb BD. Myopathic Cardiac Genotypes Increase Risk for Myocarditis. JACC Basic Transl Sci 2021; 6:584-592. [PMID: 34368507 PMCID: PMC8326270 DOI: 10.1016/j.jacbts.2021.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022]
Abstract
Impairments in certain cardiac genes confer risk for myocarditis in children. To determine the extent of this association, we performed genomic sequencing in predominantly adult patients with acute myocarditis and matched control subjects. Putatively deleterious variants in a broad set of cardiac genes were found in 19 of 117 acute myocarditis cases vs 34 of 468 control subjects (P = 0.003). Thirteen genes classically associated with cardiomyopathy or neuromuscular disorders with cardiac involvement were implicated, including >1 associated damaging variant in DYSF, DSP, and TTN. Phenotypes of subjects who have acute myocarditis with or without deleterious variants were similar, indicating that genetic testing is necessary to differentiate them.
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Key Words
- ACM, arrhythmogenic cardiomyopathy
- AM, acute myocarditis
- AM1, acute myocarditis registry 1
- CMP, cardiomyopathy
- DV, deleterious variant
- EF, ejection fraction
- ES, exome sequencing
- NMD, neuromuscular disorder
- OR, odds ratio
- TGP, targeted gene panel
- acute myocarditis
- cardiomyopathy
- genetics
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Affiliation(s)
- Amy R. Kontorovich
- Zena and Michael A. Weiner Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nihir Patel
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Felix Richter
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Simina Ramona Selejan
- Department of Internal Medicine III (Cardiology, Angiology and Intensive Care), Saarland University Medical Center, Saarland University, Homburg/Saar, Germany
| | - Ingrid Kindermann
- Department of Internal Medicine III (Cardiology, Angiology and Intensive Care), Saarland University Medical Center, Saarland University, Homburg/Saar, Germany
| | - Jeffrey A. Towbin
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Michael Bohm
- Department of Internal Medicine III (Cardiology, Angiology and Intensive Care), Saarland University Medical Center, Saarland University, Homburg/Saar, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Bruce D. Gelb
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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20
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Agrawal M, Sabino J, Frias-Gomes C, Hillenbrand CM, Soudant C, Axelrad JE, Shah SC, Ribeiro-Mourão F, Lambin T, Peter I, Colombel JF, Narula N, Torres J. Early life exposures and the risk of inflammatory bowel disease: Systematic review and meta-analyses. EClinicalMedicine 2021; 36:100884. [PMID: 34308303 PMCID: PMC8257976 DOI: 10.1016/j.eclinm.2021.100884] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/12/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Early life exposures impact immune system development and therefore the risk of immune-mediated diseases, including inflammatory bowel disease (IBD). We systematically reviewed the impact of pre-, peri‑, and postnatal exposures up to the age of five years on subsequent IBD diagnosis. METHODS We identified case-control and cohort studies reporting on the association between early life environmental factors and Crohn's disease (CD), ulcerative colitis (UC), or IBD overall. Databases were search from their inception until May 24th, 2019 until July 14th, 2020. We conducted meta-analyses for quantitative review of relevant risk factors that were comparable across studies and qualitative synthesis of the literature for a wide range of early life exposures, including maternal health and exposures during pregnancy, perinatal factors, birth month and related-factors, breastfeeding, hygiene-related factors and social factors, immigration, antibiotics, offspring health, including infections, and passive smoking. PROSPERO registration: CRD42019134980. FINDINGS Prenatal exposure to antibiotics (OR 1.8; 95% CI 1.2-2.5) and tobacco smoke (OR 1.5; 95% CI 1.2-1.9), and early life otitis media (OR 2.1; 95% CI 1.2-3.6) were associated with IBD. There was a trend towards an association between exposure to antibiotics in infancy and IBD (OR: 1.7, 95% CI 0.97, 2.9), supported by positive data on population-based data. Breastfeeding was protective against IBD. Other early life risk factors had no association with IBD, but data were limited and heterogenous. INTERPRETATION Early life is an important period of susceptibility for IBD development later in life. Tobacco smoke, infections and antibiotics were associated positively, and breastfeeding was associated negatively with IBD. Our findings offer an opportunity to develop primary prevention strategies. FUNDING This study did not receive any funding.
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Affiliation(s)
- Manasi Agrawal
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - João Sabino
- Gastroenterology Division, University Hospital of Leuven, Leuven, Belgium
| | - Catarina Frias-Gomes
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures 2674-514, Portugal
| | - Christen M. Hillenbrand
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Celine Soudant
- Levy Library, The Mount Sinai Medical Center, New York, NY, United States
- Medical Library, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jordan E. Axelrad
- Division of Gastroenterology, New York University Grossman School of Medicine, New York, NY, United States
| | - Shailja C. Shah
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
- Section of Gastroenterology, Veterans Affairs Tennessee Valley Healthcare System, Nashville campus, Nashville, TN, United States
| | - Francisco Ribeiro-Mourão
- Pediatrics Department, Unidade Local de Saúde do Alto Minho, Viana do Castelo, Portugal
- Pediatrics Department, Centro Materno Infantil do Norte – Centro Hospitalar e Universitário do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Thomas Lambin
- Department of Gastroenterology, Claude Huriez Hospital, University of Lille, Lille, France
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Neeraj Narula
- Department of Medicine (Division of Gastroenterology) and Farncombe Family Digestive, Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Joana Torres
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures 2674-514, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Portugal
- Corresponding author.
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21
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Cheng H, Sewda A, Marquez-Luna C, White SR, Whitney BM, Williams-Nguyen J, Nance RM, Lee WJ, Kitahata MM, Saag MS, Willig A, Eron JJ, Mathews WC, Hunt PW, Moore RD, Webel A, Mayer KH, Delaney JA, Crane PK, Crane HM, Hao K, Peter I. Correction to: Genetic architecture of cardiometabolic risks in people living with HIV. BMC Med 2021; 19:114. [PMID: 33947393 PMCID: PMC8097782 DOI: 10.1186/s12916-021-01976-9] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Anshuman Sewda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.,Institute of Health Management Research, IIHMR University, Jaipur, Rajasthan, India
| | - Carla Marquez-Luna
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sierra R White
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Bridget M Whitney
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Jessica Williams-Nguyen
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Robin M Nance
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Won Jun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Mari M Kitahata
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America.,Center for AIDS Research, University of Washington, Seattle, WA, United States of America
| | - Michael S Saag
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda Willig
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Joseph J Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States of America
| | - W Christopher Mathews
- Department of Medicine, University of California San Diego, San Diego, CA, United States of America
| | - Peter W Hunt
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States of America.,Department of Epidemiology,
- Johns Hopkins University, Baltimore, MD, United States of America
| | - Allison Webel
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, United States of America
| | - Kenneth H Mayer
- The Fenway Institute at Fenway Health, Boston, MA, United States of America
| | - Joseph A Delaney
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Paul K Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Heidi M Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America.,Center for AIDS Research, University of Washington, Seattle, WA, United States of America
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.
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22
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Di Narzo AF, Hart A, Kosoy R, Peters L, Stojmirovic A, Cheng H, Zhang Z, Shan M, Cho J, Kasarskis A, Argmann C, Peter I, Schadt EE, Hao K. Polygenic risk score for alcohol drinking behavior improves prediction of inflammatory bowel disease risk. Hum Mol Genet 2021; 30:514-523. [PMID: 33601420 PMCID: PMC8599895 DOI: 10.1093/hmg/ddab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/21/2020] [Revised: 01/23/2021] [Accepted: 02/03/2021] [Indexed: 02/05/2023] Open
Abstract
Epidemiological studies have long recognized risky behaviors as potentially modifiable factors for the onset and flares of inflammatory bowel disease (IBD); yet, the underlying mechanisms are largely unknown. Recently, the genetic susceptibilities to cigarette smoking, alcohol and cannabis use [i.e. substance use (SU)] have been characterized by well-powered genome-wide association studies (GWASs). We aimed to assess the impact of genetic determinants of SU on IBD risk. Using Mount Sinai Crohn's and Colitis Registry (MSCCR) cohort of 1058 IBD cases and 188 healthy controls, we computed the polygenic risk score (PRS) for SU and correlated them with the observed IBD diagnoses, while adjusting for genetic ancestry, PRS for IBD and SU behavior at enrollment. The results were validated in a pediatric cohort with no SU exposure. PRS of alcohol consumption (DrnkWk), smoking cessation and age of smoking initiation, were associated with IBD risk in MSCCR even after adjustment for PRSIBD and actual smoking status. One interquartile range decrease in PRSDrnkWk was significantly associated to higher IBD risk (i.e. inverse association) (with odds ratio = 1.65 and 95% confidence interval: 1.32, 2.06). The association was replicated in a pediatric Crohn's disease cohort. Colocalization analysis identified a locus on chromosome 16 with polymorphisms in IL27, SULT1A2 and SH2B1, which reached genome-wide statistical significance in GWAS (P < 7.7e-9) for both alcohol consumption and IBD risk. This study demonstrated that the genetic predisposition to SU was associated with IBD risk, independent of PRSIBD and in the absence of SU behaviors. Our study may help further stratify individuals at risk of IBD.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amy Hart
- Immunology Translational Sciences, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | | | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mingxu Shan
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
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23
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Chen E, Chuang LS, Giri M, Villaverde N, Hsu NY, Sabic K, Joshowitz S, Gettler K, Nayar S, Chai Z, Alter IL, Chasteau CC, Korie UM, Dzedzik S, Thin TH, Jain A, Moscati A, Bongers G, Duerr RH, Silverberg MS, Brant SR, Rioux JD, Peter I, Schumm LP, Haritunians T, McGovern DP, Itan Y, Cho JH. Inflamed Ulcerative Colitis Regions Associated With MRGPRX2-Mediated Mast Cell Degranulation and Cell Activation Modules, Defining a New Therapeutic Target. Gastroenterology 2021; 160:1709-1724. [PMID: 33421512 PMCID: PMC8494017 DOI: 10.1053/j.gastro.2020.12.076] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Recent literature has implicated a key role for mast cells in murine models of colonic inflammation, but their role in human ulcerative colitis (UC) is not well established. A major advance has been the identification of mrgprb2 (human orthologue, MRGPX2) as mediating IgE-independent mast cell activation. We sought to define mechanisms of mast cell activation and MRGPRX2 in human UC. METHODS Colon tissues were collected from patients with UC for bulk RNA sequencing and lamina propria cells were isolated for MRGPRX2 activation studies and single-cell RNA sequencing. Genetic association of all protein-altering G-protein coupled receptor single-nucleotide polymorphism was performed in an Ashkenazi Jewish UC case-control cohort. Variants of MRGPRX2 were transfected into Chinese hamster ovary (CHO) and human mast cell (HMC) 1.1 cells to detect genotype-dependent effects on β-arrestin recruitment, IP-1 accumulation, and phosphorylated extracellular signal-regulated kinase. RESULTS Mast cell-specific mediators and adrenomedullin (proteolytic precursor of PAMP-12, an MRGPRX2 agonist) are up-regulated in inflamed compared to uninflamed UC. MRGPRX2 stimulation induces carboxypeptidase secretion from inflamed UC. Of all protein-altering GPCR alleles, a unique variant of MRGPRX2, Asn62Ser, was most associated with and was bioinformatically predicted to alter arrestin recruitment. We validated that the UC protective serine allele enhances β-arrestin recruitment, decreases IP-1, and increases phosphorylated extracellular signal-regulated kinase with MRGPRX2 agonists. Single-cell RNA sequencing defines that adrenomedullin is expressed by activated fibroblasts and epithelial cells and that interferon gamma is a key upstream regulator of mast cell gene expression. CONCLUSION Inflamed UC regions are distinguished by MRGPRX2-mediated activation of mast cells, with decreased activation observed with a UC-protective genetic variant. These results define cell modules of UC activation and a new therapeutic target.
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Affiliation(s)
- Ernie Chen
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ling-shiang Chuang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Mamta Giri
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nicole Villaverde
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nai-yun Hsu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ksenija Sabic
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Sari Joshowitz
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Kyle Gettler
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Shikha Nayar
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Zhi Chai
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Isaac L. Alter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Colleen C. Chasteau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ujunwa M. Korie
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Siarhei Dzedzik
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Tin Htwe Thin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Aayushee Jain
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Gerardus Bongers
- Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai, New York
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Ontario, Canada, Toronto, Ontario, Canada
| | - Steven R. Brant
- Crohns and Colitis Center of New Jersey, Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States
| | - John D. Rioux
- Research Centre, Montreal Heart Institute, Montréal, QC, Canada. Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Inga Peter
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - L. Philip Schumm
- Department of Health Sciences, University of Chicago, Chicago, Illinois, United States
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Dermot P. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States,To whom correspondence should be addressed: Judy Cho, Hess CSM Building Floor 8th Room 118, 1470 Madison Avenue, New York, NY 10029, TEL. (212) 824-8940, FAX. (646) 537-9452,
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24
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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25
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Kim ES, Tarassishin L, Eisele C, Barre A, Nair N, Rendon A, Hawkins K, Debebe A, White S, Thjømøe A, Mørk E, Bento-Miranda M, Panchal H, Agrawal M, Patel A, Chen CL, Kornbluth A, George J, Legnani P, Maser E, Loudon H, Mella MT, Stone J, Dubinsky M, Sabino J, Torres J, Colombel JF, Peter I, Hu J. Longitudinal Changes in Fecal Calprotectin Levels Among Pregnant Women With and Without Inflammatory Bowel Disease and Their Babies. Gastroenterology 2021; 160:1118-1130.e3. [PMID: 33307026 DOI: 10.1053/j.gastro.2020.11.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The effect of pregnancy on inflammatory bowel disease (IBD) remains poorly understood. We aimed to monitor intestinal inflammation using fecal calprotectin (FC) in pregnant women and their babies during early life. METHODS Pregnant women with or without IBD and their infants were prospectively enrolled. FC levels were measured at each trimester of pregnancy and in babies throughout the first 3 years of life. Repeated-measures analysis was applied to investigate changes in FC levels while adjusting for confounders. The FC levels were correlated with the bacterial abundance in both mothers and babies. RESULTS Six hundred and fourteen fecal samples from 358 mothers (98 with IBD) and 1005 fecal samples from 289 infants (76 born to IBD mothers) were analyzed. Pregnant Patients with IBD maintained higher FC levels through pregnancy compared with controls (P = 7.5 × 10-54). FC gradually increased in controls and declined in Patients with IBD throughout pregnancy (P for interaction = 5.8 × 10-7). Babies born to mothers with IBD presented with significantly higher FC levels than those born to controls up to 3 years of age, after adjusting for sex, delivery mode, feeding behavior, and antibiotics exposure (2 weeks to 3 months of age, P = .015; 12-36 months of age, P = .00003). Subdoligranulum, Roseburia, Fusicatenibacter, and Alistipes negatively correlated, and Streptococcus, Prevotella, Escherichia-Shigella, and Bifidobacterium positively correlated with maternal FC levels at T3. Faecalibacterium, Bifidobacterium, and Alistipes showed negative correlations, and Streptococcus were positively correlated with FC levels within 3 months of birth. CONCLUSIONS Pregnancy is associated with decreased inflammatory activity in mothers with IBD. Higher FC levels in babies born to mothers with IBD suggest subclinical inflammation in early life, the long-term consequences of which are uncertain.
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Affiliation(s)
- Eun Soo Kim
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology, Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Leonid Tarassishin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Eisele
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amelie Barre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology, Cochin Hospital, Université de Paris, Paris, France
| | - Nilendra Nair
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Alexa Rendon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kelly Hawkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anketse Debebe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sierra White
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Mario Bento-Miranda
- Division of Gastroenterology, Hospital and University Center of Coimbra, Coimbra, Portugal
| | - Hinaben Panchal
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manasi Agrawal
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anish Patel
- Division of Gastroenterology, Brooke Army Medical Center, San Antonio, Texas
| | - Ching-Lynn Chen
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Asher Kornbluth
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - James George
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter Legnani
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elana Maser
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Holly Loudon
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Maria-Teresa Mella
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joanne Stone
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla Dubinsky
- Department of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine at Mount Sinai, New York, New York
| | - João Sabino
- Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Joana Torres
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology, Surgical Department, Hospital Beatriz Ângelo, Loures, Portugal
| | - Jean-Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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26
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Di Narzo A, Frades I, Crane HM, Crane PK, Hulot JS, Kasarskis A, Hart A, Argmann C, Dubinsky M, Peter I, Hao K. Meta-analysis of sample-level dbGaP data reveals novel shared genetic link between body height and Crohn's disease. Hum Genet 2021; 140:865-877. [PMID: 33452914 DOI: 10.1007/s00439-020-02250-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/19/2020] [Indexed: 12/29/2022]
Abstract
To further explore genetic links between complex traits, we developed a comprehensive framework to harmonize and integrate extensive genotype and phenotype data from the four well-characterized cohorts with the focus on cardiometabolic diseases deposited to the database of Genotypes and Phenotypes (dbGaP). We generated a series of polygenic risk scores (PRS) to investigate pleiotropic effects of loci that confer genetic risk for 19 common diseases and traits on body height, type 2 diabetes (T2D), and myocardial infarction (MI). In a meta-analysis of 20,021 subjects, we identified shared genetic determinants of Crohn's Disease (CD), a type of inflammatory bowel disease, and body height (p = 5.5 × 10-5). The association of PRS-CD with height was replicated in UK Biobank (p = 1.1 × 10-5) and an independent cohort of 510 CD cases and controls (1.57 cm shorter height per PRS-CD interquartile increase, p = 5.0 × 10-3 and a 28% reduction in CD risk per interquartile increase in PRS-height, p = 1.1 × 10-3, with the effect independent of CD diagnosis). A pathway analysis of the variants overlapping between PRS-height and PRS-CD detected significant enrichment of genes from the inflammatory, immune-mediated and growth factor regulation pathways. This finding supports the clinical observation of growth failure in patients with childhood-onset CD and demonstrates the value of using individual-level data from dbGaP in searching for shared genetic determinants. This information can help provide a refined insight into disease pathogenesis and may have major implications for novel therapies and drug repurposing.
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Affiliation(s)
- Antonio Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.,Icahn School of Medicine At Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Itziar Frades
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.,Computational Biology and Systems Biomedicine Research Group, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Heidi M Crane
- Department of Medicine, University of Washington, Seattle, WA, USA.,Center for AIDS Research, University of Washington, Seattle, WA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jean-Sebastian Hulot
- Université de Paris, INSERM, PARCC, CIC1418, F-75015, Paris, France.,Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.,Icahn School of Medicine At Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amy Hart
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.,Icahn School of Medicine At Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Marla Dubinsky
- Department of Pediatric Gastroenterology and Nutrition, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.,Icahn School of Medicine At Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA. .,Icahn School of Medicine At Mount Sinai, Icahn Institute for Data Science and Genomic Technology, New York, NY, USA.
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27
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Cheng H, Sewda A, Marquez-Luna C, White SR, Whitney BM, Williams-Nguyen J, Nance RM, Lee WJ, Kitahata MM, Saag MS, Willig A, Eron JJ, Mathews WC, Hunt PW, Moore RD, Webel A, Mayer KH, Delaney JA, Crane PK, Crane HM, Hao K, Peter I. Genetic architecture of cardiometabolic risks in people living with HIV. BMC Med 2020; 18:288. [PMID: 33109212 PMCID: PMC7592520 DOI: 10.1186/s12916-020-01762-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Advances in antiretroviral therapies have greatly improved the survival of people living with human immunodeficiency virus (HIV) infection (PLWH); yet, PLWH have a higher risk of cardiovascular disease than those without HIV. While numerous genetic loci have been linked to cardiometabolic risk in the general population, genetic predictors of the excessive risk in PLWH are largely unknown. METHODS We screened for common and HIV-specific genetic variants associated with variation in lipid levels in 6284 PLWH (3095 European Americans [EA] and 3189 African Americans [AA]), from the Centers for AIDS Research Network of Integrated Clinical Systems cohort. Genetic hits found exclusively in the PLWH cohort were tested for association with other traits. We then assessed the predictive value of a series of polygenic risk scores (PRS) recapitulating the genetic burden for lipid levels, type 2 diabetes (T2D), and myocardial infarction (MI) in EA and AA PLWH. RESULTS We confirmed the impact of previously reported lipid-related susceptibility loci in PLWH. Furthermore, we identified PLWH-specific variants in genes involved in immune cell regulation and previously linked to HIV control, body composition, smoking, and alcohol consumption. Moreover, PLWH at the top of European-based PRS for T2D distribution demonstrated a > 2-fold increased risk of T2D compared to the remaining 95% in EA PLWH but to a much lesser degree in AA. Importantly, while PRS for MI was not predictive of MI risk in AA PLWH, multiethnic PRS significantly improved risk stratification for T2D and MI. CONCLUSIONS Our findings suggest that genetic loci involved in the regulation of the immune system and predisposition to risky behaviors contribute to dyslipidemia in the presence of HIV infection. Moreover, we demonstrate the utility of the European-based and multiethnic PRS for stratification of PLWH at a high risk of cardiometabolic diseases who may benefit from preventive therapies.
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Affiliation(s)
- Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Anshuman Sewda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.,Institute of Health Management Research, IIHMR University, Jaipur, Rajasthan, India
| | - Carla Marquez-Luna
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sierra R White
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Bridget M Whitney
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Jessica Williams-Nguyen
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Robin M Nance
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Won Jun Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Mari M Kitahata
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America.,Center for AIDS Research, University of Washington, Seattle, WA, United States of America
| | - Michael S Saag
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Amanda Willig
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Joseph J Eron
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, United States of America
| | - W Christopher Mathews
- Department of Medicine, University of California San Diego, San Diego, CA, United States of America
| | - Peter W Hunt
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, United States of America
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, MD, United States of America.,Department of Epidemiology,
- Johns Hopkins University, Baltimore, MD, United States of America
| | - Allison Webel
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, United States of America
| | - Kenneth H Mayer
- The Fenway Institute at Fenway Health, Boston, MA, United States of America
| | - Joseph A Delaney
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, United States of America
| | - Paul K Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Heidi M Crane
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States of America.,Center for AIDS Research, University of Washington, Seattle, WA, United States of America
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States of America.
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28
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Hu J, Benny P, Wang M, Ma Y, Lambertini L, Peter I, Xu Y, Lee MJ. Intrauterine Growth Restriction Is Associated with Unique Features of the Reproductive Microbiome. Reprod Sci 2020; 28:828-837. [PMID: 33107014 DOI: 10.1007/s43032-020-00374-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 07/25/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Intrauterine growth restriction (IUGR) is an obstetrical complication with an increased risk of perinatal mortality and morbidity. The uterus, once considered to be a sterile environment, has now been described in recent microbiome studies to harbor diverse commensal placenta microbiota, as well as potentially pathogenic flora known to cause infection. Therefore, in this pilot study, we tested whether IUGR was associated with changes to the reproductive microbiome. The reproductive microbiome was surveyed using 16S sequencing (20 IUGR, 20 controls). Alpha and beta diversity were compared, and differential taxa features associated with IUGR were identified. Microbial screening of the placenta demonstrated a diverse range of flora predominantly including Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes. Neither alpha- nor beta-diversity was significantly different by IUGR status. However, at the taxa level, IUGR patients had significantly higher prevalence of Neisseriaceae, mucosal β-hemolytic bacteria known to uptake iron-bound host proteins including hemoglobin. Moreover, the increase in anaerobic bacteria such as Desulfovibrio reflects the emergence of a hypoxic environment in the IUGR placenta. Further analysis of the reproductive microbiome of IUGR samples showed lower levels of H202-producing Bifidobacterium and Lactobacillus that switch from respiration to fermentation, a less energetic metabolic process, when oxygen levels decrease. Source tracking analysis showed that the placental microbial contents were predominantly contributed from an oral source, as compared to a gut or vaginal source. Our results suggest that the reproductive microbiome profiles may, in the future, constitute potential biomarkers for fetal health during pregnancy, while Neisseriaceae may constitute promising therapeutic targets for IUGR treatment.
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Affiliation(s)
- Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paula Benny
- Department of Obstetrics, Gynecology and Women's Health, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Michelle Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Washington University at St. Louis, Saint Louis, MO, USA
| | - Yula Ma
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luca Lambertini
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yajuan Xu
- The Third Affiliated Hospital of Zhangzhou University, Zhengzhou, Henan, China
| | - Men-Jean Lee
- Department of Obstetrics, Gynecology and Women's Health, University of Hawaii at Manoa, Honolulu, HI, USA.
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29
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Stahl E, Roda G, Dobbyn A, Hu J, Zhang Z, Westerlind H, Bonfiglio F, Raj T, Torres J, Chen A, Petras R, Pardi DS, Iuga AC, Levi GS, Cao W, Jain P, Rieder F, Gordon IO, Cho JH, D’Amato M, Harpaz N, Hao K, Colombel JF, Peter I. Collagenous Colitis Is Associated With HLA Signature and Shares Genetic Risks With Other Immune-Mediated Diseases. Gastroenterology 2020; 159:549-561.e8. [PMID: 32371109 PMCID: PMC7483815 DOI: 10.1053/j.gastro.2020.04.063] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Collagenous colitis (CC) is an inflammatory bowel disorder with unknown etiopathogenesis involving HLA-related immune-mediated responses and environmental and genetic risk factors. We carried out an array-based genetic association study in a cohort of patients with CC and investigated the common genetic basis between CC and Crohn's disease (CD), ulcerative colitis (UC), and celiac disease. METHODS DNA from 804 CC formalin-fixed, paraffin-embedded tissue samples was genotyped with Illumina Immunochip. Matching genotype data on control samples and CD, UC, and celiac disease cases were provided by the respective consortia. A discovery association study followed by meta-analysis with an independent cohort, polygenic risk score calculation, and cross-phenotype analyses were performed. Enrichment of regulatory expression quantitative trait loci among the CC variants was assessed in hemopoietic and intestinal cells. RESULTS Three HLA alleles (HLA-B∗08:01, HLA-DRB1∗03:01, and HLA-DQB1∗02:01), related to the ancestral haplotype 8.1, were significantly associated with increased CC risk. We also identified an independent protective effect of HLA-DRB1∗04:01 on CC risk. Polygenic risk score quantifying the risk across multiple susceptibility loci was strongly associated with CC risk. An enrichment of expression quantitative trait loci was detected among the CC-susceptibility variants in various cell types. The cross-phenotype analysis identified a complex pattern of polygenic pleiotropy between CC and other immune-mediated diseases. CONCLUSIONS In this largest genetic study of CC to date with histologically confirmed diagnosis, we strongly implicated the HLA locus and proposed potential non-HLA mechanisms in disease pathogenesis. We also detected a shared genetic risk between CC, celiac disease, CD, and UC, which supports clinical observations of comorbidity.
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Affiliation(s)
- Eli Stahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giulia Roda
- IBD Center, Humanitas Research Hospital, Milan, Italy
| | - Amanda Dobbyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Helga Westerlind
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden
| | - Ferdinando Bonfiglio
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden
| | - Towfique Raj
- Ronald M. Loeb Center for Alzheimer’s Disease, Departments of Neuroscience, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joana Torres
- Department of Gastroenterology, Hospital Beatriz Angelo, Loures, Portugal
| | - Anli Chen
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Robert Petras
- AmeriPath Institute of Gastrointestinal Pathology and Digestive Disease, Cleveland, OH, USA
| | - Darrell S. Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Alina C. Iuga
- Department of Biology and Cell Pathology, Columbia University, New York, NY, USA
| | - Gabriel S. Levi
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Wenqing Cao
- Division of Anatomic Pathology, New York University Langone Medical Center, New York, NY, USA
| | - Prantesh Jain
- Department of Hematology and Oncology, University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Florian Rieder
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | - Ilyssa O. Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | - Judy H. Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mauro D’Amato
- Department of Medicine, Karolinska Institutet, Solna, SE-17176, Stockholm, Sweden,School of Biological Sciences, Monash University, Clayton, VIC Australia
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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30
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Nair N, Austin C, Curtin P, Gouveia C, Arora M, Torres J, Colombel JF, Peter I. Association Between Early-life Exposures and Inflammatory Bowel Diseases, Based on Analyses of Deciduous Teeth. Gastroenterology 2020; 159:383-385. [PMID: 32224130 DOI: 10.1053/j.gastro.2020.03.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 01/27/2023]
Affiliation(s)
- Nilendra Nair
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY
| | - Christine Austin
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Paul Curtin
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Catarina Gouveia
- Surgical Department, Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joana Torres
- Surgical Department, Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal; Division of Gastroenterology, Department of Medicine, Icahn School of Medicine, New York, NY.
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31
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Williams-Nguyen J, Hawes SE, Nance RM, Lindström S, Heckbert SR, Kim HN, Mathews WC, Cachay ER, Budoff M, Hurt CB, Hunt PW, Geng E, Moore RD, Mugavero MJ, Peter I, Kitahata MM, Saag MS, Crane HM, Delaney JA. Association Between Chronic Hepatitis C Virus Infection and Myocardial Infarction Among People Living With HIV in the United States. Am J Epidemiol 2020; 189:554-563. [PMID: 31712804 DOI: 10.1093/aje/kwz236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Hepatitis C virus (HCV) infection is common among people living with human immunodeficiency virus (PLWH). Extrahepatic manifestations of HCV, including myocardial infarction (MI), are a topic of active research. MI is classified into types, predominantly atheroembolic type 1 MI (T1MI) and supply-demand mismatch type 2 MI (T2MI). We examined the association between HCV and MI among patients in the Centers for AIDS Research (CFAR) Network of Integrated Clinical Systems, a US multicenter clinical cohort of PLWH. MIs were centrally adjudicated and categorized by type using the Third Universal Definition of Myocardial Infarction. We estimated the association between chronic HCV (RNA+) and time to MI while adjusting for demographic characteristics, cardiovascular risk factors, clinical characteristics, and history of injecting drug use. Among 23,407 PLWH aged ≥18 years, there were 336 T1MIs and 330 T2MIs during a median of 4.7 years of follow-up between 1998 and 2016. HCV was associated with a 46% greater risk of T2MI (adjusted hazard ratio (aHR) = 1.46, 95% confidence interval (CI): 1.09, 1.97) but not T1MI (aHR = 0.87, 95% CI: 0.58, 1.29). In an exploratory cause-specific analysis of T2MI, HCV was associated with a 2-fold greater risk of T2MI attributed to sepsis (aHR = 2.01, 95% CI: 1.25, 3.24). Extrahepatic manifestations of HCV in this high-risk population are an important area for continued research.
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32
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Granot-Hershkovitz E, Wu P, Karasik D, Peter I, Peloso GM, Levy D, Vasan RS, Adrienne Cupples L, Liu CT, Meigs JB, Siscovick DS, Dupuis J, Friedlander Y, Hochner H. Searching for parent-of-origin effects on cardiometabolic traits in imprinted genomic regions. Eur J Hum Genet 2020; 28:646-655. [PMID: 31896779 PMCID: PMC7170899 DOI: 10.1038/s41431-019-0568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/27/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
Cardiometabolic traits pose a major global public health burden. Large-scale genome-wide association studies (GWAS) have identified multiple loci accounting for up to 30% of the genetic variance in complex traits such as cardiometabolic traits. However, the contribution of parent-of-origin effects (POEs) to complex traits has been largely ignored in GWAS. Family-based studies enable the assessment of POEs in genetic association analyses. We investigated POEs on a range of complex traits in 3 family-based studies. The discovery phase was carried out in large pedigrees from the Kibbutzim Family Study (n = 901 individuals) and in 872 parent-offspring trios from the Jerusalem Perinatal Study. Focusing on imprinted genomic regions, we examined parent-specific associations with 12 complex traits (i.e., body-size, blood pressure, lipids), mostly cardiometabolic risk traits. Forty five of the 11,967 SNPs initially found to have POE were evaluated for replication (p value < 1 × 10-4) in Framingham Heart Study families (max n = 8000 individuals). Three common variants yielded evidence of POE in the meta-analysis. Two variants, located on chr6 in the HLA region, showed a paternal effect on height (rs1042136: βpaternal = -0.023, p value = 1.5 × 10-8 and rs1431403: βpaternal = -0.011, p value = 5.4 × 10-6). The corresponding maternally-derived effects were statistically nonsignificant. The variant rs9332053, located on chr13 in RCBTB2 gene, demonstrated a maternal effect on hip circumference (βmaternal = -4.24, p value = 9.6 × 10-6; βpaternal = 1.29, p value = 0.23). These findings provide evidence for the utility of incorporating POEs into association studies of cardiometabolic traits, especially anthropometric traits. The study highlights the benefits of using family-based data for deciphering the genetic architecture of complex traits.
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Affiliation(s)
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Daniel Levy
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Ramachandran S Vasan
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston University Schools of Medicine and Public health, Boston, MA, 02118, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David S Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel.
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33
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Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, Tarassishin L, Jharap B, Cote-Daigneault J, Mao Q, Mogno I, Britton GJ, Uzzan M, Chen CL, Kornbluth A, George J, Legnani P, Maser E, Loudon H, Stone J, Dubinsky M, Faith JJ, Clemente JC, Mehandru S, Colombel JF, Peter I. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut 2020; 69:42-51. [PMID: 31036757 DOI: 10.1136/gutjnl-2018-317855] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Prenatal and early life bacterial colonisation is thought to play a major role in shaping the immune system. Furthermore, accumulating evidence links early life exposures to the risk of developing IBD later in life. We aimed to assess the effect of maternal IBD on the composition of the microbiome during pregnancy and on the offspring's microbiome. METHODS We prospectively examined the diversity and taxonomy of the microbiome of pregnant women with and without IBD and their babies at multiple time points. We evaluated the role of maternal IBD diagnosis, the mode of delivery, antibiotic use and feeding behaviour on the microbiome composition during early life. To assess the effects of IBD-associated maternal and infant microbiota on the enteric immune system, we inoculated germ-free mice (GFM) with the respective stool and profiled adaptive and innate immune cell populations in the murine intestines. RESULTS Pregnant women with IBD and their offspring presented with lower bacterial diversity and altered bacterial composition compared with control women and their babies. Maternal IBD was the main predictor of the microbiota diversity in the infant gut at 7, 14, 30, 60 and 90 days of life. Babies born to mothers with IBD demonstrated enrichment in Gammaproteobacteria and depletion in Bifidobacteria. Finally, GFM inoculated with third trimester IBD mother and 90-day infant stools showed significantly reduced microbial diversity and fewer class-switched memory B cells and regulatory T cells in the colon. CONCLUSION Aberrant gut microbiota composition persists during pregnancy with IBD and alters the bacterial diversity and abundance in the infant stool. The dysbiotic microbiota triggered abnormal imprinting of the intestinal immune system in GFM.
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Affiliation(s)
- Joana Torres
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Gastroenterology, Hospital Beatriz Angelo, Loures, Portugal
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Akihiro Seki
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Caroline Eisele
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nilendra Nair
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ruiqi Huang
- Department of Health Evidence and Policy, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Leonid Tarassishin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Bindia Jharap
- Department of Gastroenterology and Hepatology, Meander Medical Center, Amersfoort, The Netherlands
| | - Justin Cote-Daigneault
- Department of Gastroenterology, Centre Hospitalier de L'Universite de Montreal, Montreal, Quebec, Canada
| | - Qixing Mao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Naijing, China
| | - Ilaria Mogno
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Graham J Britton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Mathieu Uzzan
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ching-Lynn Chen
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Asher Kornbluth
- Department of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - James George
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Peter Legnani
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Elana Maser
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Holly Loudon
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Joanne Stone
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Marla Dubinsky
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Saurabh Mehandru
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jean-Frederic Colombel
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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34
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Sabino J, Torres J, Colombel JF, Peter I. Neonatal Life Events and the Risk of Inflammatory Bowel Disease. Gastroenterology 2019; 157:1440-1441. [PMID: 31442434 DOI: 10.1053/j.gastro.2019.04.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 12/02/2022]
Affiliation(s)
- João Sabino
- The Dr. Henry D. Janowitz Division of Gastroenterology and, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Joana Torres
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York; Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
| | - Jean-Fréderic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology and, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Peter I, Dubinsky M, Bressman S, Park A, Lu C, Chen N, Wang A. Anti-Tumor Necrosis Factor Therapy and Incidence of Parkinson Disease Among Patients With Inflammatory Bowel Disease. JAMA Neurol 2019; 75:939-946. [PMID: 29710331 DOI: 10.1001/jamaneurol.2018.0605] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Importance Despite established genetic and pathophysiologic links between inflammatory bowel disease (IBD) and Parkinson disease (PD), clinical data supporting this association remain scarce. Although systemic inflammation is considered a potential biological mechanism shared between the 2 diseases, the role of reduced systemic inflammation through IBD-directed anti-tumor necrosis factor (anti-TNF) therapy in PD risk is largely unknown. Objective To compare the incidence of PD among individuals with or without IBD and to assess whether PD risk among patients with IBD is altered by anti-TNF therapy. Design, Setting, and Participants This is a retrospective cohort study analyzing information in the Truven Health MarketScan administrative claims database and the Medicare Supplemental Database between January 1, 2000, and March 31, 2016. Individuals were selected who had at least 2 claims for IBD diagnoses, at least 6 months of follow-up, and no prior diagnosis of PD on or before the IBD index date. Exposure to Anti-TNF therapy was measured from the anti-TNF index date to the last date of anti-TNF coverage or the end of enrollment or PD index date, whichever was earliest. Incidence rates per 1000 person-years were calculated, and crude and adjusted incidence rate ratios were estimated by Poisson regression models and presented with 95% CIs. Main Outcomes and Measures Incidence of PD among patients with IBD with or without exposure to anti-TNF therapy. Results In total, 144 018 individuals with IBD were matched on age, sex, and year of index date with 720 090 unaffected controls. Of them, 1796 individuals had at least 2 PD diagnoses and at least 1 filled PD-related prescription. The mean (SD) age of individuals with IBD was 51 (17) years, and 44% were men. The incidence of PD among patients with IBD was 28% higher than that among unaffected matched controls (adjusted incidence rate ratio, 1.28; 95% CI, 1.14-1.44; P < .001). A 78% reduction in the incidence rate of PD was detected among patients with IBD who were exposed to anti-TNF therapy compared with those who were not exposed (adjusted incidence rate ratio, 0.22; 95% CI, 0.05-0.88; P = .03). Conclusions and Relevance A higher incidence of PD was observed among patients with IBD than among individuals without IBD. Early exposure to antiinflammatory anti-TNF therapy was associated with substantially reduced PD incidence. These findings support a role of systemic inflammation in the pathogenesis of both diseases. Further studies are required to determine whether anti-TNF treatment administered to high-risk individuals may mitigate PD risk.
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Affiliation(s)
- Inga Peter
- Department of Genetics and Genomic Sciences, ISMMS (Icahn School of Medicine at Mount Sinai), New York, New York
| | - Marla Dubinsky
- Division of Gastroenterology, Department of Medicine, ISMMS, New York, New York
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Takagawa T, Kitani A, Fuss I, Levine B, Brant SR, Peter I, Tajima M, Nakamura S, Strober W. An increase in LRRK2 suppresses autophagy and enhances Dectin-1-induced immunity in a mouse model of colitis. Sci Transl Med 2019; 10:10/444/eaan8162. [PMID: 29875204 DOI: 10.1126/scitranslmed.aan8162] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 05/23/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022]
Abstract
The LRRK2/MUC19 gene region constitutes a high-risk genetic locus for the occurrence of both inflammatory bowel diseases (IBDs) and Parkinson's disease. We show that dendritic cells (DCs) from patients with Crohn's disease (CD) and lymphoblastoid cell lines derived from patients without CD but bearing a high-risk allele (rs11564258) at this locus as heterozygotes exhibited increased LRRK2 expression in vitro. To investigate the immunological consequences of this increased LRRK2 expression, we conducted studies in transgenic mice overexpressing Lrrk2 and showed that these mice exhibited more severe colitis induced by dextran sodium sulfate (DSS) than did littermate control animals. This increase in colitis severity was associated with lamina propria DCs that showed increased Dectin-1-induced NF-κB activation and proinflammatory cytokine secretion. Colitis severity was driven by LRRK2 activation of NF-κB pathway components including the TAK1 complex and TRAF6. Next, we found that membrane-associated LRRK2 (in association with TAB2) caused inactivation of Beclin-1 and inhibition of autophagy. HCT116 colon epithelial cells lacking Beclin-1 exhibited increased LRRK2 expression compared to wild-type cells, suggesting that inhibition of autophagy potentially could augment LRRK2 proinflammatory signaling. We then showed that LRRK2 inhibitors decreased Dectin-1-induced TNF-α production by mouse DCs and ameliorated DSS-induced colitis, both in control and Lrrk2 transgenic animals. Finally, we demonstrated that LRRK2 inhibitors blocked TNF-α production by cultured DCs from patients with CD. Our findings suggest that normalization of LRRK2 activation could be a therapeutic approach for treating IBD, regardless of whether a LRRK2 risk allele is involved.
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Affiliation(s)
- Tetsuya Takagawa
- Division of Internal Medicine, Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Nishinomiya 663-8501, Japan.,Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Atsushi Kitani
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Fuss
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Beth Levine
- Departments of Internal Medicine and Microbiology, Center for Autophagy Research, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins School of Medicine, and Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Masaki Tajima
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiro Nakamura
- Division of Internal Medicine, Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Nishinomiya 663-8501, Japan
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Weimers P, Halfvarson J, Saunders-Pullman R, Ludvigsson JF, Peter I, Olén O, Burisch J. Inflammatory Bowel Disease and Parkinson's Disease: A Reply to Letter to the Editor of Shih-Wei Lai. Inflamm Bowel Dis 2019; 25:e127. [PMID: 31406980 DOI: 10.1093/ibd/izz181] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Petra Weimers
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Jonas F Ludvigsson
- Department Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ola Olén
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark.,Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Gastroenterology and Nutrition, Sachs' Children and Youth Hospital, Stockholm, Sweden
| | - Johan Burisch
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
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Affiliation(s)
- Joana Torres
- Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2019; 15:e1008190. [PMID: 31145742 PMCID: PMC6542503 DOI: 10.1371/journal.pgen.1008190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Crane HM, Paramsothy P, Drozd DR, Nance RM, Delaney JAC, Heckbert SR, Budoff MJ, Burkholder GA, Willig JH, Mugavero MJ, Mathews WC, Crane PK, Moore RD, Eron JJ, Napravnik S, Hunt PW, Geng E, Hsue P, Rodriguez C, Peter I, Barnes GS, McReynolds J, Lober WB, Crothers K, Feinstein MJ, Grunfeld C, Saag MS, Kitahata MM. Types of Myocardial Infarction Among Human Immunodeficiency Virus-Infected Individuals in the United States. JAMA Cardiol 2019; 2:260-267. [PMID: 28052152 DOI: 10.1001/jamacardio.2016.5139] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Importance The Second Universal Definition of Myocardial Infarction (MI) divides MIs into different types. Type 1 MIs result spontaneously from instability of atherosclerotic plaque, whereas type 2 MIs occur in the setting of a mismatch between oxygen demand and supply, as with severe hypotension. Type 2 MIs are uncommon in the general population, but their frequency in human immunodeficiency virus (HIV)-infected individuals is unknown. Objectives To characterize MIs, including type; identify causes of type 2 MIs; and compare demographic and clinical characteristics among HIV-infected individuals with type 1 vs type 2 MIs. Design, Setting, and Participants This longitudinal study identified potential MIs among patients with HIV receiving clinical care at 6 US sites from January 1, 1996, to March 1, 2014, using diagnoses and cardiac biomarkers recorded in the centralized data repository. Sites assembled deidentified packets, including physician notes and electrocardiograms, procedures, and clinical laboratory tests. Two physician experts adjudicated each event, categorizing each definite or probable MI as type 1 or type 2 and identifying the causes of type 2 MI. Main Outcomes and Measures The number and proportion of type 1 vs type 2 MIs, demographic and clinical characteristics among those with type 1 vs type 2 MIs, and the causes of type 2 MIs. Results Among 571 patients (median age, 49 years [interquartile range, 43-55 years]; 430 men and 141 women) with definite or probable MIs, 288 MIs (50.4%) were type 2 and 283 (49.6%) were type 1. In analyses of type 1 MIs, 79 patients who underwent cardiac interventions, such as coronary artery bypass graft surgery, were also included, totaling 362 patients. Sepsis or bacteremia (100 [34.7%]) and recent use of cocaine or other illicit drugs (39 [13.5%]) were the most common causes of type 2 MIs. A higher proportion of patients with type 2 MIs were younger than 40 years (47 of 288 [16.3%] vs 32 of 362 [8.8%]) and had lower current CD4 cell counts (median, 230 vs 383 cells/µL), lipid levels (mean [SD] total cholesterol level, 167 [63] vs 190 [54] mg/dL, and mean (SD) Framingham risk scores (8% [7%] vs 10% [8%]) than those with type 1 MIs or who underwent cardiac interventions. Conclusions and Relevance Approximately half of all MIs among HIV-infected individuals were type 2 MIs caused by heterogeneous clinical conditions, including sepsis or bacteremia and recent use of cocaine or other illicit drugs. Demographic characteristics and cardiovascular risk factors among those with type 1 and type 2 MIs differed, suggesting the need to specifically consider type among HIV-infected individuals to further understand MI outcomes and to guide prevention and treatment.
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Affiliation(s)
- Heidi M Crane
- Department of Medicine, University of Washington, Seattle
| | | | - Daniel R Drozd
- Department of Medicine, University of Washington, Seattle
| | - Robin M Nance
- Department of Medicine, University of Washington, Seattle
| | - J A Chris Delaney
- Department of Medicine, University of Washington, Seattle2Department of Epidemiology, University of Washington, Seattle
| | | | | | | | - James H Willig
- Department of Medicine, University of Alabama at Birmingham
| | | | | | - Paul K Crane
- Department of Medicine, University of Washington, Seattle
| | - Richard D Moore
- Department of Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Joseph J Eron
- Department of Medicine, The University of North Carolina at Chapel Hill
| | - Sonia Napravnik
- Department of Medicine, The University of North Carolina at Chapel Hill
| | - Peter W Hunt
- Department of Medicine, University of California-San Francisco
| | - Elvin Geng
- Department of Medicine, University of California-San Francisco
| | - Priscilla Hsue
- Department of Medicine, University of California-San Francisco
| | | | - Inga Peter
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Greg S Barnes
- Department of Medicine, University of Washington, Seattle10Department of Biobehavioral Nursing and Health Systems, University of Washington, Seattle
| | - Justin McReynolds
- Department of Medicine, University of Washington, Seattle10Department of Biobehavioral Nursing and Health Systems, University of Washington, Seattle
| | - William B Lober
- Department of Medicine, University of Washington, Seattle10Department of Biobehavioral Nursing and Health Systems, University of Washington, Seattle
| | | | | | - Carl Grunfeld
- Department of Medicine, University of California-San Francisco
| | - Michael S Saag
- Department of Medicine, University of Alabama at Birmingham
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Frades I, Readhead B, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK, Kovacic JC, Dudley JT, Giannarelli C, Björkegren JLM, Peter I. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy. Circ Genom Precis Med 2019; 12:e002390. [PMID: 31059280 DOI: 10.1161/circgen.118.002390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Antiretroviral therapy (ART) for HIV infection increases risk for coronary artery disease (CAD), presumably by causing dyslipidemia and increased atherosclerosis. We applied systems pharmacology to identify and validate specific regulatory gene networks through which ART drugs may promote CAD. METHODS Transcriptional responses of human cell lines to 15 ART drugs retrieved from the Library of Integrated Cellular Signatures (overall 1127 experiments) were used to establish consensus ART gene/transcriptional signatures. Next, enrichments of differentially expressed genes and gene-gene connectivity within these ART-consensus signatures were sought in 30 regulatory gene networks associated with CAD and CAD-related phenotypes in the Stockholm Atherosclerosis Gene Expression study. RESULTS Ten of 15 ART signatures were significantly enriched both for differential expression and connectivity in a specific atherosclerotic arterial wall regulatory gene network (AR-RGN) causal for CAD involving RNA processing genes. An atherosclerosis in vitro model of cholestryl ester-loaded foam cells was then used for experimental validation. Treatments of these foam cells with ritonavir, nelfinavir, and saquinavir at least doubled cholestryl ester accumulation ( P=0.02, 0.0009, and 0.02, respectively), whereas RNA silencing of the AR-RGN top key driver, PQBP1 (polyglutamine binding protein 1), significantly curbed cholestryl ester accumulation following treatment with any of these ART drugs by >37% ( P<0.05). CONCLUSIONS By applying a novel systems pharmacology data analysis framework, 3 commonly used ARTs (ritonavir, nelfinavir, and saquinavir) were found altering the activity of AR-RGN, a regulatory gene network promoting foam cell formation and risk of CAD. Targeting AR-RGN or its top key driver PQBP1 may help reduce CAD side effects of these ART drugs.
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Affiliation(s)
- Itziar Frades
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ben Readhead
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Institute for Next Generation Healthcare (B.R., J.T.D.), Icahn School of Medicine at Mount Sinai, New York, NY.,ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe (B.R.)
| | - Letizia Amadori
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Simon Koplev
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Husain A Talukdar
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (H.A.T., J.L.M.B.)
| | - Heidi M Crane
- Department of Medicine, University of Washington, Seattle (H.M.C., P.K.C.)
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle (H.M.C., P.K.C.)
| | - Jason C Kovacic
- Department of Medicine (J.C.K.), Icahn School of Medicine at Mount Sinai, New York, NY.,Cardiovascular Research Center (J.C.K., C.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Institute for Next Generation Healthcare (B.R., J.T.D.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Chiara Giannarelli
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Cardiovascular Research Center (J.C.K., C.G.), Icahn School of Medicine at Mount Sinai, New York, NY.,Precision Immunology Institute (C.G.), Icahn School of Medicine at Mount Sinai, New York, NY
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden (H.A.T., J.L.M.B.)
| | - Inga Peter
- Department of Genetics and Genomic Sciences (I.F., B.R., L.A., S.K., J.T.D., C.G., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY.,Icahn Institute for Data Science and Genomic Technology (B.R., J.T.D., J.L.M.B., I.P.), Icahn School of Medicine at Mount Sinai, New York, NY
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Hirten RP, Grinspan A, Fu SC, Luo Y, Suarez-Farinas M, Rowland J, Contijoch EJ, Mogno I, Yang N, Luong T, Labrias PR, Peter I, Cho JH, Sands BE, Colombel JF, Faith JJ, Clemente JC. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:969-979. [PMID: 30852592 PMCID: PMC6499938 DOI: 10.1093/ibd/izy398] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recurrent and severe Clostridium difficile infections (CDI) are treated with fecal microbiota transplant (FMT). Uncertainty exists regarding FMT effectiveness for CDI with underlying inflammatory bowel disease (IBD) and regarding its effects on disease activity and effectiveness in transferring the donor microbiota to patients with and without IBD. METHODS Subjects with and without IBD who underwent FMT for recurrent or severe CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) frequency of IBD flare after FMT; (3) microbiota engraftment after FMT; (and 4) predictors of CDI recurrence. RESULTS One hundred thirty-four patients, 46 with IBD, were treated with FMT. Follow-up was available in 83 and 118 patients at 6 and 2 months, respectively. There was no difference in recurrence in patients with and without IBD at 6 months (38.7% vs 36.5%; P > 0.99) and 2 months (22.5% vs 17.9%; P = 0.63). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. Pre-FMT microbiota was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment, with no difference in engraftment based on CDI recurrence or IBD endoscopic severity at FMT. CONCLUSIONS Inflammatory bowel disease did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiota was not predictive of recurrence, and microbial engraftment was impacted in those requiring IBD treatment escalation, though not by CDI recurrence or IBD disease severity.
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Affiliation(s)
- Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shih-Chen Fu
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Yuying Luo
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Rowland
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ilaria Mogno
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Nancy Yang
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tramy Luong
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Philippe R Labrias
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Inga Peter
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Judy H Cho
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
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Hu J, Ly J, Zhang W, Huang Y, Glover V, Peter I, Hurd YL, Nomura Y. Microbiota of newborn meconium is associated with maternal anxiety experienced during pregnancy. Dev Psychobiol 2019; 61:640-649. [PMID: 30908632 DOI: 10.1002/dev.21837] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 06/22/2018] [Revised: 12/18/2018] [Accepted: 01/13/2019] [Indexed: 12/11/2022]
Abstract
Little is known about whether a mother's psychological state during pregnancy influences her offspring's microbiome. This study examined whether maternal anxiety, depression, and stress during pregnancy is associated with the diversity of meconium microbiome, the first internal discharge, in 75 newborns from an existing birth cohort study. The meconium microbiome was profiled using multibarcode16S rRNA sequencing at V3-V4 hypervariable region followed by taxonomic assignment to the green gene 16S references at 97% similarity and diversity analysis at the genus level. Results showed that the meconium contained diversified microbiota, and greater pregnancy-related anxiety was significantly associated with a less diverse meconium microbiota community (p = 0.001). At the specific taxa level, greater pregnancy-related anxiety was correlated with a lower level of the Enterococcaceae family (p = 2e-4, Spearman rho = -0.43). These findings support a significant role of prenatal maternal mood in the early-life bacteria colonization of their offspring.
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Affiliation(s)
- Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jenny Ly
- Department of Psychology, Queens College, City University of New York, New York, New York
| | - Wei Zhang
- Department of Psychology, Queens College, City University of New York, New York, New York.,Department of Psychology, New Jersey City University, Jersey City, New Jerse, New Jersey
| | - Yonglin Huang
- Graduate Center, City University of New York, Brooklyn, New York, NY
| | - Vivette Glover
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yoko Nomura
- Department of Psychology, Queens College, City University of New York, New York, New York.,Graduate Center, City University of New York, Brooklyn, New York, NY.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
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44
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Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 2019; 10:10/423/eaai7795. [PMID: 29321258 DOI: 10.1126/scitranslmed.aai7795] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/31/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Abstract
Crohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3.3 × 10-8). These variants affected CD age of onset, disease location, LRRK2 activity, and autophagy. Bayesian network analysis of CD patient intestinal tissue further implicated LRRK2 in CD pathogenesis. Analysis of the extended LRRK2 locus in 24,570 CD cases, patients with Parkinson's disease (PD), and healthy controls revealed extensive pleiotropy, with shared genetic effects between CD and PD in both Ashkenazi Jewish and non-Jewish cohorts. The LRRK2 N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. Like the G2019S mutation, the N2081D variant was associated with increased kinase activity, whereas neither N551K nor R1398H variants on the protective haplotype altered kinase activity. We also confirmed that R1398H, but not N551K, increased guanosine triphosphate binding and hydrolyzing enzyme (GTPase) activity, thereby deactivating LRRK2. The presence of shared LRRK2 alleles in CD and PD provides refined insight into disease mechanisms and may have major implications for the treatment of these two seemingly unrelated diseases.
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Affiliation(s)
- Ken Y Hui
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | | | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Schaffner
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianting Li
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manual Rivas
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Xiuliang Bao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philippe R Labrias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Talin Haritunians
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Darren Ruane
- Department of Immunology and Inflammation, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Kyle Gettler
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Ernie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dalin Li
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Elena R Schiff
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nikolas Pontikos
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nir Barzilai
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Susan Bressman
- Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Adam S Cheifetz
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark J Daly
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Seymour Katz
- New York University School of Medicine, New York City, NY 10016, USA.,North Shore University-Long Island Jewish Medical Center, Manhasset, NY, USA.,St. Francis Hospital, Roslyn, NY 11576, USA
| | - Todd Lencz
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA 02114, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Deparment of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Haydeh Payami
- Departments of Neurology and Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35805, USA
| | - Yakov Peter
- Department of Biology, Touro College, Queens, NY 10033, USA.,Department of Pulmonary Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10033, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, Quebec H1T1C8, Canada.,Faculté de Médecine, Université de Montréal, Montreal, Quebec H1T1C8, Canada
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - William K Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario M5T3L9, USA.,Department of Medicine, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Jeffery M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gil Atzmon
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Itsik Pe'er
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Yiannis Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dermot P B McGovern
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Judy H Cho
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics, Yale University, New Haven, CT 06520, USA.,Section of Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. .,Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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45
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Sewda A, White SR, Erazo M, Hao K, García-Fructuoso G, Fernández-Rodriguez I, Heuzé Y, Richtsmeier JT, Romitti PA, Reva B, Jabs EW, Peter I. Nonsyndromic craniosynostosis: novel coding variants. Pediatr Res 2019; 85:463-468. [PMID: 30651579 PMCID: PMC6398438 DOI: 10.1038/s41390-019-0274-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/09/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Craniosynostosis (CS), the premature fusion of one or more neurocranial sutures, is associated with approximately 200 syndromes; however, about 65-85% of patients present with no additional major birth defects. METHODS We conducted targeted next-generation sequencing of 60 known syndromic and other candidate genes in patients with sagittal nonsyndromic CS (sNCS, n = 40) and coronal nonsyndromic CS (cNCS, n = 19). RESULTS We identified 18 previously published and 5 novel pathogenic variants, including three de novo variants. Novel variants included a paternally inherited c.2209C>G:p.(Leu737Val) variant in BBS9 of a patient with cNCS. Common variants in BBS9, a gene required for ciliogenesis during cranial suture development, have been associated with sNCS risk in a previous genome-wide association study. We also identified c.313G>T:p.(Glu105*) variant in EFNB1 and c.435G>C:p.(Lys145Asn) variant in TWIST1, both in patients with cNCS. Mutations in EFNB1 and TWIST1 have been linked to craniofrontonasal and Saethre-Chotzen syndrome, respectively; both present with coronal CS. CONCLUSIONS We provide additional evidence that variants in genes implicated in syndromic CS play a role in isolated CS, supporting their inclusion in genetic panels for screening patients with NCS. We also identified a novel BBS9 variant that further shows the potential involvement of BBS9 in the pathogenesis of CS.
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Affiliation(s)
- Anshuman Sewda
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Sierra R. White
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Monica Erazo
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ke Hao
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Yann Heuzé
- University Bordeaux, CNRS, MCC, PACEA, UMR5199, Bordeaux Archaeological Sciences Cluster of Excellence, Pessac, France
| | - Joan T. Richtsmeier
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Boris Reva
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ethylin Wang Jabs
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inga Peter
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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46
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Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, Llewellyn SR, Hira S, Johnson C, Rabinowitz KM, Barkan R, Dotan I, Hirten RP, Fu SC, Luo Y, Yang N, Luong T, Labrias PR, Lira S, Peter I, Grinspan A, Clemente JC, Kosoy R, Kim-Schulze S, Qin X, Castillo A, Hurley A, Atreja A, Rogers J, Fasihuddin F, Saliaj M, Nolan A, Reyes-Mercedes P, Rodriguez C, Aly S, Santa-Cruz K, Peters L, Suárez-Fariñas M, Huang R, Hao K, Zhu J, Zhang B, Losic B, Irizar H, Song WM, Di Narzo A, Wang W, Cohen BL, DiMaio C, Greenwald D, Itzkowitz S, Lucas A, Marion J, Maser E, Ungaro R, Naymagon S, Novak J, Shah B, Ullman T, Rubin P, George J, Legnani P, Telesco SE, Friedman JR, Brodmerkel C, Plevy S, Cho JH, Colombel JF, Schadt EE, Argmann C, Dubinsky M, Kasarskis A, Sands B, Faith JJ. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife 2019; 8:e40553. [PMID: 30666957 PMCID: PMC6342524 DOI: 10.7554/elife.40553] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 07/28/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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47
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Weimers P, Halfvarson J, Sachs MC, Saunders-Pullman R, Ludvigsson JF, Peter I, Burisch J, Olén O. Inflammatory Bowel Disease and Parkinson's Disease: A Nationwide Swedish Cohort Study. Inflamm Bowel Dis 2019; 25:111-123. [PMID: 29788069 DOI: 10.1093/ibd/izy190] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Few studies have examined the association between inflammatory bowel disease (IBD) and Parkinson's disease (PD). METHODS To estimate the incidence and relative risk of PD development in a cohort of adult IBD, we included all incident IBD patients (n = 39,652) in the Swedish National Patient Register (NPR) between 2002 and 2014 (ulcerative colitis [UC]: n = 24,422; Crohn's disease [CD]: n = 11,418; IBD-unclassified [IBD-U]: n = 3812). Each IBD patient was matched for sex, age, year, and place of residence with up to 10 reference individuals (n = 396,520). In a cohort design, all incident PD occurring after the index date was included from the NPR. In a case-control design, all incident PD occurring before the index date was included. The association between IBD and PD and vice versa was investigated by multivariable Cox and logistic regression. RESULTS In IBD, there were 103 cases of incident PD, resulting in hazard ratios (HRs) for PD of 1.3 (95% confidence interval [CI], 1.0-1.7; P = 0.04) in UC, 1.1 (95% CI, 0.7-1.7) in CD, and 1.7 (95% CI, 0.8-3.0) in IBD-U. However, these effects disappeared when adjusting for number of medical visits during follow-up to minimize potential surveillance bias. In a case-control analysis, IBD patients were more likely to have prevalent PD at the time of IBD diagnosis than matched controls, with odds ratios of 1.4 (95% CI, 1.2-1.8) in all IBD patients, 1.4 (95% CI, 1.1-1.9) for UC, and 1.6 (95% CI, 1.1-2.3) for CD patients alone. CONCLUSIONS IBD is associated with an increased risk of PD, but some of this association might be explained by surveillance bias. 10.1093/ibd/izy190_video1izy190.video15785623138001.
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Affiliation(s)
- Petra Weimers
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michael C Sachs
- Unit of Biostatistics, Institute of Environmental Medicine, Stockholm, Sweden
| | | | - Jonas F Ludvigsson
- Department Medical Epidemiology and Biostatistics, Stockholm, Sweden.,Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Ola Olén
- Clinical Epidemiology Unit, Department of Medicine Solna, Stockholm, Sweden.,Department of Pediatric gastroenterology and nutrition, Sachs' Children and Youth Hospital, Stockholm, Sweden.,Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
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48
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Weimers P, Halfvarson J, Sachs MC, Ludvigsson JF, Peter I, Olén O, Burisch J. Association between inflammatory bowel disease and Parkinson's disease: seek and you shall find? Gut 2019; 68:175-176. [PMID: 30021791 DOI: 10.1136/gutjnl-2018-316937] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 12/08/2022]
Affiliation(s)
- Petra Weimers
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michael C Sachs
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ola Olén
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Gastroenterology and Nutrition, Sachs' Children and Youth Hospital, Stockholm, Sweden.,Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
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49
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Granot-Hershkovitz E, Karasik D, Friedlander Y, Rodriguez-Murillo L, Dorajoo R, Liu J, Sewda A, Peter I, Carmi S, Hochner H. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. Eur J Hum Genet 2018; 26:1848-1858. [PMID: 30108283 PMCID: PMC6244281 DOI: 10.1038/s41431-018-0230-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 01/15/2018] [Revised: 06/24/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022] Open
Abstract
Genetic studies in isolated populations often increase power for identifying loci associated with complex diseases and traits. We present here the Kibbutzim Family Study (KFS), aimed at investigating the genetic basis of cardiometabolic traits in extended Israeli families characterized by long-term social stability and a homogeneous environment. Extensive information on cardiometabolic traits, as well as genome-wide genotypes, were collected on 901 individuals. We observed that most KFS participants were of Ashkenazi Jewish (AJ) genetic origin, confirmed a recent severe bottleneck in the AJ recent history, and detected a subtle within-AJ population structure. Focusing on genetic variants relatively common in the KFS but very rare in Europeans, we observed that AJ-enriched variants appear in cancer-related pathways more than expected by chance. We conducted an association study of the AJ-enriched variants against 16 cardiometabolic traits, and found seven loci (24 variants) to be significantly associated. The strongest association, which we also replicated in an independent study, was between a variant upstream of MSRA (frequency ≈1% in the KFS and nearly absent in Europeans) and weight (P = 3.6∙10-8). In conclusion, the KFS is a valuable resource for the study of the population genetics of Israel as well as the genetics of cardiometabolic traits.
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Affiliation(s)
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Laura Rodriguez-Murillo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anshuman Sewda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shai Carmi
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Hagit Hochner
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
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50
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Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet 2018; 14:e1007329. [PMID: 29795570 PMCID: PMC5967709 DOI: 10.1371/journal.pgen.1007329] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 02/05/2023] Open
Abstract
As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also available in gnomAD at http://gnomad.broadinstitute.org). We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations. As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10-100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohn's disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically attempt to evaluate whether strong acting rare alleles, particularly protein-truncating or otherwise large effect-size alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohn's disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are enriched in AJ (p < 0.005), including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC (sites VCF available via FTP at ftp.broadinstitute.org/pub/ExAC_release/release0.3/) to pinpoint genetic variation that contributes to variable disease predisposition across populations.
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Affiliation(s)
- Manuel A. Rivas
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States of America
| | - Brandon E. Avila
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jukka Koskela
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hailiang Huang
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Christine Stevens
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Benjamin M. Neale
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Mitja Kurki
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Andrea Ganna
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Daniel Graham
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Benjamin Glaser
- Hadassah-Hebrew University Medical Center, Endocrinology and Metabolism Service Department of Internal Medicine, Jerusalem, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gil Atzmon
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Nir Barzilai
- Department of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Adam P. Levine
- Division of Medicine, University College London, London, United Kingdom
| | - Elena Schiff
- Division of Medicine, University College London, London, United Kingdom
| | - Nikolas Pontikos
- Division of Medicine, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Ben Weisburd
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Monkol Lek
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Konrad J. Karczewski
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Jonathan Bloom
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Eric V. Minikel
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laurent Beaugerie
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Philippe Seksik
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Jacques Cosnes
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Stefan Schreiber
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Johannes Bethge
- Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | | | | | - Graham Heap
- IBD Pharmacogenetics, Royal Devon and Exeter NHS Trust, Exeter, United Kingdom
| | - Tariq Ahmad
- Peninsula College of Medicine and Dentistry, Exeter, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Anthony W. Segal
- Division of Medicine, University College London, London, United Kingdom
| | - Stephan Targan
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paivi Saavalainen
- Research Programs Unit, Immunobiology, and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Martti Farkkila
- Department of Medicine, Division of Gastroenterology, Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Kontula
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Aarno Palotie
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Richard H. Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States of America
| | - Mark S. Silverberg
- Inflammatory Bowel Disease Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - John D. Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jeffrey C. Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel G. MacArthur
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
| | - Chaim Jalas
- Bonei Olam, Center for Rare Jewish Genetic Disorders, Brooklyn, NY, United States of America
| | - Harry Sokol
- Gastroenterology Department, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris, Paris, France
| | - Ramnik J. Xavier
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Ann Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Judy H. Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, NY, United States of America
| | - Dermot P. B. McGovern
- Translational Genomics Unit, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Mark J. Daly
- Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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