1
|
Stonebraker JR, Pace RG, Gallins PJ, Dang H, Aksit MA, Faino AV, Gordon WW, MacParland S, Bamshad MJ, Gibson RL, Cutting GR, Durie PR, Wright FA, Zhou YH, Blackman SM, O'Neal WK, Ling SC, Knowles MR. Genetic variation in severe cystic fibrosis liver disease is associated with novel mechanisms for disease pathogenesis. Hepatology 2024:01515467-990000000-00819. [PMID: 38536042 DOI: 10.1097/hep.0000000000000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/11/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND AND AIMS It is not known why severe cystic fibrosis (CF) liver disease (CFLD) with portal hypertension occurs in only ~7% of people with CF. We aimed to identify genetic modifiers for severe CFLD to improve understanding of disease mechanisms. APPROACH AND RESULTS Whole-genome sequencing was available in 4082 people with CF with pancreatic insufficiency (n = 516 with severe CFLD; n = 3566 without CFLD). We tested ~15.9 million single nucleotide polymorphisms (SNPs) for association with severe CFLD versus no-CFLD, using pre-modulator clinical phenotypes including (1) genetic variant ( SERPINA1 ; Z allele) previously associated with severe CFLD; (2) candidate SNPs (n = 205) associated with non-CF liver diseases; (3) genome-wide association study of common/rare SNPs; (4) transcriptome-wide association; and (5) gene-level and pathway analyses. The Z allele was significantly associated with severe CFLD ( p = 1.1 × 10 -4 ). No significant candidate SNPs were identified. A genome-wide association study identified genome-wide significant SNPs in 2 loci and 2 suggestive loci. These 4 loci contained genes [significant, PKD1 ( p = 8.05 × 10 -10 ) and FNBP1 ( p = 4.74 × 10 -9 ); suggestive, DUSP6 ( p = 1.51 × 10 -7 ) and ANKUB1 ( p = 4.69 × 10 -7 )] relevant to severe CFLD pathophysiology. The transcriptome-wide association identified 3 genes [ CXCR1 ( p = 1.01 × 10 -6 ) , AAMP ( p = 1.07 × 10 -6 ), and TRBV24 ( p = 1.23 × 10 -5 )] involved in hepatic inflammation and innate immunity. Gene-ranked analyses identified pathways enriched in genes linked to multiple liver pathologies. CONCLUSION These results identify loci/genes associated with severe CFLD that point to disease mechanisms involving hepatic fibrosis, inflammation, innate immune function, vascular pathology, intracellular signaling, actin cytoskeleton and tight junction integrity and mechanisms of hepatic steatosis and insulin resistance. These discoveries will facilitate mechanistic studies and the development of therapeutics for severe CFLD.
Collapse
Affiliation(s)
- Jaclyn R Stonebraker
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul J Gallins
- Bioinformatics Research Center, Departments of Statistics and Biological Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melis A Aksit
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anna V Faino
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - William W Gordon
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Sonya MacParland
- Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ronald L Gibson
- Department of Pediatrics, Division of Pulmonary & Respiratory Diseases, Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Fred A Wright
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, Departments of Statistics and Biological Science, North Carolina State University, Raleigh, North Carolina, USA
- Departments of Statistics and Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Scott M Blackman
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Division of Pediatric Endocrinology and Diabetes, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wanda K O'Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Simon C Ling
- Division of Gastroenterology, Hepatology, and Nutrition, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
2
|
Blue EE, White JJ, Dush MK, Gordon WW, Wyatt BH, White P, Marvin CT, Helle E, Ojala T, Priest JR, Jenkins MM, Almli LM, Reefhuis J, Pangilinan F, Brody LC, McBride KL, Garg V, Shaw GM, Romitti PA, Nembhard WN, Browne ML, Werler MM, Kay DM, Mital S, Chong JX, Nascone-Yoder NM, Bamshad MJ. Rare variants in CAPN2 increase risk for isolated hypoplastic left heart syndrome. HGG Adv 2023; 4:100232. [PMID: 37663545 PMCID: PMC10474499 DOI: 10.1016/j.xhgg.2023.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a severe congenital heart defect (CHD) characterized by hypoplasia of the left ventricle and aorta along with stenosis or atresia of the aortic and mitral valves. HLHS represents only ∼4%-8% of all CHDs but accounts for ∼25% of deaths. HLHS is an isolated defect (i.e., iHLHS) in 70% of families, the vast majority of which are simplex. Despite intense investigation, the genetic basis of iHLHS remains largely unknown. We performed exome sequencing on 331 families with iHLHS aggregated from four independent cohorts. A Mendelian-model-based analysis demonstrated that iHLHS was not due to single, large-effect alleles in genes previously reported to underlie iHLHS or CHD in >90% of families in this cohort. Gene-based association testing identified increased risk for iHLHS associated with variation in CAPN2 (p = 1.8 × 10-5), encoding a protein involved in functional adhesion. Functional validation studies in a vertebrate animal model (Xenopus laevis) confirmed CAPN2 is essential for cardiac ventricle morphogenesis and that in vivo loss of calpain function causes hypoplastic ventricle phenotypes and suggest that human CAPN2707C>T and CAPN21112C>T variants, each found in multiple individuals with iHLHS, are hypomorphic alleles. Collectively, our findings show that iHLHS is typically not a Mendelian condition, demonstrate that CAPN2 variants increase risk of iHLHS, and identify a novel pathway involved in HLHS pathogenesis.
Collapse
Affiliation(s)
- Elizabeth E. Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Michael K. Dush
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - William W. Gordon
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Brent H. Wyatt
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Peter White
- Institute for Genomic Medicine, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Colby T. Marvin
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Emmi Helle
- New Children’s Hospital and Pediatric Research Center, Helsinki University Hospital, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Ojala
- New Children’s Hospital and Pediatric Research Center, Helsinki University Hospital, Helsinki, Finland
| | - James R. Priest
- Stanford University School of Medicine, Lucile Packard Children’s Hospital, Stanford, CA, USA
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lynn M. Almli
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennita Reefhuis
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Faith Pangilinan
- Genetics and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence C. Brody
- Genetics and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kim L. McBride
- Center for Cardiovascular Research, Nationwide Children’s Hospital, and Division of Genetic and Genomic Medicine, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Vidu Garg
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
| | | | - Marilyn L. Browne
- Birth Defects Registry, New York State Department of Health, Albany, NY, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, USA
| | - Martha M. Werler
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Denise M. Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - National Birth Defects Prevention Study
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Invitae, San Francisco, CA, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Genomic Medicine, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- New Children’s Hospital and Pediatric Research Center, Helsinki University Hospital, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Stanford University School of Medicine, Lucile Packard Children’s Hospital, Stanford, CA, USA
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Genetics and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Center for Cardiovascular Research, Nationwide Children’s Hospital, and Division of Genetic and Genomic Medicine, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Birth Defects Registry, New York State Department of Health, Albany, NY, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - University of Washington Center for Mendelian Genomics
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Invitae, San Francisco, CA, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Genomic Medicine, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- New Children’s Hospital and Pediatric Research Center, Helsinki University Hospital, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Stanford University School of Medicine, Lucile Packard Children’s Hospital, Stanford, CA, USA
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Genetics and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Center for Cardiovascular Research, Nationwide Children’s Hospital, and Division of Genetic and Genomic Medicine, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Cardiovascular Research and The Heart Center, Nationwide Children’s Hospital, and Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, USA
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Birth Defects Registry, New York State Department of Health, Albany, NY, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Seema Mital
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
3
|
Rosenfeld M, Faino AV, Qu P, Onchiri FM, Blue EE, Collaco JM, Gordon WW, Szczesniak R, Zhou YH, Bamshad MJ, Gibson RL. Association of Pseudomonas aeruginosa infection stage with lung function trajectory in children with cystic fibrosis. J Cyst Fibros 2023; 22:857-863. [PMID: 37217389 DOI: 10.1016/j.jcf.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/25/2023] [Accepted: 05/06/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa (Pa) infection in cystic fibrosis (CF) is characterized in stages: never (prior to first positive culture) to incident (first positive culture) to chronic. The association of Pa infection stage with lung function trajectory is poorly understood and the impact of age on this association has not been examined. We hypothesized that FEV1 decline would be slowest prior to Pa infection, intermediate after incident infection and greatest after chronic Pa infection. METHODS Participants in a large US prospective cohort study diagnosed with CF prior to age 3 contributed data through the U.S. CF Patient Registry. Cubic spline linear mixed effects models were used to evaluate the longitudinal association of Pa stage (never, incident, chronic using 4 different definitions) with FEV1 adjusted for relevant covariates. Models contained interaction terms between age and Pa stage. RESULTS 1,264 subjects born 1992-2006 provided a median 9.5 (IQR 0.25 to 15.75) years of follow up through 2017. 89% developed incident Pa; 39-58% developed chronic Pa depending on the definition. Compared to never Pa, incident Pa infection was associated with greater annual FEV1 decline and chronic Pa infection with the greatest FEV1 decline. The most rapid FEV1 decline and strongest association with Pa infection stage was seen in early adolescence (ages 12-15). CONCLUSIONS Annual FEV1 decline worsens significantly with each Pa infection stage in children with CF. Our findings suggest that measures to prevent chronic infection, particularly during the high-risk period of early adolescence, could mitigate FEV1 decline and improve survival.
Collapse
Affiliation(s)
- Margaret Rosenfeld
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA.
| | - Anna V Faino
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Pingping Qu
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William W Gordon
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Rhonda Szczesniak
- Department of Pediatrics, Cincinnati Children's Hospital and Medical Center, Cincinnati, OH USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Hospital, Seattle, WA, USA; Brotman Baty Institute, Seattle, WA USA
| | - Ronald L Gibson
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| |
Collapse
|
4
|
Zhou YH, Gallins PJ, Pace RG, Dang H, Aksit MA, Blue EE, Buckingham KJ, Collaco JM, Faino AV, Gordon WW, Hetrick KN, Ling H, Liu W, Onchiri FM, Pagel K, Pugh EW, Raraigh KS, Rosenfeld M, Sun Q, Wen J, Li Y, Corvol H, Strug LJ, Bamshad MJ, Blackman SM, Cutting GR, Gibson RL, O’Neal WK, Wright FA, Knowles MR. Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Am J Respir Crit Care Med 2023; 207:1324-1333. [PMID: 36921087 PMCID: PMC10595435 DOI: 10.1164/rccm.202209-1653oc] [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: 09/02/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.
Collapse
Affiliation(s)
- Yi-Hui Zhou
- Bioinformatics Research Center
- Department of Biological Sciences, and
| | | | - Rhonda G. Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Hong Dang
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | | | - Elizabeth E. Blue
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Medical Genetics, Department of Medicine
| | | | | | - Anna V. Faino
- Children’s Core for Biostatistics, Epidemiology and Analytics in Research and
| | | | - Kurt N. Hetrick
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | - Hua Ling
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | | | - Kymberleigh Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth W. Pugh
- Department of Genetic Medicine, Center for Inherited Disease Research, and
| | | | - Margaret Rosenfeld
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Yun Li
- Department of Biostatistics
- Department of Genetics, and
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Harriet Corvol
- Pediatric Pulmonary Department, Assistance Publique-Hôpitaux de Paris, Hôpital Trousseau, Paris, France
- Centre de Recherche Saint Antoine, Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health
- Department of Statistical Sciences, and
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; and
- Program in Genetics and Genome Biology and
- The Center for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Genetic Medicine, Department of Pediatrics
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Scott M. Blackman
- McKusick-Nathans Department of Genetic Medicine
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ronald L. Gibson
- Department of Pediatrics, and
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine
| | - Fred A. Wright
- Bioinformatics Research Center
- Department of Biological Sciences, and
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | | |
Collapse
|
5
|
Esterhuizen AI, Tiffin N, Riordan G, Wessels M, Burman RJ, Aziz MC, Calhoun JD, Gunti J, Amiri EE, Ramamurthy A, Bamshad MJ, Mefford HC, Ramesar R, Wilmshurst JM, Carvill GL, Leal SM, Nickerson DA, Anderson P, Bacus TJ, Blue EE, Brower K, Buckingham KJ, Chong JX, Cornejo Sánchez D, Davis CP, Davis CJ, Frazar CD, Gomeztagle-Burgess K, Gordon WW, Horike-Pyne M, Hurless JR, Jarvik GP, Johanson E, Thomas Kolar J, Marvin CT, McGee S, McGoldrick DJ, Mekonnen B, Nielsen PM, Patterson K, Radhakrishnan A, Richardson MA, Roote GT, Ryke EL, Schrauwen I, Shively KM, Smith JD, Tackett M, Wang G, Weiss JM, Wheeler MM, Yi Q, Zhang X. Precision medicine for developmental and epileptic encephalopathies in Africa-strategies for a resource-limited setting. Genet Med 2023; 25:100333. [PMID: 36480001 DOI: 10.1016/j.gim.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Sub-Saharan Africa bears the highest burden of epilepsy worldwide. A presumed proportion is genetic, but this etiology is buried under the burden of infections and perinatal insults in a setting of limited awareness and few options for testing. Children with developmental and epileptic encephalopathies (DEEs) are most severely affected by this diagnostic gap in Africa, because the rate of actionable findings is highest in DEE-associated genes. METHODS We tested 234 genetically naive South African children diagnosed with/possible DEE using gene panels, exome sequencing, and chromosomal microarray. Statistical comparison of electroclinical features in children with and children without candidate variants was performed to identify characteristics most likely predictive of a positive genetic finding. RESULTS Of the 41 (of 234) children with likely/pathogenic variants, 26 had variants supporting precision therapy. Multivariate regression modeling highlighted neonatal or infantile-onset seizures and movement abnormalities as predictive of a positive genetic finding. We used this, coupled with an emphasis on precision medicine outcomes, to propose the pragmatic "Think-Genetics" strategy for early recognition of a possible genetic etiology. CONCLUSION Our findings emphasize the importance of an early genetic diagnosis in DEE. We designed the Think-Genetics strategy for early recognition, appropriate interim management, and genetic testing for DEE in resource-constrained settings.
Collapse
Affiliation(s)
- Alina I Esterhuizen
- The South African MRC/UCT Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicki Tiffin
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Gillian Riordan
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Marie Wessels
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Richard J Burman
- Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Miriam C Aziz
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jeffrey D Calhoun
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jonathan Gunti
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ezra E Amiri
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Aishwarya Ramamurthy
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA; Department of Genome Sciences, University of Washington, Seattle, WA; Brotman Baty Institute, Seattle, WA
| | | | - Heather C Mefford
- Centre for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN
| | - Raj Ramesar
- The South African MRC/UCT Genomic and Precision Medicine Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Jo M Wilmshurst
- Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Pharmacology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Rosenfeld M, Faino AV, Onchiri F, Aksit MA, Blackman SM, Blue EE, Collaco JM, Gordon WW, Pace RG, Raraigh KS, Zhou YH, Cutting GR, Knowles MR, Bamshad MJ, Gibson RL. Comparing encounter-based and annualized chronic pseudomonas infection definitions in cystic fibrosis. J Cyst Fibros 2021; 21:40-44. [PMID: 34393091 DOI: 10.1016/j.jcf.2021.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/07/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Chronic Pseudomonas aeruginosa (Pa) infection is associated with increased morbidity and mortality in people with cystic fibrosis (CF). There is no gold standard definition of chronic Pa infection in CF. We compared chronic Pa definitions using encounter-based versus annualized data in the Early Pseudomonas Infection Control (EPIC) Observational study cohort, and subsequently compared annualized chronic Pa definitions across a range of U.S. cohorts spanning decades of CF care. We found that an annualized chronic Pa definition requiring at least 1 Pa+ culture in 3 of 4 consecutive years ("Green 3/4") resulted in chronic Pa metrics similar to established encounter-based modified Leeds criteria definitions, including a similar age at and proportion who fulfilled chronic Pa criteria, and a similar proportion with sustained Pa infection after meeting the chronic Pa definition. The Green 3/4 chronic Pa definition will be valuable for longitudinal analyses in cohorts with limited culture frequency.
Collapse
Affiliation(s)
- Margaret Rosenfeld
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
| | - Anna V Faino
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Frankline Onchiri
- Children's Core for Biostatistics, Epidemiology and Analytics in Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Melis A Aksit
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Scott M Blackman
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - William W Gordon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rhonda G Pace
- Marsico Lung Institute/Cystic Fibrosis Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen S Raraigh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA; Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Michael R Knowles
- Marsico Lung Institute/Cystic Fibrosis Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
7
|
Gordon WW. Primary reticulum cell sarcoma (histiocytic lymphoma) of the mandible. Pathological quiz case 2. Arch Otolaryngol 1977; 103:62-4. [PMID: 318833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
8
|
Abstract
Nasal sarcoidosis may affect nasal skin, mucosa, or bone separately or simulataneously. Its incidence in patients with systemic sarcoid was once thought to be low, but this may be due to lack of proper intranasal examination and awareness of its existence by physicians who are more preoccupied with lung and other visceral involvement. The otolaryngologist should be aware of nasal sarcoidosis because nasal obstruction or drainage secondary to nasal sarcoidosis may be the first and only manifestation of systemic sarcoidosis. The otolaryngologist can diagnose this disease earlier in its course by being aware of its existence.
Collapse
|
9
|
Gordon WW. Pathologic quiz case 1. Squamous cell carcinoma. Arch Otolaryngol 1975; 101:202-4. [PMID: 1120005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
10
|
|