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Ohiri JC, Dellefave-Castillo L, Tomar G, Wilsbacher L, Choudhury L, Barefield DY, Fullenkamp D, Gacita AM, Monroe TO, Pesce L, Blancard M, Vaught L, George AL, Demonbreun AR, Puckelwartz MJ, McNally EM. Reduction of Filamin C Results in Altered Proteostasis, Cardiomyopathy, and Arrhythmias. J Am Heart Assoc 2024:e030467. [PMID: 38761081 DOI: 10.1161/jaha.123.030467] [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: 04/04/2023] [Accepted: 04/17/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Many cardiomyopathy-associated FLNC pathogenic variants are heterozygous truncations, and FLNC pathogenic variants are associated with arrhythmias. Arrhythmia triggers in filaminopathy are incompletely understood. METHODS AND RESULTS We describe an individual with biallelic FLNC pathogenic variants, p.Arg650X and c.970-4A>G, with peripartum cardiomyopathy and ventricular arrhythmias. We also describe clinical findings in probands with FLNC variants including Val2715fs87X, Glu2458Serfs71X, Phe106Leu, and c.970-4A>G with hypertrophic and dilated cardiomyopathy, atrial fibrillation, and ventricular tachycardia. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) were generated. The FLNC truncation, Arg650X/c.970-4A>G, showed a marked reduction in filamin C protein consistent with biallelic loss of function mutations. To assess loss of filamin C, gene editing of a healthy control iPSC line was used to generate a homozygous FLNC disruption in the actin binding domain. Because filamin C has been linked to protein quality control, we assessed the necessity of filamin C in iPSC-CMs for response to the proteasome inhibitor bortezomib. After exposure to low-dose bortezomib, FLNC-null iPSC-CMs showed an increase in the chaperone proteins BAG3, HSP70 (heat shock protein 70), and HSPB8 (small heat shock protein B8) and in the autophagy marker LC3I/II. FLNC null iPSC-CMs had prolonged electric field potential, which was further prolonged in the presence of low-dose bortezomib. FLNC null engineered heart tissues had impaired function after low-dose bortezomib. CONCLUSIONS FLNC pathogenic variants associate with a predisposition to arrhythmias, which can be modeled in iPSC-CMs. Reduction of filamin C prolonged field potential, a surrogate for action potential, and with bortezomib-induced proteasome inhibition, reduced filamin C led to greater arrhythmia potential and impaired function.
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Affiliation(s)
- Joyce C Ohiri
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Garima Tomar
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Lisa Wilsbacher
- Feinberg Cardiovascular and Renal Research Institute, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Lubna Choudhury
- Bluhm Cardiovascular Institute Northwestern Medicine Chicago IL USA
| | - David Y Barefield
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
- Cell and Molecular Physiology Loyola University Stritch School of Medicine Maywood IL USA
| | - Dominic Fullenkamp
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Anthony M Gacita
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Tanner O Monroe
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Lorenzo Pesce
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Malorie Blancard
- Department of Pharmacology, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Lauren Vaught
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Alexis R Demonbreun
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
- Department of Pharmacology, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
- Department of Pharmacology, Feinberg School of Medicine Northwestern University Chicago IL USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine Northwestern University Chicago IL USA
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2
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Lewis ACF, Chisholm RL, Connolly JJ, Esplin ED, Glessner J, Gordon A, Green RC, Hakonarson H, Harr M, Holm IA, Jarvik GP, Karlson E, Kenny EE, Kottyan L, Lennon N, Linder JE, Luo Y, Martin LJ, Perez E, Puckelwartz MJ, Rasmussen-Torvik LJ, Sabatello M, Sharp RR, Smoller JW, Sterling R, Terek S, Wei WQ, Fullerton SM. Managing differential performance of polygenic risk scores across groups: Real-world experience of the eMERGE Network. Am J Hum Genet 2024:S0002-9297(24)00120-4. [PMID: 38688278 DOI: 10.1016/j.ajhg.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
The differential performance of polygenic risk scores (PRSs) by group is one of the major ethical barriers to their clinical use. It is also one of the main practical challenges for any implementation effort. The social repercussions of how people are grouped in PRS research must be considered in communications with research participants, including return of results. Here, we outline the decisions faced and choices made by a large multi-site clinical implementation study returning PRSs to diverse participants in handling this issue of differential performance. Our approach to managing the complexities associated with the differential performance of PRSs serves as a case study that can help future implementers of PRSs to plot an anticipatory course in response to this issue.
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Affiliation(s)
- Anna C F Lewis
- Edmond and Lily Safra Center for Ethics, Harvard University, Cambridge, MA, USA; Department of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Joe Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Pharmacology, Northwestern University, Evanston, IL, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Mass General Brigham Personalized Medicine, Boston, MA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine, New York City, NY, USA; Center for Clinical Translational Genomics, Icahn School of Medicine, New York City, NY, USA; Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine, New York City, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York City, NY, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Evanston, IL, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Boston, MA, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Pharmacology, Northwestern University, Evanston, IL, USA
| | - Laura J Rasmussen-Torvik
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Preventive Medicine, Northwestern University, Evanston, IL, USA
| | - Maya Sabatello
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Irving Medical Center, New York City, NY, USA; Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York City, NY, USA
| | | | - Jordan W Smoller
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA; Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
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3
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Hui D, Dudek S, Kiryluk K, Walunas TL, Kullo IJ, Wei WQ, Tiwari HK, Peterson JF, Chung WK, Davis B, Khan A, Kottyan L, Limdi NA, Feng Q, Puckelwartz MJ, Weng C, Smith JL, Karlson EW, Center RG, Jarvik GP, Ritchie MD. Risk factors affecting polygenic score performance across diverse cohorts. medRxiv 2024:2023.05.10.23289777. [PMID: 38645167 PMCID: PMC11030495 DOI: 10.1101/2023.05.10.23289777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Apart from ancestry, personal or environmental covariates may contribute to differences in polygenic score (PGS) performance. We analyzed effects of covariate stratification and interaction on body mass index (BMI) PGS (PGS BMI ) across four cohorts of European (N=491,111) and African (N=21,612) ancestry. Stratifying on binary covariates and quintiles for continuous covariates, 18/62 covariates had significant and replicable R 2 differences among strata. Covariates with the largest differences included age, sex, blood lipids, physical activity, and alcohol consumption, with R 2 being nearly double between best and worst performing quintiles for certain covariates. 28 covariates had significant PGS BMI -covariate interaction effects, modifying PGS BMI effects by nearly 20% per standard deviation change. We observed overlap between covariates that had significant R 2 differences among strata and interaction effects - across all covariates, their main effects on BMI were correlated with their maximum R 2 differences and interaction effects (0.56 and 0.58, respectively), suggesting high-PGS BMI individuals have highest R 2 and increase in PGS effect. Using quantile regression, we show the effect of PGS BMI increases as BMI itself increases, and that these differences in effects are directly related to differences in R 2 when stratifying by different covariates. Given significant and replicable evidence for context-specific PGS BMI performance and effects, we investigated ways to increase model performance taking into account non-linear effects. Machine learning models (neural networks) increased relative model R 2 (mean 23%) across datasets. Finally, creating PGS BMI directly from GxAge GWAS effects increased relative R 2 by 7.8%. These results demonstrate that certain covariates, especially those most associated with BMI, significantly affect both PGS BMI performance and effects across diverse cohorts and ancestries, and we provide avenues to improve model performance that consider these effects.
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 2024; 30:480-487. [PMID: 38374346 PMCID: PMC10878968 DOI: 10.1038/s41591-024-02796-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.
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Affiliation(s)
| | - Leah C Kottyan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Josh Arias
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sonja I Berndt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - James J Cimino
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - David R Crosslin
- Tulane University, New Orleans, LA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - QiPing Feng
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Tian Ge
- Mass General Brigham, Boston, MA, USA
| | | | | | | | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Clive Hoggart
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Hsu
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | - Amit Khera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nita Limdi
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Northwestern University, Evanston, IL, USA
| | | | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Li McCarthy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nihal Pai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Zhe Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Karthik F, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Faulkner M, MacLeod HM, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. Genome Med 2024; 16:13. [PMID: 38229148 PMCID: PMC10792876 DOI: 10.1186/s13073-024-01284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. METHODS The SDY Case Registry is a National Institutes of Health/Centers for Disease Control and Prevention surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases < 20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015 to 2019. The cohort included 211 children (median age 0.33 year; range 0-20 years), determined to have died suddenly and unexpectedly and from whom DNA biospecimens for DNA extractions and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex- and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy, and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, pathogenic and likely pathogenic genetic variation was identified using a Bayesian-based artificial intelligence (AI) tool. RESULTS The SDY cohort was 43% European, 29% African, 3% Asian, 16% Hispanic, and 9% with mixed ancestries and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy, or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, potentially damaging variants in epilepsy, cardiomyopathy, and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. CONCLUSIONS While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
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Affiliation(s)
- Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Lorenzo L Pesce
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Gregory Webster
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Mark W Russell
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Sarah S Geisler
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Samuel D Kearns
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Felix Karthik
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan P Etheridge
- Division of Pediatric Cardiology, University of Utah, Salt Lake City, UT, USA
| | - Tanner O Monroe
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tess D Pottinger
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Prince J Kannankeril
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Darlene Fountain
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Kristin M Burns
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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6
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Agrawal V, Manouchehri A, Vaitinadin NS, Shi M, Bagheri M, Gupta DK, Kullo IJ, Luo Y, McNally EM, Puckelwartz MJ, Ferguson JF, Wells QS, Mosley JD. Identification of Clinical Drivers of Left Atrial Enlargement Through Genomics of Left Atrial Size. Circ Heart Fail 2024; 17:e010557. [PMID: 38126226 PMCID: PMC10842187 DOI: 10.1161/circheartfailure.123.010557] [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: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Greater left atrial size is associated with a higher incidence of cardiovascular disease and mortality, but the full spectrum of diagnoses associated with left atrial enlargement in sex-stratified clinical populations is not well known. Our study sought to identify genetic risk mechanisms affecting left atrial diameter (LAD) in a clinical cohort. METHODS Using Vanderbilt deidentified electronic health record, we studied 6163 females and 5993 males of European ancestry who had at least 1 LAD measure and available genotyping. A sex-stratified polygenic score was constructed for LAD variation and tested for association against 1680 International Classification of Diseases code-based phenotypes. Two-sample univariable and multivariable Mendelian randomization approaches were used to assess etiologic relationships between candidate associations and LAD. RESULTS A phenome-wide association study identified 25 International Classification of Diseases code-based diagnoses in females and 11 in males associated with a polygenic score of LAD (false discovery rate q<0.01), 5 of which were further evaluated by Mendelian randomization (waist circumference [WC], atrial fibrillation, heart failure, systolic blood pressure, and coronary artery disease). Sex-stratified differences in the genetic associations between risk factors and a polygenic score for LAD were observed (WC for females; heart failure, systolic blood pressure, atrial fibrillation, and WC for males). By multivariable Mendelian randomization, higher WC remained significantly associated with larger LAD in females, whereas coronary artery disease, WC, and atrial fibrillation remained significantly associated with larger LAD in males. CONCLUSIONS In a clinical population, we identified, by genomic approaches, potential etiologic risk factors for larger LAD. Further studies are needed to confirm the extent to which these risk factors may be modified to prevent or reverse adverse left atrial remodeling and the extent to which sex modifies these risk factors.
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Affiliation(s)
- Vineet Agrawal
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Veterans Affairs, Nashville, TN, USA
| | - Ali Manouchehri
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nataraja Sarma Vaitinadin
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Minoo Bagheri
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Deepak K. Gupta
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Northwestern Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, Northwestern Feinberg School of Medicine, Chicago, IL, USA
| | - Jane F. Ferguson
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S. Wells
- Vanderbilt Translational and Clinical Cardiovascular Research Center and Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan D. Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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Lee DSM, Cardone KM, Zhang DY, Abramowitz S, DePaolo JS, Aragam KG, Biddinger K, Conery M, Dilitikas O, Hoffman-Andrews L, Judy RL, Khan A, Kulo I, Puckelwartz MJ, Reza N, Satterfield BA, Singhal P, Arany ZP, Cappola TP, Carruth E, Day SM, Do R, Haggarty CM, Joseph J, McNally E, Nadkarni G, Owens AT, Rader DJ, Ritchie MD, Sun Y, Voight BF, Levin MG, Damrauer SM. Common- and rare-variant genetic architecture of heart failure across the allele frequency spectrum. medRxiv 2023:2023.07.16.23292724. [PMID: 37503172 PMCID: PMC10371173 DOI: 10.1101/2023.07.16.23292724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Heart failure (HF) is a complex trait, influenced by environmental and genetic factors, that affects over 30 million individuals worldwide. Historically, the genetics of HF have been studied in Mendelian forms of disease, where rare genetic variants have been linked to familial cardiomyopathies. More recently, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with risk of HF. However, the relative importance of genetic variants across the allele-frequency spectrum remains incompletely characterized. Here, we report the results of common- and rare-variant association studies of all-cause heart failure, applying recently developed methods to quantify the heritability of HF attributable to different classes of genetic variation. We combine GWAS data across multiple populations including 207,346 individuals with HF and 2,151,210 without, identifying 176 risk loci at genome-wide significance (p < 5×10-8). Signals at newly identified common-variant loci include coding variants in Mendelian cardiomyopathy genes (MYBPC3, BAG3), as well as regulators of lipoprotein (LPL) and glucose metabolism (GIPR, GLP1R), and are enriched in cardiac, muscle, nerve, and vascular tissues, as well as myocyte and adipocyte cell types. Gene burden studies across three biobanks (PMBB, UKB, AOU) including 27,208 individuals with HF and 349,126 without uncover exome-wide significant (p < 3.15×10-6) associations for HF and rare predicted loss-of-function (pLoF) variants in TTN, MYBPC3, FLNC, and BAG3. Total burden heritability of rare coding variants (2.2%, 95% CI 0.99-3.5%) is highly concentrated in a small set of Mendelian cardiomyopathy genes, and is lower than heritability attributable to common variants (4.3%, 95% CI 3.9-4.7%) which is more diffusely spread throughout the genome. Finally, we demonstrate that common-variant background, in the form of a polygenic risk score (PRS), significantly modifies the risk of HF among carriers of pathogenic truncating variants in the Mendelian cardiomyopathy gene TTN. These findings suggest a significant polygenic component to HF exists that is not captured by current clinical genetic testing.
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Affiliation(s)
- David S M Lee
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Katie M Cardone
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David Y Zhang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah Abramowitz
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - John S DePaolo
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Krishna G Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kiran Biddinger
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mitchell Conery
- Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ozan Dilitikas
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Lily Hoffman-Andrews
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Renae L Judy
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Iftikhar Kulo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Megan J Puckelwartz
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Nosheen Reza
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | | | - Pankhuri Singhal
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Zoltan P Arany
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Thomas P Cappola
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Eric Carruth
- Department of Translational Data Science and Informatics, Geisinger, Danville, PA
| | - Sharlene M Day
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Mount Sinai Icahn School of Medicine, New York, NY
- Biome Phenomics Center, Mount Sinai Icahn School of Medicine, New York, NY
- Department of Genetics and Genomic Sciences, Mount Sinai Icahn School of Medicine, New York, NY
| | | | - Jacob Joseph
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elizabeth McNally
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Girish Nadkarni
- Division of Nephrology, Department of Medicine, Mount Sinai Icahn School of Medicine, New York, NY
| | - Anjali T Owens
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yan Sun
- Deparment of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Michael G Levin
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Scott M Damrauer
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn N, Arias J, Belbin G, Below JE, Berndt S, Chung W, Cimino JJ, Clayton EW, Connolly JJ, Crosslin D, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth R, Ge T, Glessner JT, Gordon A, Guiducci C, Hakonarson H, Harden M, Harr M, Hirschhorn J, Hoggart C, Hsu L, Irvin R, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos R, Luo Y, Malolepsza E, Manolio T, Martin LJ, McCarthy L, Meigs JB, Mersha TB, Mosley J, Namjou B, Pai N, Pesce LL, Peters U, Peterson J, Prows CA, Puckelwartz MJ, Rehm H, Roden D, Rosenthal EA, Rowley R, Sawicki KT, Schaid D, Schmidlen T, Smit R, Smith J, Smoller JW, Thomas M, Tiwari H, Toledo D, Vaitinadin NS, Veenstra D, Walunas T, Wang Z, Wei WQ, Weng C, Wiesner G, Xianyong Y, Kenny E. Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations. medRxiv 2023:2023.05.25.23290535. [PMID: 37333246 PMCID: PMC10275001 DOI: 10.1101/2023.05.25.23290535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Polygenic risk scores (PRS) have improved in predictive performance supporting their use in clinical practice. Reduced predictive performance of PRS in diverse populations can exacerbate existing health disparities. The NHGRI-funded eMERGE Network is returning a PRS-based genome-informed risk assessment to 25,000 diverse adults and children. We assessed PRS performance, medical actionability, and potential clinical utility for 23 conditions. Standardized metrics were considered in the selection process with additional consideration given to strength of evidence in African and Hispanic populations. Ten conditions were selected with a range of high-risk thresholds: atrial fibrillation, breast cancer, chronic kidney disease, coronary heart disease, hypercholesterolemia, prostate cancer, asthma, type 1 diabetes, obesity, and type 2 diabetes. We developed a pipeline for clinical PRS implementation, used genetic ancestry to calibrate PRS mean and variance, created a framework for regulatory compliance, and developed a PRS clinical report. eMERGE's experience informs the infrastructure needed to implement PRS-based implementation in diverse clinical settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Li Hsu
- Fred Hutchinson Cancer Center and University of Washington
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ulrike Peters
- Fred Hutchinson Cancer Center and University of Washington
| | | | | | | | | | - Dan Roden
- Vanderbilt University Medical Center
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9
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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10
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Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Etheridge FK, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, MacLeod H, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. medRxiv 2023:2023.03.27.23287711. [PMID: 37034657 PMCID: PMC10081419 DOI: 10.1101/2023.03.27.23287711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Sudden unexpected death in children is a tragic event. Understanding the genetics of sudden death in the young (SDY) enables family counseling and cascade screening. The objective of this study was to characterize genetic variation in an SDY cohort using whole genome sequencing. Methods The SDY Case Registry is a National Institutes of Health/Centers for Disease Control surveillance effort to discern the prevalence, causes, and risk factors for SDY. The SDY Case Registry prospectively collected clinical data and DNA biospecimens from SDY cases <20 years of age. SDY cases were collected from medical examiner and coroner offices spanning 13 US jurisdictions from 2015-2019. The cohort included 211 children (mean age 1 year; range 0-20 years), determined to have died suddenly and unexpectedly and in whom DNA biospecimens and next-of-kin consent were ascertained. A control cohort consisted of 211 randomly sampled, sex-and ancestry-matched individuals from the 1000 Genomes Project. Genetic variation was evaluated in epilepsy, cardiomyopathy and arrhythmia genes in the SDY and control cohorts. American College of Medical Genetics/Genomics guidelines were used to classify variants as pathogenic or likely pathogenic. Additionally, genetic variation predicted to be damaging was identified using a Bayesian-based artificial intelligence (AI) tool. Results The SDY cohort was 42% European, 30% African, 17% Hispanic, and 11% with mixed ancestries, and 39% female. Six percent of the cohort was found to harbor a pathogenic or likely pathogenic genetic variant in an epilepsy, cardiomyopathy or arrhythmia gene. The genomes of SDY cases, but not controls, were enriched for rare, damaging variants in epilepsy, cardiomyopathy and arrhythmia-related genes. A greater number of rare epilepsy genetic variants correlated with younger age at death. Conclusions While damaging cardiomyopathy and arrhythmia genes are recognized contributors to SDY, we also observed an enrichment in epilepsy-related genes in the SDY cohort, and a correlation between rare epilepsy variation and younger age at death. These findings emphasize the importance of considering epilepsy genes when evaluating SDY.
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11
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Fischer JA, Monroe TO, Pesce LL, Sawicki KT, Quattrocelli M, Bauer R, Kearns SD, Wolf MJ, Puckelwartz MJ, McNally EM. Opposing effects of genetic variation in MTCH2 for obesity versus heart failure. Hum Mol Genet 2023; 32:15-29. [PMID: 35904451 PMCID: PMC9837833 DOI: 10.1093/hmg/ddac176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/04/2022] [Accepted: 07/26/2022] [Indexed: 01/25/2023] Open
Abstract
Genetic variation in genes regulating metabolism may be advantageous in some settings but not others. The non-failing adult heart relies heavily on fatty acids as a fuel substrate and source of ATP. In contrast, the failing heart favors glucose as a fuel source. A bootstrap analysis for genes with deviant allele frequencies in cardiomyopathy cases versus controls identified the MTCH2 gene as having unusual variation. MTCH2 encodes an outer mitochondrial membrane protein, and prior genome-wide studies associated MTCH2 variants with body mass index, consistent with its role in metabolism. We identified the referent allele of rs1064608 (p.Pro290) as being overrepresented in cardiomyopathy cases compared to controls, and linkage disequilibrium analysis associated this variant with the MTCH2 cis eQTL rs10838738 and lower MTCH2 expression. To evaluate MTCH2, we knocked down Mtch in Drosophila heart tubes which produced a dilated and poorly functioning heart tube, reduced adiposity and shortened life span. Cardiac Mtch mutants generated more lactate at baseline, and they displayed impaired oxygen consumption in the presence of glucose but not palmitate. Treatment of cardiac Mtch mutants with dichloroacetate, a pyruvate dehydrogenase kinase inhibitor, reduced lactate and rescued lifespan. Deletion of MTCH2 in human cells similarly impaired oxygen consumption in the presence of glucose but not fatty acids. These data support a model in which MTCH2 reduction may be favorable when fatty acids are the major fuel source, favoring lean body mass. However, in settings like heart failure, where the heart shifts toward using more glucose, reduction of MTCH2 is maladaptive.
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Affiliation(s)
- Julie A Fischer
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tanner O Monroe
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lorenzo L Pesce
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Konrad T Sawicki
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mattia Quattrocelli
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Rosemary Bauer
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel D Kearns
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthew J Wolf
- Department of Medicine, Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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12
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Hui D, Xiao B, Dikilitas O, Freimuth RR, Irvin MR, Jarvik GP, Kottyan L, Kullo I, Limdi NA, Liu C, Luo Y, Namjou B, Puckelwartz MJ, Schaid D, Tiwari H, Wei WQ, Verma S, Kim D, Ritchie MD. Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index. Pac Symp Biocomput 2023; 28:437-448. [PMID: 36540998 PMCID: PMC10018532] [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] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polygenic risk scores (PRS) have led to enthusiasm for precision medicine. However, it is well documented that PRS do not generalize across groups differing in ancestry or sample characteristics e.g., age. Quantifying performance of PRS across different groups of study participants, using genome-wide association study (GWAS) summary statistics from multiple ancestry groups and sample sizes, and using different linkage disequilibrium (LD) reference panels may clarify which factors are limiting PRS transferability. To evaluate these factors in the PRS generation process, we generated body mass index (BMI) PRS (PRSBMI) in the Electronic Medical Records and Genomics (eMERGE) network (N=75,661). Analyses were conducted in two ancestry groups (European and African) and three age ranges (adult, teenagers, and children). For PRSBMI calculations, we evaluated five LD reference panels and three sets of GWAS summary statistics of varying sample size and ancestry. PRSBMI performance increased for both African and European ancestry individuals using cross-ancestry GWAS summary statistics compared to European-only summary statistics (6.3% and 3.7% relative R2 increase, respectively, pAfrican=0.038, pEuropean=6.26x10-4). The effects of LD reference panels were more pronounced in African ancestry study datasets. PRSBMI performance degraded in children; R2 was less than half of teenagers or adults. The effect of GWAS summary statistics sample size was small when modeled with the other factors. Additionally, the potential of using a PRS generated for one trait to predict risk for comorbid diseases is not well understood especially in the context of cross-ancestry analyses - we explored clinical comorbidities from the electronic health record associated with PRSBMI and identified significant associations with type 2 diabetes and coronary atherosclerosis. In summary, this study quantifies the effects that ancestry, GWAS summary statistic sample size, and LD reference panel have on PRS performance, especially in cross-ancestry and age-specific analyses.
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Affiliation(s)
- Daniel Hui
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brenda Xiao
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ozan Dikilitas
- Department of Internal Medicine, Department of Cardiovascular Medicine, Clinician-Investigator Training Program, Mayo Clinic, Rochester MN
| | - Robert R. Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gail P. Jarvik
- Departments of Medicine and Genome Sciences, University of Washington, Seattle WA, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Iftikhar Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Yuan Luo
- Department of Preventive Medicine (Health and Biomedical Informatics), Northwestern University, Chicago, IL USA
| | - Bahram Namjou
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Daniel Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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13
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Levin MG, Tsao NL, Singhal P, Liu C, Vy HMT, Paranjpe I, Backman JD, Bellomo TR, Bone WP, Biddinger KJ, Hui Q, Dikilitas O, Satterfield BA, Yang Y, Morley MP, Bradford Y, Burke M, Reza N, Charest B, Judy RL, Puckelwartz MJ, Hakonarson H, Khan A, Kottyan LC, Kullo I, Luo Y, McNally EM, Rasmussen-Torvik LJ, Day SM, Do R, Phillips LS, Ellinor PT, Nadkarni GN, Ritchie MD, Arany Z, Cappola TP, Margulies KB, Aragam KG, Haggerty CM, Joseph J, Sun YV, Voight BF, Damrauer SM. Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure. Nat Commun 2022; 13:6914. [PMID: 36376295 PMCID: PMC9663424 DOI: 10.1038/s41467-022-34216-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Heart failure is a leading cause of cardiovascular morbidity and mortality. However, the contribution of common genetic variation to heart failure risk has not been fully elucidated, particularly in comparison to other common cardiometabolic traits. We report a multi-ancestry genome-wide association study meta-analysis of all-cause heart failure including up to 115,150 cases and 1,550,331 controls of diverse genetic ancestry, identifying 47 risk loci. We also perform multivariate genome-wide association studies that integrate heart failure with related cardiac magnetic resonance imaging endophenotypes, identifying 61 risk loci. Gene-prioritization analyses including colocalization and transcriptome-wide association studies identify known and previously unreported candidate cardiomyopathy genes and cellular processes, which we validate in gene-expression profiling of failing and healthy human hearts. Colocalization, gene expression profiling, and Mendelian randomization provide convergent evidence for the roles of BCKDHA and circulating branch-chain amino acids in heart failure and cardiac structure. Finally, proteome-wide Mendelian randomization identifies 9 circulating proteins associated with heart failure or quantitative imaging traits. These analyses highlight similarities and differences among heart failure and associated cardiovascular imaging endophenotypes, implicate common genetic variation in the pathogenesis of heart failure, and identify circulating proteins that may represent cardiomyopathy treatment targets.
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Affiliation(s)
- Michael G Levin
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Noah L Tsao
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pankhuri Singhal
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Chang Liu
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Ha My T Vy
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ishan Paranjpe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tiffany R Bellomo
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - William P Bone
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran J Biddinger
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Qin Hui
- Emory University School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Ozan Dikilitas
- Departments of Internal Medicine and Cardiovascular Medicine, and Mayo Clinician-Investigator Training Program, Mayo Clinic, Rochester, MN, USA
| | | | - Yifan Yang
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P Morley
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Megan Burke
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nosheen Reza
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian Charest
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Renae L Judy
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Megan J Puckelwartz
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Leah C Kottyan
- Department of Pediatrics, Division of Human Genetics and Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Iftikhar Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sharlene M Day
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, BioMe Phenomics Center, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lawrence S Phillips
- Atlanta VA Health Care System, Decatur, GA, USA
- Division of Endocrinology, Emory University School of Medicine, Atlanta, GA, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
| | - Girish N Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Zoltan Arany
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas P Cappola
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth B Margulies
- Division of Cardiovascular Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Krishna G Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher M Haggerty
- Department of Translational Data Science and Informatics and Heart Institute, Geisinger, Danville, PA, USA
| | - Jacob Joseph
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yan V Sun
- Emory University School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute of Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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14
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Barefield DY, Yamakawa S, Tahtah I, Sell JJ, Broman M, Laforest B, Harris S, Alvarez AA, Araujo KN, Puckelwartz MJ, Wasserstrom JA, Fishman GI, McNally EM. Partial and complete loss of myosin binding protein H-like cause cardiac conduction defects. J Mol Cell Cardiol 2022; 169:28-40. [PMID: 35533732 PMCID: PMC9329245 DOI: 10.1016/j.yjmcc.2022.04.012] [Citation(s) in RCA: 2] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/25/2022] [Accepted: 04/15/2022] [Indexed: 02/04/2023]
Abstract
A premature truncation of MYBPHL in humans and a loss of Mybphl in mice is associated with dilated cardiomyopathy, atrial and ventricular arrhythmias, and atrial enlargement. MYBPHL encodes myosin binding protein H-like (MyBP-HL). Prior work in mice indirectly identified Mybphl expression in the atria and in small puncta throughout the ventricle. Because of its genetic association with human and mouse cardiac conduction system disease, we evaluated the anatomical localization of MyBP-HL and the consequences of loss of MyBP-HL on conduction system function. Immunofluorescence microscopy of normal adult mouse ventricles identified MyBP-HL-positive ventricular cardiomyocytes that co-localized with the ventricular conduction system marker contactin-2 near the atrioventricular node and in a subset of Purkinje fibers. Mybphl heterozygous ventricles had a marked reduction of MyBP-HL-positive cells compared to controls. Lightsheet microscopy of normal perinatal day 5 mouse hearts showed enrichment of MyBP-HL-positive cells within and immediately adjacent to the contactin-2-positive ventricular conduction system, but this association was not apparent in Mybphl heterozygous hearts. Surface telemetry of Mybphl-null mice revealed atrioventricular block and atrial bigeminy, while intracardiac pacing revealed a shorter atrial relative refractory period and atrial tachycardia. Calcium transient analysis of isolated Mybphl-null atrial cardiomyocytes demonstrated an increased heterogeneity of calcium release and faster rates of calcium release compared to wild type controls. Super-resolution microscopy of Mybphl heterozygous and homozygous null atrial cardiomyocytes showed ryanodine receptor disorganization compared to wild type controls. Abnormal calcium release, shorter atrial refractory period, and atrial dilation seen in Mybphl null, but not wild type control hearts, agree with the observed atrial arrhythmias, bigeminy, and atrial tachycardia, whereas the proximity of MyBP-HL-positive cells with the ventricular conduction system provides insight into how a predominantly atrial expressed gene contributes to ventricular arrhythmias and ventricular dysfunction.
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Affiliation(s)
- David Y. Barefield
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL;,Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL;,Correspondence to: David Y. Barefield, PhD, Department of Cell and Molecular Physiology Loyola University Chicago, 2160 S. 1st Ave. Maywood, IL 60153,
| | - Sean Yamakawa
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Ibrahim Tahtah
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Jordan J. Sell
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Michael Broman
- Section of Cardiology, Department of Medicine, University of Chicago, Chicago, IL
| | - Brigitte Laforest
- Section of Cardiology, Department of Medicine, University of Chicago, Chicago, IL
| | - Sloane Harris
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Alejandro A. Alvarez
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Kelly N. Araujo
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - J. Andrew Wasserstrom
- Department of Medicine and The Feinberg Cardiovascular and Renal Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Glenn I. Fishman
- Division of Cardiology, NYU Grossman School of Medicine, New York, New York
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL;,Correspondence to: Elizabeth McNally, MD, PhD, Center for Genetic Medicine, Northwestern University, 303 E. Superior St. Chicago, IL 60611,
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15
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Pensa AV, Baman JR, Puckelwartz MJ, Wilcox JE. Genetically Based Atrial Fibrillation: Current Considerations for Diagnosis and Management. J Cardiovasc Electrophysiol 2022; 33:1944-1953. [PMID: 35262243 DOI: 10.1111/jce.15446] [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: 01/09/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
Atrial fibrillation (AF) is the most common atrial arrhythmia and is subcategorized into numerous clinical phenotypes. Given its heterogeneity, investigations into the genetic mechanisms underlying AF have been pursued in recent decades, with predominant analyses focusing on early onset or lone AF. Linkage analyses, genome wide association studies (GWAS), and single gene analyses have led to the identification of rare and common genetic variants associated with AF risk. Significant overlap with genetic variants implicated in dilated cardiomyopathy syndromes, including truncating variants of the sarcomere protein titin, have been identified through these analyses, in addition to other genes associated with cardiac structure and function. Despite this, widespread utilization of genetic testing in AF remains hindered by the unclear impact of genetic risk identification on clinical outcomes and the high prevalence of variants of unknown significance (VUS). However, genetic testing is a reasonable option for patients with early onset AF and in those with significant family history of arrhythmia. While many knowledge gaps remain, emerging data support genotyping to inform selection of AF therapeutics. In this review we highlight the current understanding of the complex genetic basis of AF and explore the overlap of AF with inherited cardiomyopathy syndromes. We propose a set of criteria for clinical genetic testing in AF patients and outline future steps for the integration of genetics into AF care. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Anthony V Pensa
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jayson R Baman
- Department of Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Megan J Puckelwartz
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jane E Wilcox
- Department of Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL
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16
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Bazrafshan S, Sibilia R, Girgla S, Viswanathan SK, Puckelwartz MJ, Sangha KS, Singh RR, Kakroo M, Jandarov R, Harris DM, Rubinstein J, Becker RC, McNally EM, Sadayappan S. South Asian-Specific MYBPC3 Δ25bp Deletion Carriers Display Hypercontraction and Impaired Diastolic Function Under Exercise Stress. Front Cardiovasc Med 2021; 8:766339. [PMID: 35004883 PMCID: PMC8733148 DOI: 10.3389/fcvm.2021.766339] [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] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background: A 25-base pair (25bp) intronic deletion in the MYBPC3 gene enriched in South Asians (SAs) is a risk allele for late-onset left ventricular (LV) dysfunction, hypertrophy, and heart failure (HF) with several forms of cardiomyopathy. However, the effect of this variant on exercise parameters has not been evaluated. Methods: As a pilot study, 10 asymptomatic SA carriers of the MYBPC3 Δ25bp variant (52.9 ± 2.14 years) and 10 age- and gender-matched non-carriers (NCs) (50.1 ± 2.7 years) were evaluated at baseline and under exercise stress conditions using bicycle exercise echocardiography and continuous cardiac monitoring. Results: Baseline echocardiography parameters were not different between the two groups. However, in response to exercise stress, the carriers of Δ25bp had significantly higher LV ejection fraction (%) (CI: 4.57 ± 1.93; p < 0.0001), LV outflow tract peak velocity (m/s) (CI: 0.19 ± 0.07; p < 0.0001), and higher aortic valve (AV) peak velocity (m/s) (CI: 0.103 ± 0.08; p = 0.01) in comparison to NCs, and E/A ratio, a marker of diastolic compliance, was significantly lower in Δ25bp carriers (CI: 0.107 ± 0.102; p = 0.038). Interestingly, LV end-diastolic diameter (LVIDdia) was augmented in NCs in response to stress, while it did not increase in Δ25bp carriers (CI: 0.239 ± 0.125; p = 0.0002). Further, stress-induced right ventricular systolic excursion velocity s' (m/s), as a marker of right ventricle function, increased similarly in both groups, but tricuspid annular plane systolic excursion increased more in carriers (slope: 0.008; p = 0.0001), suggesting right ventricle functional differences between the two groups. Conclusions: These data support that MYBPC3 Δ25bp is associated with LV hypercontraction under stress conditions with evidence of diastolic impairment.
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Affiliation(s)
- Sholeh Bazrafshan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Robert Sibilia
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Saavia Girgla
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Shiv Kumar Viswanathan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Kiranpal S. Sangha
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Rohit R. Singh
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Mashhood Kakroo
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Roman Jandarov
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - David M. Harris
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Jack Rubinstein
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Richard C. Becker
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Sakthivel Sadayappan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
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17
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Webster G, Puckelwartz MJ, Pesce LL, Dellefave-Castillo LM, Vanoye CG, Potet F, Page P, Kearns SD, Pottinger T, White S, Arunkumar P, Olson R, Kofman A, Ibrahim N, Ing A, Brew C, Yap KL, Kadri S, George AL, McNally EM. Genomic Autopsy of Sudden Deaths in Young Individuals. JAMA Cardiol 2021; 6:1247-1256. [PMID: 34379075 DOI: 10.1001/jamacardio.2021.2789] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 11/14/2022]
Abstract
Importance Postmortem genetic testing of young individuals with sudden death has previously identified pathogenic gene variants. However, prior studies primarily considered highly penetrant monogenic variants, often without detailed decedent and family clinical information. Objective To assess genotype and phenotype risk in a diverse cohort of young decedents with sudden death and their families. Design, Setting, and Participants Pathological and whole-genome sequence analysis was conducted in a cohort referred from a national network of medical examiners. Cases were accrued prospectively from May 2015 to March 2019 across 24 US states. Analysis began September 2016 and ended November 2020. Exposures Evaluation of autopsy and clinical data integrated with whole-genome sequence data and family member evaluation. Results A total of 103 decedents (mean [SD] age at death, 23.7 [11.9] years; age range, 1-44 years), their surviving family members, and 140 sex- and genetic ancestry-matched controls were analyzed. Among 103 decedents, autopsy and clinical data review categorized 36 decedents with postmortem diagnoses, 23 decedents with findings of uncertain significance, and 44 with sudden unexplained death. Pathogenic/likely pathogenic (P/LP) genetic variants in arrhythmia or cardiomyopathy genes were identified in 13 decedents (12.6%). A multivariable analysis including decedent phenotype, ancestry, and sex demonstrated that younger decedents had a higher burden of P/LP variants and select variants of uncertain significance (effect size, -1.64; P = .001). These select, curated variants of uncertain significance in cardiac genes were more common in decedents than controls (83 of 103 decedents [86%] vs 100 of 140 controls [71%]; P = .005), and decedents harbored more rare cardiac variants than controls (2.3 variants per individual vs 1.8 in controls; P = .006). Genetic testing of 31 parent-decedent trios and 14 parent-decedent dyads revealed 8 transmitted P/LP variants and 1 de novo P/LP variant. Incomplete penetrance was present in 6 of 8 parents who transmitted a P/LP variant. Conclusions and Relevance Whole-genome sequencing effectively identified P/LP variants in cases of sudden death in young individuals, implicating both arrhythmia and cardiomyopathy genes. Genomic analyses and familial phenotype association suggest potentially additive, oligogenic risk mechanisms for sudden death in this cohort.
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Affiliation(s)
- Gregory Webster
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Megan J Puckelwartz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lorenzo L Pesce
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Carlos G Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Franck Potet
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Patrick Page
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Samuel D Kearns
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Tess Pottinger
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Steven White
- Cook County Medical Examiner's Office, Chicago, Illinois
| | | | - Rachael Olson
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Amber Kofman
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Nora Ibrahim
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alexander Ing
- Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Casey Brew
- Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kai Lee Yap
- Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Sabah Kadri
- Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elizabeth M McNally
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Section Editor, JAMA Cardiology
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18
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Khan SS, Shah SJ, Strande JL, Baldridge AS, Flevaris P, Puckelwartz MJ, McNally EM, Rasmussen-Torvik LJ, Lee DC, Carr JC, Benefield BC, Afzal MZ, Heiman M, Gupta S, Shapiro AD, Vaughan DE. Identification of Cardiac Fibrosis in Young Adults With a Homozygous Frameshift Variant in SERPINE1. JAMA Cardiol 2021; 6:841-846. [PMID: 33439236 DOI: 10.1001/jamacardio.2020.6909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/26/2023]
Abstract
Importance Cardiac fibrosis is exceedingly rare in young adults. Identification of genetic variants that cause early-onset cardiomyopathy may inform novel biological pathways. Experimental models and a single case report have linked genetic deficiency of plasminogen activator inhibitor-1 (PAI-1), a downstream target of cardiac transforming growth factor β, with cardiac fibrosis. Objective To perform detailed cardiovascular phenotyping and genotyping in young adults from an Amish family with a frameshift variant (c.699_700dupTA) in SERPINE1, the gene that codes for PAI-1. Design, Setting, and Participants This observational study included participants from 3 related nuclear families from an Amish community in the primary analysis and participants from the extended family in the secondary analysis. Participants were recruited from May 2015 to December 2016, and analysis took place from June 2015 to June 2020. Main Outcomes and Measures (1) Multimodality cardiovascular imaging (transthoracic echocardiography and cardiac magnetic resonance imaging), (2) whole-exome sequencing, and (3) induced pluripotent stem cell-derived cardiomyocytes. Results Among 17 participants included in the primary analysis, the mean (interquartile range) age was 23.7 (20.9-29.9) years and 9 individuals (52.9%) were confirmed to be homozygous for the SERPINE1 c.699_700dupTA variant. Late gadolinium enhancement was present in 6 of 9 homozygous participants (67%) with absolute PAI-1 deficiency vs 0 of 8 in the control group (P = .001). Late gadolinium enhancement patterns tended to be dense and linear, usually subepicardial but also midmyocardial and transmural with noncoronary distributions. Targeted whole-exome sequencing analysis identified that homozygosity for c.699_700dupTA SERPINE1 was the only shared pathogenic variant or variant of uncertain significance after examination of cardiomyopathy genes among those with late gadolinium enhancement. Induced pluripotent stem cell-derived cardiomyocytes from participants homozygous for the SERPINE1 c.699_700dupTA variant exhibited susceptibility to cardiomyocyte injury in response to angiotensin II (increased transforming growth factor β1 secretion and release of lactate dehydrogenase) compared with control induced pluripotent stem cell-derived cardiomyocytes. In a secondary analysis based on echocardiography in 155 individuals across 3 generations in the extended family, no difference in global longitudinal strain was observed in carriers for the SERPINE1 c.699_700dupTA variant compared with wild-type participants, supporting an autosomal recessive inheritance pattern. Conclusions and Relevance In this study, a highly penetrant, autosomal recessive, cardiac fibrosis phenotype among young adults with homozygous frameshift variant for SERPINE1 was identified, suggesting an optimal range of PAI-1 levels are needed for cardiac homeostasis.
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Affiliation(s)
- Sadiya S Khan
- Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sanjiv J Shah
- Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Associate Editor, JAMA Cardiology
| | - Jennifer L Strande
- Department of Medicine and Cardiovascular Center, Medical College of Wisconsin, Milwaukee
| | - Abigail S Baldridge
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Panagiotis Flevaris
- Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elizabeth M McNally
- Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Daniel C Lee
- Division of Cardiology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - James C Carr
- Department of Radiology, Northwestern University, Chicago, Illinois
| | - Brandon C Benefield
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Muhammad Zeeshan Afzal
- Department of Medicine and Cardiovascular Center, Medical College of Wisconsin, Milwaukee
| | - Meadow Heiman
- Indiana Hemophilia and Thrombosis Center, Indianapolis
| | - Sweta Gupta
- Indiana Hemophilia and Thrombosis Center, Indianapolis
| | - Amy D Shapiro
- Indiana Hemophilia and Thrombosis Center, Indianapolis
| | - Douglas E Vaughan
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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19
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Affiliation(s)
- Dominic E Fullenkamp
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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20
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Webster G, Reynolds M, Arva NC, Dellefave-Castillo LM, McElligott HS, Kofman A, Laboski A, Magnetta D, George AL, McNally EM, Puckelwartz MJ. Mitochondrial cardiomyopathy and ventricular arrhythmias associated with biallelic variants in C1QBP. Am J Med Genet A 2021; 185:2496-2501. [PMID: 34003581 DOI: 10.1002/ajmg.a.62262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/03/2020] [Revised: 03/23/2021] [Accepted: 04/24/2021] [Indexed: 11/06/2022]
Abstract
Patients with biallelic mutations in the nuclear-encoded mitochondrial gene C1QBP/p32 have been described with syndromic features and autosomal recessive cardiomyopathy. We describe the clinical course in two siblings who developed cardiomyopathy and ventricular fibrillation in infancy. We provide genomic analysis and clinical-pathologic correlation. Both siblings had profound cardiac failure with ventricular arrhythmia. One child died suddenly. The second sibling survived resuscitation but required extracorporeal cardiopulmonary support and died shortly afterward. On cardiac autopsy, the left ventricle was hypertrophied in both children. Histological examination revealed prominent cardiomyocyte cytoplasmic clearing, and electron microscopy confirmed abnormal mitochondrial structure within cardiomyocytes. DNA sequencing revealed compound heterozygous variants in C1QBP (p.Thr40Asnfs*45 and p.Phe204Leu) in both children. Family segregation analysis demonstrated each variant was inherited from an unaffected, heterozygous parent. Inherited loss of C1QBP/p32 is associated with recessive cardiomyopathy, ventricular fibrillation, and sudden death in early life. Ultrastructural mitochondrial evaluation in the second child was similar to findings in engineered C1qbp-deficient mice. Rapid trio analysis can define rare biallelic variants in genes that may be implicated in sudden death and facilitate medical management and family planning. (184/200).
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Affiliation(s)
- Gregory Webster
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Meredith Reynolds
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicoleta C Arva
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Amber Kofman
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Aleksandra Laboski
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Defne Magnetta
- Division of Cardiology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Bluhm Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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21
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Khan SS, Hoell C, Castillo LM, Connolly JJ, Crosslin DR, Chung WK, Gordon AS, Harr M, Jarvik GP, Kullo I, Larson EB, Leppig KA, Manolio T, Pacheco JA, Ralston JD, Puckelwartz MJ, Smith ME, Wells Q, McNally EM, Rasmussen-Torvik LJ. Practice Patterns After Return of Rare Variants Associated With Cardiomyopathy in the Electronic Medical Records and Genomics Network. Circ Heart Fail 2021; 14:e008155. [PMID: 33951936 DOI: 10.1161/circheartfailure.120.008155] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/16/2022]
Affiliation(s)
- Sadiya S Khan
- Division of Cardiology, Department of Medicine (S.S.K., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (S.S.K., L.J.R.-T.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Christin Hoell
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Lisa M Castillo
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, PA (J.J.C., M.H.)
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education (D.R.C.), University of Washington Medical Center, Seattle
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University School of Medicine, New York, NY (W.K.C.)
| | - Adam S Gordon
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Margaret Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, PA (J.J.C., M.H.)
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences (G.P.J.), University of Washington Medical Center, Seattle
| | - Iftikhar Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN (I.K.)
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Kathleen A Leppig
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Teri Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD (T.M.)
| | - Jennifer A Pacheco
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - James D Ralston
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Megan J Puckelwartz
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Maureen E Smith
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Quinn Wells
- Department of Medicine, Vanderbilt University Medical Center. Nashville, TN (Q.W.)
| | - Elizabeth M McNally
- Division of Cardiology, Department of Medicine (S.S.K., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine (S.S.K., L.J.R.-T.), Feinberg School of Medicine, Northwestern University, Chicago, IL
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22
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Puckelwartz MJ, Pesce LL, Dellefave‐Castillo LM, Wheeler MT, Pottinger TD, Robinson AC, Kearns SD, Gacita AM, Schoppen ZJ, Pan W, Kim G, Wilcox JE, Anderson AS, Ashley EA, Day SM, Cappola T, Dorn GW, McNally EM. Genomic Context Differs Between Human Dilated Cardiomyopathy and Hypertrophic Cardiomyopathy. J Am Heart Assoc 2021; 10:e019944. [PMID: 33764162 PMCID: PMC8174318 DOI: 10.1161/jaha.120.019944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
Background Inherited cardiomyopathies display variable penetrance and expression, and a component of phenotypic variation is genetically determined. To evaluate the genetic contribution to this variable expression, we compared protein coding variation in the genomes of those with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). Methods and Results Nonsynonymous single-nucleotide variants (nsSNVs) were ascertained using whole genome sequencing from familial cases of HCM (n=56) or DCM (n=70) and correlated with echocardiographic information. Focusing on nsSNVs in 102 genes linked to inherited cardiomyopathies, we correlated the number of nsSNVs per person with left ventricular measurements. Principal component analysis and generalized linear models were applied to identify the probability of cardiomyopathy type as it related to the number of nsSNVs in cardiomyopathy genes. The probability of having DCM significantly increased as the number of cardiomyopathy gene nsSNVs per person increased. The increase in nsSNVs in cardiomyopathy genes significantly associated with reduced left ventricular ejection fraction and increased left ventricular diameter for individuals carrying a DCM diagnosis, but not for those with HCM. Resampling was used to identify genes with aberrant cumulative allele frequencies, identifying potential modifier genes for cardiomyopathy. Conclusions Participants with DCM had more nsSNVs per person in cardiomyopathy genes than participants with HCM. The nsSNV burden in cardiomyopathy genes did not correlate with the probability or manifestation of left ventricular measures in HCM. These findings support the concept that increased variation in cardiomyopathy genes creates a genetic background that predisposes to DCM and increased disease severity.
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Affiliation(s)
- Megan J. Puckelwartz
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIL
- Department of Medicine/Cardiovascular MedicineStanford UniversityStanfordCA
| | - Lorenzo L. Pesce
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | | | - Matthew T. Wheeler
- Department of Medicine/Cardiovascular MedicineStanford UniversityStanfordCA
| | - Tess D. Pottinger
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Avery C. Robinson
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Samuel D. Kearns
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Anthony M. Gacita
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Zachary J. Schoppen
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Wenyu Pan
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Gene Kim
- Department of MedicineUniversity of ChicagoChicagoIL
| | - Jane E. Wilcox
- Department of MedicineBluhm Cardiovascular InstituteNorthwestern UniversityChicagoIL
| | - Allen S. Anderson
- Department of MedicineBluhm Cardiovascular InstituteNorthwestern UniversityChicagoIL
| | - Euan A. Ashley
- Department of MedicineBluhm Cardiovascular InstituteNorthwestern UniversityChicagoIL
| | - Sharlene M. Day
- Department of Internal MedicineThe University of MichiganAnn ArborMI
- Perelman School of MedicineDivision of Cardiovascular Medicine and Penn CardiovascularInstitute and Department of MedicineUniversity of PennsylvaniaPhiladelphiaPA
| | - Thomas Cappola
- Perelman School of MedicineDivision of Cardiovascular Medicine and Penn CardiovascularInstitute and Department of MedicineUniversity of PennsylvaniaPhiladelphiaPA
| | | | - Elizabeth M. McNally
- Center for Genetic MedicineNorthwestern University Feinberg School of MedicineChicagoIL
- Department of Internal MedicineThe University of MichiganAnn ArborMI
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23
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Abstract
BACKGROUND Inherited cardiomyopathy associates with a range of phenotypes, mediated by genetic and nongenetic factors. Noninherited cardiomyopathy also displays varying progression and outcomes. Expression of cardiomyopathy genes is under the regulatory control of promoters and enhancers, and human genetic variation in promoters and enhancers may contribute to this variability. METHODS We superimposed epigenomic profiling from hearts and cardiomyocytes, including promoter-capture chromatin conformation information, to identify enhancers for 2 cardiomyopathy genes, MYH7 and LMNA. Enhancer function was validated in human cardiomyocytes derived from induced pluripotent stem cells. We also conducted a genome-wide search to ascertain genomic variation in enhancers positioned to alter cardiac expression and correlated one of these variants to cardiomyopathy progression using biobank data. RESULTS Multiple enhancers were identified and validated for LMNA and MYH7, including a key enhancer that regulates the switch from MYH6 expression to MYH7 expression. Deletion of this enhancer resulted in a dose-dependent increase in MYH6 and faster contractile rate in engineered heart tissues. We searched for genomic variation in enhancer sequences across the genome, with a focus on nucleotide changes that create or interrupt transcription factor binding sites. The sequence variant, rs875908, disrupts a T-Box Transcription Factor 5 binding motif and maps to an enhancer region 2 kilobases from the transcriptional start site of MYH7. Gene editing to remove the enhancer that harbors this variant markedly reduced MYH7 expression in human cardiomyocytes. Using biobank-derived data, rs875908 associated with longitudinal echocardiographic features of cardiomyopathy. CONCLUSIONS Enhancers regulate cardiomyopathy gene expression, and genomic variation within these enhancer regions associates with cardiomyopathic progression over time. This integrated approach identified noncoding modifiers of cardiomyopathy and is applicable to other cardiac genes.
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Affiliation(s)
- Anthony M. Gacita
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Dominic E. Fullenkamp
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Joyce Ohiri
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Tess Pottinger
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Megan J. Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
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24
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Gacita AM, Dellefave-Castillo L, Page PGT, Barefield DY, Wasserstrom JA, Puckelwartz MJ, Nobrega MA, McNally EM. Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart. Circ Heart Fail 2020; 13:e006926. [PMID: 32993371 PMCID: PMC7577963 DOI: 10.1161/circheartfailure.120.006926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Indexed: 01/08/2023]
Abstract
BACKGROUND The failing heart is characterized by changes in gene expression. However, the regulatory regions of the genome that drive these gene expression changes have not been well defined in human hearts. METHODS To define genome-wide enhancer and promoter use in heart failure, cap analysis of gene expression sequencing was applied to 3 healthy and 4 failed human hearts to identify promoter and enhancer regions used in left ventricles. Healthy hearts were derived from donors unused for transplantation and failed hearts were obtained as discarded tissue after transplantation. RESULTS Cap analysis of gene expression sequencing identified a combined potential for ≈23 000 promoters and ≈5000 enhancers active in human left ventricles. Of these, 17 000 promoters and 1800 enhancers had additional support for their regulatory function. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered aminoterminal protein sequences. Enhancer usage between healthy and failed hearts identified a majority of differentially used heart failure enhancers were intronic and primarily localized within the first intron, revealing this position as a common feature associated with tissue-specific gene expression changes in the heart. CONCLUSIONS This data set defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction. Additionally, regulatory changes contributing to heart failure are attractive therapeutic targets for controlling ventricular remodeling and clinical progression.
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Affiliation(s)
- Anthony M Gacita
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Lisa Dellefave-Castillo
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Patrick G T Page
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - David Y Barefield
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - J Andrew Wasserstrom
- Department of Medicine (Cardiology) (J.A.W.), Northwestern University Feinberg School of Medicine, Chicago IL
| | - Megan J Puckelwartz
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
| | | | - Elizabeth M McNally
- Center for Genetic Medicine (A.M.G., L.D.-C., P.G.T.P., D.Y.B., M.J.P., E.M.M.), Northwestern University Feinberg School of Medicine, Chicago IL
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25
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Schoppen ZJ, Balmert LC, White S, Olson R, Arunkumar P, Dellefave‐Castillo LM, Puckelwartz MJ, George AL, McNally EM, Webster G. Prevalence of Abnormal Heart Weight After Sudden Death in People Younger than 40 Years of Age. J Am Heart Assoc 2020; 9:e015699. [PMID: 32885733 PMCID: PMC7726998 DOI: 10.1161/jaha.120.015699] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background After sudden cardiac death in people aged <40 years, heart weight is a surrogate for cardiomegaly and a marker for cardiomyopathy. However, thresholds for cardiomegaly based on heart weight have not been validated in a cohort of cases of sudden cardiac death in young people. Methods and Results We surveyed medical examiner offices to determine which tools were used to assess heart weight norms. The survey determined that there was no gold standard for cardiomegaly (52 centers reported 22 different methods). We used a collection of heart weight data from sudden deaths in the Northwestern Sudden Death Collaboration (NSDC) to test the 22 methods. We found that the methods reported in our survey had little consistency: they classified between 18% and 81% of NSDC hearts with cardiomegaly. Therefore, we obtained biometric and postmortem data from a reference population of 3398 decedents aged <40 years. The reference population was ethnically diverse and had no known cardiac pathology on autopsy or histology. We derived and validated a multivariable regression model to predict normal heart weights and a threshold for cardiomegaly (upper 95% CI limit) in the young reference population (the Chicago model). Using the new model, the prevalence of cardiomegaly in hearts from the NSDC was 19%. Conclusions Medical examiner offices use a variety of tools to classify cardiomegaly. These approaches produce inconsistent results, and many overinterpret cardiomegaly. We recommend the model proposed to classify postmortem cardiomegaly in cases of sudden cardiac death in young people.
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Affiliation(s)
- Zachary J. Schoppen
- Division of CardiologyAnn & Robert H. Lurie Children’s Hospital of ChicagoNorthwestern University Feinberg School of MedicineChicagoIL
| | - Lauren C. Balmert
- Department of Preventive Medicine (Biostatistics)Northwestern University Feinberg School of MedicineChicagoIL
| | | | - Rachael Olson
- Division of CardiologyAnn & Robert H. Lurie Children’s Hospital of ChicagoNorthwestern University Feinberg School of MedicineChicagoIL
| | | | - Lisa M. Dellefave‐Castillo
- Center for Genetic Medicine and Division of CardiologyDepartment of MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Megan J. Puckelwartz
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIL
- Center for Genetic Medicine and Division of CardiologyDepartment of MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Alfred L. George
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIL
| | - Elizabeth M. McNally
- Center for Genetic Medicine and Division of CardiologyDepartment of MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Gregory Webster
- Division of CardiologyAnn & Robert H. Lurie Children’s Hospital of ChicagoNorthwestern University Feinberg School of MedicineChicagoIL
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26
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Pottinger T, Puckelwartz MJ, Pesce LL, Gacita A, Salamone I, Kearns S, Pacheco JA, Nobrega M, Rasmussen-Torvik LJ, Smith ME, Chisholm R, McNally EM. Abstract 439: Trajectory Analysis of Left Ventricular Dimensions From Biobank Data Uncovers Novel Genetic Associations. Circ Res 2020. [DOI: 10.1161/res.127.suppl_1.439] [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] [Indexed: 11/16/2022]
Abstract
Background:
Approximately 6 million adults in the United States have heart failure. The progression of heart failure is variable arising from differences in sex, age, genetic background including ancestry, and medication response. Many population-based genetic studies of heart failure have been cross-sectional in nature, failing to gain additional power from longitudinal analyses. As heart failure is known to change over time, using longitudinal data trajectories as a quantitative trait will increase power in genome wide association studies (GWAS).
Methods:
We used the electronic health record in a racially and ethnically diverse medical biobank from a single, metropolitan US center. We used whole genome data from 896 unrelated participants analyzed, including 494 who had at least 1 electrocardiogram and 324 who had more than 1 echocardiogram (average of 3 observations per person). A mixture model based semiparametric latent growth curve model was used to cluster outcome measures used for genome-wide analyses.
Results:
GWAS on the trajectory probability of QTc interval identified significant associations with variants in regulatory regions proximal to the
WLS
gene, which encodes Wntless, a Wnt ligand secretion mediator.
WLS
was previously associated with QTc and myocardial infarction, thus confirming the power of the method. GWAS on the trajectory probability of left ventricular diameter (LVIDd) identified significant associations with variants in regulatory regions near
MYO10
, which encodes unconventional Myosin-10.
MYO10
was previously associated with obesity and metabolic syndrome.
Conclusions:
This is the first study to show an association with variants in or near
MYO10
and left ventricular dimension changes over time. Further, we found that using trajectory probabilities can provide increased power to find novel associations with longitudinal data. This reduces the need for larger cohorts, and increases yield from smaller, well-phenotyped cohorts, such as those found in biobanks. This approach should be useful in the study of rare diseases and underrepresented populations.
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27
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Sadayappan S, Puckelwartz MJ, McNally EM. South Asian-Specific MYBPC3Δ25bp Intronic Deletion and Its Role in Cardiomyopathies and Heart Failure. Circ Genom Precis Med 2020; 13:e002986. [PMID: 32543992 DOI: 10.1161/circgen.120.002986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sakthivel Sadayappan
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, OH. Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Megan J Puckelwartz
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, OH. Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Elizabeth M McNally
- Division of Cardiovascular Health and Disease, Department of Internal Medicine, Heart, Lung and Vascular Institute, College of Medicine, University of Cincinnati, OH. Center for Genetic Medicine, Northwestern University, Chicago, IL
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Pottinger TD, Puckelwartz MJ, Pesce LL, Robinson A, Kearns S, Pacheco JA, Rasmussen-Torvik LJ, Smith ME, Chisholm R, McNally EM. Pathogenic and Uncertain Genetic Variants Have Clinical Cardiac Correlates in Diverse Biobank Participants. J Am Heart Assoc 2020; 9:e013808. [PMID: 32009526 PMCID: PMC7033893 DOI: 10.1161/jaha.119.013808] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Genome sequencing coupled with electronic heath record data can uncover medically important genetic variation. Interpretation of rare genetic variation and its role in mediating cardiovascular phenotypes is confounded by variants of uncertain significance. Methods and Results We analyzed the whole genome sequence of 900 racially and ethnically diverse biobank participants selected from a single US center. Participants were equally divided among European, African, Hispanic, and mixed races/ethnicities. We evaluated the American College of Medical Genetics and Genomics medically actionable list of 59 genes, focusing on the cardiac genes. Variation was interpreted using the most recent reports in ClinVar, a database of medically relevant human variation. We identified 19 individuals with pathogenic or likely pathogenic variants in cardiac actionable genes (2%) and found evidence of related clinical correlates in the electronic health record. Participants of African ancestry, compared with those of European ancestry, had more variants of uncertain significance in the medically actionable genes including the 30 cardiac actionable genes, even when normalized to total variant count per person. Longitudinal measures of left ventricle size from ≈400 biobank participants (1723 patient‐years) were correlated with genetic findings. The presence of ≥1 uncertain variant in the actionable cardiac genes and a cardiomyopathy diagnosis correlated with increased left ventricular internal diameter in diastole and in systole. In particular, MYBPC3 was identified as a gene with excess variants of uncertain significance. Conclusions These data indicate that a subset of uncertain genetic variants may confer risk and should not be considered benign.
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Affiliation(s)
- Tess D Pottinger
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Megan J Puckelwartz
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
- Department of Pharmacology Northwestern University Feinberg School of Medicine Chicago IL
| | | | - Avery Robinson
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Samuel Kearns
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Jennifer A Pacheco
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Maureen E Smith
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
| | - Rex Chisholm
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
- Department of Cell and Molecular Biology Northwestern University Feinberg School of Medicine Chicago IL
| | - Elizabeth M McNally
- Center for Genetic Medicine Northwestern University Feinberg School of Medicine Chicago IL
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29
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Vanoye CG, Desai RR, Adusumili S, Meiler J, Sanders CR, Mirshahi T, Puckelwartz MJ, McNally EM, George AL. Functional Consequences of Incidentally Discovered KCNQ1 Variants Determined by Automated Electrophysiology. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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30
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Viswanathan SK, Puckelwartz MJ, Mehta A, Ramachandra CJA, Jagadeesan A, Fritsche-Danielson R, Bhat RV, Wong P, Kandoi S, Schwanekamp JA, Kuffel G, Pesce LL, Zilliox MJ, Durai UNB, Verma RS, Molokie RE, Suresh DP, Khoury PR, Thomas A, Sanagala T, Tang HC, Becker RC, Knöll R, Shim W, McNally EM, Sadayappan S. Association of Cardiomyopathy With MYBPC3 D389V and MYBPC3Δ25bpIntronic Deletion in South Asian Descendants. JAMA Cardiol 2019; 3:481-488. [PMID: 29641836 DOI: 10.1001/jamacardio.2018.0618] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Importance The genetic variant MYBPC3Δ25bp occurs in 4% of South Asian descendants, with an estimated 100 million carriers worldwide. MYBPC3 Δ25bp has been linked to cardiomyopathy and heart failure. However, the high prevalence of MYBPC3Δ25bp suggests that other stressors act in concert with MYBPC3Δ25bp. Objective To determine whether there are additional genetic factors that contribute to the cardiomyopathic expression of MYBPC3Δ25bp. Design, Setting, andParticipants South Asian individuals living in the United States were screened for MYBPC3Δ25bp, and a subgroup was clinically evaluated using electrocardiograms and echocardiograms at Loyola University, Chicago, Illinois, between January 2015 and July 2016. Main Outcomes and Measures Next-generation sequencing of 174 cardiovascular disease genes was applied to identify additional modifying gene mutations and correlate genotype-phenotype parameters. Cardiomyocytes derived from human-induced pluripotent stem cells were established and examined to assess the role of MYBPC3Δ25bp. Results In this genotype-phenotype study, individuals of South Asian descent living in the United States from both sexes (36.23% female) with a mean population age of 48.92 years (range, 18-84 years) were recruited. Genetic screening of 2401 US South Asian individuals found an MYBPC3Δ25bpcarrier frequency of 6%. A higher frequency of missense TTN variation was found in MYBPC3Δ25bp carriers compared with noncarriers, identifying distinct genetic backgrounds within the MYBPC3Δ25bp carrier group. Strikingly, 9.6% of MYBPC3Δ25bp carriers also had a novel MYBPC3 variant, D389V. Family studies documented D389V was in tandem on the same allele as MYBPC3Δ25bp, and D389V was only seen in the presence of MYBPC3Δ25bp. In contrast to MYBPC3Δ25bp, MYBPC3Δ25bp/D389V was associated with hyperdynamic left ventricular performance (mean [SEM] left ventricular ejection fraction, 66.7 [0.7%]; left ventricular fractional shortening, 36.6 [0.6%]; P < .03) and stem cell-derived cardiomyocytes exhibited cellular hypertrophy with abnormal Ca2+ transients. Conclusions and Relevance MYBPC3Δ25bp/D389V is associated with hyperdynamic features, which are an early finding in hypertrophic cardiomyopathy and thought to reflect an unfavorable energetic state. These findings support that a subset of MYBPC3Δ25bp carriers, those with D389V, account for the increased risk attributed to MYBPC3Δ25bp.
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Affiliation(s)
- Shiv Kumar Viswanathan
- Heart, Lung and Vascular Institute, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio.,Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
| | | | - Ashish Mehta
- National Heart Research Institute Singapore.,Cardiovascular Academic Clinical Program, DUKE-NUS Medical School, Singapore.,PSC and Phenotyping Laboratory, Victor Chang Cardiac Research Institute, Sydney, Australia
| | | | | | - Regina Fritsche-Danielson
- Cardiovascular and Metabolic Disease Innovative Medicines and Early Development Unit, AstraZeneca Research and Development, Gothenburg, Sweden
| | - Ratan V Bhat
- Cardiovascular and Metabolic Disease Innovative Medicines and Early Development Unit, AstraZeneca Research and Development, Gothenburg, Sweden
| | - Philip Wong
- National Heart Research Institute Singapore.,Cardiovascular and Metabolic Disorders Program, DUKE-NUS Medical School, Singapore.,Department of Cardiology, National Heart Centre Singapore, Singapore
| | - Sangeetha Kandoi
- Heart, Lung and Vascular Institute, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio.,Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois.,Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Jennifer A Schwanekamp
- Heart, Lung and Vascular Institute, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Gina Kuffel
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois
| | - Lorenzo L Pesce
- Computation Institute, The University of Chicago, Chicago, Illinois
| | - Michael J Zilliox
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois
| | - U Nalla B Durai
- Divison of Hematology and Oncology, University of Illinois at Chicago
| | - Rama Shanker Verma
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - Robert E Molokie
- Divison of Hematology and Oncology, University of Illinois at Chicago
| | | | - Philip R Khoury
- Heart Institute, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Annie Thomas
- Marcella Niehoff School of Nursing, Loyola University Chicago, Maywood, Illinois
| | - Thriveni Sanagala
- Department of Cardiology and Echocardiography and Cardiographics, Loyola University Chicago, Maywood, Illinois
| | - Hak Chiaw Tang
- Department of Cardiology, National Heart Centre Singapore, Singapore
| | - Richard C Becker
- Heart, Lung and Vascular Institute, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ralph Knöll
- Cardiovascular and Metabolic Disease Innovative Medicines and Early Development Unit, AstraZeneca Research and Development, Gothenburg, Sweden.,Integrated Cardio-Metabolic Centre, Myocardial Genetics, Karolinska Institutet, University Hospital, Heart and Vascular Theme, Stockholm, Sweden
| | - Winston Shim
- National Heart Research Institute Singapore.,Cardiovascular and Metabolic Disorders Program, DUKE-NUS Medical School, Singapore
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois.,Associate Editor for Translational Science
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio.,Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, Illinois
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31
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Zouk H, Venner E, Lennon NJ, Muzny DM, Abrams D, Adunyah S, Albertson-Junkans L, Ames DC, Appelbaum P, Aronson S, Aufox S, Babb LJ, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski SJ, Bland HT, Blout C, Borthwick K, Bottinger EP, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Almoguera B, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm RL, Christensen KD, Chung W, Chute CG, City B, Cobb BL, Connolly JJ, Crane P, Crew K, Crosslin D, De Andrade M, De la Cruz J, Denson S, Denny J, DeSmet T, Dikilitas O, Friedrich C, Fullerton SM, Funke B, Gabriel S, Gainer V, Gharavi A, Glazer AM, Glessner JT, Goehringer J, Gordon AS, Graham C, Green RC, Gundelach JH, Dayal J, Hain HS, Hakonarson H, Harden MV, Harley J, Harr M, Hartzler A, Hayes MG, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell KM, Hripcsak G, Hu J, Jarvik GP, Jayaseelan JC, Jiang Y, Joo YY, Jose S, Josyula NS, Justice AE, Kalla SE, Kalra D, Karlson E, Kelly MA, Keating BJ, Kenny EE, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan DC, Korchina V, Kottyan L, Kovar C, Kudalkar E, Kullo IJ, Lammers P, Larson EB, Lebo MS, Leduc M, Lee MT(M, Leppig KA, Leslie ND, Li R, Liang WH, Lin CF, Linder J, Lindor NM, Lingren T, Linneman JG, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, Dinsmore MJ, Dodge S, Hynes ED, Dunlea P, Edwards TL, Eng CM, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, McGowan ML, McNally E, Meldrim J, Mentch F, Mosley J, Mukherjee S, Mullen TE, Muniz J, Murdock DR, Murphy S, Murugan M, Myers MF, Namjou B, Ni Y, Obeng AO, Onofrio RC, Taylor CO, Person TN, Peterson JF, Petukhova L, Pisieczko CJ, Pratap S, Prows CA, Puckelwartz MJ, Rahm AK, Raj R, Ralston JD, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Rasouly HM, Raychaudhuri S, Ritchie MD, Rives C, Riza B, Roden D, Rosenthal EA, Santani A, Schaid D, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp RR, Singh R, Sleiman PM, Slowik K, Smith JC, Smith ME, Smoller JW, Sohn S, Stanaway IB, Starren J, Stroud M, Su J, Tolwinski K, Van Driest SL, Vargas SM, Varugheese M, Veenstra D, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei WQ, Weiss ST, Wiesner GL, Wells Q, Weng C, White PS, Wiley KL, Williams JL, Williams MS, Wilson MW, Witkowski L, Woods LA, Woolf B, Wu TJ, Wynn J, Yang Y, Yi V, Zhang G, Zhang L, Rehm HL, Gibbs RA. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network. Am J Hum Genet 2019; 105:588-605. [PMID: 31447099 PMCID: PMC6731372 DOI: 10.1016/j.ajhg.2019.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [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: 10/26/2018] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.
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32
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Affiliation(s)
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Associate Editor
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33
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Puckelwartz MJ, Pesce LL, Dellefave-Castillo LM, Wheeler MT, Pottinger TD, Robinson AC, Gacita AM, Schoppen ZJ, Pan W, Kim G, Wilcox JE, Anderson AS, Ashley EA, Day SM, Cappola T, Dorn GW, McNally EM. Abstract 469: Genomic Context Predicts Dilated but Not Hypertrophic Cardiomyopathy. Circ Res 2019. [DOI: 10.1161/res.125.suppl_1.469] [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] [Indexed: 11/16/2022]
Abstract
Rationale:
Cardiomyopathies are a major cause of heart failure and have a strong heritable component.
Objective:
Determine the role of both common and rare nonsynonymous genetic variation in hypertrophic (HCM) and dilated familial cardiomyopathy (DCM).
Methods and Results:
Whole genome sequencing was used to determine common and rare nonsynonymous genetic variation in familial cases of HCM (n=56) or DCM (n=71). Variation was evaluated in 102 cardiomyopathy genes routinely assayed in clinical and commercial gene testing panels. We used cardiac gene expression data from GTEx (Genotype-Tissue Expression database) to define additional genes expressed in the heart. The number of nonsynonymous single nucleotide variants (nsSNVs), the majority of which were missense variants, was correlated with echocardiographic measurements. Principal component analysis (PCA) of left ventricular measures separated HCM and DCM. Regression of the first principal component using all nonsynonymous single nucleotide variants (nsSNVs) in cardiomyopathy genes showed the number of nsSNVs predicted DCM but not HCM. DCM probability in the cohort significantly increased as the number of cardiomyopathy gene nsSNVs increased (p<0.02). The increase in nsSNVs in cardiomyopathy genes significantly associated with reduced left ventricular ejection fraction and increased left ventricular diameter in DCM. Resampling methods identified genes with deviant cumulative allele frequencies, identifying potential modifier genes for cardiomyopathy.
Conclusions:
DCM subjects carry a greater burden of nsSNVs in cardiomyopathy genes. This genomic burden translates to impaired systolic cardiac function in DCM. In contrast, nsSNV burden in cardiomyopathy genes did not correlate with the probability or manifestation of left ventricular measures in HCM. These findings support a complex inheritance for DCM where increased variation in cardiomyopathy genes creates a genetic background that predisposes to DCM and increased disease severity. The distinct genetic landscapes of HCM and DCM suggest that greater genetic variation in cardiac genes provokes unfavorable ventricular remodeling with reduced systolic function.
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34
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Affiliation(s)
- Megan J Puckelwartz
- From the Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Elizabeth M McNally
- From the Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.
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35
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Affiliation(s)
- Megan J Puckelwartz
- From the Department of Pharmacology, Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.
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36
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Barefield DY, Rahmanseresht S, O'Leary T, Sell JJ, Puckelwartz MJ, Wilsbacher LD, Previs MJ, McNally EM. Myosin Binding Protein H-Like Regulates Myofilament Content in Atrial and a Subset of Ventricular Conduction System Cardiomyocytes. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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37
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Affiliation(s)
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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38
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Levy Y, Ross JA, Niglas M, Snetkov VA, Lynham S, Liao CY, Puckelwartz MJ, Hsu YM, McNally EM, Alsheimer M, Harridge SD, Young SG, Fong LG, Español Y, Lopez-Otin C, Kennedy BK, Lowe DA, Ochala J. Prelamin A causes aberrant myonuclear arrangement and results in muscle fiber weakness. JCI Insight 2018; 3:120920. [PMID: 30282816 PMCID: PMC6237469 DOI: 10.1172/jci.insight.120920] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/23/2018] [Indexed: 01/06/2023] Open
Abstract
Physiological and premature aging are frequently associated with an accumulation of prelamin A, a precursor of lamin A, in the nuclear envelope of various cell types. Here, we aimed to underpin the hitherto unknown mechanisms by which prelamin A alters myonuclear organization and muscle fiber function. By experimentally studying membrane-permeabilized myofibers from various transgenic mouse lines, our results indicate that, in the presence of prelamin A, the abundance of nuclei and myosin content is markedly reduced within muscle fibers. This leads to a concept by which the remaining myonuclei are very distant from each other and are pushed to function beyond their maximum cytoplasmic capacity, ultimately inducing muscle fiber weakness.
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Affiliation(s)
- Yotam Levy
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
| | - Jacob A Ross
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
| | - Marili Niglas
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
| | - Vladimir A Snetkov
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, United Kingdom
| | - Chen-Yu Liao
- Buck Institute for Research on Aging, Novato, California, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Yueh-Mei Hsu
- Buck Institute for Research on Aging, Novato, California, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | - Manfred Alsheimer
- Department of Cell and Developmental Biology, University of Würzburg, Würzburg, Germany
| | - Stephen Dr Harridge
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
| | - Stephen G Young
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Loren G Fong
- Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Yaiza Español
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, California, USA.,Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Centre for Healthy Ageing, National University Health System, Singapore.,Singapore Institute for Clinical Sciences, Singapore
| | - Dawn A Lowe
- Divisions of Rehabilitation Science and Physical Therapy, Department of Rehabilitation Medicine, School of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Julien Ochala
- School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, and
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Barefield DY, Sell JJ, Puckelwartz MJ, Wilsbacher LD, Fishman GI, McNally EM. Abstract 116:
Mybphl
is a Novel Myofilament Component Implicated in Arrhythmia and Dilated Cardiomyopathy. Circ Res 2018. [DOI: 10.1161/res.123.suppl_1.116] [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] [Indexed: 11/16/2022]
Abstract
Dilated cardiomyopathy is under significant genetic influence. Using whole-genome sequencing, we found a premature stop variant (R255X) in the
MYBPHL
gene in a family with DCM and conduction system disease. A
Mybphl
null mouse model revealed systolic dysfunction with atrial and ventricular conduction system (VCS) abnormalities. We found MyBP-HL protein highly expressed in both human and mouse atria and in a subset of ventricular cardiomyocytes. We hypothesize that MyBP-HL regulates VCS function and loss of MyBP-HL causes ventricular arrhythmia and cardiac dysfunction. We now examined hearts and isolated VCMs from
Mybphl
WT, het, and null mice using immunofluorescence microscopy (IFM). Clusters of MyBP-HL+ ventricular cardiomyocytes were evident in WT hearts (~1/200,000), with only 10% as many MyBP-HL+ cardiomyocytes in het samples. In WT hearts, MyBP-HL+ cells localized in the right ventricular free wall, with significantly fewer MyBP-HL+ cells in the right ventricular free wall in het hearts. The VCS marker contactin-2 (Cntn2) was used to assess MyBP-HL co-localization in the VCS. MyBP-HL co-localized with Cntn2+ cardiomyocytes in the transition zone between the atria and ventricle near the AV node, as well as in a subset of Cntn2+ Purkinje fibers. MyBP-HL+ ventricular cardiomyocytes were also found outside the VCS, suggesting other roles for those cells in regulating ventricular function. To discern MyBP-HL myofilament localization, we used super-resolution structured illumination microscopy on atrial cardiomyocytes. MyBP-HL co-localized with cMyBP-C in the C-zone of the A-band but also occupied space in the inner portion of the A-band near the M-line. This localization was not altered in het mice; however, the ratio of MyBP-HL in the inner portion of the A-band was diminished in het mice compared to WT. This suggests that MyBP-HL may bind the light meromyosin coiled-coil tail that originates from the M-line. Following the discovery that loss of MyBP-HL is associated with DCM and arrhythmia, we identified that MyBP-HL associates with the VCS and reduced MyBP-HL levels reduce the amount of MyBP-HL positive VCMs. These data suggest that loss of MyBP-HL may impair the development and function of the VCS, resulting in arrhythmias.
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Wyatt EJ, Demonbreun AR, Kim EY, Puckelwartz MJ, Vo AH, Dellefave-Castillo LM, Gao QQ, Vainzof M, Pavanello RCM, Zatz M, McNally EM. Efficient exon skipping of SGCG mutations mediated by phosphorodiamidate morpholino oligomers. JCI Insight 2018; 3:99357. [PMID: 29720576 DOI: 10.1172/jci.insight.99357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/05/2018] [Indexed: 12/15/2022] Open
Abstract
Exon skipping uses chemically modified antisense oligonucleotides to modulate RNA splicing. Therapeutically, exon skipping can bypass mutations and restore reading frame disruption by generating internally truncated, functional proteins to rescue the loss of native gene expression. Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the SGCG gene, which encodes the dystrophin-associated protein γ-sarcoglycan. The most common SGCG mutations disrupt the transcript reading frame abrogating γ-sarcoglycan protein expression. In order to treat most SGCG gene mutations, it is necessary to skip 4 exons in order to restore the SGCG transcript reading frame, creating an internally truncated protein referred to as Mini-Gamma. Using direct reprogramming of human cells with MyoD, myogenic cells were tested with 2 antisense oligonucleotide chemistries, 2'-O-methyl phosphorothioate oligonucleotides and vivo-phosphorodiamidate morpholino oligomers, to induce exon skipping. Treatment with vivo-phosphorodiamidate morpholino oligomers demonstrated efficient skipping of the targeted exons and corrected the mutant reading frame, resulting in the expression of a functional Mini-Gamma protein. Antisense-induced exon skipping of SGCG occurred in normal cells and those with multiple distinct SGCG mutations, including the most common 521ΔT mutation. These findings demonstrate a multiexon-skipping strategy applicable to the majority of limb-girdle muscular dystrophy 2C patients.
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Affiliation(s)
- Eugene J Wyatt
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alexis R Demonbreun
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ellis Y Kim
- Committee on Molecular Medicine and Molecular Pathogenesis and
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Andy H Vo
- Committee on Developmental Biology and Regenerative Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Lisa M Dellefave-Castillo
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Quan Q Gao
- Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mariz Vainzof
- Human Genome and Stem-Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Rita C M Pavanello
- Human Genome and Stem-Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem-Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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41
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Zhou C, Li C, Zhou B, Sun H, Koullourou V, Holt I, Puckelwartz MJ, Warren DT, Hayward R, Lin Z, Zhang L, Morris GE, McNally EM, Shackleton S, Rao L, Shanahan CM, Zhang Q. Novel nesprin-1 mutations associated with dilated cardiomyopathy cause nuclear envelope disruption and defects in myogenesis. Hum Mol Genet 2017; 26:2258-2276. [PMID: 28398466 PMCID: PMC5458344 DOI: 10.1093/hmg/ddx116] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/22/2017] [Indexed: 02/05/2023] Open
Abstract
Nesprins-1 and -2 are highly expressed in skeletal and cardiac muscle and together with SUN (Sad1p/UNC84)-domain containing proteins and lamin A/C form the LInker of Nucleoskeleton-and-Cytoskeleton (LINC) bridging complex at the nuclear envelope (NE). Mutations in nesprin-1/2 have previously been found in patients with autosomal dominant Emery–Dreifuss muscular dystrophy (EDMD) as well as dilated cardiomyopathy (DCM). In this study, three novel rare variants (R8272Q, S8381C and N8406K) in the C-terminus of the SYNE1 gene (nesprin-1) were identified in seven DCM patients by mutation screening. Expression of these mutants caused nuclear morphology defects and reduced lamin A/C and SUN2 staining at the NE. GST pull-down indicated that nesprin-1/lamin/SUN interactions were disrupted. Nesprin-1 mutations were also associated with augmented activation of the ERK pathway in vitro and in hearts in vivo. During C2C12 muscle cell differentiation, nesprin-1 levels are increased concomitantly with kinesin light chain (KLC-1/2) and immunoprecipitation and GST pull-down showed that these proteins interacted via a recently identified LEWD domain in the C-terminus of nesprin-1. Expression of nesprin-1 mutants in C2C12 cells caused defects in myoblast differentiation and fusion associated with dysregulation of myogenic transcription factors and disruption of the nesprin-1 and KLC-1/2 interaction at the outer nuclear membrane. Expression of nesprin-1α2 WT and mutants in zebrafish embryos caused heart developmental defects that varied in severity. These findings support a role for nesprin-1 in myogenesis and muscle disease, and uncover a novel mechanism whereby disruption of the LINC complex may contribute to the pathogenesis of DCM.
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Affiliation(s)
- Can Zhou
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5 9NU, UK.,Department of Cardiology, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Chen Li
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5 9NU, UK.,Department of Cardiology, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Bin Zhou
- Laboratory of Molecular Translational Medicine.,Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education
| | - Huaqin Sun
- Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Victoria Koullourou
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5 9NU, UK.,Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Ian Holt
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10?7AG, UK and Institute for Science and Technology in Medicine, Keele University, ST5?5BG, UK
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Derek T Warren
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5?9NU, UK
| | - Robert Hayward
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5?9NU, UK
| | - Ziyuan Lin
- Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Lin Zhang
- Laboratory of Molecular Translational Medicine.,Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education
| | - Glenn E Morris
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry SY10?7AG, UK and Institute for Science and Technology in Medicine, Keele University, ST5?5BG, UK
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sue Shackleton
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1?9HN, UK
| | - Li Rao
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Catherine M Shanahan
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5?9NU, UK
| | - Qiuping Zhang
- King's College London British Heart Foundation Centre of Research Excellence, Cardiovascular Division, London SE5?9NU, UK
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42
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Barefield DY, Puckelwartz MJ, Kim EY, Wilsbacher LD, Vo AH, Waters EA, Earley JU, Hadhazy M, Dellefave-Castillo L, Pesce LL, McNally EM. Experimental Modeling Supports a Role for MyBP-HL as a Novel Myofilament Component in Arrhythmia and Dilated Cardiomyopathy. Circulation 2017; 136:1477-1491. [PMID: 28778945 DOI: 10.1161/circulationaha.117.028585] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 07/21/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cardiomyopathy and arrhythmias are under significant genetic influence. Here, we studied a family with dilated cardiomyopathy and associated conduction system disease in whom prior clinical cardiac gene panel testing was unrevealing. METHODS Whole-genome sequencing and induced pluripotent stem cells were used to examine a family with dilated cardiomyopathy and atrial and ventricular arrhythmias. We also characterized a mouse model with heterozygous and homozygous deletion of Mybphl. RESULTS Whole-genome sequencing identified a premature stop codon, R255X, in the MYBPHL gene encoding MyBP-HL (myosin-binding protein-H like), a novel member of the myosin-binding protein family. MYBPHL was found to have high atrial expression with low ventricular expression. We determined that MyBP-HL protein was myofilament associated in the atria, and truncated MyBP-HL protein failed to incorporate into the myofilament. Human cell modeling demonstrated reduced expression from the mutant MYBPHL allele. Echocardiography of Mybphl heterozygous and null mouse hearts exhibited a 36% reduction in fractional shortening and an increased diastolic ventricular chamber size. Atria weight normalized to total heart weight was significantly increased in Mybphl heterozygous and null mice. Using a reporter system, we detected robust expression of Mybphl in the atria, and in discrete puncta throughout the right ventricular wall and septum, as well. Telemetric electrocardiogram recordings in Mybphl mice revealed cardiac conduction system abnormalities with aberrant atrioventricular conduction and an increased rate of arrhythmia in heterozygous and null mice. CONCLUSIONS The findings of reduced ventricular function and conduction system defects in Mybphl mice support that MYBPHL truncations may increase risk for human arrhythmias and cardiomyopathy.
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Affiliation(s)
- David Y Barefield
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Megan J Puckelwartz
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Ellis Y Kim
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Lisa D Wilsbacher
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Andy H Vo
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Emily A Waters
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Judy U Earley
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Michele Hadhazy
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Lisa Dellefave-Castillo
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Lorenzo L Pesce
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.)
| | - Elizabeth M McNally
- From Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL (D.Y.B., M.J.P., J.U.E., M.H., L.D.-C., E.M.M.); Molecular Pathogenesis and Molecular Medicine, University of Chicago, IL (E.Y.K.); Feinberg Cardiovascular Institute, Northwestern University Feinberg School of Medicine, Chicago, IL (L.D.W.); Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, IL (A.H.V.); Northwestern University Center for Advanced Molecular Imaging, Evanston, IL (E.A.W.); and Computation Institute, University of Chicago, IL (L.L.P.).
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43
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Pan W, Puckelwartz MJ, Dellefave-Castillo L, Pesce LL, McNally EM. Abstract 74: Whole Genome Sequencing as a Diagnostic Tool for Cardiomyopathy. Circ Res 2017. [DOI: 10.1161/res.121.suppl_1.74] [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] [Indexed: 11/16/2022]
Abstract
Background:
Congestive heart failure (CHF) is an increasing medical problem that is disabling and costly, and CHF currently affects more than 5 million Americans. A leading cause of CHF is cardiomyopathy, a disorder with a high heritable component. Genetic studies of familial cardiomyopathy have identified more than 50 responsible genes. Knowledge of the genetic underpinnings of disease provides prognostic information and can guide clinical decision- making. Clinical genetic testing employs gene panels for diagnosis, and typical panels include 20-100 genes. We assessed the viability of whole genome sequencing (WGS) to identify potentially pathogenic cardiomyopathy-associated genetic variants in established and novel genes.
Methods:
WGS was conducted on 91 families (99 individuals) with cardiomyopathy. In 46/91 (50%) families, there was a prior history of unrevealing panel-based clinical genetic testing. WGS was performed using Illumina next generation sequencing. Variants were called and annotated using MegaSeq and MegaSeq2. MegaSeq2 refines the number of candidate variants from ~4 million to <30 using variant effect prediction, conservation at variant site, frequency, and expression data.
Results:
MegaSeq2 was applied to 99 cardiomyopathy genomes and in 45/91 families (49%), a potentially pathogenic or likely pathogenic variant was identified. Here we describe identification and segregation analysis in 4 families. Two families have unique
RBM20
variants that segregate with cardiomyopathy. One family was found to carry a premature stop in
SCN5A
and exhibits variable phenotypes including sudden death, arrhythmia and cardiomyopathy. The fourth family has cardiomyopathy that segregates with a
BAG3
early termination variant.
Conclusions:
WGS was able to identify potentially pathogenic variants in nearly half (45/91). While some of the variants identified were in novel genes, the majority of pathogenic variants were in established cardiomyopathy genes despite previous panel-based testing. More comprehensive analysis, like WGS, allows for re-evaluation of variation as additional genetic information becomes available.
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Affiliation(s)
- Wenyu Pan
- Cntr for Genetic Medicine, Northwestern Univ, Chicago, IL
| | - Megan J Puckelwartz
- Cntr for Genetic Medicine and Dept of Pharmacology, Northwestern Univ, Chicago, IL
| | | | | | - Elizabeth M McNally
- Cntr for Genetic Medicine and Dept of Medicine, Northwestern Univ, Chicago, IL
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44
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Barefield DY, Puckelwartz MJ, Dellefave-Castillo L, McNally EM. Abstract 391: The Pathophysiological Role of MYBPHL in Dilated Cardiomyopathy. Circ Res 2016. [DOI: 10.1161/res.119.suppl_1.391] [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] [Indexed: 11/16/2022]
Abstract
Background:
Cardiomyopathy is a leading cause of heart failure and is highly heritable. One common form of cardiomyopathy is dilated cardiomyopathy (DCM), which currently has over 70 identified genes that have been described as causative for the disease. Genetic testing for DCM employs gene panels and has a sensitivity of mutation detection less than 50%, indicating that additional genes contribute to DCM. Here, we employed whole genome sequencing (WGS) in a family with DCM and heart block who had previously undergone unrevealing genetic testing. We identified a premature stop codon in the
MYBPHL
gene, a gene that has not previously been linked to DCM as a likely cause of DCM in this family. Myosin binding protein H Like (MyBP-HL) is a muscle-expressed protein bearing structural similarity to myosin binding protein C (MyBP-C), which is commonly mutated gene in cardiomyopathies.
Objective:
Determine the physiological and pathophysiological role of
Mybphl
.
Results:
RNA-seq and qPCR from mouse hearts revealed that
Mybphl
is highly expressed in the right and left atria with lower expression in the ventricle and virtually no expression in skeletal muscle. As MyBP-HL shares a high homology with the myofilament proteins cardiac myosin binding protein-C and H, we investigated if MyBP-HL is also myofilament-associated. We determined that MyBP-HL protein is myofilament-associated in the atria although not clearly so in ventricle. To assess the requirement of MyBP-HL in cardiac function, we used a mouse model with an insertional disruption of the
Mybphl
gene. These mice have deficits in
in vivo
cardiac function, with reduced fractional shortening. In addition, ECG recordings from the
Mybphl
null mice show conduction system abnormalities affecting atrioventricular conduction.
Conclusions:
WGS identified a premature stop codon in
MYBPHL
in human DCM. A mouse model with a disrupted
Mybphl
gene showed similar pathophysiological features as the humans with reduced ventricular function and cardiac conduction system abnormalities. MyBP-HL is an important protein for normal cardiac function.
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45
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Abstract
With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.
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Affiliation(s)
- Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine
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46
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Depreux FF, Puckelwartz MJ, Augustynowicz A, Wolfgeher D, Labno CM, Pierre-Louis D, Cicka D, Kron SJ, Holaska J, McNally EM. Disruption of the lamin A and matrin-3 interaction by myopathic LMNA mutations. Hum Mol Genet 2015; 24:4284-95. [PMID: 25948554 DOI: 10.1093/hmg/ddv160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
The nuclear face of the nuclear membrane is enriched with the intermediate filament protein lamin A. Mutations in LMNA, the gene encoding lamin A, lead to a diverse set of inherited conditions including myopathies that affect both the heart and skeletal muscle. To gain insight about lamin A protein interactions, binding proteins associated with the tail of lamin A were characterized. Of 130 nuclear proteins found associated with the lamin A tail, 17 (13%) were previously described lamin A binding partners. One protein not previously linked to lamin A, matrin-3, was selected for further study, because like LMNA mutations, matrin-3 has also been implicated in inherited myopathy. Matrin-3 binds RNA and DNA and is a nucleoplasmic protein originally identified from the insoluble nuclear fraction, referred to as the nuclear matrix. Anti-matrin-3 antibodies were found to co-immunoprecipitate lamin A, and the lamin-A binding domain was mapped to the carboxy-terminal half of matrin-3. Three-dimensional mapping of the lamin A-matrin-3 interface showed that the LMNA truncating mutation Δ303, which lacks the matrin-3 binding domain, was associated with an increased distance between lamin A and matrin-3. LMNA mutant cells are known to have altered biophysical properties and the matrin-3-lamin A interface is positioned to contribute to these defects.
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Affiliation(s)
| | - Megan J Puckelwartz
- Department of Medicine, Center for Genetic Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Don Wolfgeher
- Department of Molecular of Genetics and Cell Biology, Proteomics Core Facility
| | - Christine M Labno
- Integrated Microscopy Facility, Office of Shared Research Facilities
| | | | | | | | | | - Elizabeth M McNally
- Department of Medicine, Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA and Center for Genetic Medicine, Northwestern University, Chicago, IL, 60611, USA
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47
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Abstract
Heart failure is highly influenced by heritability, and nearly 100 genes link to familial cardiomyopathy. Despite the marked genetic diversity that underlies these complex cardiovascular phenotypes, several key genes and pathways have emerged. Hypertrophic cardiomyopathy is characterized by increased contractility and a greater energetic cost of cardiac output. Dilated cardiomyopathy is often triggered by mutations that disrupt the giant protein titin. The energetic consequences of these mutations offer molecular targets and opportunities for new drug development and gene correction therapies.
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Affiliation(s)
- Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - David Y Barefield
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
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48
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Golbus JR, Puckelwartz MJ, Dellefave-Castillo L, Fahrenbach JP, Nelakuditi V, Pesce LL, Pytel P, McNally EM. Targeted analysis of whole genome sequence data to diagnose genetic cardiomyopathy. ACTA ACUST UNITED AC 2014; 7:751-759. [PMID: 25179549 DOI: 10.1161/circgenetics.113.000578] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Cardiomyopathy is highly heritable but genetically diverse. At present, genetic testing for cardiomyopathy uses targeted sequencing to simultaneously assess the coding regions of >50 genes. New genes are routinely added to panels to improve the diagnostic yield. With the anticipated $1000 genome, it is expected that genetic testing will shift toward comprehensive genome sequencing accompanied by targeted gene analysis. Therefore, we assessed the reliability of whole genome sequencing and targeted analysis to identify cardiomyopathy variants in 11 subjects with cardiomyopathy. METHODS AND RESULTS Whole genome sequencing with an average of 37× coverage was combined with targeted analysis focused on 204 genes linked to cardiomyopathy. Genetic variants were scored using multiple prediction algorithms combined with frequency data from public databases. This pipeline yielded 1 to 14 potentially pathogenic variants per individual. Variants were further analyzed using clinical criteria and segregation analysis, where available. Three of 3 previously identified primary mutations were detected by this analysis. In 6 subjects for whom the primary mutation was previously unknown, we identified mutations that segregated with disease, had clinical correlates, and had additional pathological correlation to provide evidence for causality. For 2 subjects with previously known primary mutations, we identified additional variants that may act as modifiers of disease severity. In total, we identified the likely pathological mutation in 9 of 11 (82%) subjects. CONCLUSIONS These pilot data demonstrate that ≈30 to 40× coverage whole genome sequencing combined with targeted analysis is feasible and sensitive to identify rare variants in cardiomyopathy-associated genes.
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Affiliation(s)
- Jessica R Golbus
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Megan J Puckelwartz
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Lisa Dellefave-Castillo
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - John P Fahrenbach
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Viswateja Nelakuditi
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Lorenzo L Pesce
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Peter Pytel
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
| | - Elizabeth M McNally
- Department of Medicine, Department of Human Genetics, Department of Pathology, The Computation Institute, The University of Chicago & Argonne National Laboratories, Chicago, IL
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Puckelwartz MJ, McNally EM. Genetic profiling for risk reduction in human cardiovascular disease. Genes (Basel) 2014; 5:214-34. [PMID: 24705294 PMCID: PMC3978520 DOI: 10.3390/genes5010214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 11/16/2022] Open
Abstract
Cardiovascular disease is a major health concern affecting over 80,000,000 people in the U.S. alone. Heart failure, cardiomyopathy, heart rhythm disorders, atherosclerosis and aneurysm formation have significant heritable contribution. Supported by familial aggregation and twin studies, these cardiovascular diseases are influenced by genetic variation. Family-based linkage studies and population-based genome-wide association studies (GWAS) have each identified genes and variants important for the pathogenesis of cardiovascular disease. The advent of next generation sequencing has ushered in a new era in the genetic diagnosis of cardiovascular disease, and this is especially evident when considering cardiomyopathy, a leading cause of heart failure. Cardiomyopathy is a genetically heterogeneous disorder characterized by morphologically abnormal heart with abnormal function. Genetic testing for cardiomyopathy employs gene panels, and these panels assess more than 50 genes simultaneously. Despite the large size of these panels, the sensitivity for detecting the primary genetic defect is still only approximately 50%. Recently, there has been a shift towards applying broader exome and/or genome sequencing to interrogate more of the genome to provide a genetic diagnosis for cardiomyopathy. Genetic mutations in cardiomyopathy offer the capacity to predict clinical outcome, including arrhythmia risk, and genetic diagnosis often provides an early window in which to institute therapy. This discussion is an overview as to how genomic data is shaping the current understanding and treatment of cardiovascular disease.
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Puckelwartz MJ, Pesce LL, Nelakuditi V, Dellefave-Castillo L, Golbus JR, Day SM, Cappola TP, Dorn GW, Foster IT, McNally EM. Supercomputing for the parallelization of whole genome analysis. Bioinformatics 2014; 30:1508-13. [PMID: 24526712 DOI: 10.1093/bioinformatics/btu071] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION The declining cost of generating DNA sequence is promoting an increase in whole genome sequencing, especially as applied to the human genome. Whole genome analysis requires the alignment and comparison of raw sequence data, and results in a computational bottleneck because of limited ability to analyze multiple genomes simultaneously. RESULTS We now adapted a Cray XE6 supercomputer to achieve the parallelization required for concurrent multiple genome analysis. This approach not only markedly speeds computational time but also results in increased usable sequence per genome. Relying on publically available software, the Cray XE6 has the capacity to align and call variants on 240 whole genomes in ∼50 h. Multisample variant calling is also accelerated. AVAILABILITY AND IMPLEMENTATION The MegaSeq workflow is designed to harness the size and memory of the Cray XE6, housed at Argonne National Laboratory, for whole genome analysis in a platform designed to better match current and emerging sequencing volume.
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Affiliation(s)
- Megan J Puckelwartz
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Lorenzo L Pesce
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Viswateja Nelakuditi
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Lisa Dellefave-Castillo
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Jessica R Golbus
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Sharlene M Day
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Thomas P Cappola
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Gerald W Dorn
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Ian T Foster
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
| | - Elizabeth M McNally
- Department of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USADepartment of Medicine, Computation Institute and Argonne National Laboratory, 9700 S. Cass Ave. Argonne, IL 60439, USA, Department of Human Genetics, The University of Chicago, 5841 S. Maryland Ave Chicago, IL 60637, USA, Department of Internal Medicine, The University of Michigan, 1150 W Medical Center Dr. Ann Arbor, MI 48109, USA, Perelman School of Medicine, Penn Cardiovascular Institute and Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd. Philadelphia, PA 19104, USA and Washington University School of Medicine, 660 S. Euclid Ave. St. Louis, MO 63110, USA
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