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Kadagandla S, Kapoor A. Identification of candidate causal cis -regulatory variants underlying electrocardiographic QT interval GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584880. [PMID: 38585875 PMCID: PMC10996567 DOI: 10.1101/2024.03.13.584880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Identifying causal variants among tens or hundreds of associated variants at each locus mapped by genome-wide association studies (GWAS) of complex traits is a challenge. As vast majority of GWAS variants are noncoding, sequence variation at cis -regulatory elements affecting transcriptional expression of specific genes is a widely accepted molecular hypothesis. Following this cis -regulatory hypothesis and combining it with the observation that nucleosome-free open chromatin is a universal hallmark of all types of cis -regulatory elements, we aimed to identify candidate causal regulatory variants underlying electrocardiographic QT interval GWAS loci. At a dozen loci, selected for higher effect sizes and a better understanding of the likely causal gene, we identified and included all common variants in high linkage disequilibrium with the GWAS variants as candidate variants. Using ENCODE DNase-seq and ATAC-seq from multiple human adult cardiac left ventricle tissue samples, we generated genome-wide maps of open chromatin regions marking putative regulatory elements. QT interval associated candidate variants were filtered for overlap with cardiac left ventricle open chromatin regions to identify candidate causal cis -regulatory variants, which were further assessed for colocalizing with a known cardiac GTEx expression quantitative trait locus variant as additional evidence for their causal role. Together, these efforts have generated a comprehensive set of candidate causal variants that are expected to be enriched for cis -regulatory potential and thereby, explaining the observed genetic associations.
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Gunamalai L, Singh P, Berg B, Shi L, Sanchez E, Smith A, Breton G, Bedford MT, Balciunas D, Kapoor A. Functional characterization of QT interval associated SCN5A enhancer variants identify combined additive effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584440. [PMID: 38559211 PMCID: PMC10979898 DOI: 10.1101/2024.03.11.584440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Several empirical and theoretical studies suggest presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual variability in gene expression. However, for vast majority of genes, enhancers and the underlying regulatory variation remains unknown. Even for the genes with well-characterized enhancers, the nature of the combined effects from multiple enhancers and their variants, when known, on gene expression regulation remains unexplored. Here, we have evaluated the combined effects from five SCN5A enhancers and their regulatory variants that are known to collectively correlate with SCN5A cardiac expression and underlie QT interval association in the general population. Using small deletions centered at the regulatory variants in episomal reporter assays in a mouse cardiomyocyte cell line we demonstrate that the variants and their flanking sequences play critical role in individual enhancer activities, likely being a transcription factor (TF) binding site. By performing oligonucleotide-based pulldown assays on predicted TFs we identify the TFs likely driving allele-specific enhancer activities. Using all 32 possible allelic synthetic constructs in reporter assays, representing the five biallelic enhancers in tandem in their genomic order, we demonstrate combined additive effects on overall enhancer activities. Using transient enhancer assays in developing zebrafish embryos we demonstrate the four out the five enhancer elements act as enhancers in vivo . Together, these studies extend the previous findings to uncover the TFs driving the enhancer activities of QT interval associated SCN5A regulatory variants, reveal the additive effects from allelic combinations of these regulatory variants, and prove their potential to act as enhancers in vivo .
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Jonker T, Barnett P, Boink GJJ, Christoffels VM. Role of Genetic Variation in Transcriptional Regulatory Elements in Heart Rhythm. Cells 2023; 13:4. [PMID: 38201209 PMCID: PMC10777909 DOI: 10.3390/cells13010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Genetic predisposition to cardiac arrhythmias has been a field of intense investigation. Research initially focused on rare hereditary arrhythmias, but over the last two decades, the role of genetic variation (single nucleotide polymorphisms) in heart rate, rhythm, and arrhythmias has been taken into consideration as well. In particular, genome-wide association studies have identified hundreds of genomic loci associated with quantitative electrocardiographic traits, atrial fibrillation, and less common arrhythmias such as Brugada syndrome. A significant number of associated variants have been found to systematically localize in non-coding regulatory elements that control the tissue-specific and temporal transcription of genes encoding transcription factors, ion channels, and other proteins. However, the identification of causal variants and the mechanism underlying their impact on phenotype has proven difficult due to the complex tissue-specific, time-resolved, condition-dependent, and combinatorial function of regulatory elements, as well as their modest conservation across different model species. In this review, we discuss research efforts aimed at identifying and characterizing-trait-associated variant regulatory elements and the molecular mechanisms underlying their impact on heart rate or rhythm.
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Affiliation(s)
- Timo Jonker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
| | - Gerard J. J. Boink
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
- Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
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4
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Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023; 14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Genome-wide association studies (GWAS) have linked hundreds of loci to cardiac diseases. However, in most loci the causal variants and their target genes remain unknown. We developed a combined experimental and analytical approach that integrates single cell epigenomics with GWAS to prioritize risk variants and genes. We profiled accessible chromatin in single cells obtained from human hearts and leveraged the data to study genetics of Atrial Fibrillation (AF), the most common cardiac arrhythmia. Enrichment analysis of AF risk variants using cell-type-resolved open chromatin regions (OCRs) implicated cardiomyocytes as the main mediator of AF risk. We then performed statistical fine-mapping, leveraging the information in OCRs, and identified putative causal variants in 122 AF-associated loci. Taking advantage of the fine-mapping results, our novel statistical procedure for gene discovery prioritized 46 high-confidence risk genes, highlighting transcription factors and signal transduction pathways important for heart development. In summary, our analysis provides a comprehensive map of AF risk variants and genes, and a general framework to integrate single-cell genomics with genetic studies of complex traits.
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Affiliation(s)
- Alan Selewa
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael Wasney
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Linsin Smith
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chenwei Tang
- The College, The University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ivan P Moskowitz
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anindita Basu
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Sebastian Pott
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022; 24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
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6
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Lopes-Marques M, Silva R, Serrano C, Gomes V, Cardoso A, Prata MJ, Amorim A, Azevedo L. Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (Na V 1.5). PeerJ 2022; 10:e13913. [PMID: 35996667 PMCID: PMC9392453 DOI: 10.7717/peerj.13913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/27/2022] [Indexed: 01/19/2023] Open
Abstract
Common genetic polymorphisms may modify the phenotypic outcome when co-occurring with a disease-causing variant, and therefore understanding their modulating role in health and disease is of great importance. The polymorphic p.His558Arg variant of the sodium voltage-gated channel alpha subunit 5 (Na V 1.5) encoded by the SCN5A gene is a case in point, as several studies have shown it can modify the clinical phenotype in a number of cardiac diseases. To evaluate the genetic backgrounds associated with this modulating effect, we reanalysed previous electrophysiological findings regarding the p.His558Arg variant and further assessed its patterns of genetic diversity in human populations. The Na V 1.5 p.His558Arg variant was found to be in linkage disequilibrium with six other polymorphic variants that previously were also associated with cardiac traits in GWAS analyses. On account of this, incongruent reports that Arg558 allele can compensate, aggravate or have no effect on Na V 1.5, likely might have arose due to a role of p.His558Arg depending on the additional linked variants. Altogether, these results indicate a major influence of the epistatic interactions between SCN5A variants, revealing also that phenotypic severity may depend on the polymorphic background associated to each individual genome.
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Affiliation(s)
- Monica Lopes-Marques
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Raquel Silva
- Center for Interdisciplinary Research in Health (CIIS), Universidade Católica Portuguesa, Faculdade de Medicina Dentária, Viseu, Portugal
| | - Catarina Serrano
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Verónica Gomes
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Ana Cardoso
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Maria João Prata
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Antonio Amorim
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
| | - Luisa Azevedo
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal,Population Genetics and Evolution, Institute of Innovation and Investigation in Health (i3S), Porto, Portugal
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Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Yue MCS, Sung WWL, Thiruvahindrapuram B, Lougheed J, Oechslin E, Mondal T, Bergin L, Smythe J, Jayappa S, Rao VJ, Shenthar J, Dhandapany PS, Semsarian C, Weintraub RG, Bagnall RD, Ingles J, Melé M, Maass PG, Ellis J, Scherer SW, Mital S. Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. NPJ Genom Med 2022; 7:18. [PMID: 35288587 PMCID: PMC8921194 DOI: 10.1038/s41525-022-00288-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10-7 versus controls). Genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) were most highly enriched for regulatory variants (odds ratio 6.7-58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.
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Affiliation(s)
- Robert Lesurf
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Abdelrahman Said
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Oyediran Akinrinade
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- St. George's University School of Medicine, Grenada, Grenada
| | | | - Kathleen Delfosse
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ting Liu
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roderick Yao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabrielle Persad
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Fintan McKenna
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ramil R Noche
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Zebrafish Genetics and Disease Models Core, The Hospital for Sick Children, Toronto, ON, Canada
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shreya Shah
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anastasia Miron
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Qian Yang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Guoliang Meng
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Erwin Oechslin
- Peter Munk Cardiac Centre, Division of Cardiology, Toronto General Hospital, University of Toronto, Toronto, ON, Canada
| | - Tapas Mondal
- Department of Pediatrics, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Lynn Bergin
- Division of Cardiology, London Health Sciences Centre, London, ON, Canada
| | - John Smythe
- Department of Pediatrics, Kingston General Hospital, Kingston, ON, Canada
| | - Shashank Jayappa
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Vinay J Rao
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Jayaprakash Shenthar
- Department of Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, India
| | - Perundurai S Dhandapany
- Cardiovascular Biology and Disease Theme, Institute for Stem Cell Science and Regenerative Medicine, Bangalore (inStem), Bangalore, India
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Robert G Weintraub
- Cardiology Department, Royal Children's Hospital, Melbourne, Australia
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard D Bagnall
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, Australia
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, Australia
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain
| | - Philipp G Maass
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Seema Mital
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada.
- Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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Chatterjee S, Karasaki KM, Fries LE, Kapoor A, Chakravarti A. A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease. Genome Res 2021; 31:2199-2208. [PMID: 34782358 PMCID: PMC8647834 DOI: 10.1101/gr.275667.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/05/2021] [Indexed: 01/25/2023]
Abstract
The major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk variants attenuate binding of the transcription factors RARB, GATA2, and SOX10 to their cognate CREs, reduce RET gene expression, and dysregulate other ENS and HSCR genes in the RET-EDNRB gene regulatory network (GRN). Here, we use siRNA, ChIP, and CRISPR-Cas9 deletion analyses in the SK-N-SH cell line to ask how many additional HSCR-associated risk variants reside in RET CREs that affect its gene expression. We identify 22 HSCR-associated variants in candidate RET CREs, of which seven have differential allele-specific in vitro enhancer activity, and four of these seven affect RET gene expression; of these, two enhancers are bound by the transcription factor PAX3. We also show that deleting multiple variant-containing enhancers leads to synergistic effects on RET gene expression. These, coupled with our prior results, show that common sequence variants in at least 10 RET enhancers affect HSCR risk, seven with experimental evidence of affecting RET gene expression, extending the known RET-EDNRB GRN to reveal an extensive regulatory code modulating disease risk at a single gene.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Kameko M Karasaki
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
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9
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Kapoor A, Nandakumar P, Auer DR, Sosa MX, Ross H, Bollinger J, Yan J, Berrios C, Chakravarti A. Multiple, independent, common variants at RET, SEMA3 and NRG1 gut enhancers specify Hirschsprung disease risk in European ancestry subjects. J Pediatr Surg 2021; 56:2286-2294. [PMID: 34006365 PMCID: PMC8526751 DOI: 10.1016/j.jpedsurg.2021.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/08/2021] [Accepted: 04/06/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Hirschsprung disease (HSCR) is a developmental disorder of the enteric nervous system (ENS) characterized by congenital aganglionosis arising from coding variants in ENS genes causing partial or total loss-of-function. Low-penetrance, common, noncoding variants at RET, SEMA3 and NRG1 loci are also associated with HSCR, with small-to-moderate loss of gene expression mediated through sequence variants in cis-regulatory elements (CRE) as another causal mechanism. Since these latter variants are common, many individuals carry multiple risk variants. However, the extent and combinatorial effects of all putative CRE variants within and across these loci on HSCR is unknown. METHODS Using 583 HSCR subjects, one of the largest samples of European ancestry studied, and genotyping 56 tag variants, we evaluated association of all common variants overlapping putative gut CREs and fine-mapped causal variants at RET, SEMA3 and NRG1. RESULTS We demonstrate that 28 and 8 tag variants, several of which are genetically independent, overlap putative-enhancers at the RET and SEMA3 loci, respectively, as well as two fine-mapped tag variants at the NRG1 locus, are significantly associated with HSCR. Importantly, disease risk increases with increasing numbers of risk alleles from multiple variants within and across these loci, varying >25-fold across individuals. CONCLUSION This increasing allele number-dependent risk, we hypothesize, arises from HSCR-relevant ENS cells sensing the reduced gene expression at multiple ENS genes since their developmental effects are integrated through gene regulatory networks.
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Affiliation(s)
- Ashish Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Priyanka Nandakumar
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dallas R. Auer
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maria X. Sosa
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Holly Ross
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juli Bollinger
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jia Yan
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Courtney Berrios
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016, USA.
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10
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He XW, Li LF, Zhang F, Yun LB. Research Progress on Molecular Markers Related to Unexplained Sudden Cardiac Death and Its Forensic Application. FA YI XUE ZA ZHI 2021; 37:687-693. [PMID: 35187922 DOI: 10.12116/j.issn.1004-5619.2020.400507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Routine pathological examination of unexplained sudden cardiac death (USCD) lacks significant morphological characteristics. In the field of forensic medicine, molecular biology methods have been used to find the cause of death by detecting genes and research related to the mechanism of sudden cardiac death has been carried out. From the molecular pathology point of view, the application of multiple levels of biomarkers to resolve the causes of USCD has already shown potential and provides an important path for forensic identification of USCD. This article reviews the latest research progress on USCD-related genes, RNA, proteins and USCD, and summarizes forensic application.
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Affiliation(s)
- Xiang-Wang He
- West China School of Basic Medical Sciences & Forensic Medicine, Chengdu 610041, China
| | - Lin-Feng Li
- West China School of Basic Medical Sciences & Forensic Medicine, Chengdu 610041, China
| | - Fu Zhang
- Key Laboratory of Forensic Pathology, Guangdong Public Security Department, Guangzhou 510050, China
| | - Li-Bing Yun
- West China School of Basic Medical Sciences & Forensic Medicine, Chengdu 610041, China
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Benway CJ, Liu J, Guo F, Du F, Randell SH, Cho MH, Silverman EK, Zhou X. Chromatin Landscapes of Human Lung Cells Predict Potentially Functional Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Variants. Am J Respir Cell Mol Biol 2021; 65:92-102. [PMID: 33788674 DOI: 10.1165/rcmb.2020-0475oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified dozens of loci associated with risk of chronic obstructive pulmonary disease (COPD). However, identifying the causal variants and their functional role in the appropriate cell type remains a major challenge. We aimed to identify putative causal variants in 82 GWAS loci associated with COPD susceptibility and predict the regulatory impact of these variants in lung-cell types. We used an integrated approach featuring statistical fine mapping, open chromatin profiling, and machine learning to identify functional variants. We generated chromatin accessibility data using the Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-seq) for human primary lung-cell types implicated in COPD pathobiology. We then evaluated the enrichment of COPD risk variants in lung-specific open chromatin regions and generated cell type-specific regulatory predictions for >6,500 variants corresponding to 82 COPD GWAS loci. Integration of the fine-mapped variants with lung open chromatin regions helped prioritize 22 variants in putative regulatory elements with potential functional effects. Comparison with functional predictions from 222 Encyclopedia of DNA Elements (ENCODE) cell samples revealed cell type-specific regulatory effects of COPD variants in the lung epithelium, endothelium, and immune cells. We identified potential causal variants for COPD risk by integrating fine mapping in GWAS loci with cell-specific regulatory profiling, highlighting the importance of leveraging the chromatin status in relevant cell types to predict the molecular effects of risk variants in lung disease.
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Affiliation(s)
| | | | - Feng Guo
- Channing Division of Network Medicine and
| | - Fei Du
- Channing Division of Network Medicine and
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael H Cho
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Xiaobo Zhou
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
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12
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Man JCK, Bosada FM, Scholman KT, Offerhaus JA, Walsh R, van Duijvenboden K, van Eif VWW, Bezzina CR, Verkerk AO, Boukens BJ, Barnett P, Christoffels VM. Variant Intronic Enhancer Controls SCN10A-short Expression and Heart Conduction. Circulation 2021; 144:229-242. [PMID: 33910361 DOI: 10.1161/circulationaha.121.054083] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Genetic variants in SCN10A, encoding the neuronal voltage-gated sodium channel NaV1.8, are strongly associated with atrial fibrillation, Brugada syndrome, cardiac conduction velocities, and heart rate. The cardiac function of SCN10A has not been resolved, however, and diverging mechanisms have been proposed. Here, we investigated the cardiac expression of SCN10A and the function of a variant-sensitive intronic enhancer previously linked to the regulation of SCN5A, encoding the major essential cardiac sodium channel NaV1.5. METHODS The expression of SCN10A was investigated in mouse and human hearts. With the use of CRISPR/Cas9 genome editing, the mouse intronic enhancer was disrupted, and mutant mice were characterized by transcriptomic and electrophysiological analyses. The association of genetic variants at SCN5A-SCN10A enhancer regions and gene expression were evaluated by genome-wide association studies single-nucleotide polymorphism mapping and expression quantitative trait loci analysis. RESULTS We found that cardiomyocytes of the atria, sinoatrial node, and ventricular conduction system express a short transcript comprising the last 7 exons of the gene (Scn10a-short). Transcription occurs from an intronic enhancer-promoter complex, whereas full-length Scn10a transcript was undetectable in the human and mouse heart. Expression quantitative trait loci analysis revealed that the genetic variants in linkage disequilibrium with genetic variant rs6801957 in the intronic enhancer associate with SCN10A transcript levels in the heart. Genetic modification of the enhancer in the mouse genome led to reduced cardiac Scn10a-short expression in atria and ventricles, reduced cardiac sodium current in atrial cardiomyocytes, atrial conduction slowing and arrhythmia, whereas the expression of Scn5a, the presumed enhancer target gene, remained unaffected. In patch-clamp transfection experiments, expression of Scn10a-short-encoded NaV1.8-short increased NaV1.5-mediated sodium current. We propose that noncoding genetic variation modulates transcriptional regulation of Scn10a-short in cardiomyocytes that impacts NaV1.5-mediated sodium current and heart rhythm. CONCLUSIONS Genetic variants in and around SCN10A modulate enhancer function and expression of a cardiac-specific SCN10A-short transcript. We propose that noncoding genetic variation modulates transcriptional regulation of a functional C-terminal portion of NaV1.8 in cardiomyocytes that impacts on NaV1.5 function, cardiac conduction velocities, and arrhythmia susceptibility.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Fernanda M Bosada
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Koen T Scholman
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Joost A Offerhaus
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Karel van Duijvenboden
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent W W van Eif
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Connie R Bezzina
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Arie O Verkerk
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Phil Barnett
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
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13
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Pinsach-Abuin M, del Olmo B, Pérez-Agustin A, Mates J, Allegue C, Iglesias A, Ma Q, Merkurjev D, Konovalov S, Zhang J, Sheikh F, Telenti A, Brugada J, Brugada R, Gymrek M, di Iulio J, Garcia-Bassets I, Pagans S. Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants. Cell Rep Med 2021; 2:100250. [PMID: 33948580 PMCID: PMC8080235 DOI: 10.1016/j.xcrm.2021.100250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/07/2021] [Accepted: 03/23/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide association studies (GWASs) are instrumental in identifying loci harboring common single-nucleotide variants (SNVs) that affect human traits and diseases. GWAS hits emerge in clusters, but the focus is often on the most significant hit in each trait- or disease-associated locus. The remaining hits represent SNVs in linkage disequilibrium (LD) and are considered redundant and thus frequently marginally reported or exploited. Here, we interrogate the value of integrating the full set of GWAS hits in a locus repeatedly associated with cardiac conduction traits and arrhythmia, SCN5A-SCN10A. Our analysis reveals 5 common 7-SNV haplotypes (Hap1-5) with 2 combinations associated with life-threatening arrhythmia-Brugada syndrome (the risk Hap1/1 and protective Hap2/3 genotypes). Hap1 and Hap2 share 3 SNVs; thus, this analysis suggests that assuming redundancy among clustered GWAS hits can lead to confounding disease-risk associations and supports the need to deconstruct GWAS data in the context of haplotype composition.
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Affiliation(s)
- Mel·lina Pinsach-Abuin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Bernat del Olmo
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Adrian Pérez-Agustin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jesus Mates
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Catarina Allegue
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Anna Iglesias
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sergiy Konovalov
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jing Zhang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Farah Sheikh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Josep Brugada
- Arrhythmia Unit, Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ramon Brugada
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
- Cardiology Service, Hospital Universitari Dr. Josep Trueta, Girona, Spain
| | - Melissa Gymrek
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Julia di Iulio
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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15
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Xu L, Shi R. Generation of functional Na V1.5 current by endogenous transcriptional activation of SCN5A. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1892524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Liang Xu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Rui Shi
- Department of Gynaecology and Obstetrics, East Hospital, Tongji University School of Medicine, Shanghai, PR China
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16
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Abstract
RATIONALE There is growing evidence that common variants and rare sequence alterations in regulatory sequences can result in birth defects or predisposition to disease. Congenital heart defects are the most common birth defect and have a clear genetic component, yet only a third of cases can be attributed to structural variation in the genome or a mutation in a gene. The remaining unknown cases could be caused by alterations in regulatory sequences. OBJECTIVE Identify regulatory sequences and gene expression networks that are active during organogenesis of the human heart. Determine whether these sites and networks are enriched for disease-relevant genes and associated genetic variation. METHODS AND RESULTS We characterized ChromHMM (chromatin state) and gene expression dynamics during human heart organogenesis. We profiled 7 histone modifications in embryonic hearts from each of 9 distinct Carnegie stages (13-14, 16-21, and 23), annotated chromatin states, and compared these maps to over 100 human tissues and cell types. We also generated RNA-sequencing data, performed differential expression, and constructed weighted gene coexpression networks. We identified 177 412 heart enhancers; 12 395 had not been previously annotated as strong enhancers. We identified 92% of all functionally validated heart-positive enhancers (n=281; 7.5× enrichment; P<2.2×10-16). Integration of these data demonstrated novel heart enhancers are enriched near genes expressed more strongly in cardiac tissue and are enriched for variants associated with ECG measures and atrial fibrillation. Our gene expression network analysis identified gene modules strongly enriched for heart-related functions, regulatory control by heart-specific enhancers, and putative disease genes. CONCLUSIONS Well-connected hub genes with heart-specific expression targeted by embryonic heart-specific enhancers are likely disease candidates. Our functional annotations will allow for better interpretation of whole genome sequencing data in the large number of patients affected by congenital heart defects.
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Affiliation(s)
- Jennifer VanOudenhove
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
| | - Tara N. Yankee
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Andrea Wilderman
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington CT, USA
| | - Justin Cotney
- Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington CT, USA
- Institute for Systems Genomics, UConn, Storrs CT, USA
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17
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Wang J, Wang Y, Duan Z, Hu W. Hypoxia‐induced alterations of transcriptome and chromatin accessibility in
HL
‐1 cells. IUBMB Life 2020; 72:1737-1746. [PMID: 32351020 DOI: 10.1002/iub.2297] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Jingru Wang
- Department of Cardiovascular MedicineThe Fourth Affiliated Hospital of China Medical University Shenyang China
| | - Yang Wang
- Department of Cardiovascular MedicineThe Fourth Affiliated Hospital of China Medical University Shenyang China
| | - Zhiying Duan
- Department of Cardiovascular MedicineThe Fourth Affiliated Hospital of China Medical University Shenyang China
| | - Weina Hu
- Department of Cardiovascular MedicineThe Fourth Affiliated Hospital of China Medical University Shenyang China
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18
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Man JCK, Mohan RA, Boogaard MVD, Hilvering CRE, Jenkins C, Wakker V, Bianchi V, Laat WD, Barnett P, Boukens BJ, Christoffels VM. An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo. Nat Commun 2019; 10:4943. [PMID: 31666509 PMCID: PMC6821807 DOI: 10.1038/s41467-019-12856-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 10/03/2019] [Indexed: 12/19/2022] Open
Abstract
Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia disorders. Here, we identify an evolutionary conserved regulatory cluster with super enhancer characteristics downstream of SCN5A, which drives localized cardiac expression and contains conduction velocity-associated variants. We use genome editing to create a series of deletions in the mouse genome and show that the enhancer cluster controls the conformation of a >0.5 Mb genomic region harboring multiple interacting gene promoters and enhancers. We find that this cluster and its individual components are selectively required for cardiac Scn5a expression, normal cardiac conduction and normal embryonic development. Our studies reveal physiological roles of an enhancer cluster in the SCN5A-SCN10A locus, show that it controls the chromatin architecture of the locus and Scn5a expression, and suggest that genetic variants affecting its activity may influence cardiac function.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Rajiv A Mohan
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Malou van den Boogaard
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Catharina R E Hilvering
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Catherine Jenkins
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Valerio Bianchi
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Academic Medical Center, Amsterdam, The Netherlands.
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19
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Profile of Aravinda Chakravarti. Proc Natl Acad Sci U S A 2019; 116:10608-10610. [DOI: 10.1073/pnas.1906109116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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