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Dong Y, Lu R, Cao H, Zhang J, Wu X, Deng Y, Li JD. Deficiency in Prader-Willi syndrome gene necdin leads to attenuated cardiac contractility. iScience 2024; 27:109974. [PMID: 38832028 PMCID: PMC11144731 DOI: 10.1016/j.isci.2024.109974] [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: 09/25/2023] [Revised: 01/02/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Prader-Willi syndrome (PWS) is a genetic disorder characterized by behavioral disturbances, hyperphagia, and intellectual disability. Several surveys indicate that PWS is also associated with cardiac abnormalities, possibly contributing to a high incidence of sudden death. However, the pathological mechanisms underlying cardiac dysfunction in PWS remain unclear. In this study, we found that deficiency in necdin, an intronless gene within PWS region, led to heart systolic and diastolic dysfunction in mice. Through yeast two-hybrid screening, we identified an interaction between necdin and non-muscle myosin regulatory light chain 12a/b (MYL12 A/B). We further showed that necdin stabilized MYL12 A/B via SGT1-heat shock protein 90 (HSP90) chaperone machinery. The zebrafish lacking the MYL12 A/B analog, MYL12.1, exhibited impaired heart function, while cardiac-specific overexpression of MYL12A normalized the heart dysfunction in necdin-deficient mice. Our findings revealed necdin dysfunction as a contributing factor to cardiomyopathy in PWS patients and emphasized the importance of HSP90 chaperone machinery and non-muscle myosin in heart fitness.
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Affiliation(s)
- Yufan Dong
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
| | - Renbin Lu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
| | - Hui Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Zhang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Medical Genetics, Changsha 410078, Hunan, P.R. China
| | - Xiushan Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yun Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jia-Da Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Medical Genetics, Changsha 410078, Hunan, P.R. China
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
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Qi M, Zhang H, Xiu X, He D, Cooper DN, Yang Y, Zhao H. Genetic evidence for T-wave area from 12-lead electrocardiograms to monitor cardiovascular diseases in patients taking diabetes medications. Hum Genet 2024:10.1007/s00439-024-02661-6. [PMID: 38507016 DOI: 10.1007/s00439-024-02661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Aims Many studies indicated use of diabetes medications can influence the electrocardiogram (ECG), which remains the simplest and fastest tool for assessing cardiac functions. However, few studies have explored the role of genetic factors in determining the relationship between the use of diabetes medications and ECG trace characteristics (ETC). Methods Genome-wide association studies (GWAS) were performed for 168 ETCs extracted from the 12-lead ECGs of 42,340 Europeans in the UK Biobank. The genetic correlations, causal relationships, and phenotypic relationships of these ETCs with medication usage, as well as the risk of cardiovascular diseases (CVDs), were estimated by linkage disequilibrium score regression (LDSC), Mendelian randomization (MR), and regression model, respectively. Results The GWAS identified 124 independent single nucleotide polymorphisms (SNPs) that were study-wise and genome-wide significantly associated with at least one ETC. Regression model and LDSC identified significant phenotypic and genetic correlations of T-wave area in lead aVR (aVR_T-area) with usage of diabetes medications (ATC code: A10 drugs, and metformin), and the risks of ischemic heart disease (IHD) and coronary atherosclerosis (CA). MR analyses support a putative causal effect of the use of diabetes medications on decreasing aVR_T-area, and on increasing risk of IHD and CA. ConclusionPatients taking diabetes medications are prone to have decreased aVR_T-area and an increased risk of IHD and CA. The aVR_T-area is therefore a potential ECG marker for pre-clinical prediction of IHD and CA in patients taking diabetes medications.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Haoyang Zhang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Xuehao Xiu
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Dan He
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Yuanhao Yang
- Mater Research Institute, Translational Research Institute, Brisbane, QLD, Australia
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510006, China.
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2024; 11:385. [PMID: 38680232 PMCID: PMC11046187 DOI: 10.12688/f1000research.109488.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. METHODS A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. RESULTS Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. CONCLUSIONS Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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Affiliation(s)
- Michael P. Heaton
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Gregory P. Harhay
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S. Bassett
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Halden J. Clark
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Jaden M. Carlson
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Erin E. Jobman
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Helen R. Sadd
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Madeline C. Pelster
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Aspen M. Workman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Larry A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | | | | | | | - Greta M. Krafsur
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Dale M. Grotelueschen
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Brian L. Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2024; 11:385. [PMID: 38680232 PMCID: PMC11046187 DOI: 10.12688/f1000research.109488.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 05/01/2024] Open
Abstract
Background Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. Methods A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. Results Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Conclusions Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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Affiliation(s)
- Michael P. Heaton
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Gregory P. Harhay
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S. Bassett
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Halden J. Clark
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Jaden M. Carlson
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Erin E. Jobman
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Helen R. Sadd
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Madeline C. Pelster
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Aspen M. Workman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Larry A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | | | | | | | - Greta M. Krafsur
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Dale M. Grotelueschen
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Brian L. Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
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Zhang M, Hillegass WB, Yu X, Majumdar S, Daryl Pollard J, Jackson E, Knudson J, Wolfe D, Kato GJ, Maher JF, Mei H. Genetic variants and effect modifiers of QT interval prolongation in patients with sickle cell disease. Gene 2024; 890:147824. [PMID: 37741592 DOI: 10.1016/j.gene.2023.147824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Sickle cell disease (SCD) is a common inherited blood disorder among African Americans (AA), with premature mortality which has been associated with prolongation of the heart rate-corrected QT interval (QTc), a known risk factor for sudden cardiac death. Although numerous genetic variants have been identified as contributors to QT interval prolongation in the general population, their impact on SCD patients remains unclear. This study used an unweighted polygenic risk score (PRS) to validate the previously identified associations between SNPs and QTc interval in SCD patients, and to explore possible interactions with other factors that prolong QTc interval in AA individuals with SCD. METHODS In SCD patients, candidate genetic variants associated with the QTc interval were genotyped. To identify any risk SNPs that may be correlated with QTc interval prolongation, linear regression was employed, and an unweighted PRS was subsequently constructed. The effect of PRS on the QTc interval was evaluated using linear regression, while stratification analysis was used to assess the influence of serum alanine transaminase (ALT), a biomarker for liver disease, on the PRS effect. We also evaluated the PRS with the two subcomponents of QTc, the QRS and JTc intervals. RESULTS Out of 26 candidate SNPs, five risk SNPs were identified for QTc duration under the recessive model. For every unit increase in PRS, the QTc interval prolonged by 4.0 ms (95% CI: [2.0, 6.1]; p-value: <0.001) in the additive model and 9.4 ms in the recessive model (95% CI: [4.6, 14.1]; p-value: <0.001). Serum ALT showed a modification effect on PRS-QTc prolongation under the recessive model. In the normal ALT group, each PRS unit increased QTc interval by 11.7 ms (95% CI: [6.3, 17.1]; p-value: 2.60E-5), whereas this effect was not observed in the elevated ALT group (0.9 ms; 95% CI: [-7.0, 8.8]; p-value: 0.823). CONCLUSION Several candidate genetic variants are associated with QTc interval prolongation in SCD patients, and serum ALT acts as a modifying factor. The association of a CPS1 gene variant in both QTc and JTc duration adds to NOS1AP as evidence of involvement of the urea cycle and nitric oxide metabolism in cardiac repolarization in SCD. Larger replication studies are needed to confirm these findings and elucidate the underlying mechanisms.
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Affiliation(s)
- Mengna Zhang
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - William B Hillegass
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Xue Yu
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Suvankar Majumdar
- Division of Hematology, Children's National Hospital, Washington, DC, USA
| | - J Daryl Pollard
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Erin Jackson
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jarrod Knudson
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Douglas Wolfe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Gregory J Kato
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Joseph F Maher
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Internal Medicine/Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA.
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS 39216, USA; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
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Li N, Li YJ, Guo XJ, Wu SH, Jiang WF, Zhang DL, Wang KW, Li L, Sun YM, Xu YJ, Yang YQ, Qiu XB. Discovery of TBX20 as a Novel Gene Underlying Atrial Fibrillation. BIOLOGY 2023; 12:1186. [PMID: 37759586 PMCID: PMC10525918 DOI: 10.3390/biology12091186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
Atrial fibrillation (AF), the most prevalent type of sustained cardiac dysrhythmia globally, confers strikingly enhanced risks for cognitive dysfunction, stroke, chronic cardiac failure, and sudden cardiovascular demise. Aggregating studies underscore the crucial roles of inherited determinants in the occurrence and perpetuation of AF. However, due to conspicuous genetic heterogeneity, the inherited defects accounting for AF remain largely indefinite. Here, via whole-genome genotyping with genetic markers and a linkage assay in a family suffering from AF, a new AF-causative locus was located at human chromosome 7p14.2-p14.3, a ~4.89 cM (~4.43-Mb) interval between the markers D7S526 and D7S2250. An exome-wide sequencing assay unveiled that, at the defined locus, the mutation in the TBX20 gene, NM_001077653.2: c.695A>G; p.(His232Arg), was solely co-segregated with AF in the family. Additionally, a Sanger sequencing assay of TBX20 in another family suffering from AF uncovered a novel mutation, NM_001077653.2: c.862G>C; p.(Asp288His). Neither of the two mutations were observed in 600 unrelated control individuals. Functional investigations demonstrated that the two mutations both significantly reduced the transactivation of the target gene KCNH2 (a well-established AF-causing gene) and the ability to bind the promoter of KCNH2, while they had no effect on the nuclear distribution of TBX20. Conclusively, these findings reveal a new AF-causative locus at human chromosome 7p14.2-p14.3 and strongly indicate TBX20 as a novel AF-predisposing gene, shedding light on the mechanism underlying AF and suggesting clinical significance for the allele-specific treatment of AF patients.
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Affiliation(s)
- Ning Li
- Department of Cardiology, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, China;
| | - Yan-Jie Li
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Xiao-Juan Guo
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
| | - Shao-Hui Wu
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Wei-Feng Jiang
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
| | - Dao-Liang Zhang
- Cardiac Arrhythmia Center, Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen 518057, China;
| | - Kun-Wei Wang
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China;
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education of China, Tongji University School of Medicine, Shanghai 200092, China;
| | - Yu-Min Sun
- Department of Cardiology, Shanghai Jing’an District Central Hospital, Fudan University, Shanghai 200040, China;
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China; (X.-J.G.); (Y.-J.X.)
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People′s Hospital, Fudan University, Shanghai 200240, China
- Cardiovascular Research Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai 200240, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China; (Y.-J.L.); (S.-H.W.); (W.-F.J.)
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Cruz LA, Cooke Bailey JN, Crawford DC. Importance of Diversity in Precision Medicine: Generalizability of Genetic Associations Across Ancestry Groups Toward Better Identification of Disease Susceptibility Variants. Annu Rev Biomed Data Sci 2023; 6:339-356. [PMID: 37196357 PMCID: PMC10720270 DOI: 10.1146/annurev-biodatasci-122220-113250] [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] [Indexed: 05/19/2023]
Abstract
Genome-wide association studies (GWAS) revolutionized our understanding of common genetic variation and its impact on common human disease and traits. Developed and adopted in the mid-2000s, GWAS led to searchable genotype-phenotype catalogs and genome-wide datasets available for further data mining and analysis for the eventual development of translational applications. The GWAS revolution was swift and specific, including almost exclusively populations of European descent, to the neglect of the majority of the world's genetic diversity. In this narrative review, we recount the GWAS landscape of the early years that established a genotype-phenotype catalog that is now universally understood to be inadequate for a complete understanding of complex human genetics. We then describe approaches taken to augment the genotype-phenotype catalog, including the study populations, collaborative consortia, and study design approaches aimed to generalize and then ultimately discover genome-wide associations in non-European descent populations. The collaborations and data resources established in the efforts to diversify genomic findings undoubtedly provide the foundations of the next chapters of genetic association studies with the advent of budget-friendly whole-genome sequencing.
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Affiliation(s)
- Lauren A Cruz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA;
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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Ji Y, Temprano-Sagrera G, Holle LA, Bebo A, Brody JA, Le NQ, Kangro K, Brown MR, Martinez-Perez A, Sitlani CM, Suchon P, Kleber ME, Emmert DB, Ozel AB, Dobson DA, Tang W, Llobet D, Tracy RP, Deleuze JF, Delgado GE, Gögele M, Wiggins KL, Souto JC, Pankow JS, Taylor KD, Trégouët DA, Moissl AP, Fuchsberger C, Rosendaal FR, Morrison AC, Soria JM, Cushman M, Morange PE, März W, Hicks AA, Desch KC, Johnson AD, de Vries PS, Wolberg AS, Smith NL, Sabater-Lleal M. Antithrombin, Protein C, and Protein S: Genome and Transcriptome-Wide Association Studies Identify 7 Novel Loci Regulating Plasma Levels. Arterioscler Thromb Vasc Biol 2023; 43:e254-e269. [PMID: 37128921 PMCID: PMC10330350 DOI: 10.1161/atvbaha.122.318213] [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: 08/25/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Antithrombin, PC (protein C), and PS (protein S) are circulating natural anticoagulant proteins that regulate hemostasis and of which partial deficiencies are causes of venous thromboembolism. Previous genetic association studies involving antithrombin, PC, and PS were limited by modest sample sizes or by being restricted to candidate genes. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, we meta-analyzed across ancestries the results from 10 genome-wide association studies of plasma levels of antithrombin, PC, PS free, and PS total. METHODS Study participants were of European and African ancestries, and genotype data were imputed to TOPMed, a dense multiancestry reference panel. Each of the 10 studies conducted a genome-wide association studies for each phenotype and summary results were meta-analyzed, stratified by ancestry. Analysis of antithrombin included 25 243 European ancestry and 2688 African ancestry participants, PC analysis included 16 597 European ancestry and 2688 African ancestry participants, PSF and PST analysis included 4113 and 6409 European ancestry participants. We also conducted transcriptome-wide association analyses and multiphenotype analysis to discover additional associations. Novel genome-wide association studies and transcriptome-wide association analyses findings were validated by in vitro functional experiments. Mendelian randomization was performed to assess the causal relationship between these proteins and cardiovascular outcomes. RESULTS Genome-wide association studies meta-analyses identified 4 newly associated loci: 3 with antithrombin levels (GCKR, BAZ1B, and HP-TXNL4B) and 1 with PS levels (ORM1-ORM2). transcriptome-wide association analyses identified 3 newly associated genes: 1 with antithrombin level (FCGRT), 1 with PC (GOLM2), and 1 with PS (MYL7). In addition, we replicated 7 independent loci reported in previous studies. Functional experiments provided evidence for the involvement of GCKR, SNX17, and HP genes in antithrombin regulation. CONCLUSIONS The use of larger sample sizes, diverse populations, and a denser imputation reference panel allowed the detection of 7 novel genomic loci associated with plasma antithrombin, PC, and PS levels.
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Affiliation(s)
- Yuekai Ji
- Cardiovascular Division, Department of Medicine, University of Minnesota, MN, USA
| | - Gerard Temprano-Sagrera
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Lori A Holle
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Allison Bebo
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | | | - Ngoc-Quynh Le
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Kadri Kangro
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | - Angel Martinez-Perez
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, WA, USA
| | - Pierre Suchon
- C2VN, INSERM, INRAE, Aix Marseille Univ, France
- Laboratory of Haematology, La Timone Hospital, France
| | - Marcus E Kleber
- SYNLAB MVZ für Humangenetik Mannheim, Germany
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
| | - David B Emmert
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, C.S. Mott Children’s Hospital, MI, USA
| | - Dre’Von A Dobson
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN, USA
| | - Dolors Llobet
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, VT, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, France
- Laboratory of Excellence on Medical Genomics (GenMed), France
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Martin Gögele
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | | | - Juan Carlos Souto
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, CA, USA
| | - David-Alexandre Trégouët
- Laboratory of Excellence on Medical Genomics (GenMed), France
- INSERM UMR 1219, Bordeaux Population Health Research Center, France
| | - Angela P Moissl
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health(nutriCARD) Halle-Jena-Leipzig, Germany
| | - Christian Fuchsberger
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, the Netherlands
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | - Jose Manuel Soria
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Mary Cushman
- Larner College of Medicine, University of Vermont, VT, USA
| | - Pierre-Emmanuel Morange
- C2VN, INSERM, INRAE, Aix Marseille Univ, France
- Laboratory of Haematology, La Timone Hospital, France
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Germany
| | - Andrew A Hicks
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Karl C Desch
- Department of Pediatrics, University of Michigan, C.S. Mott Children’s Hospital, MI, USA
| | - Andrew D Johnson
- National Heart Lung and Blood Institute, Division of Intramural Research, Population Sciences Branch, The Framingham Heart Study, MA, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | | | | | - Alisa S Wolberg
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, WA, USA
| | - Maria Sabater-Lleal
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
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9
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Joseph J, Liu C, Hui Q, Aragam K, Wang Z, Charest B, Huffman JE, Keaton JM, Edwards TL, Demissie S, Djousse L, Casas JP, Gaziano JM, Cho K, Wilson PWF, Phillips LS, O’Donnell CJ, Sun YV. Genetic architecture of heart failure with preserved versus reduced ejection fraction. Nat Commun 2022; 13:7753. [PMID: 36517512 PMCID: PMC9751124 DOI: 10.1038/s41467-022-35323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Pharmacologic clinical trials for heart failure with preserved ejection fraction have been largely unsuccessful as compared to those for heart failure with reduced ejection fraction. Whether differences in the genetic underpinnings of these major heart failure subtypes may provide insights into the disparate outcomes of clinical trials remains unknown. We utilize a large, uniformly phenotyped, single cohort of heart failure sub-classified into heart failure with reduced and with preserved ejection fractions based on current clinical definitions, to conduct detailed genetic analyses of the two heart failure sub-types. We find different genetic architectures and distinct genetic association profiles between heart failure with reduced and with preserved ejection fraction suggesting differences in underlying pathobiology. The modest genetic discovery for heart failure with preserved ejection fraction (one locus) compared to heart failure with reduced ejection fraction (13 loci) despite comparable sample sizes indicates that clinically defined heart failure with preserved ejection fraction likely represents the amalgamation of several, distinct pathobiological entities. Development of consensus sub-phenotyping of heart failure with preserved ejection fraction is paramount to better dissect the underlying genetic signals and contributors to this highly prevalent condition.
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Affiliation(s)
- Jacob Joseph
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA ,Cardiology Section (111A), VA Providence Healthcare System, 830 Chalkstone Avenue, Providence, RI 02908 USA
| | - Chang Liu
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA
| | - Qin Hui
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
| | - Krishna Aragam
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Zeyuan Wang
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
| | - Brian Charest
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA
| | - Jennifer E. Huffman
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA
| | - Jacob M. Keaton
- grid.94365.3d0000 0001 2297 5165Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA ,grid.412807.80000 0004 1936 9916Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Todd L. Edwards
- grid.412807.80000 0004 1936 9916Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Serkalem Demissie
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University School of Medicine, Boston, MA USA
| | - Luc Djousse
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Juan P. Casas
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - J. Michael Gaziano
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Kelly Cho
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Peter W. F. Wilson
- grid.484294.7Atlanta VA Health Care System, Decatur, GA USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Atlanta, GA USA
| | - Lawrence S. Phillips
- grid.484294.7Atlanta VA Health Care System, Decatur, GA USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Atlanta, GA USA
| | | | - Christopher J. O’Donnell
- grid.410370.10000 0004 4657 1992Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Yan V. Sun
- grid.189967.80000 0001 0941 6502Emory University Rollins School of Public Health, Atlanta, GA USA ,grid.484294.7Atlanta VA Health Care System, Decatur, GA USA
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10
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Hoffmann TJ, Lu M, Oni-Orisan A, Lee C, Risch N, Iribarren C. A large genome-wide association study of QT interval length utilizing electronic health records. Genetics 2022; 222:iyac157. [PMID: 36271874 PMCID: PMC9713425 DOI: 10.1093/genetics/iyac157] [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: 07/09/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022] Open
Abstract
QT interval length is an important risk factor for adverse cardiovascular outcomes; however, the genetic architecture of QT interval remains incompletely understood. We conducted a genome-wide association study of 76,995 ancestrally diverse Kaiser Permanente Northern California members enrolled in the Genetic Epidemiology Research on Adult Health and Aging cohort using 448,517 longitudinal QT interval measurements, uncovering 9 novel variants, most replicating in 40,537 individuals in the UK Biobank and Population Architecture using Genomics and Epidemiology studies. A meta-analysis of all 3 cohorts (n = 117,532) uncovered an additional 19 novel variants. Conditional analysis identified 15 additional variants, 3 of which were novel. Little, if any, difference was seen when adjusting for putative QT interval lengthening medications genome-wide. Using multiple measurements in Genetic Epidemiology Research on Adult Health and Aging increased variance explained by 163%, and we show that the ≈6 measurements in Genetic Epidemiology Research on Adult Health and Aging was equivalent to a 2.4× increase in sample size of a design with a single measurement. The array heritability was estimated at ≈17%, approximately half of our estimate of 36% from family correlations. Heritability enrichment was estimated highest and most significant in cardiovascular tissue (enrichment 7.2, 95% CI = 5.7-8.7, P = 2.1e-10), and many of the novel variants included expression quantitative trait loci in heart and other relevant tissues. Comparing our results to other cardiac function traits, it appears that QT interval has a multifactorial genetic etiology.
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Affiliation(s)
- Thomas J Hoffmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Meng Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Akinyemi Oni-Orisan
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
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11
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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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12
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Yang D, Chung T, Kim D. DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator. Bioinformatics 2022; 38:3501-3512. [PMID: 35640981 DOI: 10.1093/bioinformatics/btac373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/17/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The importance of chromatin loops in gene regulation is broadly accepted. There are mainly two approaches to predict chromatin loops: transcription factor (TF) binding-dependent approach and genomic variation-based approach. However, neither of these approaches provides an adequate understanding of gene regulation in human tissues. To address this issue, we developed a deep learning-based chromatin loop prediction model called DeepLUCIA (Deep Learning-based Universal Chromatin Interaction Annotator). RESULTS Although DeepLUCIA does not use TF binding profile data which previous TF binding-dependent methods critically rely on, its prediction accuracies are comparable to those of the previous TF binding-dependent methods. More importantly, DeepLUCIA enables the tissue-specific chromatin loop predictions from tissue-specific epigenomes that cannot be handled by genomic variation-based approach. We demonstrated the utility of the DeepLUCIA by predicting several novel target genes of SNPs identified in genome-wide association studies targeting Brugada syndrome, COVID-19 severity, and age-related macular degeneration. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dongchan Yang
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Taesu Chung
- Biotechnology & Healthcare Examination Division, KIPO, Daejeon, 35208, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
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13
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Loh M, Zhang W, Ng HK, Schmid K, Lamri A, Tong L, Ahmad M, Lee JJ, Ng MCY, Petty LE, Spracklen CN, Takeuchi F, Islam MT, Jasmine F, Kasturiratne A, Kibriya M, Mohlke KL, Paré G, Prasad G, Shahriar M, Chee ML, de Silva HJ, Engert JC, Gerstein HC, Mani KR, Sabanayagam C, Vujkovic M, Wickremasinghe AR, Wong TY, Yajnik CS, Yusuf S, Ahsan H, Bharadwaj D, Anand SS, Below JE, Boehnke M, Bowden DW, Chandak GR, Cheng CY, Kato N, Mahajan A, Sim X, McCarthy MI, Morris AP, Kooner JS, Saleheen D, Chambers JC. Identification of genetic effects underlying type 2 diabetes in South Asian and European populations. Commun Biol 2022; 5:329. [PMID: 35393509 PMCID: PMC8991226 DOI: 10.1038/s42003-022-03248-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/08/2022] [Indexed: 02/08/2023] Open
Abstract
South Asians are at high risk of developing type 2 diabetes (T2D). We carried out a genome-wide association meta-analysis with South Asian T2D cases (n = 16,677) and controls (n = 33,856), followed by combined analyses with Europeans (neff = 231,420). We identify 21 novel genetic loci for significant association with T2D (P = 4.7 × 10-8 to 5.2 × 10-12), to the best of our knowledge at the point of analysis. The loci are enriched for regulatory features, including DNA methylation and gene expression in relevant tissues, and highlight CHMP4B, PDHB, LRIG1 and other genes linked to adiposity and glucose metabolism. A polygenic risk score based on South Asian-derived summary statistics shows ~4-fold higher risk for T2D between the top and bottom quartile. Our results provide further insights into the genetic mechanisms underlying T2D, and highlight the opportunities for discovery from joint analysis of data from across ancestral populations.
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Affiliation(s)
- Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Katharina Schmid
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, 85748, Garching bei München, Neuherberg, Germany
| | - Amel Lamri
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Lin Tong
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Meraj Ahmad
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Jung-Jin Lee
- Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Mayo Hospital, Lahore, Pakistan
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, 37215, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Md Tariqul Islam
- U Chicago Research Bangladesh, House#4, Road#2b, Sector#4, Uttara, Dhaka, 1230, Bangladesh
| | - Farzana Jasmine
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Anuradhani Kasturiratne
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - Muhammad Kibriya
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Gauri Prasad
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohammad Shahriar
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Miao Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - James C Engert
- Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Hertzel C Gerstein
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - K Radha Mani
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Marijana Vujkovic
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Ananda R Wickremasinghe
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Salim Yusuf
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Habibul Ahsan
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sonia S Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Donald W Bowden
- Department of Medicine, Mayo Hospital, Lahore, Pakistan
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 37215, USA
| | - Giriraj R Chandak
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- JSS Academy of Health Education of Research, Mysuru, India
- Science and Engineering Research Board, Department of Science and Technology, Ministry of Science and technology, Government of India, New Delhi, India
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Anubha Mahajan
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hosptial, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK.
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK.
- MRC-PHE Centre for Enviroment and Health, Imperial College London, London, W2 1PG, UK.
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK.
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK.
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK.
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK.
- MRC-PHE Centre for Enviroment and Health, Imperial College London, London, W2 1PG, UK.
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14
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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15
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Glinge C, Lahrouchi N, Jabbari R, Tfelt-Hansen J, Bezzina CR. Genome-wide association studies of cardiac electrical phenotypes. Cardiovasc Res 2021; 116:1620-1634. [PMID: 32428210 PMCID: PMC7341169 DOI: 10.1093/cvr/cvaa144] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022] Open
Abstract
The genetic basis of cardiac electrical phenotypes has in the last 25 years been the subject of intense investigation. While in the first years, such efforts were dominated by the study of familial arrhythmia syndromes, in recent years, large consortia of investigators have successfully pursued genome-wide association studies (GWAS) for the identification of single-nucleotide polymorphisms that govern inter-individual variability in electrocardiographic parameters in the general population. We here provide a review of GWAS conducted on cardiac electrical phenotypes in the last 14 years and discuss the implications of these discoveries for our understanding of the genetic basis of disease susceptibility and variability in disease severity. Furthermore, we review functional follow-up studies that have been conducted on GWAS loci associated with cardiac electrical phenotypes and highlight the challenges and opportunities offered by such studies.
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Affiliation(s)
- Charlotte Glinge
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 7, 2100 Copenhagen, Denmark
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Reza Jabbari
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 7, 2100 Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 7, 2100 Copenhagen, Denmark.,Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Frederik V's Vej, 2100 Copenhagen, Denmark
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Amsterdam University Medical Center, University of Amsterdam, Heart Center, Amsterdam Cardiovascular Sciences, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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16
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Vincentz JW, Firulli BA, Toolan KP, Osterwalder M, Pennacchio LA, Firulli AB. HAND transcription factors cooperatively specify the aorta and pulmonary trunk. Dev Biol 2021; 476:1-10. [PMID: 33757801 DOI: 10.1016/j.ydbio.2021.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023]
Abstract
Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart field (SHF) derived myocardium and endocardium. The related transcription factors HAND1 and HAND2 have been implicated in human CHDs involving the OFT. Although Hand1 is expressed within the OFT, Hand1 NCC-specific conditional knockout mice (H1CKOs) are viable. Here we show that these H1CKOs present a low penetrance of OFT phenotypes, whereas SHF-specific Hand1 ablation does not reveal any cardiac phenotypes. Further, HAND1 and HAND2 appear functionally redundant within the cNCCs, as a reduction/ablation of Hand2 on an NCC-specific H1CKO background causes pronounced OFT defects. Double conditional Hand1 and Hand2 NCC knockouts exhibit persistent truncus arteriosus (PTA) with 100% penetrance. NCC lineage-tracing and Sema3c in situ mRNA expression reveal that Sema3c-expressing cells are mis-localized, resulting in a malformed septal bridge within the OFTs of H1CKO;H2CKO embryos. Interestingly, Hand1 and Hand2 also genetically interact within the SHF, as SHF H1CKOs on a heterozygous Hand2 background exhibit Ventricular Septal Defects (VSDs) with incomplete penetrance. Previously, we identified a BMP, HAND2, and GATA-dependent Hand1 OFT enhancer sufficient to drive reporter gene expression within the nascent OFT and aorta. Using these transcription inputs as a probe, we identify a novel Hand2 OFT enhancer, suggesting that a conserved BMP-GATA dependent mechanism transcriptionally regulates both HAND factors. These findings support the hypothesis that HAND factors interpret BMP signaling within the cNCCs to cooperatively coordinate OFT morphogenesis.
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Affiliation(s)
- Joshua W Vincentz
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
| | - Beth A Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Kevin P Toolan
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA; Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research Department of Pediatrics, Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202-5225, USA.
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17
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Gou D, Zhou J, Song Q, Wang Z, Bai X, Zhang Y, Zuo M, Wang F, Chen A, Yousaf M, Yang Z, Peng H, Li K, Xie W, Tang J, Yao Y, Han M, Ke T, Chen Q, Xu C, Wang Q. Mog1 knockout causes cardiac hypertrophy and heart failure by downregulating tbx5-cryab-hspb2 signalling in zebrafish. Acta Physiol (Oxf) 2021; 231:e13567. [PMID: 33032360 DOI: 10.1111/apha.13567] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/09/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022]
Abstract
AIMS MOG1 is a small protein that can bind to small GTPase RAN and regulate transport of RNA and proteins between the cytoplasm and nucleus. However, the in vivo physiological role of mog1 in the heart needs to be fully defined. METHODS Mog1 knockout zebrafish was generated by TALEN. Echocardiography, histological analysis, and electrocardiograms were used to examine cardiac structure and function. RNA sequencing and real-time RT-PCR were used to elucidate the molecular mechanism and to analyse the gene expression. Isoproterenol was used to induce cardiac hypertrophy. Whole-mount in situ hybridization was used to observe cardiac morphogenesis. RESULTS Mog1 knockout zebrafish developed cardiac hypertrophy and heart failure (enlarged pericardium, increased nppa and nppb expression and ventricular wall thickness, and reduced ejection fraction), which was aggravated by isoproterenol. RNAseq and KEGG pathway analyses revealed the effect of mog1 knockout on the pathways of cardiac hypertrophy, dilatation and contraction. Mechanistic studies revealed that mog1 knockout decreased expression of tbx5, which reduced expression of cryab and hspb2, resulting in cardiac hypertrophy and heart failure. Overexpression of cryab, hspb2 and tbx5 rescued the cardiac oedema phenotype of mog1 KO zebrafish. Telemetry electrocardiogram monitoring showed QRS and QTc prolongation and a reduced heart rate in mog1 knockout zebrafish, which was associated with reduced scn1b expression. Moreover, mog1 knockout resulted in abnormal cardiac looping during embryogenesis because of the reduced expression of nkx2.5, gata4 and hand2. CONCLUSION Our data identified an important molecular determinant for cardiac hypertrophy and heart failure, and rhythm maintenance of the heart.
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Affiliation(s)
- Dongzhi Gou
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Juan Zhou
- School of Basic Medicine Gannan Medical University Ganzhou P. R. China
| | - Qixue Song
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Zhijie Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Xuemei Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Yidan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Mengxia Zuo
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Fan Wang
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
| | - Ailan Chen
- Department of Cardiology Guangzhou Medical University Guangzhou P. R. China
| | - Muhammad Yousaf
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Zhongcheng Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Huixing Peng
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Ke Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Wen Xie
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Jingluo Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Yufeng Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Meng Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Tie Ke
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Qiuyun Chen
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
| | - Chengqi Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education College of Life Science and Technology and Center for Human Genome Research Huazhong University of Science and Technology Wuhan P. R. China
- Department of Cardiovascular and Metabolic Sciences Lerner Research Institute Department of Cardiovascular Medicine Cleveland Clinic Cleveland OH USA
- Department of Molecular Medicine Cleveland Clinic Lerner College of Medicine of CaseWestern Reserve University Cleveland OH USA
- Department of Genetics and Genome Science Case Western Reserve University School of Medicine Cleveland OH USA
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18
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Chen Y, Xiao D, Zhang L, Cai CL, Li BY, Liu Y. The Role of Tbx20 in Cardiovascular Development and Function. Front Cell Dev Biol 2021; 9:638542. [PMID: 33585493 PMCID: PMC7876368 DOI: 10.3389/fcell.2021.638542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/08/2021] [Indexed: 01/05/2023] Open
Abstract
Tbx20 is a member of the Tbx1 subfamily of T-box-containing genes and is known to play a variety of fundamental roles in cardiovascular development and homeostasis as well as cardiac remodeling in response to pathophysiological stresses. Mutations in TBX20 are widely associated with the complex spectrum of congenital heart defects (CHDs) in humans, which includes defects in chamber septation, chamber growth, and valvulogenesis. In addition, genetic variants of TBX20 have been found to be associated with dilated cardiomyopathy and heart arrhythmia. This broad spectrum of cardiac morphogenetic and functional defects is likely due to its broad expression pattern in multiple cardiogenic cell lineages and its critical regulation of transcriptional networks during cardiac development. In this review, we summarize recent findings in our general understanding of the role of Tbx20 in regulating several important aspects of cardiac development and homeostasis and heart function.
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Affiliation(s)
- Yuwen Chen
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China.,Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Deyong Xiao
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Lu Zhang
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Chen-Leng Cai
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
| | - Bai-Yan Li
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Ying Liu
- Cardiovascular Developmental Biology Program, Herman B Wells Center for Pediatric Research, Indianapolis, IN, United States
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19
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Li X, Guo LZ, Liu N, Du X, Bai R, Dong JZ, Ma CS. Association of T66A polymorphism in CASQ2 with PR interval in a Chinese population. Herz 2020; 46:123-129. [PMID: 32291483 DOI: 10.1007/s00059-020-04913-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/18/2020] [Accepted: 03/18/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE The aim of this study was to explore the relationship between arrhythmia-associated or electrocardiogram (ECG)-associated common variants and PR interval, QRS duration, QTcorrected, and heart rate in a Chinese cohort. METHODS We studied the association between 26 single-nucleotide polymorphisms (SNPs) and digital ECG data from 379 unrelated Han Chinese individuals collected in an epidemiological survey in Beijing. All subjects were 45 years of age or older and were free of cardiovascular diseases and diabetes. The SNPs were genotyped in a multiplex panel using the Sequenom MassARRAY platform. RESULTS Missense variant T66A (Thr66Ala, rs4074536) of the CASQ2 gene, which was previously reported to be associated with QRS complex in European populations, was significantly associated with PR interval prolongation in our sample (padjusted = 0.006, betaadjusted = 3.983 ms). A two-tailed t test showed that the CC genotype (n = 86) had a significantly longer PR interval (162.9 ± 19.4 ms) than the non-CC genotypes (n = 288, PR interval: 154.6 ± 20.9 ms), with a remarkable difference of 8.2 ms between the groups (p = 0.001). Interestingly, this association between T66A of CASQ2 and PR interval was more evident in females (padjusted = 0.007, betaadjusted = 5.723 ms) than in males (padjusted = 0.177, betaadjusted = 2.725 ms). In addition, rs3822714 in the HAND1 locus might be associated with QRS duration (padjusted = 0.034, betaadjusted = -2.268 ms). CONCLUSION We identified a novel signal of an association between the CC genotype of T66A in CASQ2 and PR interval prolongation in a Chinese population, particularly in females. This association deserves further exploration given its possible effects on calcium handling in cardiac electrophysiology.
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Affiliation(s)
- Xin Li
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Li-Zhu Guo
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Nian Liu
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Xin Du
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Rong Bai
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Jian-Zeng Dong
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China
| | - Chang-Sheng Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine for Cardiovascular Diseases, Beijing, China.
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20
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Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Lin Y, Le Marchand L, Matise TC, Monroe KR, Moreland L, North KE, Park SL, Reiner A, Wallace R, Wilkens LR, Kooperberg C, Ritchie MD, Crawford DC. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. PLoS One 2019; 14:e0226771. [PMID: 31891604 PMCID: PMC6938343 DOI: 10.1371/journal.pone.0226771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/11/2022] Open
Abstract
We performed a hypothesis-generating phenome-wide association study (PheWAS) to identify and characterize cross-phenotype associations, where one SNP is associated with two or more phenotypes, between thousands of genetic variants assayed on the Metabochip and hundreds of phenotypes in 5,897 African Americans as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study. The PAGE I study was a National Human Genome Research Institute-funded collaboration of four study sites accessing diverse epidemiologic studies genotyped on the Metabochip, a custom genotyping chip that has dense coverage of regions in the genome previously associated with cardio-metabolic traits and outcomes in mostly European-descent populations. Here we focus on identifying novel phenome-genome relationships, where SNPs are associated with more than one phenotype. To do this, we performed a PheWAS, testing each SNP on the Metabochip for an association with up to 273 phenotypes in the participating PAGE I study sites. We identified 133 putative pleiotropic variants, defined as SNPs associated at an empirically derived p-value threshold of p<0.01 in two or more PAGE study sites for two or more phenotype classes. We further annotated these PheWAS-identified variants using publicly available functional data and local genetic ancestry. Amongst our novel findings is SPARC rs4958487, associated with increased glucose levels and hypertension. SPARC has been implicated in the pathogenesis of diabetes and is also known to have a potential role in fibrosis, a common consequence of multiple conditions including hypertension. The SPARC example and others highlight the potential that PheWAS approaches have in improving our understanding of complex disease architecture by identifying novel relationships between genetic variants and an array of common human phenotypes.
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Affiliation(s)
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Janina M. Jeff
- Illumina, Inc., San Diego, California, United States of America
| | - Alex Frase
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Scott Dudek
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yuki Bradford
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jose-Luis Ambite
- Information Sciences Institute; University of Southern California, Marina del Rey, California, United States of America
| | - Christy L. Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Ewa Deelman
- Information Sciences Institute; University of Southern California, Marina del Rey, California, United States of America
| | | | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucia A. Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chun-Nan Hsu
- Center for Research in Biological Systems, Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | | | - Yi Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Kristine R. Monroe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Larry Moreland
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sungshim L. Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Robert Wallace
- Departments of Epidemiology and Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dana C. Crawford
- Cleveland Institute for Computational Biology, Cleveland, Ohio, United States of America
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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21
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Sequence variants with large effects on cardiac electrophysiology and disease. Nat Commun 2019; 10:4803. [PMID: 31641117 PMCID: PMC6805929 DOI: 10.1038/s41467-019-12682-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Features of the QRS complex of the electrocardiogram, reflecting ventricular depolarisation, associate with various physiologic functions and several pathologic conditions. We test 32.5 million variants for association with ten measures of the QRS complex in 12 leads, using 405,732 electrocardiograms from 81,192 Icelanders. We identify 190 associations at 130 loci, the majority of which have not been reported before, including associations with 21 rare or low-frequency coding variants. Assessment of genes expressed in the heart yields an additional 13 rare QRS coding variants at 12 loci. We find 51 unreported associations between the QRS variants and echocardiographic traits and cardiovascular diseases, including atrial fibrillation, complete AV block, heart failure and supraventricular tachycardia. We demonstrate the advantage of in-depth analysis of the QRS complex in conjunction with other cardiovascular phenotypes to enhance our understanding of the genetic basis of myocardial mass, cardiac conduction and disease. Aberrant morphology of the QRS complex in an electrocardiogram can be associated with cardiac morbidity and mortality. Here, the authors perform genome-wide association studies for ten measures of the QRS complex in 81,192 individuals and find 86 previously unreported loci that associate with at least one parameter.
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22
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Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H, Drees F, Singhal S, Matsui H, van Setten J, Sotoodehnia N, Gaulton KJ, Smith EN, D'Antonio M, Rosenfeld MG, Frazer KA. Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. Nat Genet 2019; 51:1506-1517. [PMID: 31570892 PMCID: PMC6858543 DOI: 10.1038/s41588-019-0499-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/15/2019] [Indexed: 12/15/2022]
Abstract
The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes.
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Affiliation(s)
- Paola Benaglio
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Wubin Ma
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Margaret K R Donovan
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Christopher DeBoever
- Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frauke Drees
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sanghamitra Singhal
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Nona Sotoodehnia
- Department of Medicine, Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Erin N Smith
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Kelly A Frazer
- Department of Pediatrics, Rady Children's Hospital, Division of Genome Information Sciences, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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23
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Vincentz JW, Firulli BA, Toolan KP, Arking DE, Sotoodehnia N, Wan J, Chen PS, de Gier-de Vries C, Christoffels VM, Rubart-von der Lohe M, Firulli AB. Variation in a Left Ventricle-Specific Hand1 Enhancer Impairs GATA Transcription Factor Binding and Disrupts Conduction System Development and Function. Circ Res 2019; 125:575-589. [PMID: 31366290 DOI: 10.1161/circresaha.119.315313] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RATIONALE The ventricular conduction system (VCS) rapidly propagates electrical impulses through the working myocardium of the ventricles to coordinate chamber contraction. GWAS (Genome-wide association studies) have associated nucleotide polymorphisms, most are located within regulatory intergenic or intronic sequences, with variation in VCS function. Two highly correlated polymorphisms (r2>0.99) associated with VCS functional variation (rs13165478 and rs13185595) occur 5' to the gene encoding the basic helix-loop-helix transcription factor HAND1 (heart- and neural crest derivatives-expressed protein 1). OBJECTIVE Here, we test the hypothesis that these polymorphisms influence HAND1 transcription thereby influencing VCS development and function. METHODS AND RESULTS We employed transgenic mouse models to identify an enhancer that is sufficient for left ventricle (LV) cis-regulatory activity. Two evolutionarily conserved GATA transcription factor cis-binding elements within this enhancer are bound by GATA4 and are necessary for cis-regulatory activity, as shown by in vitro DNA binding assays. CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9-mediated deletion of this enhancer dramatically reduces Hand1 expression solely within the LV but does not phenocopy previously published mouse models of cardiac Hand1 loss-of-function. Electrophysiological and morphological analyses reveals that mice homozygous for this deleted enhancer display a morphologically abnormal VCS and a conduction system phenotype consistent with right bundle branch block. Using 1000 Genomes Project data, we identify 3 additional single nucleotide polymorphisms (SNPs), located within the Hand1 LV enhancer, that compose a haplotype with rs13165478 and rs13185595. One of these SNPs, rs10054375, overlaps with a critical GATA cis-regulatory element within the Hand1 LV enhancer. This SNP, when tested in electrophoretic mobility shift assays, disrupts GATA4 DNA-binding. Modeling 2 of these SNPs in mice causes diminished Hand1 expression and mice present with abnormal VCS function. CONCLUSIONS Together, these findings reveal that SNP rs10054375, which is located within a necessary and sufficient LV-specific Hand1 enhancer, exhibits reduces GATA DNA-binding in electrophoretic mobility shift assay, and this enhancer in total, is required for VCS development and function in mice and perhaps humans.
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Affiliation(s)
- Joshua W Vincentz
- From the Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis (J.W.V., B.A.F., K.P.T., M.R.L., A.B.F.)
| | - Beth A Firulli
- From the Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis (J.W.V., B.A.F., K.P.T., M.R.L., A.B.F.)
| | - Kevin P Toolan
- From the Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis (J.W.V., B.A.F., K.P.T., M.R.L., A.B.F.)
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (D.E.A.)
| | - Nona Sotoodehnia
- Department of Epidemiology, Division of Cardiology, University of Washington, Seattle (N.S.)
| | - Juyi Wan
- Division of Cardiology, Department of Medicine, Krannert Institute of Cardiology, Indianapolis (J.W., P.-S.C.).,Department of Cardiothoracic Surgery, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China (J.W.)
| | - Peng-Sheng Chen
- Division of Cardiology, Department of Medicine, Krannert Institute of Cardiology, Indianapolis (J.W., P.-S.C.)
| | - Corrie de Gier-de Vries
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, the Netherlands (C.d.G.V., V.M.C.)
| | - Vincent M Christoffels
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, the Netherlands (C.d.G.V., V.M.C.)
| | - Michael Rubart-von der Lohe
- From the Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis (J.W.V., B.A.F., K.P.T., M.R.L., A.B.F.)
| | - Anthony B Firulli
- From the Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis (J.W.V., B.A.F., K.P.T., M.R.L., A.B.F.)
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24
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Swenson BR, Louie T, Lin HJ, Méndez-Giráldez R, Below JE, Laurie CC, Kerr KF, Highland H, Thornton TA, Ryckman KK, Kooperberg C, Soliman EZ, Seyerle AA, Guo X, Taylor KD, Yao J, Heckbert SR, Darbar D, Petty LE, McKnight B, Cheng S, Bello NA, Whitsel EA, Hanis CL, Nalls MA, Evans DS, Rotter JI, Sofer T, Avery CL, Sotoodehnia N. GWAS of QRS duration identifies new loci specific to Hispanic/Latino populations. PLoS One 2019; 14:e0217796. [PMID: 31251759 PMCID: PMC6599128 DOI: 10.1371/journal.pone.0217796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/17/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The electrocardiographically quantified QRS duration measures ventricular depolarization and conduction. QRS prolongation has been associated with poor heart failure prognosis and cardiovascular mortality, including sudden death. While previous genome-wide association studies (GWAS) have identified 32 QRS SNPs across 26 loci among European, African, and Asian-descent populations, the genetics of QRS among Hispanics/Latinos has not been previously explored. METHODS We performed a GWAS of QRS duration among Hispanic/Latino ancestry populations (n = 15,124) from four studies using 1000 Genomes imputed genotype data (adjusted for age, sex, global ancestry, clinical and study-specific covariates). Study-specific results were combined using fixed-effects, inverse variance-weighted meta-analysis. RESULTS We identified six loci associated with QRS (P<5x10-8), including two novel loci: MYOCD, a nuclear protein expressed in the heart, and SYT1, an integral membrane protein. The top SNP in the MYOCD locus, intronic SNP rs16946539, was found in Hispanics/Latinos with a minor allele frequency (MAF) of 0.04, but is monomorphic in European and African descent populations. The most significant QRS duration association was with intronic SNP rs3922344 (P = 1.19x10-24) in SCN5A/SCN10A. Three other previously identified loci, CDKN1A, VTI1A, and HAND1, also exceeded the GWAS significance threshold among Hispanics/Latinos. A total of 27 of 32 previously identified QRS duration SNPs were shown to generalize in Hispanics/Latinos. CONCLUSIONS Our QRS duration GWAS, the first in Hispanic/Latino populations, identified two new loci, underscoring the utility of extending large scale genomic studies to currently under-examined populations.
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Affiliation(s)
- Brenton R. Swenson
- Institute for Public Health Genetics, University of Washington, Seattle, WA, United States of America
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States of America
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Henry J. Lin
- The Institute for Translational Genomics and Population Sciences, and Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, United States of America
- Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Raúl Méndez-Giráldez
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jennifer E. Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Kathleen F. Kerr
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Heather Highland
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Kelli K. Ryckman
- Departments of Epidemiology and Pediatrics, University of Iowa, Iowa City, IA, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Elsayed Z. Soliman
- Department of Internal Medicine, Section on Cardiology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
- Epidemiological Cardiology Research Center (EPICARE), Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Amanda A. Seyerle
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States of America
- Carolina Health Informatics Program, University of North Carolina, Chapel Hill, NC, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, and Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, and Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, and Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States of America
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Lauren E. Petty
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Barbara McKnight
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States of America
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Natalie A. Bello
- Brigham and Women's Hospital, Division of Cardiovascular Medicine, Boston, MA, United States of America
- Division of Cardiology, Columbia University Medical Center, New York, NY, United States of America
| | - Eric A. Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Craig L. Hanis
- Human Genetics Center, University of Texas, Health Science Center at Houston, Houston, TX, United States of America
| | - Mike A. Nalls
- Data Technical International, Glen Echo, MD, United States of America
- Laboratory of Neurogenetics, National Institute of Aging, Bethesda, MD, United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, and Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Christy L. Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, United States of America
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States of America
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, United States of America
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25
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Demola P, Crocamo A, Ceriello L, Botti A, Cremonini I, Pattoneri P, Corradi D, Visioli F, Goldoni M, Pelà G. Hemodynamic and ECG responses to stress test in early adolescent athletes explain ethnicity-related cardiac differences. Int J Cardiol 2019; 289:125-130. [PMID: 31072636 DOI: 10.1016/j.ijcard.2019.04.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/10/2019] [Accepted: 04/26/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Ethnicity is an important determinant of athletes' cardiovascular adaptation. Black adolescent and adult athletes exhibit a left ventricular (LV) hypertrophy with a concentric remodelling higher than their Caucasian counterparts. Scant data, however, are available on race-related differences in hemodynamic response of adolescent athletes to exercise and its relation with heart remodelling. We evaluated if race-specific, sport-related structural and electrical remodelling in adolescent athletes of Caucasian and African ethnicity exclusively depends on race itself rather than on different cardiovascular responses to physical exercise. METHODS We examined 90 adolescent athletes, 60 Caucasian (WA) and 30 Black (BA). All participants underwent thorough clinical, echocardiographic and stress test evaluations. RESULTS BA had greater indexed LV mass (LVM/BSA) with increased relative wall thickness (RWT) implying a concentric remodelling. BA showed higher systolic blood pressure (SBP) compared to WA during the whole exercise test. ECG data showed that BA vs WA had a significant shorter QRS duration in each step considered with a significant greater QT dispersion. BA reached a higher relative pressure peak as compared to WA. RWT was strongly influenced by ethnicity and less by SBP at peak of exercise (PE), although LVM/BSA was significantly related to SBP at PE and just marginally to age and not significantly to race. CONCLUSIONS Black adolescent athletes showed higher SBP during all steps of exercise associated to a different trend. Ethnicity was the main determinant of RWT, suggesting that LV geometry is principally race-related rather than influenced by a different hemodynamic profile to physical activity.
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Affiliation(s)
- Pierluigi Demola
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Antonio Crocamo
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Laura Ceriello
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Andrea Botti
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Isabella Cremonini
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | | | - Domenico Corradi
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Francesco Visioli
- Department of Molecular Medicine, University of Padova, Italy; IMDEA-Food, CEI UAM+CSIC, Madrid, Spain
| | - Matteo Goldoni
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy
| | - Giovanna Pelà
- Department of Medicine and Surgery, University Medical School and University Hospital of Parma, Italy.
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26
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Genomic approaches for the elucidation of genes and gene networks underlying cardiovascular traits. Biophys Rev 2018; 10:1053-1060. [PMID: 29934864 PMCID: PMC6082306 DOI: 10.1007/s12551-018-0435-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies have shed light on the association between natural genetic variation and cardiovascular traits. However, linking a cardiovascular trait associated locus to a candidate gene or set of candidate genes for prioritization for follow-up mechanistic studies is all but straightforward. Genomic technologies based on next-generation sequencing technology nowadays offer multiple opportunities to dissect gene regulatory networks underlying genetic cardiovascular trait associations, thereby aiding in the identification of candidate genes at unprecedented scale. RNA sequencing in particular becomes a powerful tool when combined with genotyping to identify loci that modulate transcript abundance, known as expression quantitative trait loci (eQTL), or loci modulating transcript splicing known as splicing quantitative trait loci (sQTL). Additionally, the allele-specific resolution of RNA-sequencing technology enables estimation of allelic imbalance, a state where the two alleles of a gene are expressed at a ratio differing from the expected 1:1 ratio. When multiple high-throughput approaches are combined with deep phenotyping in a single study, a comprehensive elucidation of the relationship between genotype and phenotype comes into view, an approach known as systems genetics. In this review, we cover key applications of systems genetics in the broad cardiovascular field.
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Méndez-Giráldez R, Gogarten SM, Below JE, Yao J, Seyerle AA, Highland HM, Kooperberg C, Soliman EZ, Rotter JI, Kerr KF, Ryckman KK, Taylor KD, Petty LE, Shah SJ, Conomos MP, Sotoodehnia N, Cheng S, Heckbert SR, Sofer T, Guo X, Whitsel EA, Lin HJ, Hanis CL, Laurie CC, Avery CL. GWAS of the electrocardiographic QT interval in Hispanics/Latinos generalizes previously identified loci and identifies population-specific signals. Sci Rep 2017; 7:17075. [PMID: 29213071 PMCID: PMC5719082 DOI: 10.1038/s41598-017-17136-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023] Open
Abstract
QT interval prolongation is a heritable risk factor for ventricular arrhythmias and can predispose to sudden death. Most genome-wide association studies (GWAS) of QT were performed in European ancestral populations, leaving other groups uncharacterized. Herein we present the first QT GWAS of Hispanic/Latinos using data on 15,997 participants from four studies. Study-specific summary results of the association between 1000 Genomes Project (1000G) imputed SNPs and electrocardiographically measured QT were combined using fixed-effects meta-analysis. We identified 41 genome-wide significant SNPs that mapped to 13 previously identified QT loci. Conditional analyses distinguished six secondary signals at NOS1AP (n = 2), ATP1B1 (n = 2), SCN5A (n = 1), and KCNQ1 (n = 1). Comparison of linkage disequilibrium patterns between the 13 lead SNPs and six secondary signals with previously reported index SNPs in 1000G super populations suggested that the SCN5A and KCNE1 lead SNPs were potentially novel and population-specific. Finally, of the 42 suggestively associated loci, AJAP1 was suggestively associated with QT in a prior East Asian GWAS; in contrast BVES and CAP2 murine knockouts caused cardiac conduction defects. Our results indicate that whereas the same loci influence QT across populations, population-specific variation exists, motivating future trans-ethnic and ancestrally diverse QT GWAS.
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Affiliation(s)
| | | | - Jennifer E Below
- The Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Amanda A Seyerle
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.,Division of Epidemiology and Community, University of Minnesota, Minneapolis, MN, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elsayed Z Soliman
- Department of Internal Medicine, Section on Cardiology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Epidemiological Cardio Research Center (EPICARE), Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kelli K Ryckman
- Departments of Epidemiology and Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lauren E Petty
- Human Genetics Center, University of Texas, Health Science Center at Houston, Houston, TX, USA.,Center for Precision Medicine, University of Texas, Health Science Center at Houston, Houston, TX, USA
| | - Sanjiv J Shah
- Division of Cardiology, Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Susan Cheng
- Brigham and Women's Hospital, Division of Cardiovascular Medicine, Boston, MA, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA.,Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Craig L Hanis
- Human Genetics Center, University of Texas, Health Science Center at Houston, Houston, TX, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA. .,Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA.
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Affiliation(s)
- Teri A Manolio
- Division of Genomic Medicine, the National Human Genome Research Institute, Bethesda, Maryland 20892, USA
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