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Dungan JR, Qin X, Gregory SG, Cooper-Dehoff R, Duarte JD, Qin H, Gulati M, Taylor JY, Pepine CJ, Hauser ER, Kraus WE. Sex-dimorphic gene effects on survival outcomes in people with coronary artery disease. AMERICAN HEART JOURNAL PLUS: CARDIOLOGY RESEARCH AND PRACTICE 2022; 17. [PMID: 35959094 PMCID: PMC9365120 DOI: 10.1016/j.ahjo.2022.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Ischemic coronary heart disease (IHD) is the leading cause of death worldwide. Genetic variation is presumed to be a major factor underlying sex differences for IHD events, including mortality. The purpose of this study was to identify sex-specific candidate genes associated with all-cause mortality among people diagnosed with coronary artery disease (CAD). Methods: We performed a sex-stratified, exploratory genome-wide association (GWAS) screen using existing data from CAD-diagnosed males (n = 510) and females (n = 174) who reported European ancestry from the Duke Catheterization Genetics biorepository. Extant genotype data for 785,945 autosomal SNPs generated with the Human Omni1-Quad BeadChip (Illumina, CA, USA) were analyzed using an additive inheritance model. We estimated instantaneous risk of all-cause mortality by genotype groups across the 11-year follow-up using Cox multivariate regression, covarying for age and genomic ancestry. Results: The top GWAS hits associated with all-cause mortality among people with CAD included 8 SNPs among males and 15 among females (p = 1 × 10−6 or 10−7), adjusted for covariates. Cross-sex comparisons revealed distinct candidate genes. Biologically relevant candidates included rs9932462 (EMP2/TEKT5) and rs2835913 (KCNJ6) among males and rs7217169 (RAP1GAP2), rs8021816 (PRKD1), rs8133010 (PDE9A), and rs12145981 (LPGAT1) among females. Conclusions: We report 20 sex-specific candidate genes having suggestive association with all-cause mortality among CAD-diagnosed subjects. Findings demonstrate proof of principle for identifying sex-associated genetic factors that may help explain differential mortality risk in people with CAD. Replication and meta-analyses in larger studies with more diverse samples will strengthen future work in this area.
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van Andel MM, Groenink M, van den Berg MP, Timmermans J, Scholte AJHA, Mulder BJM, Zwinderman AH, de Waard V. Genome-wide methylation patterns in Marfan syndrome. Clin Epigenetics 2021; 13:217. [PMID: 34895303 PMCID: PMC8665617 DOI: 10.1186/s13148-021-01204-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/27/2021] [Indexed: 12/29/2022] Open
Abstract
Background Marfan syndrome (MFS) is a connective tissue disorder caused by mutations in the Fibrillin-1 gene (FBN1). Here, we undertook the first epigenome-wide association study (EWAS) in patients with MFS aiming at identifying DNA methylation loci associated with MFS phenotypes that may shed light on the disease process. Methods The Illumina 450 k DNA-methylation array was used on stored peripheral whole-blood samples of 190 patients with MFS originally included in the COMPARE trial. An unbiased genome-wide approach was used, and methylation of CpG-sites across the entire genome was evaluated. Additionally, we investigated CpG-sites across the FBN1-locus (15q21.1) more closely, since this is the gene defective in MFS. Differentially Methylated Positions (DMPs) and Differentially Methylated Regions (DMRs) were identified through regression analysis. Associations between methylation levels and aortic diameters and presence or absence of 21 clinical features of MFS at baseline were analyzed. Moreover, associations between aortic diameter change, and the occurrence of clinical events (death any cause, type-A or -B dissection/rupture, or aortic surgery) and methylation levels were analyzed. Results We identified 28 DMPs that are significantly associated with aortic diameters in patients with MFS. Seven of these DMPs (25%) could be allocated to a gene that was previously associated with cardiovascular diseases (HDAC4, IGF2BP3, CASZ1, SDK1, PCDHGA1, DIO3, PTPRN2). Moreover, we identified seven DMPs that were significantly associated with aortic diameter change and five DMP’s that associated with clinical events. No significant associations at p < 10–8 or p < 10–6 were found with any of the non-cardiovascular phenotypic MFS features. Investigating DMRs, clusters were seen mostly on X- and Y, and chromosome 18–22. The remaining DMRs indicated involvement of a large family of protocadherins on chromosome 5, which were not reported in MFS before. Conclusion This EWAS in patients with MFS has identified a number of methylation loci significantly associated with aortic diameters, aortic dilatation rate and aortic events. Our findings add to the slowly growing literature on the regulation of gene expression in MFS patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01204-4.
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Affiliation(s)
- Mitzi M van Andel
- Department of Cardiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Maarten Groenink
- Department of Cardiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Department of Radiology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Maarten P van den Berg
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Janneke Timmermans
- Department of Cardiology, Radboud University Hospital, Nijmegen, The Netherlands
| | - Arthur J H A Scholte
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Barbara J M Mulder
- Department of Cardiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Vivian de Waard
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
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Dungan JR, Qin X, Hurdle M, Haynes CS, Hauser ER, Kraus WE. Genome-Wide Variants Associated With Longitudinal Survival Outcomes Among Individuals With Coronary Artery Disease. Front Genet 2021; 12:661497. [PMID: 34140969 PMCID: PMC8204081 DOI: 10.3389/fgene.2021.661497] [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: 01/30/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022] Open
Abstract
Objective Coronary artery disease (CAD) is an age-associated condition that greatly increases the risk of mortality. The purpose of this study was to identify gene variants associated with all-cause mortality among individuals with clinically phenotyped CAD using a genome-wide screening approach. Approach and Results We performed discovery (n = 684), replication (n = 1,088), and meta-analyses (N = 1,503) for association of genomic variants with survival outcome using secondary data from White participants with CAD from two GWAS sub-studies of the Duke Catheterization Genetics Biorepository. We modeled time from catheterization to death or last follow-up (median 7.1 years, max 12 years) using Cox multivariable regression analysis. Target statistical screening thresholds were p × 10–8 for the discovery phase and Bonferroni-calculated p-values for the replication (p < 5.3 × 10–4) and meta-analysis (p < 1.6 × 10–3) phases. Genome-wide analysis of 785,945 autosomal SNPs revealed two SNPs (rs13007553 and rs587936) that had the same direction of effect across all three phases of the analysis, with suggestive p-value association in discovery and replication and significant meta-analysis association in models adjusted for clinical covariates. The rs13007553 SNP variant, LINC01250, which resides between MYTIL and EIPR1, conferred increased risk for all-cause mortality even after controlling for clinical covariates [HR 1.47, 95% CI 1.17–1.86, p(adj) = 1.07 × 10–3 (discovery), p(adj) = 0.03 (replication), p(adj) = 9.53 × 10–5 (meta-analysis)]. MYT1L is involved in neuronal differentiation. TSSC1 is involved in endosomal recycling and is implicated in breast cancer. The rs587936 variant annotated to DAB2IP was associated with increased survival time [HR 0.65, 95% CI 0.51–0.83, p(adj) = 4.79 × 10–4 (discovery), p(adj) = 0.02 (replication), p(adj) = 2.25 × 10–5 (meta-analysis)]. DAB2IP is a ras/GAP tumor suppressor gene which is highly expressed in vascular tissue. DAB2IP has multiple lines of evidence for protection against atherosclerosis. Conclusion Replicated findings identified two candidate genes for further study regarding association with survival in high-risk CAD patients: novel loci LINC01250 (rs13007553) and biologically relevant candidate DAB2IP (rs587936). These candidates did not overlap with validated longevity candidate genes. Future research could further define the role of common variants in survival outcomes for people with CAD and, ultimately, improve longitudinal outcomes for these patients.
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Affiliation(s)
- Jennifer R Dungan
- Division of Healthcare in Adult Populations, School of Nursing, Duke University, Durham, NC, United States
| | - Xue Qin
- School of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, NC, United States
| | - Melissa Hurdle
- School of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, NC, United States
| | - Carol S Haynes
- School of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, NC, United States
| | - Elizabeth R Hauser
- School of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, NC, United States.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States.,Cooperative Studies Program Epidemiology Center, Durham VA Medical Center, Durham, NC, United States
| | - William E Kraus
- School of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, NC, United States.,Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States
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Hu YJ, Schmidt AF, Dudbridge F, Holmes MV, Brophy JM, Tragante V, Li Z, Liao P, Quyyumi AA, McCubrey RO, Horne BD, Hingorani AD, Asselbergs FW, Patel R, Long Q. Impact of Selection Bias on Estimation of Subsequent Event Risk. CIRCULATION. CARDIOVASCULAR GENETICS 2017; 10:e001616. [PMID: 28986451 PMCID: PMC5659743 DOI: 10.1161/circgenetics.116.001616] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 07/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Studies of recurrent or subsequent disease events may be susceptible to bias caused by selection of subjects who both experience and survive the primary indexing event. Currently, the magnitude of any selection bias, particularly for subsequent time-to-event analysis in genetic association studies, is unknown. METHODS AND RESULTS We used empirically inspired simulation studies to explore the impact of selection bias on the marginal hazard ratio for risk of subsequent events among those with established coronary heart disease. The extent of selection bias was determined by the magnitudes of genetic and nongenetic effects on the indexing (first) coronary heart disease event. Unless the genetic hazard ratio was unrealistically large (>1.6 per allele) and assuming the sum of all nongenetic hazard ratios was <10, bias was usually <10% (downward toward the null). Despite the low bias, the probability that a confidence interval included the true effect decreased (undercoverage) with increasing sample size because of increasing precision. Importantly, false-positive rates were not affected by selection bias. CONCLUSIONS In most empirical settings, selection bias is expected to have a limited impact on genetic effect estimates of subsequent event risk. Nevertheless, because of undercoverage increasing with sample size, most confidence intervals will be over precise (not wide enough). When there is no effect modification by history of coronary heart disease, the false-positive rates of association tests will be close to nominal.
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Affiliation(s)
- Yi-Juan Hu
- Dept of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
| | - Amand F Schmidt
- Institute of Cardiovascular Science & The Farr Institute, University College London, UK
| | - Frank Dudbridge
- Dept of Non-communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine & Dept of Health Sciences, University of Leicester, UK
| | - Michael V Holmes
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, UK
- Medical Research Council Population Health Research Unit at the University of Oxford, UK
| | - James M Brophy
- Dept of Medicine, McGill University, Montreal Quebec, Canada
| | - Vinicius Tragante
- Dept of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ziyi Li
- Dept of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
| | - Peizhou Liao
- Dept of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
| | - Arshed A Quyyumi
- Division of Cardiology, Dept of Medicine, Emory Clinical Cardiovascular Research Institute, Emory University School of Medicine, Atlanta, GA
| | - Raymond O. McCubrey
- Intermountain Heart Institute, Intermountain Medical Center, University of Utah, Salt Lake City, UT
| | - Benjamin D. Horne
- Intermountain Heart Institute, Intermountain Medical Center, University of Utah, Salt Lake City, UT
- Dept of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Aroon D Hingorani
- Institute of Cardiovascular Science & The Farr Institute, University College London, UK
| | - Folkert W. Asselbergs
- Institute of Cardiovascular Science & The Farr Institute, University College London, UK
- Dept of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Riyaz Patel
- Institute of Cardiovascular Science & The Farr Institute, University College London, UK
| | - Qi Long
- Dept of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Dungan JR. Biases in Genetic Association of Coronary Heart Disease Events May Be Less Likely Than Suspected: Here Is When to Check for Them. CIRCULATION. CARDIOVASCULAR GENETICS 2017; 10:CIRCGENETICS.117.001912. [PMID: 28986456 DOI: 10.1161/circgenetics.117.001912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Jennifer R Dungan
- From the Healthcare in Adult Populations Division, Duke University School of Nursing, Durham, NC.
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Vanaveski T, Singh K, Narvik J, Eskla KL, Visnapuu T, Heinla I, Jayaram M, Innos J, Lilleväli K, Philips MA, Vasar E. Promoter-Specific Expression and Genomic Structure of IgLON Family Genes in Mouse. Front Neurosci 2017; 11:38. [PMID: 28210208 PMCID: PMC5288359 DOI: 10.3389/fnins.2017.00038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/19/2017] [Indexed: 01/20/2023] Open
Abstract
IgLON family is composed of five genes: Lsamp, Ntm, Opcml, Negr1, and Iglon5; encoding for five highly homologous neural adhesion proteins that regulate neurite outgrowth and synapse formation. In the current study we performed in silico analysis revealing that Ntm and Opcml display similar genomic structure as previously reported for Lsamp, characterized by two alternative promotors 1a and 1b. Negr1 and Iglon5 transcripts have uniform 5′ region, suggesting single promoter. Iglon5, the recently characterized family member, shares high level of conservation and structural qualities characteristic to IgLON family such as N-terminal signal peptide, three Ig domains, and GPI anchor binding site. By using custom 5′-isoform-specific TaqMan gene-expression assay, we demonstrated heterogeneous expression of IgLON transcripts in different areas of mouse brain and several-fold lower expression in selected tissues outside central nervous system. As an example, the expression of IgLON transcripts in urogenital and reproductive system is in line with repeated reports of urogenital tumors accompanied by mutations in IgLON genes. Considering the high levels of intra-family homology shared by IgLONs, we investigated potential compensatory effects at the level of IgLON isoforms in the brains of mice deficient of one or two family members. We found that the lack of IgLONs is not compensated by a systematic quantitative increase of the other family members. On the contrary, the expression of Ntm 1a transcript and NEGR1 protein was significantly reduced in the frontal cortex of Lsamp-deficient mice suggesting that the expression patterns within IgLON family are balanced coherently. The actions of individual IgLONs, however, can be antagonistic as demonstrated by differential expression of Syp in deletion mutants of IgLONs. In conclusion, we show that the genomic twin-promoter structure has impact on both anatomical distribution and intra-family interactions of IgLON family members. Remarkable variety in the activity levels of 1a and 1b promoters both in the brain and in other tissues, suggests complex functional regulation of IgLONs by alternative signal peptides driven by 1a and 1b promoters.
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Affiliation(s)
- Taavi Vanaveski
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Katyayani Singh
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Jane Narvik
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Kattri-Liis Eskla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Tanel Visnapuu
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of TartuTartu, Estonia; Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of HelsinkiHelsinki, Finland
| | - Indrek Heinla
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Mohan Jayaram
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Jürgen Innos
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Kersti Lilleväli
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu Tartu, Estonia
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