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Weng LC, Guan W, Steffen LM, Pankow JS, Pankratz N, Chen MH, Cushman M, Basu S, Folsom AR, Tang W. Pleiotropic effects of n-6 and n-3 fatty acid-related genetic variants on circulating hemostatic variables. Thromb Res 2018; 168:53-59. [PMID: 29902632 PMCID: PMC6089352 DOI: 10.1016/j.thromres.2018.05.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/15/2018] [Accepted: 05/30/2018] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Data from epidemiological studies and clinical trials suggest an influence of dietary and circulating polyunsaturated fatty acids (PUFAs) on the hemostasis profile. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) related to plasma PUFAs levels. We aimed to investigate whether the SNPs related to plasma PUFAs levels were also associated with plasma levels of hemostatic variables. MATERIALS AND METHODS We tested the associations between 9 PUFA-related SNPs and 6 hemostatic variables in 9035 European Americans (EAs) and 2702 African Americans (AAs) in the Atherosclerosis Risk in Communities (ARIC) Study. We then conducted a replication study by looking-up our novel observed associations in three published GWAS for hemostatic factors in different EA populations. RESULTS We observed a novel linoleic acid-related locus at the JMJD1C region associated with factor VII activity (FVIIc): rs10740118 and rs1935, Beta (p) = -1.31 (1 × 10-3) and 1.37 (5 × 10-4) in EAs, respectively, and - 1.24 (5 × 10-4) and 1.28 (3 × 10-4) in meta-analysis of EAs and AAs of ARIC. This novel association was replicated in two of three independent EA populations (p = 0.01 and 0.03 in meta-analyses). We confirmed previously reported associations at the docosapentaenoic acid-related GCKR locus with protein C and FVIIc and at JMJD1C with fibrinogen. Adjustment for plasma PUFAs did not abolish the associations between these loci and hemostatic variables. CONCLUSIONS Our study identified a novel association for FVIIc at JMJD1C, a histone demethylase that plays a role in DNA repair and possibly transcription regulation and RNA processing.
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Affiliation(s)
- Lu-Chen Weng
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, WBOB 300, Minneapolis, MN 55454, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455, USA
| | - Lyn M Steffen
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, WBOB 300, Minneapolis, MN 55454, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, WBOB 300, Minneapolis, MN 55454, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Mayo Mail Code 609, 420 Delaware Street S.E., Minneapolis, MN 55455, USA
| | - Ming-Huei Chen
- National Heart, Lung and Blood Institute's The Framingham Heart Study, Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont, Colchester Research Facility, 360 South Park Dr., Colchester, VT 05446, USA
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455, USA
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, WBOB 300, Minneapolis, MN 55454, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, WBOB 300, Minneapolis, MN 55454, USA.
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Nolte IM, van der Most PJ, Alizadeh BZ, de Bakker PI, Boezen HM, Bruinenberg M, Franke L, van der Harst P, Navis G, Postma DS, Rots MG, Stolk RP, Swertz MA, Wolffenbuttel BH, Wijmenga C, Snieder H. Missing heritability: is the gap closing? An analysis of 32 complex traits in the Lifelines Cohort Study. Eur J Hum Genet 2017; 25:877-885. [PMID: 28401901 DOI: 10.1038/ejhg.2017.50] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 02/03/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023] Open
Abstract
Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is closing, we first identified genome-wide significant SNPs from the literature and performed replication analyses for 32 highly relevant traits from five broad disease areas in 13 436 subjects of the Lifelines Cohort. Next, we calculated the variance explained by multi-SNP genetic risk scores (GRSs) for each trait, and compared it to their broad- and narrow-sense heritabilities captured by all common SNPs. The majority of all previously-associated SNPs (median=75%) were significantly associated with their respective traits. All GRSs were significant, with unweighted GRSs generally explaining less phenotypic variance than weighted GRSs, for which the explained variance was highest for height (15.5%) and varied between 0.02 and 6.7% for the other traits. Broad-sense common-SNP heritability estimates were significant for all traits, with the additive effect of common SNPs explaining 48.9% of the variance for height and between 5.6 and 39.2% for the other traits. Dominance effects were uniformly small (0-1.5%) and not significant. On average, the variance explained by the weighted GRSs accounted for only 10.7% of the common-SNP heritability of the 32 traits. These results indicate that GRSs may not yet be ready for accurate personalized prediction of complex disease traits limiting widespread adoption in clinical practice.
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Affiliation(s)
- Ilja M Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter J van der Most
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Behrooz Z Alizadeh
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Paul Iw de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H Marike Boezen
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerjan Navis
- Department of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirkje S Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald P Stolk
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bruce Hr Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Flister MJ, Hoffman MJ, Lemke A, Prisco SZ, Rudemiller N, O'Meara CC, Tsaih SW, Moreno C, Geurts AM, Lazar J, Adhikari N, Hall JL, Jacob HJ. SH2B3 Is a Genetic Determinant of Cardiac Inflammation and Fibrosis. ACTA ACUST UNITED AC 2015; 8:294-304. [PMID: 25628389 DOI: 10.1161/circgenetics.114.000527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/14/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND Genome-wide association studies are powerful tools for nominating pathogenic variants, but offer little insight as to how candidate genes affect disease outcome. Such is the case for SH2B adaptor protein 3 (SH2B3), which is a negative regulator of multiple cytokine signaling pathways and is associated with increased risk of myocardial infarction (MI), but its role in post-MI inflammation and fibrosis is completely unknown. METHODS AND RESULTS Using an experimental model of MI (left anterior descending artery occlusion/reperfusion injury) in wild-type and Sh2b3 knockout rats (Sh2b3(em2Mcwi)), we assessed the role of Sh2b3 in post-MI fibrosis, leukocyte infiltration, angiogenesis, left ventricle contractility, and inflammatory gene expression. Compared with wild-type, Sh2b3(em2Mcwi) rats had significantly increased fibrosis (2.2-fold; P<0.05) and elevated leukocyte infiltration (>2-fold; P<0.05), which coincided with decreased left ventricle fractional shortening (-Δ11%; P<0.05) at 7 days post left anterior descending artery occlusion/reperfusion injury. Despite an increased angiogenic potential in Sh2b3(em2Mcwi) rats (1.7-fold; P<0.05), we observed no significant differences in left ventricle capillary density between wild-type and Sh2b3(em2Mcwi) rats. In total, 12 genes were significantly elevated in the post left anterior descending artery occluded/reperfused hearts of Sh2b3(em2Mcwi) rats relative to wild-type, of which 3 (NLRP12, CCR2, and IFNγ) were significantly elevated in the left ventricle of heart failure patients carrying the MI-associated rs3184504 [T] SH2B3 risk allele. CONCLUSIONS These data demonstrate for the first time that SH2B3 is a crucial mediator of post-MI inflammation and fibrosis.
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Affiliation(s)
- Michael J Flister
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Matthew J Hoffman
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Angela Lemke
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Sasha Z Prisco
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Nathan Rudemiller
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Caitlin C O'Meara
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Shirng-Wern Tsaih
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Carol Moreno
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Aron M Geurts
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Jozef Lazar
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Neeta Adhikari
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Jennifer L Hall
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.)
| | - Howard J Jacob
- From the Human and Molecular Genetics Center (M.J.F., M.J.H., A.L., S.Z.P., S.-W.T., A.M.G., J.L., H.J.J.), Departments of Physiology (M.J.F., M.J.H., A.L., S.Z.P., N.R., A.M.G., H.J.J.), Dermatology (J.L.), and Pediatrics (H.J.J.), Medical College of Wisconsin, Milwaukee; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (C.C.O'M.); Department of Cardiovascular and Metabolic Disease at MedImmune, Cambridge, United Kingdom (C.M.); and Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis (N.A., J.L.H.).
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