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Dueker ND, Beecham A, Wang L, Dong C, Sacco RL, Blanton SH, Rundek T. Rare variants in previously identified linkage regions associated with carotid plaque in Dominican Republic families. PLoS One 2022; 17:e0250799. [PMID: 35020748 PMCID: PMC8754284 DOI: 10.1371/journal.pone.0250799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/13/2021] [Indexed: 11/18/2022] Open
Abstract
Carotid plaque is a subclinical measure of atherosclerosis. We have previously shown measures of carotid plaque to be heritable in a sample of 100 Dominican families and found evidence for linkage and association of common variants (CVs) on 7q36, 11p15, 14q32 and 15q23 with plaque presence. Our current study aimed to refine these regions further and identify rare variants (RVs) influencing plaque presence. Therefore, we performed targeted sequencing of the one LOD unit down region on 7q36, 11p15, 14q32 and 15q23 in 12 Dominican families with evidence for linkage to plaque presence. Gene-based RV analyses were performed using the Sequence Association Test for familial data (F-SKAT) under two filtering algorithms; 1. all exonic RVs and 2. non-synonymous RVs. Replication analyses were performed using a sample of 22 Dominican families and 556 unrelated Dominicans with Exome Array data. To identify additional non-synonymous RVs influencing plaque, we looked for co-segregation of RVs with plaque in each of the sequenced families. Our most strongly associated gene with evidence for replication was AMPD3 which showed suggestive association with plaque presence in the sequenced families (exonic RV p = 0.003, nonsynonymous RV p = 0.005) and replication families (exonic RV p = 0.04, nonsynonymous RV p = 0.02). Examination of the sequenced family pedigrees revealed two missense variants on chromosome 11 which co-segregated with plaque presence in one of our families; rs61751342 (located in DENND2B), and rs61760882 (located in RNF141). The rs61751342 missense variant is an eQTL for SCUBE2 in the atrial appendage. Notably, SCUBE2 encodes a protein which interacts with vascular endothelial growth factor (VEGF) receptor 2 to regulate VEGF-induced angiogenesis, thus providing biologic plausibility for this gene in atherosclerosis. In conclusion, using targeted sequencing of previously-identified linkage regions, we have identified suggestive evidence for the role of RVs in carotid plaque pathogenesis.
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MESH Headings
- AMP Deaminase/genetics
- Adaptor Proteins, Signal Transducing/genetics
- Adult
- Aged
- Calcium-Binding Proteins/genetics
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 7/genetics
- DNA-Binding Proteins/genetics
- Dominican Republic
- Genetic Linkage
- Genotype
- Humans
- Middle Aged
- Pedigree
- Plaque, Atherosclerotic/genetics
- Plaque, Atherosclerotic/pathology
- Polymorphism, Genetic
- Quantitative Trait Loci
- Transcription Factors/genetics
- Tumor Suppressor Proteins/genetics
- Vascular Endothelial Growth Factor Receptor-2/genetics
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Affiliation(s)
- Nicole D. Dueker
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States of America
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States of America
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States of America
| | - Chuanhui Dong
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Ralph L. Sacco
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States of America
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Evelyn F. McKnight Brain Institute, Department of Neurology, University of Miami, Miami, FL, United States of America
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States of America
| | - Tatjana Rundek
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Evelyn F. McKnight Brain Institute, Department of Neurology, University of Miami, Miami, FL, United States of America
- * E-mail:
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Wojczynski MK, Lin SJ, Sebastiani P, Perls TT, Lee J, Kulminski A, Newman A, Zmuda JM, Christensen K, Province MA. NIA Long Life Family Study: Objectives, Design, and Heritability of Cross Sectional and Longitudinal Phenotypes. J Gerontol A Biol Sci Med Sci 2021; 77:717-727. [PMID: 34739053 PMCID: PMC8974329 DOI: 10.1093/gerona/glab333] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
The NIA Long Life Family Study (LLFS) is a longitudinal, multicenter, multinational, population-based multigenerational family study of the genetic and nongenetic determinants of exceptional longevity and healthy aging. The Visit 1 in-person evaluation (2006–2009) recruited 4 953 individuals from 539 two-generation families, selected from the upper 1% tail of the Family Longevity Selection Score (FLoSS, which quantifies the degree of familial clustering of longevity). Demographic, anthropometric, cognitive, activities of daily living, ankle-brachial index, blood pressure, physical performance, and pulmonary function, along with serum, plasma, lymphocytes, red cells, and DNA, were collected. A Genome Wide Association Scan (GWAS) (Ilumina Omni 2.5M chip) followed by imputation was conducted. Visit 2 (2014–2017) repeated all Visit 1 protocols and added carotid ultrasonography of atherosclerotic plaque and wall thickness, additional cognitive testing, and perceived fatigability. On average, LLFS families show healthier aging profiles than reference populations, such as the Framingham Heart Study, at all age/sex groups, for many critical healthy aging phenotypes. However, participants are not uniformly protected. There is considerable heterogeneity among the pedigrees, with some showing exceptional cognition, others showing exceptional grip strength, others exceptional pulmonary function, etc. with little overlap in these families. There is strong heritability for key healthy aging phenotypes, both cross-sectionally and longitudinally, suggesting that at least some of this protection may be genetic. Little of the variance in these heritable phenotypes is explained by the common genome (GWAS + Imputation), which may indicate that rare protective variants for specific phenotypes may be running in selected families.
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Affiliation(s)
- Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Shiow Jiuan Lin
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Thomas T Perls
- Department of Medicine, Geriatrics Section, Boston Medical Center, Boston University School of Medicine, MA, USA
| | - Joseph Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA
| | - Anne Newman
- Departments of Epidemiology and Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Joe M Zmuda
- Departments of Epidemiology and Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, Southern Denmark University, Odense, Denmark
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
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Yudkovicz JJ, Minster RL, Barinas-Mitchell E, Christensen K, Feitosa M, Barker MS, Newman AB, Kuipers AL. Pleiotropic effects between cardiovascular disease risk factors and measures of cognitive and physical function in long-lived adults. Sci Rep 2021; 11:17980. [PMID: 34504188 PMCID: PMC8429644 DOI: 10.1038/s41598-021-97298-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Cardiovacular disease (CVD) is the leading cause of death among older adults and is often accompanied by functional decline. It is unclear what is driving this co-occurrence, but it may be behavioral, environmental and/or genetic. We used a family-based study to estimate the phenotypic and shared genetic correlation between CVD risk factors and physical and cognitive functional measures. Participants (n = 1,881) were from the Long Life Family Study, which enrolled families based on their exceptional longevity (sample mean age = 69.4 years, 44% female). Cardiovascular disease risk factors included carotid vessel measures [intima-media thickness and inter-adventitial diameter], obesity [body mass index (BMI) and waist circumference], and hypertension [systolic and diastolic blood pressures]. Function was measured in the physical [gait speed, grip strength, chair stand] and cognitive [digital symbol substitution test, retained and working memory, semantic fluency, and trail making tests] domains. We used SOLAR to estimate the genetic, environmental, and phenotypic correlation between each pair adjusting for age, age2, sex, field center, smoking, height, and weight. There were significant phenotypic correlations (range |0.05–0.22|) between CVD risk factors and physical and cognitive function (all P < 0.05). Most significant genetic correlations (range |0.21–0.62|) were between CVD risk factorsand cognitive function, although BMI and waist circumference had significant genetic correlation with gait speed and chair stand time (range |0.29–0.53|; all P < 0.05). These results suggest that CVD risk factors may share a common genetic-and thus, biologic-basis with both cognitive and physical function. This is particularly informative for research into the genetic determinants of chronic disease.
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Affiliation(s)
- Julia J Yudkovicz
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Kaare Christensen
- Department of Epidemiology, Biostatistics and Biodemography, Danish Aging Research Center, University of Southern Denmark, Odense C, Denmark
| | - Mary Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan S Barker
- Department of Neurology, Columbia University, New York, NY, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Allison L Kuipers
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA.
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Binder CJ, Borén J, Catapano AL, Dallinga-Thie G, Kronenberg F, Mallat Z, Negrini S, Raggi P, von Eckardstein A. The year 2019 in Atherosclerosis. Atherosclerosis 2020; 299:67-75. [PMID: 32248950 DOI: 10.1016/j.atherosclerosis.2020.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Christoph J Binder
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Jan Borén
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alberico L Catapano
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy; IRCCS Multimedica Hospital, Milan, Italy
| | - Geesje Dallinga-Thie
- Department of Vascular Medicine, Amsterdam University Medical Centers, AMC, Amsterdam, the Netherlands
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Austria
| | - Ziad Mallat
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom; University of Paris, PARCC, INSERM, Paris, France
| | - Simona Negrini
- Institute of Clinical Chemistry, University of Zurich, University Hospital of Zurich, Zurich, Switzerland
| | - Paolo Raggi
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada; Department of Medicine, University of Alberta, Edmonton, AB, Canada; Division of Cardiology, University of Alberta, Edmonton, AB, Canada
| | - Arnold von Eckardstein
- Institute of Clinical Chemistry, University of Zurich, University Hospital of Zurich, Zurich, Switzerland.
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