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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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Feng J, Jiang W, Cheng X, Zou B, Varley AW, Liu T, Qian G, Zeng W, Tang J, Zhao Q, Chu Y, Wei Y, Li X, Munford RS, Lu M. A host lipase prevents lipopolysaccharide-induced foam cell formation. iScience 2021; 24:103004. [PMID: 34522852 PMCID: PMC8426562 DOI: 10.1016/j.isci.2021.103004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 08/15/2021] [Indexed: 01/04/2023] Open
Abstract
Although microbe-associated molecular pattern (MAMP) molecules can promote cholesterol accumulation in macrophages, the existence of a host-derived MAMP inactivation mechanism that prevents foam cell formation has not been described. Here, we tested the ability of acyloxyacyl hydrolase (AOAH), the host lipase that inactivates gram-negative bacterial lipopolysaccharides (LPSs), to prevent foam cell formation in mice. Following exposure to small intraperitoneal dose(s) of LPSs, Aoah -/- macrophages produced more low-density lipoprotein receptor and less apolipoprotein E and accumulated more cholesterol than did Aoah +/+ macrophages. The Aoah -/- macrophages also maintained several pro-inflammatory features. Using a perivascular collar placement model, we found that Aoah -/- mice developed more carotid artery foam cells than did Aoah +/+ mice after they had been fed a high fat, high cholesterol diet, and received small doses of LPSs. This is the first demonstration that an enzyme that inactivates a stimulatory MAMP in vivo can reduce cholesterol accumulation and inflammation in arterial macrophages.
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Affiliation(s)
- Jintao Feng
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Jiang
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Trauma-Emergency & Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200040, China
| | - Xiaofang Cheng
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Benkun Zou
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Alan W. Varley
- Department of Internal Medicine, UT-Southwestern Medical Center at Dallas, Texas 75390, USA
| | - Ting Liu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Guojun Qian
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenjiao Zeng
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianguo Tang
- Department of Trauma-Emergency & Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200040, China
| | - Qiang Zhao
- Department of Cardiac Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Yiwei Chu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuanyuan Wei
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaobo Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Robert S. Munford
- Antibacterial Host Defense Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mingfang Lu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Trauma-Emergency & Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200040, China
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Targeted sequencing of linkage region in Dominican families implicates PRIMA1 and the SPATA7-PTPN21-ZC3H14-EML5-TTC8 locus in carotid-intima media thickness and atherosclerotic events. Sci Rep 2019; 9:11621. [PMID: 31406157 PMCID: PMC6691113 DOI: 10.1038/s41598-019-48186-1] [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: 09/25/2018] [Accepted: 07/29/2019] [Indexed: 11/22/2022] Open
Abstract
Carotid intima-media thickness (cIMT) is a subclinical marker for atherosclerosis. Previously, we reported a quantitative trait locus (QTL) for total cIMT on chromosome 14q and identified PRiMA1, FOXN3 and CCDC88C as candidate genes using a common variants (CVs)-based approach. Herein, we further evaluated the genetic contribution of the QTL to cIMT by resequencing. We sequenced all exons within the QTL and genomic regions of PRiMA1, FOXN3 and CCDC88C in Dominican families with evidence for linkage to the QTL. Unrelated Dominicans from the Northern Manhattan Study (NOMAS) were used for validation. Single-variant-based and gene-based analyses were performed for CVs and rare variants (RVs). The strongest evidence for association with CVs was found in PRiMA1 (p = 8.2 × 10−5 in families, p = 0.01 in NOMAS at rs12587586), and in the five-gene cluster SPATA7-PTPN21-ZC3H14-EML5-TTC8 locus (p = 1.3 × 10−4 in families, p = 0.01 in NOMAS at rs2274736). No evidence for association with RVs was found in PRiMA1. The top marker from previous study in PRiMA1 (rs7152362) was associated with fewer atherosclerotic events (OR = 0.67; p = 0.02 in NOMAS) and smaller cIMT (β = −0.58, p = 2.8 × 10−4 in Family). Within the five-gene cluster, evidence for association was found for exonic RVs (p = 0.02 in families, p = 0.28 in NOMAS), which was enriched among RVs with higher functional potentials (p = 0.05 in NOMAS for RVs in the top functional tertile). In summary, targeted resequencing provided validation and novel insights into the genetic architecture of cIMT, suggesting stronger effects for RVs with higher functional potentials. Furthermore, our data support the clinical relevance of CVs associated with subclinical atherosclerosis.
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Dueker ND, Guo S, Beecham A, Wang L, Blanton SH, Di Tullio MR, Rundek T, Sacco RL. Sequencing of Linkage Region on Chromosome 12p11 Identifies PKP2 as a Candidate Gene for Left Ventricular Mass in Dominican Families. G3 (BETHESDA, MD.) 2018; 8:659-668. [PMID: 29288195 PMCID: PMC5919734 DOI: 10.1534/g3.117.300358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/10/2017] [Indexed: 12/16/2022]
Abstract
Increased left ventricular mass (LVM) is an intermediate phenotype for cardiovascular disease (CVD) and a predictor of stroke. Using families from the Dominican Republic, we have previously shown LVM to be heritable and found evidence for linkage to chromosome 12p11. Our current study aimed to further characterize the QTL by sequencing the 1 LOD unit down region in 10 families from the Dominican Republic with evidence for linkage to LVM. Within this region, we tested 5477 common variants [CVs; minor allele frequency (MAF) ≥5%] using the Quantitative Transmission-Disequilibrium Test (QTDT). Gene-based analyses were performed to test rare variants (RVs; MAF < 5%) in 181 genes using the family-based sequence kernel association test. A sample of 618 unrelated Dominicans from the Northern Manhattan Study (NOMAS) and 12 Dominican families with Exome Array data were used for replication analyses. The most strongly associated CV with evidence for replication was rs1046116 (Discovery families P = 9.0 × 10-4; NOMAS P = 0.03; replication families P = 0.46), a missense variant in PKP2 In nonsynonymous RV analyses, PKP2 was one of the most strongly associated genes (P = 0.05) with suggestive evidence for replication in NOMAS (P = 0.05). PKP2 encodes the plakophilin 2 protein and is a desmosomal gene implicated in arrythmogenic right ventricular cardiomyopathy and recently in arrhythmogenic left ventricular cardiomyopathy, which makes PKP2 an excellent candidate gene for LVM. In conclusion, sequencing of our previously reported QTL identified common and rare variants within PKP2 to be associated with LVM. Future studies are necessary to elucidate the role these variants play in influencing LVM.
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Affiliation(s)
- Nicole D Dueker
- John P. Hussman Institute for Human Genomics, University of Miami, Florida 33136
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami, Florida 33136
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Florida 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Florida 33136
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Florida 33136
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami, Florida 33136
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Florida 33136
| | - Marco R Di Tullio
- Department of Medicine, Columbia University, New York, New York 10032
| | - Tatjana Rundek
- Department of Neurology, Miller School of Medicine, University of Miami, Florida 33136
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Florida 33136
| | - Ralph L Sacco
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Florida 33136
- Department of Neurology, Miller School of Medicine, University of Miami, Florida 33136
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Florida 33136
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Dueker ND, Beecham A, Wang L, Blanton SH, Guo S, Rundek T, Sacco RL. Rare Variants in NOD1 Associated with Carotid Bifurcation Intima-Media Thickness in Dominican Republic Families. PLoS One 2016; 11:e0167202. [PMID: 27936005 PMCID: PMC5147882 DOI: 10.1371/journal.pone.0167202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 11/10/2016] [Indexed: 12/19/2022] Open
Abstract
Cardiovascular disorders including ischemic stroke (IS) and myocardial infarction (MI) are heritable; however, few replicated loci have been identified. One strategy to identify loci influencing these complex disorders is to study subclinical phenotypes, such as carotid bifurcation intima-media thickness (bIMT). We have previously shown bIMT to be heritable and found evidence for linkage and association with common variants on chromosome 7p for bIMT. In this study, we aimed to characterize contributions of rare variants (RVs) in 7p to bIMT. To achieve this aim, we sequenced the 1 LOD unit down region on 7p in nine extended families from the Dominican Republic (DR) with strong evidence for linkage to bIMT. We then performed the family-based sequence kernel association test (famSKAT) on genes within the 7p region. Analyses were restricted to single nucleotide variants (SNVs) with population based minor allele frequency (MAF) <5%. We first analyzed all exonic RVs and then the subset of only non-synonymous RVs. There were 68 genes in our analyses. Nucleotide-binding oligomerization domain (NOD1) was the most significantly associated gene when analyzing exonic RVs (famSKAT p = 9.2x10-4; number of SNVs = 14). We achieved suggestive replication of NOD1 in an independent sample of twelve extended families from the DR (p = 0.055). Our study provides suggestive statistical evidence for a role of rare variants in NOD1 in bIMT. Studies in mice have shown Nod1 to play a role in heart function and atherosclerosis, providing biologic plausibility for a role in bIMT thus making NOD1 an excellent bIMT candidate.
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Affiliation(s)
- Nicole D. Dueker
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States of America
| | - Tatjana Rundek
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Ralph L. Sacco
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, United States of America
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
- * E-mail:
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