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Huang K, Ma T, Li Q, Zhong Z, Zhou Y, Zhang W, Qin T, Tang S, Zhong J, Lu S. CYP4V2 rs56413992 C > T was associated with the risk of coronary heart disease in the Chinese Han population: a case-control study. BMC Med Genomics 2023; 16:322. [PMID: 38066650 PMCID: PMC10709878 DOI: 10.1186/s12920-023-01737-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/12/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE The research aimed to detect the association between single nucleotide polymorphisms (SNPs) in CYP4V2 gene and coronary heart disease (CHD) risk. METHODS This case-control study included 487 CHD subjects and 487 healthy individuals. Logistic regression was performed to analyze the connection between five SNPs in CYP4V2 (rs1398007, rs13146272, rs3736455, rs1053094, and rs56413992) and CHD risk, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to evaluate the connection. RESULTS As a result, we found that rs56413992 T allele (OR = 1.36, 95% CI = 1.09-1.70, p = 0.007) and CT genotype (OR = 1.40, 95% CI = 1.06-1.83, p = 0.017) were significantly associated with an increased risk of CHD in the overall analysis. Precisely, rs56413992 was linked to an elevated risk of CHD in people aged > 60, males, smokers and drinkers. The study also indicated that rs1398007 was linked to an increased CHD risk in drinkers. In addition, rs1053094 was correlated with a decreased risk of CHD complicated with diabetes mellitus (DM), and rs1398007 was correlated with a decreased risk of CHD complicated with hypertension (HTN). CONCLUSION This study was the first to experimentally demonstrate that CYP4V2 rs56413992 was associated with the risk of CHD, which will provide a certain reference for revealing the pathogenesis of CHD.
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Affiliation(s)
- Kang Huang
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Tianyi Ma
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Qiang Li
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Zanrui Zhong
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Yilei Zhou
- School of Medicine, Jingchu University of Technology, Jingmen, Hubei, China
| | - Wei Zhang
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Ting Qin
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Shilin Tang
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China
| | - Jianghua Zhong
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China.
| | - Shijuan Lu
- Department of Cardiology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No. 43, Renmin Avenue, Haikou, Hainan, China.
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2
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Jaago M, Pupina N, Rähni A, Pihlak A, Sadam H, Vrana NE, Sinisalo J, Pussinen P, Palm K. Antibody response to oral biofilm is a biomarker for acute coronary syndrome in periodontal disease. Commun Biol 2022; 5:205. [PMID: 35246599 PMCID: PMC8897497 DOI: 10.1038/s42003-022-03122-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Cumulative evidence over the last decades have supported the role of gum infections as a risk for future major cardiovascular events. The precise mechanism connecting coronary artery disease (CAD) with periodontal findings has remained elusive. Here, we employ next generation phage display mimotope-variation analysis (MVA) to identify the features of dysfunctional immune system that associate CAD with periodontitis. We identify a fine molecular description of the antigenic epitope repertoires of CAD and its most severe form - acute coronary syndrome (ACS) by profiling the antibody reactivity in a patient cohort with invasive heart examination and complete clinical oral assessment. Specifically, we identify a strong immune response to an EBV VP26 epitope mimicking multiple antigens of oral biofilm as a biomarker for the no-CAD group. With a 2-step biomarker test, we stratify subjects with periodontitis from healthy controls (balanced accuracy 84%), and then assess the risk for ACS with sensitivity 71-89% and specificity 67-100%, depending on the oral health status. Our findings highlight the importance of resolving the immune mechanisms related to severe heart conditions such as ACS in the background of oral health. Prospective validation of these findings will support incorporation of these non-invasive biomarkers into clinical practice.
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Affiliation(s)
- Mariliis Jaago
- Protobios Llc, Mäealuse 4, 12618, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | | | - Annika Rähni
- Protobios Llc, Mäealuse 4, 12618, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Arno Pihlak
- Protobios Llc, Mäealuse 4, 12618, Tallinn, Estonia
| | - Helle Sadam
- Protobios Llc, Mäealuse 4, 12618, Tallinn, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Nihal Engin Vrana
- Spartha Medical, 14B Rue de la Canardiere, 67100, Strasbourg, France
| | - Juha Sinisalo
- Heart and Lung Center, Helsinki University Hospital, and Helsinki University, Helsinki, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, University of Helsinki, FI-00014, Helsinki, Finland
| | - Kaia Palm
- Protobios Llc, Mäealuse 4, 12618, Tallinn, Estonia. .,Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
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3
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Zhang H, Shen LY, Xu ZC, Kramer LM, Yu JQ, Zhang XY, Na W, Yang LL, Cao ZP, Luan P, Reecy JM, Li H. Haplotype-based genome-wide association studies for carcass and growth traits in chicken. Poult Sci 2020; 99:2349-2361. [PMID: 32359570 PMCID: PMC7597553 DOI: 10.1016/j.psj.2020.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
There have been several genome-wide association study (GWAS) reported for carcass, growth, and meat traits in chickens. Most of these studies have been based on single SNPs GWAS. In contrast, haplotype-based GWAS reports have been limited. In the present study, 2 Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) and genotyped with the chicken 60K SNP chip were used to perform a haplotype-based GWAS. The lean and fat chicken lines were selected for abdominal fat content for 11 yr. Abdominal fat weight was significantly different between the 2 lines; however, there was no difference for body weight between the lean and fat lines. A total of 132 haplotype windows were significantly associated with abdominal fat weight. These significantly associated haplotype windows were primarily located on chromosomes 2, 4, 8, 10, and 26. Seven candidate genes, including SHH, LMBR1, FGF7, IL16, PLIN1, IGF1R, and SLC16A1, were located within these associated regions. These genes may play important roles in the control of abdominal fat content. Two regions on chromosomes 3 and 10 were significantly associated with testis weight. These 2 regions were previously detected by the single SNP GWAS using this same resource population. TCF21 on chromosome 3 was identified as a potentially important candidate gene for testis growth and development based on gene expression analysis and the reported function of this gene. TCF12, which was previously detected in our SNP by SNP interaction analysis, was located in a region on chromosome 10 that was significantly associated with testis weight. Six candidate genes, including TNFRSF1B, PLOD1, NPPC, MTHFR, EPHB2, and SLC35A3, on chromosome 21 may play important roles in bone development based on the known function of these genes. In addition, several regions were significantly associated with other carcass and growth traits, but no candidate genes were identified. The results of the present study may be helpful in understanding the genetic mechanisms of carcass and growth traits in chickens.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Lin-Yong Shen
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Zi-Chun Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Luke M Kramer
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jia-Qiang Yu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Xin-Yang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Li-Li Yang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhi-Ping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
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4
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Intestinal Alkaline Phosphatase Deficiency Is Associated with Ischemic Heart Disease. DISEASE MARKERS 2019; 2019:8473565. [PMID: 31915470 PMCID: PMC6930721 DOI: 10.1155/2019/8473565] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/20/2019] [Accepted: 11/30/2019] [Indexed: 12/15/2022]
Abstract
Background We have previously shown that the deficiency of the gut enzyme intestinal alkaline phosphatase (IAP) is associated with type 2 diabetes mellitus (T2DM) in humans, and mice deficient in IAP develop the metabolic syndrome, a precipitant of T2DM and ischemic heart disease (IHD). We hypothesized that IAP deficiency might also be associated with IHD in humans. We aimed to determine the correlation between the IAP level and IHD in humans. Methods and Results The IHD patients were recruited from the National Institute of Cardiovascular Diseases (NICVD), Dhaka, Bangladesh, and the control healthy participants were recruited from a suburban community of Dhaka. We determined the IAP level in the stools of 292 IHD patients (187 males, 105 females) and 331 healthy control people (84 males, 247 females). We found that compared to controls, IHD patients have approx. 30% less IAP (mean ± SEM: 63.7 ± 3.5 vs. 44.9 ± 2.1 U/g stool, respectively; p < 0.000001), which indicates that IAP deficiency is associated with IHD, and a high level of IAP is probably protective against IHD in humans. The adjusted generalized linear model (GLM) of regression analysis predicted a strong association of IAP with IHD (p = 0.0035). Multiple logistic regression analysis showed an independent inverse relationship between the IAP level and the IHD status (odds ratio, OR = 0.993 with 95% CI 0.987-0.998; p < 0.01). Conclusions IAP deficiency is associated with IHD, and a high level of IAP might be protective against IHD.
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5
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Nanda V, Wang T, Pjanic M, Liu B, Nguyen T, Matic LP, Hedin U, Koplev S, Ma L, Franzén O, Ruusalepp A, Schadt EE, Björkegren JLM, Montgomery SB, Snyder MP, Quertermous T, Leeper NJ, Miller CL. Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus. PLoS Genet 2018; 14:e1007755. [PMID: 30444878 PMCID: PMC6268002 DOI: 10.1371/journal.pgen.1007755] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 11/30/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022] Open
Abstract
Recent genome-wide association studies (GWAS) have identified multiple new loci which appear to alter coronary artery disease (CAD) risk via arterial wall-specific mechanisms. One of the annotated genes encodes LMOD1 (Leiomodin 1), a member of the actin filament nucleator family that is highly enriched in smooth muscle-containing tissues such as the artery wall. However, it is still unknown whether LMOD1 is the causal gene at this locus and also how the associated variants alter LMOD1 expression/function and CAD risk. Using epigenomic profiling we recently identified a non-coding regulatory variant, rs34091558, which is in tight linkage disequilibrium (LD) with the lead CAD GWAS variant, rs2820315. Herein we demonstrate through expression quantitative trait loci (eQTL) and statistical fine-mapping in GTEx, STARNET, and human coronary artery smooth muscle cell (HCASMC) datasets, rs34091558 is the top regulatory variant for LMOD1 in vascular tissues. Position weight matrix (PWM) analyses identify the protective allele rs34091558-TA to form a conserved Forkhead box O3 (FOXO3) binding motif, which is disrupted by the risk allele rs34091558-A. FOXO3 chromatin immunoprecipitation and reporter assays show reduced FOXO3 binding and LMOD1 transcriptional activity by the risk allele, consistent with effects of FOXO3 downregulation on LMOD1. LMOD1 knockdown results in increased proliferation and migration and decreased cell contraction in HCASMC, and immunostaining in atherosclerotic lesions in the SMC lineage tracing reporter mouse support a key role for LMOD1 in maintaining the differentiated SMC phenotype. These results provide compelling functional evidence that genetic variation is associated with dysregulated LMOD1 expression/function in SMCs, together contributing to the heritable risk for CAD.
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Affiliation(s)
- Vivek Nanda
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ting Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Milos Pjanic
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Boxiang Liu
- Department of Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Simon Koplev
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Clinical Gene Networks AB, Stockholm, Sweden
| | - Arno Ruusalepp
- Clinical Gene Networks AB, Stockholm, Sweden
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Johan L. M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Department of Medical Biochemistry and Biophysics, Vascular Biology Unit, Karolinska Institutet, Stockholm, Sweden
- Department of Physiology, Institute of Biomedicine and Translation Medicine, University of Tartu, Tartu, Estonia
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Michael P. Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicholas J. Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Clint L. Miller
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Center for Public Health Genomics, Department of Public Health Sciences, Department of Biochemistry and Molecular Genetics, and Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
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6
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Miller CL, Leeper NJ. Genome-Wide Association Studies Candidate Gene to Dual Modifier of Nonalcoholic Steatohepatitis and Atherosclerosis. JACC Basic Transl Sci 2017; 1:680-683. [PMID: 28603781 PMCID: PMC5465816 DOI: 10.1016/j.jacbts.2016.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nonalcoholic steatohepatitis is a common disease involving chronic accumulation of fat and inflammation in the liver, often leading to advanced fibrosis, cirrhosis, and cancer. It is known that nonalcoholic steatohepatitis shares many features with atherosclerosis; however, there are still no effective therapeutics. In a recent study published in Nature, investigators demonstrated that mice lacking a high-density lipoprotein–associated gene were surprisingly protected from both steatohepatitis and atherosclerosis through the stabilization of the liver X receptor. This work reveals a timely candidate target for 2 highly prevalent cardiovascular diseases.
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Affiliation(s)
- Clint L Miller
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Nicholas J Leeper
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305.,Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305
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7
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Dennis J, Medina-Rivera A, Truong V, Antounians L, Zwingerman N, Carrasco G, Strug L, Wells P, Trégouët DA, Morange PE, Wilson MD, Gagnon F. Leveraging cell type specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels. Genet Epidemiol 2017; 41:455-466. [PMID: 28421636 DOI: 10.1002/gepi.22049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 03/07/2017] [Accepted: 03/14/2017] [Indexed: 11/10/2022]
Abstract
Tissue factor pathway inhibitor (TFPI) regulates the formation of intravascular blood clots, which manifest clinically as ischemic heart disease, ischemic stroke, and venous thromboembolism (VTE). TFPI plasma levels are heritable, but the genetics underlying TFPI plasma level variability are poorly understood. Herein we report the first genome-wide association scan (GWAS) of TFPI plasma levels, conducted in 251 individuals from five extended French-Canadian Families ascertained on VTE. To improve discovery, we also applied a hypothesis-driven (HD) GWAS approach that prioritized single nucleotide polymorphisms (SNPs) in (1) hemostasis pathway genes, and (2) vascular endothelial cell (EC) regulatory regions, which are among the highest expressers of TFPI. Our GWAS identified 131 SNPs with suggestive evidence of association (P-value < 5 × 10-8 ), but no SNPs reached the genome-wide threshold for statistical significance. Hemostasis pathway genes were not enriched for TFPI plasma level associated SNPs (global hypothesis test P-value = 0.147), but EC regulatory regions contained more TFPI plasma level associated SNPs than expected by chance (global hypothesis test P-value = 0.046). We therefore stratified our genome-wide SNPs, prioritizing those in EC regulatory regions via stratified false discovery rate (sFDR) control, and reranked the SNPs by q-value. The minimum q-value was 0.27, and the top-ranked SNPs did not show association evidence in the MARTHA replication sample of 1,033 unrelated VTE cases. Although this study did not result in new loci for TFPI, our work lays out a strategy to utilize epigenomic data in prioritization schemes for future GWAS studies.
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Affiliation(s)
- Jessica Dennis
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Alejandra Medina-Rivera
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Canada.,Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Vinh Truong
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Lina Antounians
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nora Zwingerman
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Giovana Carrasco
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Lisa Strug
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Phil Wells
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - David-Alexandre Trégouët
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France.,INSERM, UMR_S 1166, Paris, France.,ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Pierre-Emmanuel Morange
- INSERM, UMR_S 1062, Marseille, France.,Inra, UMR_INRA 1260, Marseille, France.,Aix Marseille Université, Marseille, France
| | - Michael D Wilson
- Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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8
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Zhang H, Na W, Zhang HL, Wang N, Du ZQ, Wang SZ, Wang ZP, Zhang Z, Li H. TCF21 is related to testis growth and development in broiler chickens. Genet Sel Evol 2017; 49:25. [PMID: 28235410 PMCID: PMC5326497 DOI: 10.1186/s12711-017-0299-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Background Large amounts of fat deposition often lead to loss of reproductive efficiency in humans and animals. We used broiler chickens as a model species to conduct a two-directional selection for and against abdominal fat over 19 generations, which resulted in a lean and a fat line. Direct selection for abdominal fat content also indirectly resulted in significant differences (P < 0.05) in testis weight (TeW) and in TeW as a percentage of total body weight (TeP) between the lean and fat lines. Results A total of 475 individuals from the generation 11 (G11) were genotyped. Genome-wide association studies revealed two regions on chicken chromosomes 3 and 10 that were associated with TeW and TeP. Forty G16 individuals (20 from each line), were further profiled by focusing on these two chromosomal regions, to identify candidate genes with functions that may be potentially related to testis growth and development. Of the nine candidate genes identified with database mining, a significant association was confirmed for one gene, TCF21, based on mRNA expression analysis. Gene expression analysis of the TCF21 gene was conducted again across 30 G19 individuals (15 individuals from each line) and the results confirmed the findings on the G16 animals. Conclusions This study revealed that the TCF21 gene is related to testis growth and development in male broilers. This finding will be useful to guide future studies to understand the genetic mechanisms that underlie reproductive efficiency. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0299-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Hong-Li Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Shou-Zhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Zhi-Peng Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Zhiwu Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China. .,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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9
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Abstract
Coronary artery disease (or coronary heart disease), is the leading cause of mortality in many of the developing as well as the developed countries of the world. Cholesterol-enriched plaques in the heart's blood vessels combined with inflammation lead to the lesion expansion, narrowing of blood vessels, reduced blood flow, and may subsequently cause lesion rupture and a heart attack. Even though several environmental risk factors have been established, such as high LDL-cholesterol, diabetes, and high blood pressure, the underlying genetic composition may substantially modify the disease risk; hence, genome composition and gene-environment interactions may be critical for disease progression. Ongoing scientific efforts have seen substantial advancements related to the fields of genetics and genomics, with the major breakthroughs yet to come. As genomics is the most rapidly advancing field in the life sciences, it is important to present a comprehensive overview of current efforts. Here, we present a summary of various genetic and genomics assays and approaches applied to coronary artery disease research.
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Affiliation(s)
- Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Clint L Miller
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Robert Wirka
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Juyong B Kim
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Daniel M DiRenzo
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA.
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10
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de Kovel CG, Mulder F, van Setten J, van ‘t Slot R, Al-Rubaish A, Alshehri AM, Al Faraidy K, Al-Ali A, Al-Madan M, Al Aqaili I, Larbi E, Al-Ali R, Alzahrani A, Asselbergs FW, Koeleman BPC, Al-Ali A. Exome-Wide Association Analysis of Coronary Artery Disease in the Kingdom of Saudi Arabia Population. PLoS One 2016; 11:e0146502. [PMID: 26849363 PMCID: PMC4744043 DOI: 10.1371/journal.pone.0146502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/17/2015] [Indexed: 11/28/2022] Open
Abstract
Coronary Artery Disease (CAD) remains the leading cause of mortality worldwide. Mortality rates associated with CAD have shown an exceptional increase particularly in fast developing economies like the Kingdom of Saudi Arabia (KSA). Over the past twenty years, CAD has become the leading cause of death in KSA and has reached epidemic proportions. This rise is undoubtedly caused by fast urbanization that is associated with a life-style that promotes CAD. However, the question remains whether genetics play a significant role and whether genetic susceptibility is increased in KSA compared to the well-studied Western European populations. Therefore, we performed an Exome-wide association study (EWAS) in 832 patients and 1,076 controls of Saudi Arabian origin to test whether population specific, strong genetic risk factors for CAD exist, or whether the polygenic risk score for known genetic risk factors for CAD, lipids, and Type 2 Diabetes show evidence for an enriched genetic burden. Our results do not show significant associations for a single genetic locus. However, the heritability estimate for CAD for this population was high (h(2) = 0.53, S.E. = 0.1, p = 4e(-12)) and we observed a significant association of the polygenic risk score for CAD that demonstrates that the population of KSA, at least in part, shares the genetic risk associated to CAD in Western populations.
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Affiliation(s)
- Carolien G. de Kovel
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Flip Mulder
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben van ‘t Slot
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Abdullah Al-Rubaish
- Department of Medicine, King Fahd Hospital of the University, University of Dammam, Dammam, Kingdom of Saudi Arabia
| | - Abdullah M. Alshehri
- Department of Medicine, King Fahd Hospital of the University, University of Dammam, Dammam, Kingdom of Saudi Arabia
| | - Khalid Al Faraidy
- Department of Cardiology, King Fahd Military Medical Complex, Al-Khobar, Kingdom of Saudi Arabia
| | - Abdullah Al-Ali
- Prince Sultan Cardiac Center, Al-Ahssa, Kingdom of Saudi Arabia
| | - Mohammed Al-Madan
- King Fahd Hospital of the University, University of Dammam, Dammam, Kingdom of Saudi Arabia
| | - Issa Al Aqaili
- Department of Medicine, Qatif Central Hospital, Qatif, Kingdom of Saudi Arabia
| | - Emmanuel Larbi
- Department of Medicine, King Fahd Hospital of the University, University of Dammam, Dammam, Kingdom of Saudi Arabia
| | - Rudaynah Al-Ali
- Department of Medicine, King Fahd Hospital of the University, University of Dammam, Dammam, Kingdom of Saudi Arabia
| | - Alhusain Alzahrani
- College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. C. Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Amein Al-Ali
- Prince Mohammed Center for Research & Consultation Studies, College of Medicine, University of Dammam, Dammam, Kingdom of Saudi Arabia
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11
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DuBroff R, de Lorgeril M. Cholesterol confusion and statin controversy. World J Cardiol 2015; 7:404-9. [PMID: 26225201 PMCID: PMC4513492 DOI: 10.4330/wjc.v7.i7.404] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/09/2015] [Accepted: 04/28/2015] [Indexed: 02/06/2023] Open
Abstract
The role of blood cholesterol levels in coronary heart disease (CHD) and the true effect of cholesterol-lowering statin drugs are debatable. In particular, whether statins actually decrease cardiac mortality and increase life expectancy is controversial. Concurrently, the Mediterranean diet model has been shown to prolong life and reduce the risk of diabetes, cancer, and CHD. We herein review current data related to both statins and the Mediterranean diet. We conclude that the expectation that CHD could be prevented or eliminated by simply reducing cholesterol appears unfounded. On the contrary, we should acknowledge the inconsistencies of the cholesterol theory and recognize the proven benefits of a healthy lifestyle incorporating a Mediterranean diet to prevent CHD.
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Affiliation(s)
- Robert DuBroff
- Robert DuBroff, Department of Medicine, Division of Cardiology, University of New Mexico School of Medicine, MSC 10-5550, 1 University of New Mexico, Albuquerque, NM 87131, United States
| | - Michel de Lorgeril
- Robert DuBroff, Department of Medicine, Division of Cardiology, University of New Mexico School of Medicine, MSC 10-5550, 1 University of New Mexico, Albuquerque, NM 87131, United States
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