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Prone-Olazabal D, Davies I, González-Galarza FF. Metabolic Syndrome: An Overview on Its Genetic Associations and Gene-Diet Interactions. Metab Syndr Relat Disord 2023; 21:545-560. [PMID: 37816229 DOI: 10.1089/met.2023.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] Open
Abstract
Metabolic syndrome (MetS) is a cluster of cardiometabolic risk factors that includes central obesity, hyperglycemia, hypertension, and dyslipidemias and whose inter-related occurrence may increase the odds of developing type 2 diabetes and cardiovascular diseases. MetS has become one of the most studied conditions, nevertheless, due to its complex etiology, this has not been fully elucidated. Recent evidence describes that both genetic and environmental factors play an important role on its development. With the advent of genomic-wide association studies, single nucleotide polymorphisms (SNPs) have gained special importance. In this review, we present an update of the genetics surrounding MetS as a single entity as well as its corresponding risk factors, considering SNPs and gene-diet interactions related to cardiometabolic markers. In this study, we focus on the conceptual aspects, diagnostic criteria, as well as the role of genetics, particularly on SNPs and polygenic risk scores (PRS) for interindividual analysis. In addition, this review highlights future perspectives of personalized nutrition with regard to the approach of MetS and how individualized multiomics approaches could improve the current outlook.
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Affiliation(s)
- Denisse Prone-Olazabal
- Postgraduate Department, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Ian Davies
- Research Institute of Sport and Exercise Science, The Institute for Health Research, Liverpool John Moores University, Liverpool, United Kingdom
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Song Y, Gu J, You J, Tao Y, Zhang Y, Wang L, Gao J. The functions of SID1 transmembrane family, member 2 (Sidt2). FEBS J 2023; 290:4626-4637. [PMID: 36176242 DOI: 10.1111/febs.16641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
Abstract
The SID1 transmembrane family, member 2, namely, Sidt2, is a highly glycosylated multichannel lysosomal transmembrane protein, but its specific physiological function remains unknown. Lysosomal membrane proteins are very important for the executive functioning of lysosomes. As an important part of the lysosomal membrane, Sidt2 can maintain the normal morphology of lysosomes and help stabilize them from the acidic pH environment within. As a receptor/transporter, it binds and transports nucleic acids and mediates the uptake and degradation of RNA and DNA by the lysosome. During glucose metabolism, deletion of Sidt2 can cause an increase in fasting blood glucose and the impairment of grape tolerance, which is closely related to the secretion of insulin. During lipid metabolism, the loss of Sidt2 can cause hepatic steatosis and lipid metabolism disorders and can also play a role in signal regulation and transport. Here, we review the function of the lysosomal membrane protein Sidt2, and focus on its role in glucose and lipid metabolism, autophagy and nucleotide (DNA/RNA) transport.
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Affiliation(s)
- Yingying Song
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
| | - Jing Gu
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
| | - Jingya You
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Yiyang Tao
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Yao Zhang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Lizhuo Wang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Jialin Gao
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
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Swart PC, Du Plessis M, Rust C, Womersley JS, van den Heuvel LL, Seedat S, Hemmings SMJ. Identifying genetic loci that are associated with changes in gene expression in PTSD in a South African cohort. J Neurochem 2023; 166:705-719. [PMID: 37522158 PMCID: PMC10953375 DOI: 10.1111/jnc.15919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
The molecular mechanisms underlying posttraumatic stress disorder (PTSD) are yet to be fully elucidated, especially in underrepresented population groups. Expression quantitative trait loci (eQTLs) are DNA sequence variants that influence gene expression, in a local (cis-) or distal (trans-) manner, and subsequently impact cellular, tissue, and system physiology. This study aims to identify genetic loci associated with gene expression changes in a South African PTSD cohort. Genome-wide genotype and RNA-sequencing data were obtained from 32 trauma-exposed controls and 35 PTSD cases of mixed-ancestry, as part of the SHARED ROOTS project. The first approach utilised 108 937 single-nucleotide polymorphisms (SNPs) (MAF > 10%) and 11 312 genes with Matrix eQTL to map potential eQTLs, while controlling for covariates as appropriate. The second analysis was focused on 5638 SNPs related to a previously calculated PTSD polygenic risk score for this cohort. SNP-gene pairs were considered eQTLs if they surpassed Bonferroni correction and had a false discovery rate <0.05. We did not identify eQTLs that significantly influenced gene expression in a PTSD-dependent manner. However, several known cis-eQTLs, independent of PTSD diagnosis, were observed. rs8521 (C > T) was associated with TAGLN and SIDT2 expression, and rs11085906 (C > T) was associated with ZNF333 expression. This exploratory study provides insight into the molecular mechanisms associated with PTSD in a non-European, admixed sample population. This study was limited by the cross-sectional design and insufficient statistical power. Overall, this study should encourage further multi-omics approaches towards investigating PTSD in diverse populations.
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Affiliation(s)
- Patricia C. Swart
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Morne Du Plessis
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Carlien Rust
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Jacqueline S. Womersley
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Leigh L. van den Heuvel
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
| | - Sian M. J. Hemmings
- Department of Psychiatry, Faculty of Medicine and Health SciencesStellenbosch UniversityCape TownSouth Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders UnitCape TownSouth Africa
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4
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Interaction between SIDT2 and ABCA1 Variants with Nutrients on HDL-c Levels in Mexican Adults. Nutrients 2023; 15:nu15020370. [PMID: 36678241 PMCID: PMC9861312 DOI: 10.3390/nu15020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 01/13/2023] Open
Abstract
Previous studies have reported that the SIDT2 and ABCA1 genes are involved in lipid metabolism. We aimed to analyze the association-the gene x gene interaction between rs17120425 and rs1784042 on SIDT2 and rs9282541 on ABCA1 and their diet interaction on the HDL-c serum levels-in a cohort of 1982 Mexican adults from the Health Workers Cohort Study. Demographic and clinical data were collected through a structured questionnaire and standardized procedures. Genotyping was performed using a predesigned TaqMan assay. The associations and interactions of interest were estimated using linear and logistic regression. Carriers of the rs17120425-A and rs1784042-A alleles had slightly higher blood HDL-c levels compared to the non-carriers. In contrast, rs9282541-A was associated with low blood HDL-c levels (OR = 1.34, p = 0.013). The rs1784042 x rs9282541 interaction was associated with high blood HDL-c levels (p = 3.4 × 10-4). Premenopausal women who carried at least one rs17120425-A allele and consumed high dietary fat, protein, monounsaturated, or polyunsaturated fatty acids levels had higher HDL-c levels than the non-carriers. These results support the association between the genetic variants on SIDT2 and ABCA1 with HDL-c levels and suggest gene-gene and gene-diet interactions over HDL-c concentrations in Mexican adults. Our findings could be a platform for developing clinical and dietary strategies for improving the health of the Mexican population.
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Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W, Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X. A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods 2022; 19:1599-1611. [PMID: 36303018 PMCID: PMC10008172 DOI: 10.1038/s41592-022-01640-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 09/06/2022] [Indexed: 02/07/2023]
Abstract
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
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Grants
- R01 DK078616 NIDDK NIH HHS
- U01 HG007417 NHGRI NIH HHS
- KL2 TR001100 NCATS NIH HHS
- R01 HL112064 NHLBI NIH HHS
- N01-HC-95160 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35 HG010692 NHGRI NIH HHS
- U01-HL054472 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL142711 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-DK071891 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- F30 HL149180 NHLBI NIH HHS
- R01 NR019628 NINR NIH HHS
- R01 HL113323 NHLBI NIH HHS
- N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- R01 HL132947 NHLBI NIH HHS
- P30 DK040561 NIDDK NIH HHS
- U01 HL137183 NHLBI NIH HHS
- R01-HL127564 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P30 CA016672 NCI NIH HHS
- R01-HL071051 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL104135 NHLBI NIH HHS
- T32 HL144442 NHLBI NIH HHS
- R35 CA197449 NCI NIH HHS
- P30 ES010126 NIEHS NIH HHS
- DP5 OD029586 NIH HHS
- R01-NS058700 U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
- R01 HL123915 NHLBI NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL046380 NHLBI NIH HHS
- R01HL071251, R01HL071258, R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 HG003067 NHGRI NIH HHS
- 75N92020D00003 NHLBI NIH HHS
- K01 AG059898 NIA NIH HHS
- U01 DK085524 NIDDK NIH HHS
- KL2 TR002542 NCATS NIH HHS
- R01-HL055673-18S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R03 HL141439 NHLBI NIH HHS
- HHSN268201500001I NHLBI NIH HHS
- R01-MH078143, R01-MH078111, R01-MH083824 U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)
- U01 DK062413 NIDDK NIH HHS
- R01 HL109946 NHLBI NIH HHS
- U01-HL054495 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K01 HL136700 NHLBI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U01 HL080295 NHLBI NIH HHS
- NO1-HC-25195 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HG006703 NHGRI NIH HHS
- UL1-TR-001420 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HG012064 NHGRI NIH HHS
- R35-CA197449 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- P30 ES005605 NIEHS NIH HHS
- R01 AR042742 NIAMS NIH HHS
- R21 HL140385 NHLBI NIH HHS
- HHSN268201800015I NHLBI NIH HHS
- U01 HL130114 NHLBI NIH HHS
- R01 HL117191 NHLBI NIH HHS
- R01 HG009974 NHGRI NIH HHS
- U01-HL054473 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 DK113003 NIDDK NIH HHS
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL059367 NHLBI NIH HHS
- R24 AG047115 NIA NIH HHS
- U01-HL137181 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL107202 NHLBI NIH HHS
- NR0224103 U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)
- P50 HL118006 NHLBI NIH HHS
- U01-HL72518, HL087698, HL49762, HL59684, HL58625, HL071025, HL112064 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL120393 NHLBI NIH HHS
- R01 DK117445 NIDDK NIH HHS
- R01-AG058921 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R03-HL154284 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01 AG058921 NIA NIH HHS
- R01 HL129132 NHLBI NIH HHS
- R01 HL113338 NHLBI NIH HHS
- HHSN268201800012I NHLBI NIH HHS
- R01 HL153805 NHLBI NIH HHS
- R01 DK072193 NIDDK NIH HHS
- R01 HL137922 NHLBI NIH HHS
- R01 AI079139 NIAID NIH HHS
- N01-HC-95164 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK085524 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U19 AI111224 NIAID NIH HHS
- R35 HL135824 NHLBI NIH HHS
- 75N92019D00031 NHLBI NIH HHS
- R01 DK110113 NIDDK NIH HHS
- N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95165 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL138737 NHLBI NIH HHS
- P30 DK079626 NIDDK NIH HHS
- R01 NS058700 NINDS NIH HHS
- R01 HL127564 NHLBI NIH HHS
- T32 HG000040 NHGRI NIH HHS
- DK063491 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL141845 NHLBI NIH HHS
- R01 DK075787 NIDDK NIH HHS
- R01 AR072199 NIAMS NIH HHS
- R01 HL120854 NHLBI NIH HHS
- R01 HL163560 NHLBI NIH HHS
- R01HL071258 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-HG009088 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
- R01 HL163972 NHLBI NIH HHS
- K23 HL123778 NHLBI NIH HHS
- U01 HL137181 NHLBI NIH HHS
- R01 MH078111 NIMH NIH HHS
- HHSN268201700005I NHLBI NIH HHS
- N01-HC-95159 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01-HL113323 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL141944 NHLBI NIH HHS
- R01 HL119443 NHLBI NIH HHS
- R01-HL071051, R01-HL071205, R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P60-AG10484 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- 75N92020D00007 NHLBI NIH HHS
- UM1 AI068634 NIAID NIH HHS
- HHSN268201500003I NHLBI NIH HHS
- HHSN268201700004I NHLBI NIH HHS
- N01-HC-95163 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL071205 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F30 HL107066 NHLBI NIH HHS
- R01-HL153805 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL105756 NHLBI NIH HHS
- K01 HL125751 NHLBI NIH HHS
- R01 HL067348 NHLBI NIH HHS
- T32 HL007208 NHLBI NIH HHS
- R01 HL142711 NHLBI NIH HHS
- R35 HL135818 NHLBI NIH HHS
- R01-HL92301 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 GM074897 NIGMS NIH HHS
- I01 BX005295 BLRD VA
- 75N92020D00001 NHLBI NIH HHS
- R01 HL113326 NHLBI NIH HHS
- R00 HL129045 NHLBI NIH HHS
- UL1-TR-000040 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- UL1-TR-001079 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HL072524 NHLBI NIH HHS
- R35-HL135818 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL140203 NHLBI NIH HHS
- N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL141601 NHLBI NIH HHS
- 75N92020D00005 NHLBI NIH HHS
- R01-DK117445 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01-AR48797 U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- R56 AG058543 NIA NIH HHS
- U19 AI077439 NIAID NIH HHS
- R01 HL142028 NHLBI NIH HHS
- 75N92020D00004 NHLBI NIH HHS
- HHSN268201800011I NHLBI NIH HHS
- R35 GM127131 NIGMS NIH HHS
- U01 HL137880 NHLBI NIH HHS
- R01 HG010869 NHGRI NIH HHS
- R01-HL133040 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700003I NHLBI NIH HHS
- R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95168 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL148239 NHLBI NIH HHS
- U01-HL137162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 AI132476 NIAID NIH HHS
- T32 GM007205 NIGMS NIH HHS
- HHSN268201800010I NHLBI NIH HHS
- R01-HL092577-06S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01-HL104135-04S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL132320 NHLBI NIH HHS
- U01 DK078616 NIDDK NIH HHS
- HHSN268201700001I NHLBI NIH HHS
- R01-HL141944 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL137162 NHLBI NIH HHS
- R01 HG005701 NHGRI NIH HHS
- 75N92020D00001, 75N92020D00002, 75N92020D00003, 75N92020D00004 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 HL143221 NHLBI NIH HHS
- R01 HL142992 NHLBI NIH HHS
- K01 HL129039 NHLBI NIH HHS
- R01 HL133870 NHLBI NIH HHS
- R01 DA037904 NIDA NIH HHS
- R21 HL123677 NHLBI NIH HHS
- R01 DK071891 NIDDK NIH HHS
- HHSN268201800001I U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- 75N92020D00002 NHLBI NIH HHS
- K01 HL130609 NHLBI NIH HHS
- N01-HC-95167 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 HL007374 NHLBI NIH HHS
- N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 AR063611 NIAMS NIH HHS
- KL2TR002490 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R03 HL154284 NHLBI NIH HHS
- M01-RR000052 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- 75N92020D00006 NHLBI NIH HHS
- S10 OD020069 NIH HHS
- R01 MD012765 NIMHD NIH HHS
- N01-HC-95161 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700002I NHLBI NIH HHS
- R01 HL151855 NHLBI NIH HHS
- K23 HL138461 NHLBI NIH HHS
- U01 CA182913 NCI NIH HHS
- UG3 HL151865 NHLBI NIH HHS
- F32 HL150992 NHLBI NIH HHS
- R01-MD012765 U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)
- 75N92020D00005, 75N92020D00006, 75N92020D00007 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 MH101244 NIMH NIH HHS
- U01 HG009088 NHGRI NIH HHS
- N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P42 ES016454 NIEHS NIH HHS
- UM1 DK078616 NIDDK NIH HHS
- U01-HL054509 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35-HL135824 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- M01-RR07122 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- U01 DK105561 NIDDK NIH HHS
- U01-HL072524 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P20 GM121334 NIGMS NIH HHS
- N01-HC-95167, N01-HC-95168, N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL131565 NHLBI NIH HHS
- R01HL071251 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R13 CA124365 NCI NIH HHS
- R01-HL045522 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL132825 NHLBI NIH HHS
- R01 HL118267 NHLBI NIH HHS
- HHSN268201800013I NIMHD NIH HHS
- R01-HL67348 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 GM115428 NIGMS NIH HHS
- R01 HL055673 NHLBI NIH HHS
- HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL149683 NHLBI NIH HHS
- R01 HL092301 NHLBI NIH HHS
- P30 DK020595 NIDDK NIH HHS
- R01 HL149836 NHLBI NIH HHS
- K08 HL145095 NHLBI NIH HHS
- K01 HL135405 NHLBI NIH HHS
- R03 OD030608 NIH HHS
- HHSN268201800014I NHLBI NIH HHS
- R01-HL113338 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F32-HL085989 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1 AI068636 NIAID NIH HHS
- R01 AG057381 NIA NIH HHS
- U19-CA203654 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
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Affiliation(s)
- Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Theodore Arapoglou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Corbin Quick
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yaowu Liu
- School of Statistics, Southwestern University of Finance and Economics, Chengdu, China
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Harald H H Göring
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa W Martin
- Division in Cardiology, George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Departments of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel E Weeks
- Department of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Cristen J Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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6
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Jiang X, Yang Z, Wang S, Deng S. “Big Data” Approaches for Prevention of the Metabolic Syndrome. Front Genet 2022; 13:810152. [PMID: 35571045 PMCID: PMC9095427 DOI: 10.3389/fgene.2022.810152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic syndrome (MetS) is characterized by the concurrence of multiple metabolic disorders resulting in the increased risk of a variety of diseases related to disrupted metabolism homeostasis. The prevalence of MetS has reached a pandemic level worldwide. In recent years, extensive amount of data have been generated throughout the research targeted or related to the condition with techniques including high-throughput screening and artificial intelligence, and with these “big data”, the prevention of MetS could be pushed to an earlier stage with different data source, data mining tools and analytic tools at different levels. In this review we briefly summarize the recent advances in the study of “big data” applications in the three-level disease prevention for MetS, and illustrate how these technologies could contribute tobetter preventive strategies.
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Affiliation(s)
- Xinping Jiang
- Department of United Ultrasound, The First Hospital of Jilin University, Changchun, China
| | - Zhang Yang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China
| | - Shuai Wang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China
| | - Shuanglin Deng
- Department of Oncological Neurosurgery, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Shuanglin Deng,
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7
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Gentry AE, Robins J, Makowski M, Kliewer W. Differential DNA Methylation and Cardiometabolic Risk in African American Mother-Adolescent Dyads. Biol Res Nurs 2022; 24:75-84. [PMID: 34719281 PMCID: PMC9248288 DOI: 10.1177/10998004211039017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Cardiovascular disease disproportionately affects African Americans as the leading cause of morbidity and mortality. Among African Americans, compared to other racial groups, cardiovascular disease onset occurs at an earlier age due to a higher prevalence of cardiometabolic risk factors, particularly obesity, hypertension and type 2 diabetes. Emerging evidence suggests that heritable epigenetic processes are related to increased cardiovascular disease risk, but this is largely unexplored in adolescents or across generations. MATERIALS AND METHODS In a cross-sectional descriptive pilot study in low-income African American mother-adolescent dyads, we examined associations between DNA methylation and the cardiometabolic indicators of body mass index, waist circumference, and insulin resistance. RESULTS Four adjacent cytosine and guanine nucleotides (CpG) sites were significantly differentially methylated and associated with C-reactive protein (CRP), 62 with waist circumference, and none to insulin resistance in models for both mothers and adolescents. CONCLUSION Further study of the relations among psychological and environmental stressors, indicators of cardiovascular disease, risk, and epigenetic factors will improve understanding of cardiovascular disease risk so that preventive measures can be instituted earlier and more effectively. To our knowledge this work is the first to examine DNA methylation and cardiometabolic risk outcomes in mother-adolescent dyads.
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Affiliation(s)
- Amanda Elswick Gentry
- Department of Psychiatry, Virginia
Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University,
Richmond, VA, USA,Amanda Elswick Gentry, PhD, Department of
Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia
Commonwealth University, 800 East Leigh Street, Suite 100, Room 130-B, Richmond,
VA 23219, USA.
| | - Jo Robins
- School of Nursing, Virginia
Commonwealth University, Richmond, VA, USA
| | | | - Wendy Kliewer
- Department of Psychology, College of
Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, USA
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8
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Liu G, Luo S, Lei Y, Wu J, Huang Z, Wang K, Yang P, Huang X. A nine-hub-gene signature of metabolic syndrome identified using machine learning algorithms and integrated bioinformatics. Bioengineered 2021; 12:5727-5738. [PMID: 34516309 PMCID: PMC8806918 DOI: 10.1080/21655979.2021.1968249] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
Early risk assessments and interventions for metabolic syndrome (MetS) are limited because of a lack of effective biomarkers. In the present study, several candidate genes were selected as a blood-based transcriptomic signature for MetS. We collected so far the largest MetS-associated peripheral blood high-throughput transcriptomics data and put forward a novel feature selection strategy by combining weighted gene co-expression network analysis, protein-protein interaction network analysis, LASSO regression and random forest approaches. Two gene modules and 51 hub genes as well as a 9-hub-gene signature associated with metabolic syndrome were identified. Then, based on this 9-hub-gene signature, we performed logistic analysis and subsequently established a web nomogram calculator for metabolic syndrome risk (https://xjtulgz.shinyapps.io/DynNomapp/). This 9-hub-gene signature showed excellent classification and calibration performance (AUC = 0.968 in training set, AUC = 0.883 in internal validation set, AUC = 0.861 in external validation set) as well as ideal potential clinical benefit.
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Affiliation(s)
- Guanzhi Liu
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Sen Luo
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yutian Lei
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jianhua Wu
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhuo Huang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Kunzheng Wang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Pei Yang
- Bone and Joint Surgery Center, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xin Huang
- Department of Cardiovascular Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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9
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Gu J, Geng M, Qi M, Wang L, Zhang Y, Gao J. The role of lysosomal membrane proteins in glucose and lipid metabolism. FASEB J 2021; 35:e21848. [PMID: 34582051 DOI: 10.1096/fj.202002602r] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/11/2021] [Accepted: 07/26/2021] [Indexed: 11/11/2022]
Abstract
Lysosomes have long been regarded as the "garbage dump" of the cell. More recently, however, researchers have revealed novel roles for lysosomal membranes in autophagy, ion transport, nutrition sensing, and membrane fusion and repair. With active research into lysosomal membrane proteins (LMP), increasing evidence has become available showing that LMPs are inextricably linked to glucose and lipid metabolism, and this relationship represents mutual influence and regulation. In this review, we summarize the roles of LMPs in relation to glucose and lipid metabolism, and describe their roles in glucose transport, glycolysis, cholesterol transport, and lipophagy. The role of transport proteins can be traced back to the original discoveries of GLUT8, NPC1, and NPC2, which were all found to have significant roles in the pathways involved in glucose and lipid metabolism. CLC-5 and SIDT2-knockout animals show serious phenotypic disorders of metabolism, and V-ATPase and LAMP-2 have been found to interact with proteins related to glucose and lipid metabolism. These findings all emphasize the critical role of LMPs in glycolipid metabolism and help to strengthen our understanding of the independent and close relationship between LMPs and glycolipid metabolism.
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Affiliation(s)
- Jing Gu
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
| | - Mengya Geng
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Mengxiang Qi
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Lizhuo Wang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Yao Zhang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Jialin Gao
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research (Wannan Medical College), Wannan Medical College, Wuhu, China
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10
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León-Mimila P, Villamil-Ramírez H, Macías-Kauffer LR, Jacobo-Albavera L, López-Contreras BE, Posadas-Sánchez R, Posadas-Romero C, Romero-Hidalgo S, Morán-Ramos S, Domínguez-Pérez M, Olivares-Arevalo M, López-Montoya P, Nieto-Guerra R, Acuña-Alonzo V, Macín-Pérez G, Barquera-Lozano R, Del-Río-Navarro BE, González-González I, Campos-Pérez F, Gómez-Pérez F, Valdés VJ, Sampieri A, Reyes-García JG, Carrasco-Portugal MDC, Flores-Murrieta FJ, Aguilar-Salinas CA, Vargas-Alarcón G, Shih D, Meikle PJ, Calkin AC, Drew BG, Vaca L, Lusis AJ, Huertas-Vazquez A, Villarreal-Molina T, Canizales-Quinteros S. Genome-Wide Association Study Identifies a Functional SIDT2 Variant Associated With HDL-C (High-Density Lipoprotein Cholesterol) Levels and Premature Coronary Artery Disease. Arterioscler Thromb Vasc Biol 2021; 41:2494-2508. [PMID: 34233476 PMCID: PMC8664085 DOI: 10.1161/atvbaha.120.315391] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective Low HDL-C (high-density lipoprotein cholesterol) is the most frequent dyslipidemia in Mexicans, but few studies have examined the underlying genetic basis. Our purpose was to identify genetic variants associated with HDL-C levels and cardiovascular risk in the Mexican population. Approach and Results A genome-wide association studies for HDL-C levels in 2335 Mexicans, identified four loci associated with genome-wide significance: CETP, ABCA1, LIPC, and SIDT2. The SIDT2 missense Val636Ile variant was associated with HDL-C levels and was replicated in 3 independent cohorts (P=5.9×10−18 in the conjoint analysis). The SIDT2/Val636Ile variant is more frequent in Native American and derived populations than in other ethnic groups. This variant was also associated with increased ApoA1 and glycerophospholipid serum levels, decreased LDL-C (low-density lipoprotein cholesterol) and ApoB levels, and a lower risk of premature CAD. Because SIDT2 was previously identified as a protein involved in sterol transport, we tested whether the SIDT2/Ile636 protein affected this function using an in vitro site-directed mutagenesis approach. The SIDT2/Ile636 protein showed increased uptake of the cholesterol analog dehydroergosterol, suggesting this variant affects function. Finally, liver transcriptome data from humans and the Hybrid Mouse Diversity Panel are consistent with the involvement of SIDT2 in lipid and lipoprotein metabolism. Conclusions This is the first genome-wide association study for HDL-C levels seeking associations with coronary artery disease in the Mexican population. Our findings provide new insight into the genetic architecture of HDL-C and highlight SIDT2 as a new player in cholesterol and lipoprotein metabolism in humans.
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Affiliation(s)
- Paola León-Mimila
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | - Luis R Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
- Dirección de Planeación, Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Ixtapaluca, Estado de México (L.R.M.-K.)
| | - Leonor Jacobo-Albavera
- Laboratorio de Enfermedades Cardiovasculares, INMEGEN, Mexico City (L.J.-A., M.D.-P., T.V.-M.)
| | - Blanca E López-Contreras
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | - Rosalinda Posadas-Sánchez
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City (R.P.-S., C.P.-R.)
| | - Carlos Posadas-Romero
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City (R.P.-S., C.P.-R.)
| | | | - Sofía Morán-Ramos
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
- Consejo Nacional de Ciencia y Tecnología (CONACyT), Mexico City (S.M.-R.)
| | - Mayra Domínguez-Pérez
- Laboratorio de Enfermedades Cardiovasculares, INMEGEN, Mexico City (L.J.-A., M.D.-P., T.V.-M.)
| | - Marisol Olivares-Arevalo
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | - Priscilla López-Montoya
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | - Roberto Nieto-Guerra
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
| | | | - Gastón Macín-Pérez
- Escuela Nacional de Antropología e Historia, Mexico City (V.A.-A., G.M.-P.)
| | | | | | | | | | - Francisco Gómez-Pérez
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City (F.G.-P., C.A.A.-S.)
| | - Victor J Valdés
- Instituto de Fisiología Celular, UNAM, Mexico City (V.J.V., A.S., L.V.)
| | - Alicia Sampieri
- Instituto de Fisiología Celular, UNAM, Mexico City (V.J.V., A.S., L.V.)
| | - Juan G Reyes-García
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City (J.G.R.-G., F.J.F.-M.)
| | - Miriam Del C Carrasco-Portugal
- Unidad de Investigación en Farmacología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City (M.C.-P., F.J.F.-M.)
| | - Francisco J Flores-Murrieta
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City (J.G.R.-G., F.J.F.-M.)
- Unidad de Investigación en Farmacología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City (M.C.-P., F.J.F.-M.)
| | - Carlos A Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City (F.G.-P., C.A.A.-S.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, N.L. Mexico (C.A.A.-S.)
| | - Gilberto Vargas-Alarcón
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City (G.V.-A.)
| | - Diana Shih
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (D.S., A.J.L., A.H.-V.)
| | - Peter J Meikle
- Head Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (P.J.M.)
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (A.C.C., B.G.D.)
- Central Clinical School, Monash University, Melbourne, VIC, Australia (A.C.C., B.G.D.)
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC, Australia (A.C.C., B.G.D.)
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia (A.C.C., B.G.D.)
- Central Clinical School, Monash University, Melbourne, VIC, Australia (A.C.C., B.G.D.)
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC, Australia (A.C.C., B.G.D.)
| | - Luis Vaca
- Instituto de Fisiología Celular, UNAM, Mexico City (V.J.V., A.S., L.V.)
| | - Aldons J Lusis
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (D.S., A.J.L., A.H.-V.)
| | - Adriana Huertas-Vazquez
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (D.S., A.J.L., A.H.-V.)
| | | | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México (UNAM)/Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City (P.L.-M., H.V.-R., L.R.M.-K., B.E.L.-C., S.M.-R., M.O.-A., P.L.-M., R.N.-G., S.C.-Q.)
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Association of BTLA Polymorphisms with Susceptibility to Non-Small-Cell Lung Cancer in the Chinese Population. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9121824. [PMID: 33564688 PMCID: PMC7867466 DOI: 10.1155/2021/9121824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/14/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
Studies have reported that B- and T-lymphocyte attenuator (BTLA) polymorphisms may be associated with the risk to different cancers. However, the correlation between those variations and non-small-cell lung cancer (NSCLC) is still unclear. A total of 1,003 NSCLC patients and 901 noncancer controls were recruited in the study, to confirm the association of variations in BTLA gene with the risk of NSCLC. The SNPscan™ genotyping assay was used to obtain the genotypes of the four BTLA polymorphisms (BTLA rs1982809 G>A, rs16859629 T>C, rs2171513 G>A, and rs3112270 A>G). It was found that BTLA rs1982809 polymorphism reduced the risk of NSCLC (GA vs. GG: adjusted odds ratio (OR) = 0.81, 95%confidence interval (CI) = 0.66‐0.99, and P = 0.043). However, the BTLA rs16859629, rs2171513, and rs3112270 polymorphisms showed no significant association between NSCLC patients and controls in overall comparison. In subgroup analyses, we found that BTLA rs1982809 polymorphism reduced the risk of NSCLC (nonsquamous cell carcinoma: GA vs. GG: adjusted OR = 0.79, 95%CI = 0.64‐0.97, and P = 0.026; AA/GA vs. GG: adjusted OR = 0.81, 95%CI = 0.66‐0.99, and P = 0.037; ≥59 years: GA vs. GG: P = 0.036; never alcohol consumption: GA vs. GG: P = 0.013; GA/AA vs. GG: P = 0.016; body mass index (BMI) ≥ 24 kg/m2: GA vs. GG: P = 0.030; GA/AA vs. GG: P = 0.041). The BTLA rs16859629 polymorphism increased the risk of the development of squamous cell carcinoma (CC vs. TT: adjusted OR = 9.85, 95%CI = 1.37‐71.03, and P = 0.023; CC vs. TT/TC: adjusted OR = 9.55, 95%CI = 1.32‐68.66, and P = 0.025). Taken together, the findings of the present suggest that BTLA rs1982809 and rs16859629 polymorphisms may influence the susceptibility to NSCLC in the Chinese population.
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The Variant rs1784042 of the SIDT2 Gene is Associated with Metabolic Syndrome through Low HDL-c Levels in a Mexican Population. Genes (Basel) 2020; 11:genes11101192. [PMID: 33066450 PMCID: PMC7602182 DOI: 10.3390/genes11101192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
The Mexican population has one of the highest prevalences of metabolic syndrome (MetS) worldwide. The aim of this study was to investigate the association of single-nucleotide polymorphisms (SNPs) with MetS and its components. First, we performed a pilot Genome-wide association study (GWAS) scan on a sub-sample derived from the Health Workers Cohort Study (HWCS) (n = 411). Based on GWAS results, we selected the rs1784042 and rs17120425 SNPs in the SIDT1 transmembrane family member 2 (SIDT2) gene for replication in the entire cohort (n = 1963), using predesigned TaqMan assays. We observed a prevalence of MetS in the HWCS of 52.6%. The minor allele frequency for the variant rs17120425 was 10% and 29% for the rs1784042. The SNP rs1784042 showed an overall association with MetS (OR = 0.82, p = 0.01) and with low levels of high-density lipoprotein (HDL-c) (odds ratio (OR) = 0.77, p = 0.001). The SNP rs17120425 had a significant association with type 2 diabetes (T2D) risk in the overall population (OR = 1.39, p = 0.033). Our results suggest an association of the rs1784042 and rs17120425 variants with MetS, through different mechanisms in the Mexican population. Further studies in larger samples and other populations are required to validate these findings and the relevance of these SNPs in MetS.
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