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Delabays B, Trajanoska K, Walonoski J, Mooser V. Cardiovascular Pharmacogenetics: From Discovery of Genetic Association to Clinical Adoption of Derived Test. Pharmacol Rev 2024; 76:791-827. [PMID: 39122647 DOI: 10.1124/pharmrev.123.000750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 08/12/2024] Open
Abstract
Recent breakthroughs in human genetics and in information technologies have markedly expanded our understanding at the molecular level of the response to drugs, i.e., pharmacogenetics (PGx), across therapy areas. This review is restricted to PGx for cardiovascular (CV) drugs. First, we examined the PGx information in the labels approved by regulatory agencies in Europe, Japan, and North America and related recommendations from expert panels. Out of 221 marketed CV drugs, 36 had PGx information in their labels approved by one or more agencies. The level of annotations and recommendations varied markedly between agencies and expert panels. Clopidogrel is the only CV drug with consistent PGx recommendation (i.e., "actionable"). This situation prompted us to dissect the steps from discovery of a PGx association to clinical translation. We found 101 genome-wide association studies that investigated the response to CV drugs or drug classes. These studies reported significant associations for 48 PGx traits mapping to 306 genes. Six of these 306 genes are mentioned in the corresponding PGx labels or recommendations for CV drugs. Genomic analyses also highlighted the wide between-population differences in risk allele frequencies and the individual load of actionable PGx variants. Given the high attrition rate and the long road to clinical translation, additional work is warranted to identify and validate PGx variants for more CV drugs across diverse populations and to demonstrate the utility of PGx testing. To that end, pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond. SIGNIFICANCE STATEMENT: Despite spectacular breakthroughs in human molecular genetics and information technologies, consistent evidence supporting PGx testing in the cardiovascular area is limited to a few drugs. Additional work is warranted to discover and validate new PGx markers and demonstrate their utility. Pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond.
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Affiliation(s)
- Benoît Delabays
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Joshua Walonoski
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
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Elahimanesh M, Shokri N, Mahdinia E, Mohammadi P, Parvaz N, Najafi M. Differential gene expression patterns in ST-elevation Myocardial Infarction and Non-ST-elevation Myocardial Infarction. Sci Rep 2024; 14:3424. [PMID: 38341440 PMCID: PMC10858964 DOI: 10.1038/s41598-024-54086-w] [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: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
The ST-elevation Myocardial Infarction (STEMI) and Non-ST-elevation Myocardial Infarction (NSTEMI) might occur because of coronary artery stenosis. The gene biomarkers apply to the clinical diagnosis and therapeutic decisions in Myocardial Infarction. The aim of this study was to introduce, enrich and estimate timely the blood gene profiles based on the high-throughput data for the molecular distinction of STEMI and NSTEMI. The text mining data (50 genes) annotated with DisGeNET data (144 genes) were merged with the GEO gene expression data (5 datasets) using R software. Then, the STEMI and NSTEMI networks were primarily created using the STRING server, and improved using the Cytoscape software. The high-score genes were enriched using the KEGG signaling pathways and Gene Ontology (GO). Furthermore, the genes were categorized to determine the NSTEMI and STEMI gene profiles. The time cut-off points were identified statistically by monitoring the gene profiles up to 30 days after Myocardial Infarction (MI). The gene heatmaps were clearly created for the STEMI (high-fold genes 69, low-fold genes 45) and NSTEMI (high-fold genes 68, low-fold genes 36). The STEMI and NSTEMI networks suggested the high-score gene profiles. Furthermore, the gene enrichment suggested the different biological conditions for STEMI and NSTEMI. The time cut-off points for the NSTEMI (4 genes) and STEMI (13 genes) gene profiles were established up to three days after Myocardial Infarction. The study showed the different pathophysiologic conditions for STEMI and NSTEMI. Furthermore, the high-score gene profiles are suggested to measure up to 3 days after MI to distinguish the STEMI and NSTEMI.
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Affiliation(s)
- Mohammad Elahimanesh
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Nafiseh Shokri
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Elmira Mahdinia
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Payam Mohammadi
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Najmeh Parvaz
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Clinical Biochemistry Department, Faculty of Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
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Mauriello A, Ascrizzi A, Molinari R, Falco L, Caturano A, D’Andrea A, Russo V. Pharmacogenomics of Cardiovascular Drugs for Atherothrombotic, Thromboembolic and Atherosclerotic Risk. Genes (Basel) 2023; 14:2057. [PMID: 38003001 PMCID: PMC10671139 DOI: 10.3390/genes14112057] [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: 09/30/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
PURPOSE OF REVIEW Advances in pharmacogenomics have paved the way for personalized medicine. Cardiovascular diseases still represent the leading cause of mortality in the world. The aim of this review is to summarize the background, rationale, and evidence of pharmacogenomics in cardiovascular medicine, in particular, the use of antiplatelet drugs, anticoagulants, and drugs used for the treatment of dyslipidemia. RECENT FINDINGS Randomized clinical trials have supported the role of a genotype-guided approach for antiplatelet therapy in patients with coronary heart disease undergoing percutaneous coronary interventions. Numerous studies demonstrate how the risk of ineffectiveness of new oral anticoagulants and vitamin K anticoagulants is linked to various genetic polymorphisms. Furthermore, there is growing evidence to support the association of some genetic variants and poor adherence to statin therapy, for example, due to the appearance of muscular symptoms. There is evidence for resistance to some drugs for the treatment of dyslipidemia, such as anti-PCSK9. SUMMARY Pharmacogenomics has the potential to improve patient care by providing the right drug to the right patient and could guide the identification of new drug therapies for cardiovascular disease. This is very important in cardiovascular diseases, which have high morbidity and mortality. The improvement in therapy could be reflected in the reduction of healthcare costs and patient mortality.
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Affiliation(s)
- Alfredo Mauriello
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
| | - Antonia Ascrizzi
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
| | - Riccardo Molinari
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
| | - Luigi Falco
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
| | - Alfredo Caturano
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80100 Naples, Italy;
| | - Antonello D’Andrea
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
- Unit of Cardiology, “Umberto I” Hospital, Nocera Inferiore, 84014 Salerno, Italy
| | - Vincenzo Russo
- Cardiology Unit, Department of Medical Translational Science, University of Campania “Luigi Campania”—Monaldi Hospital, 80126 Naples, Italy; (A.M.); (A.A.); (R.M.); (L.F.); (A.D.)
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Zhang PP, Song JY, Li L, Xu M, Wang H, Wang HJ. Associations between genetic variants of HSD17B13 and fasting plasma glucose in Chinese children. Nutr Metab Cardiovasc Dis 2023; 33:1778-1784. [PMID: 37414661 DOI: 10.1016/j.numecd.2023.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/09/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND AIMS Genetic variants in 17-β hydroxysteroid dehydrogenase 13 (HSD17B13) were demonstrated to protect against NAFLD, which is highly related with insulin resistance and dyslipidemia. However, the effects of NAFLD associated HSD17B13 variants on circulating glucose and lipids have not been adequately investigated in children. This study aimed to investigate associations between single nucleotide polymorphisms (SNPs) of HSD17B13 and NAFLD or its related phenotypes, such as blood glucose and serum lipids in Chinese children. METHODS AND RESULTS We studied 1027 Chinese Han children aged 7-18 years old, which included 162 NAFLD children and 865 controls without NAFLD. Three SNPs (rs13112695, rs7692397, rs6834314) in HSD17B13 were genotyped. The multivariable logistic and linear regression models were applied to detect the associations between three SNPs and NAFLD or its related phenotypes [alanine transaminase (ALT), fasting plasma glucose (FPG) and serum lipids]. The effect allele A of rs7692397 was negatively associated with FPG [β (SE) = -0.088 (0.027) mmol/L, P = 0.001], whereas the effect allele G of rs6834314 was positively associated with FPG (β (SE) = 0.060 (0.019) mmol/L, P = 0.002). After Bonferroni correction, the significant associations still remained (both P < 0.0024). No significant associations were found for NAFLD or serum lipids. CONCLUSION The study firstly revealed the association between two HSD17B13 variants and FPG in Chinese children, providing evidence for HSD17B13 variants and abnormal glucose metabolism.
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Affiliation(s)
- Ping-Ping Zhang
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China; Ningbo Center for Healthy Lifestyle Research, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Jie-Yun Song
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China
| | - Li Li
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Miao Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Hui Wang
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China
| | - Hai-Jun Wang
- Department of Maternal and Child Health, School of Public Health, Peking University, Beijing, China.
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Kogiso T, Ogasawara Y, Horiuchi K, Taniai M, Tokushige K. Analysis of genetic factors associated with fatty liver disease-related hepatocellular carcinoma. Cancer Med 2023; 12:17798-17807. [PMID: 37644826 PMCID: PMC10524060 DOI: 10.1002/cam4.6410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
AIM Single-nucleotide polymorphisms (SNPs) in PNPLA3 and hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) genes are associated with fatty liver disease (FLD) progression and carcinogenesis. In the present study, we evaluated the characteristics of Japanese FLD patients according to HSD17B13 polymorphisms. METHODS We enrolled 402 patients who were clinically and pathologically diagnosed with FLD (alcoholic: 63 cases, nonalcoholic: 339 cases) at our hospital in 1990-2018 (228 males; median age: 54.9 [14.6-83.6] years). FLD patients with HSD17B13 A/A (212 cases) and others (A/AA or AA/AA; 190 cases) were compared. RESULTS Compared to patients with HSD17B13 A/A and others, those with the A/A genotype showed increased incidence of hepatocellular carcinoma (HCC) (A/A vs. others; 18.4% vs. 9.5%, p = 0.01), cardiovascular diseases (14.2% vs. 4.2%, p < 0.01), and hypertension (56.6% vs. 47.4%, p = 0.06). In patients without A/A, the HCC incidence was significantly reduced in those with alcohol-related FLD, fibrosis-4 index <2.67, and the PNPLA3 CC genotype; however, there was no significant difference in nonalcoholic-FLD. Patients without HSD17B13 A/A showed severe steatosis (77% vs. 88.6%, p < 0.01). New HCC developed in 11 cases and the 5-year incidence rate of HCC was 3.3% in patients with both PNPLA3 GG/GC and HSD17B13 A/A, which was significantly higher than the rate for those with other SNP profiles (0.6%, p = 0.03). CONCLUSIONS Inhibiting HSD17B13 activity may prevent HCC development, particularly in alcohol-related FLD and low-risk patients. Therefore, combinations of SNPs and other risk factors can be used for screening FLD-HCC.
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Affiliation(s)
- Tomomi Kogiso
- Department of Internal MedicineInstitute of Gastroenterology, Tokyo Women's Medical UniversityTokyoJapan
| | - Yuri Ogasawara
- Department of Internal MedicineInstitute of Gastroenterology, Tokyo Women's Medical UniversityTokyoJapan
| | - Kentaro Horiuchi
- Department of Internal MedicineInstitute of Gastroenterology, Tokyo Women's Medical UniversityTokyoJapan
| | - Makiko Taniai
- Department of Internal MedicineInstitute of Gastroenterology, Tokyo Women's Medical UniversityTokyoJapan
| | - Katsutoshi Tokushige
- Department of Internal MedicineInstitute of Gastroenterology, Tokyo Women's Medical UniversityTokyoJapan
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Amangurbanova M, Huang DQ, Loomba R. Review article: the role of HSD17B13 on global epidemiology, natural history, pathogenesis and treatment of NAFLD. Aliment Pharmacol Ther 2023; 57:37-51. [PMID: 36349732 PMCID: PMC10047549 DOI: 10.1111/apt.17292] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/07/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) occurs in around a quarter of the global population and is one of the leading causes of chronic liver disease. The phenotypic manifestation and the severity of NAFLD are influenced by an interplay of environmental and genetic factors. Recently, several inactivating variants in the novel 17-Beta hydroxysteroid dehydrogenase 13 (HSD17B13) gene have been found to be associated with a reduced risk of chronic liver diseases, including NAFLD. AIMS To review the existing literature on the epidemiology of HSD17B13 and discuss its role in the natural history, disease pathogenesis and treatment of NAFLD. METHODS We extensively searched relevant literature in PubMed, Google Scholar, clinicaltrials.gov and the reference list of articles included in the review. RESULTS HSD17B13 is a liver-specific, lipid droplet (LD)-associated protein that has enzymatic pathways involving steroids, pro-inflammatory lipid mediators and retinol. The estimated prevalence of the best characterised HSD17B13 variant (rs72613567) ranges from 5% in Africa to 34% in East Asia. Loss-of-function variants in HSD17B13 are protective against the progression of NAFLD from simple steatosis to non-alcoholic steatohepatitis (NASH), liver fibrosis, cirrhosis and hepatocellular carcinoma. Emerging data from mechanistic and preclinical studies with RNA interference (RNAi) and small molecule agents indicate that inhibiting HSD17B13 activity may prevent NAFLD progression. CONCLUSIONS The loss-of-function polymorphisms of the newly identified HSD17B13 gene mitigate the progression of NAFLD. It is important to understand the exact mechanism by which these variants exert a protective effect and implement the gathered knowledge in the treatment of NAFLD.
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Affiliation(s)
- Maral Amangurbanova
- NAFLD Research Center, Division of Gastroenterology. University of California at San Diego, La Jolla, CA, United States
| | - Daniel Q. Huang
- NAFLD Research Center, Division of Gastroenterology. University of California at San Diego, La Jolla, CA, United States
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Gastroenterology and Hepatology, Department of Medicine, National University Health System, Singapore
| | - Rohit Loomba
- NAFLD Research Center, Division of Gastroenterology. University of California at San Diego, La Jolla, CA, United States
- Division of Epidemiology, Department of Family Medicine and Public Health, University of California at San Diego, San Diego, CA, United States
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Wang R, Jian Q, Hu G, Du R, Xu X, Zhang F. Integrated Metabolomics and Transcriptomics Reveal Metabolic Patterns in Retina of STZ-Induced Diabetic Retinopathy Mouse Model. Metabolites 2022; 12:metabo12121245. [PMID: 36557283 PMCID: PMC9782096 DOI: 10.3390/metabo12121245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Diabetic retinopathy (DR), as the leading cause of vision loss in the working-age population, exhibits unique metabolite profiles in human plasma and vitreous. However, those in retina are not fully understood. Here, we utilized liquid and gas chromatography-tandem mass spectrometry technology to explore metabolite characteristics of streptozotocin (STZ)-induced diabetic mice retina. A total of 145 metabolites differed significantly in diabetic retinas compared with controls. These metabolites are mainly enriched in the Warburg effect, and valine, leucine and isoleucine degradation pathways. To further identify underlying regulators, RNA sequencing was performed to integrate metabolic enzyme alterations with metabolomics in STZ-induced diabetic retina. Retinol metabolism and tryptophan metabolism are the shared pathways enriched by metabolome and transcriptome. Additionally, transcriptomic analysis identified 71 differentially expressed enzyme-related genes including Hk2, Slc7a5, Aldh1a3 and Tph integrated with altered metabolic pathways. In addition, single nucleotide polymorphisms within 6 out of 71 genes are associated with increased diabetes risk. This study lays the foundation for mechanism research and the therapeutic target development of DR.
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Affiliation(s)
- Ruonan Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai 200080, China
| | - Qizhi Jian
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai 200080, China
| | - Guangyi Hu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai 200080, China
| | - Rui Du
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Xun Xu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai 200080, China
- Correspondence: (X.X.); (F.Z.)
| | - Fang Zhang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- National Clinical Research Center for Eye Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
- Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200080, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai 200080, China
- Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai 200080, China
- Correspondence: (X.X.); (F.Z.)
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Ruan D, Yang J, Zhuang Z, Ding R, Huang J, Quan J, Gu T, Hong L, Zheng E, Li Z, Cai G, Wang X, Wu Z. Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations. Front Genet 2022; 12:812456. [PMID: 35154256 PMCID: PMC8830653 DOI: 10.3389/fgene.2021.812456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/15/2021] [Indexed: 01/02/2023] Open
Abstract
Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.
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Affiliation(s)
- Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Jinyan Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Xiaopeng Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Xiaopeng Wang, ; Zhenfang Wu,
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
- *Correspondence: Xiaopeng Wang, ; Zhenfang Wu,
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Ruiz-Narváez EA. Genetic architecture of type 2 diabetes and its shared genetic component with low birth weight in African Americans. Curr Opin Clin Nutr Metab Care 2021; 24:326-332. [PMID: 33883416 DOI: 10.1097/mco.0000000000000757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Recent large-scale multiancestry efforts has contributed to our knowledge of the hereditary basis of type 2 diabetes (T2D). The present review will summarize findings of the genetic basis of T2D in African Americans, a population group with a disproportionate burden of this disease. RECENT FINDINGS To date, >400 risk genetic variants have been found to be associated with the risk of T2D across populations of different ancestries. Although these findings are based on primarily European-ancestry populations, most of the identified loci show similar associations in African Americans. Ancestry-specific analyses including genome-wide associations studies (GWAS) in African Americans, Africans; as well as admixture mapping scans in African Americans have identified additional risk variants and genomic loci associate with the risk of T2D. These efforts have also uncovered new genetic links between low birth weight and T2D. In particular, admixture mapping approaches have identified a shared genetic ancestry component of both phenotypic traits in African Americans. SUMMARY Recent findings have helped us to better understand the genetic basis of T2D in African Americans. Of particular interest are new genetic discoveries linking low birth weight and T2D, two conditions with a much higher prevalence in African Americans compared to U.S. whites. Continuing work, including large-scale sequencing efforts would add to our knowledge of the genetic architecture of T2D in African Americans, as well as genetic links with other conditions.
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Affiliation(s)
- Edward A Ruiz-Narváez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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Is HSD17B13 Genetic Variant a Protector for Liver Dysfunction? Future Perspective as a Potential Therapeutic Target. J Pers Med 2021; 11:jpm11070619. [PMID: 34208839 PMCID: PMC8304981 DOI: 10.3390/jpm11070619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/20/2022] Open
Abstract
As diet and lifestyle have changed, fatty liver disease (FLD) has become more and more prevalent. Many genetic risk factors, such as variants of PNPLA3, TM6SF2, GCKR, and MBOAT7, have previously been uncovered via genome wide association studies (GWAS) to be associated with FLD. In 2018, a genetic variant (rs72613567, T > TA) of hydroxysteroid 17-β dehydrogenase family 13 (HSD17B13) was first associated with a lower risk of developing alcoholic liver disease and non-alcoholic fatty liver disease (NAFLD) in minor allele carriers. Other HSD17B13 variants were also later linked with either lower inflammation scores among NAFLD patients or protection against NAFLD (rs6834314, A > G and rs9992651, G > A) respectively. HSD17B13 is a lipid droplet-associated protein, but its function is still ambiguous. Compared to the other genetic variants that increase risk for FLD, HSD17B13 variants serve a protective role, making this gene a potential therapeutic target. However, the mechanism by which these variants reduce the risk of developing FLD is still unclear. Because studies in cell lines and mouse models have produced conflicting results, human liver tissue modeling using induced pluripotent stem cells may be the best way to move forward and solve this mystery.
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11
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Schwantes-An TH, Darlay R, Mathurin P, Masson S, Liangpunsakul S, Mueller S, Aithal GP, Eyer F, Gleeson D, Thompson A, Muellhaupt B, Stickel F, Soyka M, Goldman D, Liang T, Lumeng L, Pirmohamed M, Nalpas B, Jacquet JM, Moirand R, Nahon P, Naveau S, Perney P, Botwin G, Haber PS, Seitz HK, Day CP, Foroud TM, Daly AK, Cordell HJ, Whitfield JB, Morgan TR, Seth D. Genome-wide Association Study and Meta-analysis on Alcohol-Associated Liver Cirrhosis Identifies Genetic Risk Factors. Hepatology 2021; 73:1920-1931. [PMID: 32853455 DOI: 10.1002/hep.31535] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Only a minority of heavy drinkers progress to alcohol-associated cirrhosis (ALC). The aim of this study was to identify common genetic variants that underlie risk for ALC. APPROACH AND RESULTS We analyzed data from 1,128 subjects of European ancestry with ALC and 614 heavy-drinking subjects without known liver disease from Australia, the United States, the United Kingdom, and three countries in Europe. A genome-wide association study (GWAS) was performed, adjusting for principal components and clinical covariates (alcohol use, age, sex, body mass index, and diabetes). We validated our GWAS findings using UK Biobank. We then performed a meta-analysis combining data from our study, the UK Biobank, and a previously published GWAS. Our GWAS found genome-wide significant risk association of rs738409 in patatin-like phospholipase domain containing 3 (PNPLA3) (odds ratio [OR] = 2.19 [G allele], P = 4.93 × 10-17 ) and rs4607179 near HSD17B13 (OR = 0.57 [C allele], P = 1.09 × 10-10 ) with ALC. Conditional analysis accounting for the PNPLA3 and HSD17B13 loci identified a protective association at rs374702773 in Fas-associated factor family member 2 (FAF2) (OR = 0.61 [del(T) allele], P = 2.56 × 10-8 ) for ALC. This association was replicated in the UK Biobank using conditional analysis (OR = 0.79, P = 0.001). Meta-analysis (without conditioning) confirmed genome-wide significance for the identified FAF2 locus as well as PNPLA3 and HSD17B13. Two other previously known loci (SERPINA1 and SUGP1/TM6SF2) were also genome-wide significant in the meta-analysis. GeneOntology pathway analysis identified lipid droplets as the target for several identified genes. In conclusion, our GWAS identified a locus at FAF2 associated with reduced risk of ALC among heavy drinkers. Like the PNPLA3 and HSD17B13 gene products, the FAF2 product has been localized to fat droplets in hepatocytes. CONCLUSIONS Our genetic findings implicate lipid droplets in the biological pathway(s) underlying ALC.
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Affiliation(s)
- Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | | | - Steven Masson
- Faculty of Medical Sciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Suthat Liangpunsakul
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University, Indianapolis, IN
| | - Sebastian Mueller
- Department of Internal Medicine, Salem Medical Center and Center for Alcohol Research, University of Heidelberg, Heidelberg, Germany
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals and the University of Nottingham, Nottingham, United Kingdom
| | - Florian Eyer
- Division of Clinical Toxicology, Department of Internal Medicine 2, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dermot Gleeson
- The Clinical Research Facility, The Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Andrew Thompson
- MRC Centre for Drug Safety Science, Liverpool Centre for Alcohol Research, University of Liverpool, The Royal Liverpool and Broadgreen University Hospitals NHS Trust, and Liverpool Health Partners, Liverpool, United Kingdom
| | - Beat Muellhaupt
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Soyka
- Psychiatric Hospital University of Munich, Munich, Germany.,Privatklinik Meiringen, Willigen, Meiringen, Switzerland
| | | | - Tiebing Liang
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University, Indianapolis, IN
| | - Lawrence Lumeng
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University, Indianapolis, IN
| | - Munir Pirmohamed
- MRC Centre for Drug Safety Science, Liverpool Centre for Alcohol Research, University of Liverpool, The Royal Liverpool and Broadgreen University Hospitals NHS Trust, and Liverpool Health Partners, Liverpool, United Kingdom
| | - Bertrand Nalpas
- Service Addictologie, CHRU Caremeau, Nîmes, France.,DISC, Inserm, Paris, France
| | | | - Romain Moirand
- University Rennes, INRAE, INSERM, CHU Rennes, Institute NUMECAN (Nutrition Metabolisms and Cancer), Rennes, France
| | - Pierre Nahon
- APHP, Liver Unit, Hospital Jean Verdier, Bondy, France.,University Paris 13, Bobigny, France.,Inserm U1162 "Functional Genomics of Solid Tumors,", Paris, France
| | | | | | - Greg Botwin
- Medical and Research Services, VA Long Beach Healthcare System, Long Beach, CA.,Translational Genomics Group, Inflammatory Bowel & Immunobiology Research Institute, Los Angeles, CA
| | - Paul S Haber
- Drug Health Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Helmut K Seitz
- Department of Internal Medicine, Salem Medical Center and Center for Alcohol Research, University of Heidelberg, Heidelberg, Germany
| | - Christopher P Day
- Faculty of Medical Sciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN
| | - Ann K Daly
- Faculty of Medical Sciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Timothy R Morgan
- Medical and Research Services, VA Long Beach Healthcare System, Long Beach, CA
| | - Devanshi Seth
- Drug Health Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
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12
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Zhang Q, Cai Z, Lhomme M, Sahana G, Lesnik P, Guerin M, Fredholm M, Karlskov-Mortensen P. Inclusion of endophenotypes in a standard GWAS facilitate a detailed mechanistic understanding of genetic elements that control blood lipid levels. Sci Rep 2020; 10:18434. [PMID: 33116219 PMCID: PMC7595098 DOI: 10.1038/s41598-020-75612-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Dyslipidemia is the primary cause of cardiovascular disease, which is a serious human health problem in large parts of the world. Therefore, it is important to understand the genetic and molecular mechanisms that regulate blood levels of cholesterol and other lipids. Discovery of genetic elements in the regulatory machinery is often based on genome wide associations studies (GWAS) focused on end-point phenotypes such as total cholesterol level or a disease diagnosis. In the present study, we add endophenotypes, such as serum levels of intermediate metabolites in the cholesterol synthesis pathways, to a GWAS analysis and use the pig as an animal model. We do this to increase statistical power and to facilitate biological interpretation of results. Although the study population was limited to ~ 300 individuals, we identify two genome-wide significant associations and ten suggestive associations. Furthermore, we identify 28 tentative associations to loci previously associated with blood lipids or dyslipidemia associated diseases. The associations with endophenotypes may inspire future studies that can dissect the biological mechanisms underlying these previously identified associations and add a new level of understanding to previously identified associations.
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Affiliation(s)
- Qianqian Zhang
- Bioinformatics Research Centre (BiRC), Aarhus University, C.F.Møllers Allé 8, 8000, Aarhus C, Denmark
| | - Zexi Cai
- Center for Quantitativ Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Danmark
| | - Marie Lhomme
- ICANalytics, Institute of Cardiometabolism and Nutrition (ICAN), 47-83 boulevard de l'hôpital, 75013, Paris, France
| | - Goutam Sahana
- Center for Quantitativ Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Danmark
| | - Philippe Lesnik
- Unité de Recherche sur les maladies cardiovasculaires, le métabolisme et la nutrition, INSERM UMR_S 1166, ICAN Institute of Cardiometabolism & Nutrition, Faculté de Médecine Sorbonne Université, Sorbonne Université, 4ème étage, Bureau 421,91, boulevard de l'Hôpital, 75634, Paris Cedex 13, France
| | - Maryse Guerin
- Unité de Recherche sur les maladies cardiovasculaires, le métabolisme et la nutrition, INSERM UMR_S 1166, ICAN Institute of Cardiometabolism & Nutrition, Faculté de Médecine Sorbonne Université, Sorbonne Université, 4ème étage, Bureau 421,91, boulevard de l'Hôpital, 75634, Paris Cedex 13, France
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Gronnegaardsvej 3, 1870, Frederikgsberg C, Denmark
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Gronnegaardsvej 3, 1870, Frederikgsberg C, Denmark.
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13
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Stickel F, Lutz P, Buch S, Nischalke HD, Silva I, Rausch V, Fischer J, Weiss KH, Gotthardt D, Rosendahl J, Marot A, Elamly M, Krawczyk M, Casper M, Lammert F, Buckley TWM, McQuillin A, Spengler U, Eyer F, Vogel A, Marhenke S, von Felden J, Wege H, Sharma R, Atkinson S, Franke A, Nehring S, Moser V, Schafmayer C, Spahr L, Lackner C, Stauber RE, Canbay A, Link A, Valenti L, Grove JI, Aithal GP, Marquardt JU, Fateen W, Zopf S, Dufour JF, Trebicka J, Datz C, Deltenre P, Mueller S, Berg T, Hampe J, Morgan MY. Genetic Variation in HSD17B13 Reduces the Risk of Developing Cirrhosis and Hepatocellular Carcinoma in Alcohol Misusers. Hepatology 2020; 72:88-102. [PMID: 31630428 DOI: 10.1002/hep.30996] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Carriage of rs738409:G in patatin-like phospholipase domain containing 3 (PNPLA3) is associated with an increased risk for developing alcohol-related cirrhosis and hepatocellular carcinoma (HCC). Recently, rs72613567:TA in hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) was shown to be associated with a reduced risk for developing alcohol-related liver disease and to attenuate the risk associated with carriage of PNPLA3 rs738409:G. This study explores the risk associations between these two genetic variants and the development of alcohol-related cirrhosis and HCC. APPROACH AND RESULTS Variants in HSD17B13 and PNPLA3 were genotyped in 6,171 participants, including 1,031 with alcohol-related cirrhosis and HCC, 1,653 with alcohol-related cirrhosis without HCC, 2,588 alcohol misusers with no liver disease, and 899 healthy controls. Genetic associations with the risks for developing alcohol-related cirrhosis and HCC were determined using logistic regression analysis. Carriage of HSD17B13 rs72613567:TA was associated with a lower risk for developing both cirrhosis (odds ratio [OR], 0.79; 95% confidence interval [CI], 0.72-0.88; P = 8.13 × 10-6 ) and HCC (OR, 0.77; 95% CI, 0.68-0.89; P = 2.27 × 10-4 ), whereas carriage of PNPLA3 rs738409:G was associated with an increased risk for developing cirrhosis (OR, 1.70; 95% CI, 1.54-1.88; P = 1.52 × 10-26 ) and HCC (OR, 1.77; 95% CI, 1.58-1.98; P = 2.31 × 10-23 ). These associations remained significant after adjusting for age, sex, body mass index, type 2 diabetes, and country. Carriage of HSD17B13 rs72613567:TA attenuated the risk for developing cirrhosis associated with PNPLA3 rs738409:G in both men and women, but the protective effect against the subsequent development of HCC was only observed in men (ORallelic , 0.75; 95% CI, 0.64-0.87; P = 1.72 × 10-4 ). CONCLUSIONS Carriage of variants in PNPLA3 and HSD17B13 differentially affect the risk for developing advanced alcohol-related liver disease. A genotypic/phenotypic risk score might facilitate earlier diagnosis of HCC in this population.
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Affiliation(s)
- Felix Stickel
- Department of Gastroenterology and Hepatology, University Hospital of Zürich, Switzerland
| | - Philipp Lutz
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | | | - Ines Silva
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Vanessa Rausch
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Janett Fischer
- Division of Hepatology, Clinic and Polyclinic for Gastroenterology, Hepatology, Infectiology and Pneumology, University Clinic Leipzig, Leipzig, Germany
| | - Karl Heinz Weiss
- Department of Internal Medicine IV, Medical University of Heidelberg, Germany
| | - Daniel Gotthardt
- Department of Internal Medicine IV, Medical University of Heidelberg, Germany
| | - Jonas Rosendahl
- Department of Gastroenterology, University Hospital Halle/Saale, Germany
| | - Astrid Marot
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Mona Elamly
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany.,Laboratory of Metabolic Liver Diseases, Department of General, Transplant and Liver Surgery, Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Markus Casper
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Homburg, Germany
| | - Thomas W M Buckley
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, UK
| | - Ulrich Spengler
- Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Florian Eyer
- Department of Clinical Toxicology, Klinikum Rechts der Isar, Technical University of Munich, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Silke Marhenke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Johann von Felden
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Wege
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rohini Sharma
- Department of Metabolism, Digestion & Reproduction, Division of Surgery and Cancer, Imperial College London, London, UK
| | - Stephen Atkinson
- Department of Metabolism, Digestion & Reproduction, Division of Surgery and Cancer, Imperial College London, London, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Sophie Nehring
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Vincent Moser
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | - Laurent Spahr
- Departments of Gastroenterology and Hepatology, University Hospitals of Geneva and Faculty of Medicine, Geneva, Switzerland
| | | | - Rudolf E Stauber
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Ali Canbay
- Ruhr-Universität Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Alexander Link
- Ruhr-Universität Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Translational Medicine - Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Jane I Grove
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Jens U Marquardt
- Department of Medicine I, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Waleed Fateen
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK.,Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK
| | - Steffen Zopf
- Medical Department 1, University of Erlangen-Nuremberg, Germany
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, Inselspital, University of Berne, Berne, Switzerland
| | - Jonel Trebicka
- Department of Internal Medicine I, Goethe University Frankfurt, Frankfurt, Germany
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private Medical University of Salzburg, Oberndorf, Austria
| | - Pierre Deltenre
- Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Switzerland
| | - Sebastian Mueller
- Department of Internal Medicine and Center for Alcohol Research, Salem Medical Center University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Berg
- Division of Hepatology, Clinic and Polyclinic for Gastroenterology, Hepatology, Infectiology and Pneumology, University Clinic Leipzig, Leipzig, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Germany
| | - Marsha Y Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, UK
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14
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In Search for Genes Related to Atherosclerosis and Dyslipidemia Using Animal Models. Int J Mol Sci 2020; 21:ijms21062097. [PMID: 32197550 PMCID: PMC7139774 DOI: 10.3390/ijms21062097] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Atherosclerosis is a multifactorial chronic disease that affects large arteries and may lead to fatal consequences. According to current understanding, inflammation and lipid accumulation are the two key mechanisms of atherosclerosis development. Animal models based on genetically modified mice have been developed to investigate these aspects. One such model is low-density lipoprotein (LDL) receptor knockout (KO) mice (ldlr-/-), which are characterized by a moderate increase of plasma LDL cholesterol levels. Another widely used genetically modified mouse strain is apolipoprotein-E KO mice (apoE-/-) that lacks the primary lipoprotein required for the uptake of lipoproteins through the hepatic receptors, leading to even greater plasma cholesterol increase than in ldlr-/- mice. These and other animal models allowed for conducting genetic studies, such as genome-wide association studies, microarrays, and genotyping methods, which helped identifying more than 100 mutations that contribute to atherosclerosis development. However, translation of the results obtained in animal models for human situations was slow and challenging. At the same time, genetic studies conducted in humans were limited by low sample sizes and high heterogeneity in predictive subclinical phenotypes. In this review, we summarize the current knowledge on the use of KO mice for identification of genes implicated in atherosclerosis and provide a list of genes involved in atherosclerosis-associated inflammatory pathways and their brief characteristics. Moreover, we discuss the approaches for candidate gene search in animals and humans and discuss the progress made in the field of epigenetic studies that appear to be promising for identification of novel biomarkers and therapeutic targets.
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15
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House JS, Motsinger-Reif AA. Fibrate pharmacogenomics: expanding past the genome. Pharmacogenomics 2020; 21:293-306. [PMID: 32180510 DOI: 10.2217/pgs-2019-0140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Fibrates are a medication class prescribed for decades as 'broad-spectrum' lipid-modifying agents used to lower blood triglyceride levels and raise high-density lipoprotein cholesterol levels. Such lipid changes are associated with a decrease in cardiovascular disease, and fibrates are commonly used to reduce risk of dangerous cardiovascular outcomes. As with most drugs, it is well established that response to fibrate treatment is variable, and this variation is heritable. This has motivated the investigation of pharmacogenomic determinants of response, and multiple studies have discovered a number of genes associated with fibrate response. Similar to other complex traits, the interrogation of single nucleotide polymorphisms using candidate gene or genome-wide approaches has not revealed a substantial portion of response variation. However, recent innovations in technological platforms and advances in statistical methodologies are revolutionizing the use and integration of other 'omes' in pharmacogenomics studies. Here, we detail successes, challenges, and recent advances in fibrate pharmacogenomics.
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Affiliation(s)
- John S House
- Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Department of Health & Human Services, Research Triangle Park, NC 27709, USA
| | - Alison A Motsinger-Reif
- Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Department of Health & Human Services, Research Triangle Park, NC 27709, USA
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16
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Balashanmugam MV, Shivanandappa TB, Nagarethinam S, Vastrad B, Vastrad C. Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. Biomolecules 2019; 10:biom10010035. [PMID: 31881747 PMCID: PMC7022900 DOI: 10.3390/biom10010035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 12/31/2022] Open
Abstract
Coronary artery disease (CAD) is a major cause of end-stage cardiac disease. Although profound efforts have been made to illuminate the pathogenesis, the molecular mechanisms of CAD remain to be analyzed. To identify the candidate genes in the advancement of CAD, microarray dataset GSE23766 was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified, and pathway and gene ontology (GO) enrichment analyses were performed. The protein-protein interaction network was constructed and the module analysis was performed using the Biological General Repository for Interaction Datasets (BioGRID) and Cytoscape. Additionally, target genes-miRNA regulatory network and target genes-TF regulatory network were constructed and analyzed. There were 894 DEGs between male human CAD samples and female human CAD samples, including 456 up regulated genes and 438 down regulated genes. Pathway enrichment analyses revealed that DEGs (up and down regulated) were mostly enriched in the superpathway of steroid hormone biosynthesis, ABC transporters, oxidative ethanol degradation III and Complement and coagulation cascades. Similarly, geneontology enrichment analyses revealed that DEGs (up and down regulated) were mostly enriched in the forebrain neuron differentiation, filopodium membrane, platelet degranulation and blood microparticle. In the PPI network and modules (up and down regulated), MYC, NPM1, TRPC7, UBC, FN1, HEMK1, IFT74 and VHL were hub genes. In the target genes-miRNA regulatory network and target genes—TF regulatory network (up and down regulated), TAOK1, KHSRP, HSD17B11 and PAH were target genes. In conclusion, the pathway and GO ontology enriched by DEGs may reveal the molecular mechanism of CAD. Its hub and target genes, MYC, NPM1, TRPC7, UBC, FN1, HEMK1, IFT74, VHL, TAOK1, KHSRP, HSD17B11 and PAH were expected to be new targets for CAD. Our finding provided clues for exploring molecular mechanism and developing new prognostics, diagnostic and therapeutic strategies for CAD.
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Affiliation(s)
- Meenashi Vanathi Balashanmugam
- Department of Biomedical Sciences, College of Pharmacy, Shaqra University, Al Dawadmi 11911, Saudi Arabia; (M.V.B.); (T.B.S.); (S.N.)
| | - Thippeswamy Boreddy Shivanandappa
- Department of Biomedical Sciences, College of Pharmacy, Shaqra University, Al Dawadmi 11911, Saudi Arabia; (M.V.B.); (T.B.S.); (S.N.)
| | - Sivagurunathan Nagarethinam
- Department of Biomedical Sciences, College of Pharmacy, Shaqra University, Al Dawadmi 11911, Saudi Arabia; (M.V.B.); (T.B.S.); (S.N.)
| | - Basavaraj Vastrad
- Department of Pharmaceutics, SET’S College of Pharmacy, Dharwad, Karnataka 580002, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka
- Correspondence: ; Tel.: +91-9480-073398
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17
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Tuteja S, Qu L, Vujkovic M, Dunbar RL, Chen J, DerOhannessian S, Rader DJ. Genetic Variants Associated With Plasma Lipids Are Associated With the Lipid Response to Niacin. J Am Heart Assoc 2019; 7:e03488. [PMID: 30371334 PMCID: PMC6404865 DOI: 10.1161/jaha.117.008461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Background Niacin is a broad-spectrum lipid-modulating drug, but its mechanism of action is unclear. Genome-wide association studies have identified multiple loci associated with blood lipid levels and lipoprotein (a). It is unknown whether these loci modulate response to niacin. Methods and Results Using data from the AIM - HIGH (Atherothrombosis Intervention in Metabolic Syndrome with Low HDL /High Triglycerides and Impact on Global Health Outcomes) trial (n=2054 genotyped participants), we determined whether genetic variations at validated loci were associated with a differential change in plasma lipids and lipoprotein (a) 1 year after randomization to either statin+placebo or statin+niacin in a variant-treatment interaction model. Nominally significant interactions ( P<0.05) were found for genetic variants in MVK , LIPC , PABPC 4, AMPD 3 with change in high-density lipoprotein cholesterol; SPTLC 3 with change in low-density lipoprotein cholesterol; TOM 1 with change in total cholesterol; PDXDC 1 and CYP 26A1 with change in triglycerides; and none for lipoprotein (a). We also investigated whether these loci were associated with cardiovascular events. The risk of coronary disease related death was higher in the minor allele carriers at the LIPC locus in the placebo group (odds ratio 2.08, 95% confidence interval 1.11-3.90, P=0.02) but not observed in the niacin group (odds ratio 0.89, 95% confidence interval 0.48-1.65, P=0.7); P-interaction =0.02. There was a greater risk for acute coronary syndrome (odds ratio 1.85, 95% confidence interval 1.16-2.77, P=0.02) and revascularization events (odds ratio 1.64, 95% confidence interval 1.2-2.22, P=0.002) in major allele carriers at the CYP 26A1 locus in the placebo group not seen in the niacin group. Conclusions Genetic variation at loci previously associated with steady-state lipid levels displays evidence for lipid response to niacin treatment. Clinical Trials Registration URL: https://www.clinicaltrials.gov . Unique identifier: NCT00120289.
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Affiliation(s)
- Sony Tuteja
- 1 Department of Medicine Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Liming Qu
- 1 Department of Medicine Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Marijana Vujkovic
- 2 Department of Biostatistics and Epidemiology Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Richard L Dunbar
- 1 Department of Medicine Perelman School of Medicine at the University of Pennsylvania Philadelphia PA.,4 Cardiometabolic and Lipid Clinic Corporal Michael J. Crescenz VA Medical Center Philadelphia PA.,5 ICON plc North Wales PA
| | - Jinbo Chen
- 2 Department of Biostatistics and Epidemiology Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Stephanie DerOhannessian
- 1 Department of Medicine Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
| | - Daniel J Rader
- 1 Department of Medicine Perelman School of Medicine at the University of Pennsylvania Philadelphia PA.,3 Department of Genetics Perelman School of Medicine at the University of Pennsylvania Philadelphia PA
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18
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Mohamadi M, Ghaedi H, Kazerouni F, Erfanian Omidvar M, Kalbasi S, Shanaki M, Miraalamy G, Rahimipour A. Deregulation of long noncoding RNA SNHG17 and TTC28-AS1 is associated with type 2 diabetes mellitus. Scandinavian Journal of Clinical and Laboratory Investigation 2019; 79:519-523. [PMID: 31509021 DOI: 10.1080/00365513.2019.1664760] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key players in several biological processes and complex diseases including type 2 diabetes mellitus (T2DM). The purpose of this study was to investigate the expression levels of SNHG17 and TTC28-AS1 in T2DM patients. Quantitative real-time RT-PCR analysis was performed using peripheral blood mononuclear cells (PBMCs) samples from patients diagnosed with T2DM and healthy controls. Binary logistic regression analysis was carried out to determine the odds of development of T2DM based on expression levels of lncRNAs and clinical characteristic of the subjects. Spearman's correlation analysis was used to clarify the correlation between SNHG17 and TTC28-AS1 expressions to metabolic features. We found that SNHG17 and TTC28-AS1were down-regulated in the T2DM group compared to the healthy control group. The logistic regression revealed that body mass index (BMI), systolic blood pressure (SBP), fasting blood glucose (FBG) and TTC28-AS1 expression substantially affect T2DM susceptibility. Furthermore, expression of SNHG17 was negatively correlated with high-density lipoprotein cholesterol (HDL-C) and expression of TTC28-AS1 was positively correlated with low-density lipoprotein cholesterol (LDL-C). Decreased expressions of lncRNAs TTC28-AS1 and SNHG17 in T2DM are possibly associated with the development of T2DM.
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Affiliation(s)
- Mahroo Mohamadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Faranak Kazerouni
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Maryam Erfanian Omidvar
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saeid Kalbasi
- Department of Endocrinology, Loghman Hospital, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Mehrnoosh Shanaki
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Ghasem Miraalamy
- Ali-Asghar Hospital, Iran University of Medical Sciences , Tehran , Iran
| | - Ali Rahimipour
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences , Tehran , Iran.,Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences , Tehran , Iran
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19
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ZRANB3 is an African-specific type 2 diabetes locus associated with beta-cell mass and insulin response. Nat Commun 2019; 10:3195. [PMID: 31324766 PMCID: PMC6642147 DOI: 10.1038/s41467-019-10967-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Genome analysis of diverse human populations has contributed to the identification of novel genomic loci for diseases of major clinical and public health impact. Here, we report a genome-wide analysis of type 2 diabetes (T2D) in sub-Saharan Africans, an understudied ancestral group. We analyze ~18 million autosomal SNPs in 5,231 individuals from Nigeria, Ghana and Kenya. We identify a previously-unreported genome-wide significant locus: ZRANB3 (Zinc Finger RANBP2-Type Containing 3, lead SNP p = 2.831 × 10−9). Knockdown or genomic knockout of the zebrafish ortholog results in reduction in pancreatic β-cell number which we demonstrate to be due to increased apoptosis in islets. siRNA transfection of murine Zranb3 in MIN6 β-cells results in impaired insulin secretion in response to high glucose, implicating Zranb3 in β-cell functional response to high glucose conditions. We also show transferability in our study of 32 established T2D loci. Our findings advance understanding of the genetics of T2D in non-European ancestry populations. Type 2 diabetes (T2D) is prevalent in populations worldwide, however, mostly studied in European and mixed-ancestry populations. Here, the authors perform a genome-wide association study for T2D in over 5,000 sub-Saharan Africans and identify a locus, ZRANB3, that is specific for this population.
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20
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Abstract
Dyslipidemia is one of the major cardiovascular risk factors, but beyond statin treatment-which represents the cornerstone of therapy-a relevant practical uncertainty regards the use of fibrate derivatives. In the lack of successful results from the main cardiovascular trials, guidelines recommend the use of peroxisome proliferator-activated receptor agonists in selected cases, i.e. patients with true atherogenic dyslipidemia. However, recent observations indicate that fenofibrate treatment may provide a reliable complementary support against residual cardiovascular risk. We therefore summarize current evidence on fenofibrate, seeking to provide an updated interpretation of recent studies in the field.
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21
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Su W, Mao Z, Liu Y, Zhang X, Zhang W, Gustafsson JA, Guan Y. Role of HSD17B13 in the liver physiology and pathophysiology. Mol Cell Endocrinol 2019; 489:119-125. [PMID: 30365983 DOI: 10.1016/j.mce.2018.10.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 02/06/2023]
Abstract
17β-Hydroxysteroid dehydrogenases (HSD17Bs) comprise a large family of 15 members that are mainly involved in sex hormone metabolism. Some HSD17Bs enzymes also play key roles in cholesterol and fatty acid metabolism. Recent study showed that hydroxysteroid 17β-dehydrogenase 13 (HSD17B13), an enzyme with unknown biological function, is a novel liver-specific lipid droplet (LD)-associated protein in mouse and humans. HSD17B13 expression is markedly upregulated in patients and mice with non-alcoholic fatty liver disease (NAFLD). Hepatic overexpression of HSD17B13 promotes lipid accumulation in the liver. In this review, we summarize recent progress regarding the role of HSD17B13 in the regulation of hepatic lipid homeostasis and discuss genetic, genomic and proteomic evidence supporting the pathogenic role of HSD17B13 in NAFLD. We also emphasize its potential as a biomarker of advanced liver disease, such as non-alcoholic steatohepatitis (NASH) and liver cancer.
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Affiliation(s)
- Wen Su
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen, China; Department of Pathology, Shenzhen University Health Science Center, Shenzhen, China
| | - Zhuo Mao
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yiao Liu
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiaoyan Zhang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning, 116044, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Weizhen Zhang
- Shenzhen University Medical Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Jan-Ake Gustafsson
- Center for Nuclear Receptors and Cell Signaling, University of Houston, 3013 Cullen Blv, 77204, Houston, TX, USA; Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
| | - Youfei Guan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning, 116044, China; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, 116044, China.
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22
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Evans KL, Wirtz HS, Li J, She R, Maya J, Gui H, Hamer A, Depre C, Lanfear DE. Genetics of heart rate in heart failure patients (GenHRate). Hum Genomics 2019; 13:22. [PMID: 31113495 PMCID: PMC6528282 DOI: 10.1186/s40246-019-0206-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/22/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Elevated resting heart rate (HR) is a risk factor and therapeutic target in patients with heart failure (HF) and reduced ejection fraction (HFrEF). Previous studies indicate a genetic contribution to HR in population samples but there is little data in patients with HFrEF. METHODS Patients who met Framingham criteria for HF and had an ejection fraction < 50% were prospectively enrolled in a genetic HF registry (2007-2015, n = 1060). All participants donated blood for DNA and underwent genome-wide genotyping with additional variants called via imputation. We performed testing of previously identified variant "hits" (43 loci) as well as a genome-wide association (GWAS) of HR, adjusted for race, using Efficient Mixed-Model Association Expedited (EMMAX). RESULTS The cohort was 35% female, 51% African American, and averaged 68 years of age. There was a 2 beats per minute (bpm) difference in HR by race, AA being slightly higher. Among 43 candidate variants, 4 single nucleotide polymorphisms (SNPs) in one gene (GJA1) were significantly associated with HR. In genome-wide testing, one statistically significant association peak was identified on chromosome 22q13, with strongest SNP rs535263906 (p = 3.3 × 10-8). The peak is located within the gene Cadherin EGF LAG Seven-Pass G-Type Receptor 1 (CELSR1), encoding a cadherin super-family cell surface protein identified in GWAS of other phenotypes (e.g., stroke). The highest associated SNP was specific to the African American population. CONCLUSIONS These data confirm GJA1 association with HR in the setting of HFrEF and identify novel candidate genes for HR in HFrEF patients, particularly CELSR1. These associations should be tested in additional cohorts.
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Affiliation(s)
- Kaleigh L. Evans
- 0000 0001 2160 8953grid.413103.4Department of Internal Medicine, Henry Ford Hospital, 2799 West Grand Blvd. K-14, Detroit, MI 48202 USA
| | - Heidi S. Wirtz
- 0000 0001 0657 5612grid.417886.4Amgen Inc, Thousand Oaks, CA USA
| | - Jia Li
- 0000 0000 8523 7701grid.239864.2Department of Public Health Sciences, Henry Ford Health System, Detroit, MI USA
| | - Ruicong She
- 0000 0000 8523 7701grid.239864.2Department of Public Health Sciences, Henry Ford Health System, Detroit, MI USA
| | - Juan Maya
- 0000 0001 0657 5612grid.417886.4Amgen Inc, Thousand Oaks, CA USA
| | - Hongsheng Gui
- 0000 0001 2160 8953grid.413103.4Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI USA
| | - Andrew Hamer
- 0000 0001 0657 5612grid.417886.4Amgen Inc, Thousand Oaks, CA USA
| | - Christophe Depre
- 0000 0001 0657 5612grid.417886.4Amgen Inc, Thousand Oaks, CA USA
| | - David E. Lanfear
- 0000 0001 2160 8953grid.413103.4Department of Internal Medicine, Henry Ford Hospital, 2799 West Grand Blvd. K-14, Detroit, MI 48202 USA
- 0000 0001 2160 8953grid.413103.4Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI USA
- 0000 0001 2160 8953grid.413103.4Heart and Vascular Institute, Henry Ford Hospital, Detroit, MI USA
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23
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Ferenci P, Pfeiffenberger J, Stättermayer AF, Stauber RE, Willheim C, Weiss KH, Munda-Steindl P, Trauner M, Schilsky M, Zoller H. HSD17B13 truncated variant is associated with a mild hepatic phenotype in Wilson's Disease. JHEP Rep 2019; 1:2-8. [PMID: 32039348 PMCID: PMC7001574 DOI: 10.1016/j.jhepr.2019.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 12/13/2022] Open
Abstract
HSD17B13 encodes hydroxysteroid 17-β dehydrogenase 13, a novel liver lipid-droplet associated protein that is involved in the regulation of lipid biosynthetic processes. A protein-truncating HSD17B13 variant (rs72613567) was shown to protect individuals from alcoholic and non-alcoholic liver disease. Since steatosis is a common feature in Wilson's disease (WD), we aimed to assess whether the HSD17B13 variant modulates the phenotypic presentation and progression of WD. METHODS The HSD17B13:TA (rs72613567) variant was determined by allelic discrimination real-time PCR in 586 patients. The HSD17B13 genotype was correlated with the phenotypic presentation. The age of onset and the type of symptoms at presentation were used as markers of the WD phenotype. RESULTS The overall HSD17B13:TA allele frequency in patients with WD was 23.3% (273/1,172), not significantly different from the reported minor allele frequency. There was a significantly lower HSD17B13:TA allele frequency in patients with fulminant WD compared to all other phenotypic WD groups (11.0% vs. 24.0%, p < 0.01). Among the patients with fulminant WD there was a trend for a gender effect; none of the male patients carried the HSD17B13:TA allele. HSD17B13:TA allele frequency was more common in patients with minimal or no fibrosis (49 [31.1%] had simple steatosis and 20 minimal changes at biopsy) than in patients with cirrhosis or advanced fibrosis (22.3%, p = 0.025). CONCLUSIONS The HSD17B13:TA allele modulates the phenotype and outcome of WD. This allele likely ameliorates hepatic fibrosis and reduces the transition from copper induced hemolysis to fulminant disease in patients with WD. LAY SUMMARY Wilson's disease is a hereditary disease caused by accumulation of copper in the liver and other tissues. It presents with a variety of clinical symptoms. In this study we explored the role of a recently described gene mutation (HSD17B13:TA) which apparently protects the liver against toxins like alcohol. The results indicate that this mutation plays a role in the evolution of liver disease. Patients with Wilson's disease who carry this mutation are more likely to have mild disease, while the absence of the mutation is associated with the most severe form - fulminant Wilson's disease.
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Affiliation(s)
- Peter Ferenci
- Internal Medicine III, Dvision of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| | | | | | | | - Claudia Willheim
- Internal Medicine III, Dvision of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| | - Karl H. Weiss
- Internal Medicine IV, Medical University of Heidelberg, Germany
| | - Petra Munda-Steindl
- Internal Medicine III, Dvision of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| | - Michael Trauner
- Internal Medicine III, Dvision of Gastroenterology and Hepatology, Medical University of Vienna, Austria
| | - Michael Schilsky
- Departments of Medicine and Surgery, Division of Digestive Diseases and Immunology and Transplant, Yale University, New Haven, CT, USA
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24
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Ma Y, Belyaeva OV, Brown PM, Fujita K, Valles K, Karki S, de Boer YS, Koh C, Chen Y, Du X, Handelman SK, Chen V, Speliotes EK, Nestlerode C, Thomas E, Kleiner DE, Zmuda JM, Sanyal AJ, Kedishvili NY, Liang TJ, Rotman Y. 17-Beta Hydroxysteroid Dehydrogenase 13 Is a Hepatic Retinol Dehydrogenase Associated With Histological Features of Nonalcoholic Fatty Liver Disease. Hepatology 2019; 69:1504-1519. [PMID: 30415504 PMCID: PMC6438737 DOI: 10.1002/hep.30350] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease. A single-nucleotide polymorphism (SNP), rs6834314, was associated with serum liver enzymes in the general population, presumably reflecting liver fat or injury. We studied rs6834314 and its nearest gene, 17-beta hydroxysteroid dehydrogenase 13 (HSD17B13), to identify associations with histological features of NAFLD and to characterize the functional role of HSD17B13 in NAFLD pathogenesis. The minor allele of rs6834314 was significantly associated with increased steatosis but decreased inflammation, ballooning, Mallory-Denk bodies, and liver enzyme levels in 768 adult Caucasians with biopsy-proven NAFLD and with cirrhosis in the general population. We found two plausible causative variants in the HSD17B13 gene. rs72613567, a splice-site SNP in high linkage with rs6834314 (r2 = 0.94) generates splice variants and shows a similar pattern of association with NAFLD histology. Its minor allele generates simultaneous expression of exon 6-skipping and G-nucleotide insertion variants. Another SNP, rs62305723 (encoding a P260S mutation), is significantly associated with decreased ballooning and inflammation. Hepatic expression of HSD17B13 is 5.9-fold higher (P = 0.003) in patients with NAFLD. HSD17B13 is targeted to lipid droplets, requiring the conserved amino acid 22-28 sequence and amino acid 71-106 region. The protein has retinol dehydrogenase (RDH) activity, with enzymatic activity dependent on lipid droplet targeting and cofactor binding site. The exon 6 deletion, G insertion, and naturally occurring P260S mutation all confer loss of enzymatic activity. Conclusion: We demonstrate the association of variants in HSD17B13 with specific features of NAFLD histology and identify the enzyme as a lipid droplet-associated RDH; our data suggest that HSD17B13 plays a role in NAFLD through its enzymatic activity.
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Affiliation(s)
- Yanling Ma
- Liver and Energy Metabolism Unit, NIDDK, NIH, Bethesda, MD,Liver Diseases Branch, NIDDK, NIH, Bethesda, MD
| | - Olga V. Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama – Birmingham, Birmingham, AL
| | - Philip M. Brown
- Liver and Energy Metabolism Unit, NIDDK, NIH, Bethesda, MD,Liver Diseases Branch, NIDDK, NIH, Bethesda, MD
| | - Koji Fujita
- Liver and Energy Metabolism Unit, NIDDK, NIH, Bethesda, MD,Liver Diseases Branch, NIDDK, NIH, Bethesda, MD
| | - Katherine Valles
- Liver and Energy Metabolism Unit, NIDDK, NIH, Bethesda, MD,Liver Diseases Branch, NIDDK, NIH, Bethesda, MD
| | - Suman Karki
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama – Birmingham, Birmingham, AL
| | | | | | - Yanhua Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Xiaomeng Du
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | - Vincent Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Elizabeth K. Speliotes
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Cara Nestlerode
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | - David E. Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joseph M. Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Arun J. Sanyal
- Department of Internal Medicine, Division of Gastroenterology, Virginia Commonwealth University, Richmond, VA
| | - Natalia Y. Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama – Birmingham, Birmingham, AL
| | | | - Yaron Rotman
- Liver and Energy Metabolism Unit, NIDDK, NIH, Bethesda, MD,Liver Diseases Branch, NIDDK, NIH, Bethesda, MD
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25
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Woo Y, Shin JS, Shim CY, Kim JS, Kim BK, Park S, Chang HJ, Hong GR, Ko YG, Kang SM, Choi D, Ha JW, Hong MK, Jang Y, Lee SH. Effect of fenofibrate in 1113 patients at low-density lipoprotein cholesterol goal but high triglyceride levels: Real-world results and factors associated with triglyceride reduction. PLoS One 2018; 13:e0205006. [PMID: 30286170 PMCID: PMC6171908 DOI: 10.1371/journal.pone.0205006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 09/18/2018] [Indexed: 01/01/2023] Open
Abstract
Fibrates are used in patients with dyslipidemia and high cardiovascular risk. However, information regarding drug response to fibrate has been highly limited. We investigated treatment results and factors associated with triglyceride reduction after fenofibrate therapy using large-scale real-world data. Patients with one or more cardiovascular risk factors, at low-density lipoprotein-cholesterol goal but with triglyceride level ≥150 mg/dL, and undergoing treatment with fenofibrate 135–160 mg for the first time were included in this retrospective observational study. The outcome variable was the percentage changes of TG levels. The achievement rate of triglyceride <150 mg/dL was additionally analyzed. Factors associated with treatment results were also analyzed. Among 2546 patients who were initially screened, 1113 patients were enrolled (median age: 61 years; male: 71%). After median follow-up of 4 months, the median change in triglyceride was -60%, and 49% of the patients reached triglyceride <150 mg/dL. After adjusting for confounding variables, female sex, non-diabetic status, coronary artery disease, lower baseline triglyceride, and no statin use were identified to be independently associated with achievement of triglyceride <150 mg/dL. Among them, female sex, non-diabetic status, and coronary artery disease were also related to median or greater percentage reduction of triglyceride. In conclusion, only half of the study patients reached triglyceride levels <150 mg/dL after real-world fenofibrate therapy. This study indicates that more attention is needed on some subgroups to obtain optimal triglyceride levels when treating with fenofibrate.
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Affiliation(s)
- Yeongmin Woo
- Division of Cardiology, Department of Internal Medicine, Gangneung Asan Hospital, University of Ulsan College of Medicine, Gangneung, Korea
| | - Jeong-soo Shin
- Department of Biostatistics and Computing, Yonsei University College of Medicine, Seoul, Korea
| | - Chi-Young Shim
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Sun Kim
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Byeong-Keuk Kim
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Sungha Park
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyuk-Jae Chang
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Geu-Ru Hong
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Young-Guk Ko
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Seok-Min Kang
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Donghoon Choi
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jong-Won Ha
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Myeong-Ki Hong
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Yangsoo Jang
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Sang-Hak Lee
- Division of Cardiology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Cardiovascular Research Institute, Yonsei University College of Medicine, Seoul, Korea
- * E-mail:
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26
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Admixture mapping and fine-mapping of type 2 diabetes susceptibility loci in African American women. J Hum Genet 2018; 63:1109-1117. [PMID: 30135545 PMCID: PMC6202164 DOI: 10.1038/s10038-018-0503-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
Abstract
African American women are disproportionately affected by type 2 diabetes. Genetic factors may explain part of the excess risk. More than 100 genetic variants have been associated with risk of type 2 diabetes, but most studies have been conducted in white populations. Two genome-wide association studies (GWAS) in African Americans have identified three novel genetic variants only. We conducted admixture mapping using 2,918 ancestral informative markers in 2,632 cases of type 2 diabetes and 2,596 controls nested in the ongoing Black Women’s Health Study cohort, with the goal of identifying genomic loci with local African ancestry associated with type 2 diabetes. In addition, we performed replication analysis of 71 previously identified index SNPs, and fine-mapped those genetic loci to identify better or new genetic variants associated with type 2 diabetes in African Americans. We found that individual African ancestry was associated with higher risk of type 2 diabetes. In addition, we identified two genomic regions, 3q26 and 12q23, with excess of African ancestry associated with higher risk of type 2 diabetes. Lastly, we replicated 8 out of 71 index SNPs from previous GWAS, including, for the first time in African Americans, the X-linked rs5945326 SNP near the DUSP9 gene. In addition, our fine-mapping efforts suggest independent signals at five loci. Our detailed analysis identified two genomic regions associated with risk of type 2 diabetes, and showed that many genetic risk variants are shared across ancestries.
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Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel) 2018; 9:E61. [PMID: 29370075 PMCID: PMC5852557 DOI: 10.3390/genes9020061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/19/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
A plethora of genetic association analyses have identified several genetic risk loci. Technological and statistical advancements have now led to the identification of not only common genetic variants, but also low-frequency variants, structural variants, and environmental factors, as well as multi-omics variations that affect the phenotypic variance of complex traits in a population, thus referred to as complex trait architecture. The concept of heritability, or the proportion of phenotypic variance due to genetic inheritance, has been studied for several decades, but its application is mainly in addressing the narrow sense heritability (or additive genetic component) from Genome-Wide Association Studies (GWAS). In this commentary, we reflect on our perspective on the complexity of understanding heritability for human traits in comparison to model organisms, highlighting another round of clues beyond GWAS and an alternative approach, investigating these clues comprehensively to help in elucidating the genetic architecture of complex traits.
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Affiliation(s)
- Shefali Setia Verma
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marylyn D Ritchie
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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