1
|
Nair JM, Bandesh K, Giri AK, Prasad G, Rajashekhar D, Jha P, Basu A, Tandon N, Bharadwaj D. Uncovering novel regulatory variants in carbohydrate metabolism: a comprehensive multi-omics study of glycemic traits in the Indian population. Mol Genet Genomics 2024; 299:85. [PMID: 39230791 DOI: 10.1007/s00438-024-02176-9] [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: 12/29/2023] [Accepted: 08/02/2024] [Indexed: 09/05/2024]
Abstract
Clinical biomarkers such as fasting glucose, HbA1c, and fasting insulin, which gauge glycemic status in the body, are highly influenced by diet. Indians are genetically predisposed to type 2 diabetes and their carbohydrate-centric diet further elevates the disease risk. Despite the combined influence of genetic and environmental risk factors, Indians have been inadequately explored in the studies of glycemic traits. Addressing this gap, we investigate the genetic architecture of glycemic traits at genome-wide level in 4927 Indians (without diabetes). Our analysis revealed numerous variants of sub-genome-wide significance, and their credibility was thoroughly assessed by integrating data from various levels. This identified key effector genes, ZNF470, DPP6, GXYLT2, PITPNM3, BEND7, and LORICRIN-PGLYRP3. While these genes were weakly linked with carbohydrate intake or glycemia earlier in other populations, our findings demonstrated a much stronger association in the Indian population. Associated genetic variants within these genes served as expression quantitative trait loci (eQTLs) in various gut tissues essential for digestion. Additionally, majority of these gut eQTLs functioned as methylation quantitative trait loci (meth-QTLs) observed in peripheral blood samples from 223 Indians, elucidating the underlying mechanism of their regulation of target gene expression. Specific co-localized eQTLs-meth-QTLs altered the binding affinity of transcription factors targeting crucial genes involved in glucose metabolism. Our study identifies previously unreported genetic variants that strongly influence the diet-glycemia relationship. These findings set the stage for future research into personalized lifestyle interventions integrating genetic insights with tailored dietary strategies to mitigate disease risk based on individual genetic profiles.
Collapse
Affiliation(s)
- Janaki M Nair
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khushdeep Bandesh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Anil K Giri
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gauri Prasad
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Donaka Rajashekhar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Punam Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, 741251, India
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
2
|
Sharma AK, Giri AK. Engineering CRISPR/Cas9 therapeutics for cancer precision medicine. Front Genet 2024; 15:1309175. [PMID: 38725484 PMCID: PMC11079134 DOI: 10.3389/fgene.2024.1309175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
The discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) technology has revolutionized field of cancer treatment. This review explores usage of CRISPR/Cas9 for editing and investigating genes involved in human carcinogenesis. It provides insights into the development of CRISPR as a genetic tool. Also, it explores recent developments and tools available in designing CRISPR/Cas9 systems for targeting oncogenic genes for cancer treatment. Further, we delve into an overview of cancer biology, highlighting key genetic alterations and signaling pathways whose deletion prevents malignancies. This fundamental knowledge enables a deeper understanding of how CRISPR/Cas9 can be tailored to address specific genetic aberrations and offer personalized therapeutic approaches. In this review, we showcase studies and preclinical trials that show the utility of CRISPR/Cas9 in disrupting oncogenic targets, modulating tumor microenvironment and increasing the efficiency of available anti treatments. It also provides insight into the use of CRISPR high throughput screens for cancer biomarker identifications and CRISPR based screening for drug discovery. In conclusion, this review offers an overview of exciting developments in engineering CRISPR/Cas9 therapeutics for cancer treatment and highlights the transformative potential of CRISPR for innovation and effective cancer treatments.
Collapse
Affiliation(s)
- Aditya Kumar Sharma
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Anil K. Giri
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| |
Collapse
|
3
|
Dabravolski S, Orekhov NA, Melnichenko A, Sukhorukov VN, Popov MA, Orekhov A. Cholesteryl Ester Transfer Protein (CETP) Variations in Relation to Lipid Profiles and Cardiovascular Diseases: An Update. Curr Pharm Des 2024; 30:742-756. [PMID: 38425105 DOI: 10.2174/0113816128284695240219093612] [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: 10/26/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 03/02/2024]
Abstract
Lipid metabolism plays an essential role in the pathogenesis of cardiovascular and metabolic diseases. Cholesteryl ester transfer protein (CETP) is a crucial glycoprotein involved in lipid metabolism by transferring cholesteryl esters (CE) and triglycerides (TG) between plasma lipoproteins. CETP activity results in reduced HDL-C and increased VLDL- and LDL-C concentrations, thus increasing the risk of cardiovascular and metabolic diseases. In this review, we discuss the structure of CETP and its mechanism of action. Furthermore, we focus on recent experiments on animal CETP-expressing models, deciphering the regulation and functions of CETP in various genetic backgrounds and interaction with different external factors. Finally, we discuss recent publications revealing the association of CETP single nucleotide polymorphisms (SNPs) with the risk of cardiovascular and metabolic diseases, lifestyle factors, diet and therapeutic interventions. While CETP SNPs can be used as effective diagnostic markers, diet, lifestyle, gender and ethnic specificity should also be considered for effective treatment.
Collapse
Affiliation(s)
- Siarhei Dabravolski
- Department of Biotechnology Engineering, ORT Braude College, Braude Academic College of Engineering, Karmiel, Israel
| | - Nikolay A Orekhov
- Laboratory of Angiopatology, Research Institute of General Pathology and Pathophysiology, The Russian Academy of Medical Sciences, Moscow, Russian Federation
| | - Alexandra Melnichenko
- Laboratory of Angiopatology, Research Institute of General Pathology and Pathophysiology, The Russian Academy of Medical Sciences, Moscow, Russian Federation
| | - Vasily N Sukhorukov
- Laboratory of Angiopatology, Research Institute of General Pathology and Pathophysiology, The Russian Academy of Medical Sciences, Moscow, Russian Federation
| | - Mikhail A Popov
- Laboratory of Angiopatology, Research Institute of General Pathology and Pathophysiology, The Russian Academy of Medical Sciences, Moscow, Russian Federation
| | - Alexander Orekhov
- Laboratory of Angiopatology, Research Institute of General Pathology and Pathophysiology, The Russian Academy of Medical Sciences, Moscow, Russian Federation
| |
Collapse
|
4
|
Ho CY, Lee JI, Huang SP, Chen SC, Geng JH. A Genome-Wide Association Study of Metabolic Syndrome in the Taiwanese Population. Nutrients 2023; 16:77. [PMID: 38201907 PMCID: PMC10780952 DOI: 10.3390/nu16010077] [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: 11/08/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
The purpose of this study was to investigate genetic factors associated with metabolic syndrome (MetS) by conducting a large-scale genome-wide association study (GWAS) in Taiwan, addressing the limited data on Asian populations compared to Western populations. Using data from the Taiwan Biobank, comprehensive clinical and genetic information from 107,230 Taiwanese individuals was analyzed. Genotyping data from the TWB1.0 and TWB2.0 chips, including over 650,000 single nucleotide polymorphisms (SNPs), were utilized. Genotype imputation using the 1000 Genomes Project was performed, resulting in more than 9 million SNPs. MetS was defined based on a modified version of the Adult Treatment Panel III criteria. Among all participants (mean age: 50 years), 23% met the MetS definition. GWAS analysis identified 549 SNPs significantly associated with MetS, collectively mapping to 10 genomic risk loci. Notable risk loci included rs1004558, rs3812316, rs326, rs4486200, rs2954038, rs10830963, rs662799, rs62033400, rs183130, and rs34342646. Gene-set analysis revealed 22 associated genes: CETP, LPL, APOA5, SIK3, ZPR1, APOC1, BUD13, MLXIPL, TOMM40, GCK, YKT6, RPS6KB1, FTO, VMP1, TUBD1, BCL7B, C19orf80 (ANGPTL8), SIDT2, SENP7, PAFAH1B2, DOCK6, and FOXA2. This study identified genomic risk loci for MetS in a large Taiwanese population through a comprehensive GWAS approach. These associations provide novel insights into the genetic basis of MetS and hold promise for the potential discovery of clinical biomarkers.
Collapse
Affiliation(s)
- Chih-Yi Ho
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Jia-In Lee
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shu-Pin Huang
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Ph.D. Program in Environmental and Occupational Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Medical Science and Technology, College of Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Szu-Chia Chen
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Internal Medicine, Kaohsiung Municipal Siaogang Hospital, Kaohsiung Medical University, Kaohsiung 812, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jiun-Hung Geng
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung 812, Taiwan
| |
Collapse
|
5
|
Prone-Olazabal D, Davies I, González-Galarza FF. Metabolic Syndrome: An Overview on Its Genetic Associations and Gene-Diet Interactions. Metab Syndr Relat Disord 2023; 21:545-560. [PMID: 37816229 DOI: 10.1089/met.2023.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] Open
Abstract
Metabolic syndrome (MetS) is a cluster of cardiometabolic risk factors that includes central obesity, hyperglycemia, hypertension, and dyslipidemias and whose inter-related occurrence may increase the odds of developing type 2 diabetes and cardiovascular diseases. MetS has become one of the most studied conditions, nevertheless, due to its complex etiology, this has not been fully elucidated. Recent evidence describes that both genetic and environmental factors play an important role on its development. With the advent of genomic-wide association studies, single nucleotide polymorphisms (SNPs) have gained special importance. In this review, we present an update of the genetics surrounding MetS as a single entity as well as its corresponding risk factors, considering SNPs and gene-diet interactions related to cardiometabolic markers. In this study, we focus on the conceptual aspects, diagnostic criteria, as well as the role of genetics, particularly on SNPs and polygenic risk scores (PRS) for interindividual analysis. In addition, this review highlights future perspectives of personalized nutrition with regard to the approach of MetS and how individualized multiomics approaches could improve the current outlook.
Collapse
Affiliation(s)
- Denisse Prone-Olazabal
- Postgraduate Department, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Ian Davies
- Research Institute of Sport and Exercise Science, The Institute for Health Research, Liverpool John Moores University, Liverpool, United Kingdom
| | | |
Collapse
|
6
|
Jiang J, Liu Y, Wang A, Zhuo Z, Shi H, Zhang X, Li W, Sun M, Jiang S, Wang Y, Zou X, Zhang Y, Jia Z, Xu J. Development and validation of a nutrition-related genetic-clinical-radiological nomogram associated with behavioral and psychological symptoms in Alzheimer's disease. Chin Med J (Engl) 2023:00029330-990000000-00878. [PMID: 38031345 PMCID: PMC11407811 DOI: 10.1097/cm9.0000000000002914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Few evidence is available in the early prediction models of behavioral and psychological symptoms of dementia (BPSD) in Alzheimer's disease (AD). This study aimed to develop and validate a novel genetic-clinical-radiological nomogram for evaluating BPSD in patients with AD and explore its underlying nutritional mechanism. METHODS This retrospective study included 165 patients with AD from the Chinese Imaging, Biomarkers, and Lifestyle (CIBL) cohort between June 1, 2021, and March 31, 2022. Data on demoimagedatas, neuropsychological assessments, single-nucleotide polymorphisms of AD risk genes, and regional brain volumes were collected. A multivariate logistic regression model identified BPSD-associated factors, for subsequently constructing a diagnostic nomogram. This nomogram was internally validated through 1000-bootstrap resampling and externally validated using a time-series split based on the CIBL cohort data between June 1, 2022, and February 1, 2023. Area under receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA) were used to assess the discrimination, calibration, and clinical applicability of the nomogram. RESULTS Factors independently associated with BPSD were: CETP rs1800775 (odds ratio [OR] = 4.137, 95% confidence interval [CI]: 1.276-13.415, P = 0.018), decreased Mini Nutritional Assessment score (OR = 0.187, 95% CI: 0.086-0.405, P <0.001), increased caregiver burden inventory score (OR = 8.993, 95% CI: 3.830-21.119, P <0.001), and decreased brain stem volume (OR = 0.006, 95% CI: 0.001-0.191, P = 0.004). These variables were incorporated into the nomogram. The area under the ROC curve was 0.925 (95% CI: 0.884-0.967, P <0.001) in the internal validation and 0.791 (95% CI: 0.686-0.895, P <0.001) in the external validation. The calibration plots showed favorable consistency between the prediction of nomogram and actual observations, and the DCA showed that the model was clinically useful in both validations. CONCLUSION A novel nomogram was established and validated based on lipid metabolism-related genes, nutritional status, and brain stem volumes, which may allow patients with AD to benefit from early triage and more intensive monitoring of BPSD. REGISTRATION Chictr.org.cn, ChiCTR2100049131.
Collapse
Affiliation(s)
- Jiwei Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Yaou Liu
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Anxin Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Zhizheng Zhuo
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Hanping Shi
- Department of Gastrointestinal Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
- Beijing International Science and Technology Cooperation Base for Cancer Metabolism and Nutrition, Beijing 100081, China
| | - Xiaoli Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Wenyi Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Mengfan Sun
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Shirui Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Yanli Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Xinying Zou
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Yuan Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Ziyan Jia
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| | - Jun Xu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- National Clinical Research Center for Neurological Diseases, Beijing 100070, China
| |
Collapse
|
7
|
Revelas M, Thalamuthu A, Zettergren A, Oldmeadow C, Najar J, Seidu NM, Armstrong NJ, Riveros C, Kwok JB, Schofield PR, Trollor JN, Waern M, Wright MJ, Zetterberg H, Ames D, Belnnow K, Brodaty H, Scott RJ, Skoog I, Attia JR, Sachdev PS, Mather KA. High polygenic risk score for exceptional longevity is associated with a healthy metabolic profile. GeroScience 2023; 45:399-413. [PMID: 35972662 PMCID: PMC9886704 DOI: 10.1007/s11357-022-00643-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/08/2022] [Indexed: 02/03/2023] Open
Abstract
Healthy metabolic measures in humans are associated with longevity. Dysregulation leads to metabolic syndrome (MetS) and negative health outcomes. Recent exceptional longevity (EL) genome wide association studies have facilitated estimation of an individual's polygenic risk score (PRS) for EL. We tested the hypothesis that individuals with high ELPRS have a low prevalence of MetS. Participants were from five cohorts of middle-aged to older adults. The primary analyses were performed in the UK Biobank (UKBB) (n = 407,800, 40-69 years). Replication analyses were undertaken using three Australian studies: Hunter Community Study (n = 2122, 55-85 years), Older Australian Twins Study (n = 539, 65-90 years) and Sydney Memory and Ageing Study (n = 925, 70-90 years), as well as the Swedish Gothenburg H70 Birth Cohort Studies (n = 2273, 70-93 years). MetS was defined using established criteria. Regressions and meta-analyses were performed with the ELPRS and MetS and its components. Generally, MetS prevalence (22-30%) was higher in the older cohorts. In the UKBB, high EL polygenic risk was associated with lower MetS prevalence (OR = 0.94, p = 1.84 × 10-42) and its components (p < 2.30 × 10-8). Meta-analyses of the replication cohorts showed nominal associations with MetS (p = 0.028) and 3 MetS components (p < 0.05). This work suggests individuals with a high polygenic risk for EL have a healthy metabolic profile promoting longevity.
Collapse
Affiliation(s)
- Mary Revelas
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia.
- Neuroscience Research Australia, Sydney, NSW, Australia.
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| | - Anna Zettergren
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | | | - Jenna Najar
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - Nazib M Seidu
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | - Nicola J Armstrong
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Mathematics and Statistics, Curtin University, Perth, Australia
| | - Carlos Riveros
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - John B Kwok
- Neuroscience Research Australia, Sydney, NSW, Australia
- School of Medical Sciences, UNSW, Sydney, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, Sydney, NSW, Australia
- School of Medical Sciences, UNSW, Sydney, Australia
| | - Julian N Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
| | - Margda Waern
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychosis Clinic, Gothenburg, Sweden
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Henrik Zetterberg
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Hong Kong Centre for Neurodegenerative Diseases, Hong Kong, China
| | - David Ames
- University of Melbourne Academic Unit for Psychiatry of Old Age, St George's Hospital, Kew, VIC, Australia
- National Ageing Research Institute, Parkville Victoria, Australia
| | - Kaj Belnnow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Dementia Centre for Research Collaboration, UNSW, Sydney, Australia
| | - Rodney J Scott
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Pathology North, John Hunter Hospital, Newcastle, NSW, Australia
| | - Ingmar Skoog
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - John R Attia
- Hunter Medical Research Institute, Newcastle, NSW, Australia
- Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, Australia
- Pathology North, John Hunter Hospital, Newcastle, NSW, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine & Health, UNSW, Sydney, Australia
- Neuroscience Research Australia, Sydney, NSW, Australia
| |
Collapse
|
8
|
Hidalgo-Bravo A, Rivera-Paredez B, León-Reyes G, Patiño N, Castillejos-López M, Salmerón J, Velázquez-Cruz R. Unravelling the Contribution of the rs7041 and rs4588 Polymorphisms of the GC Gene and Serum VDBP Levels for Developing Metabolic Syndrome in the Mexican Population. Int J Mol Sci 2022; 23:ijms231810581. [PMID: 36142493 PMCID: PMC9503453 DOI: 10.3390/ijms231810581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Metabolic syndrome (MetS) is a multifactorial disorder integrated by a constellation of cardiovascular risk factors. The genetic and environmental determinants of MetS are not fully elucidated. This study investigated the association of two common single nucleotide polymorphisms (SNPs) on GC, rs7041 and rs4588, derived haplotypes, and serum vitamin D binding protein (VDBP) levels with the susceptibility to suffer MetS in Mexican adults. We included 1924 individuals; clinical and biochemical data were obtained through standard methods. Genotyping was performed through predesigned TaqMan assays. Logistic regression models were used to assess the associations of interest. Prevalence of MetS was 52.9% in the whole population, being more frequent in women. We observed that some association results differed between sexes. The GG genotype of the rs7041 was associated with increased odds of MetS in women. For the rs4588, the CA genotype had a protective effect against MetS in women. The haplotype GC2 was associated with reduced odds for MetS and some of its components in women. Our data suggest that VDBP serum levels were influenced by genotypes/haplotypes and this interplay seems to influence the risk of MetS. Our data provide reliable evidence regarding the association of GC polymorphisms with MetS risk in Mexican women.
Collapse
Affiliation(s)
- Alberto Hidalgo-Bravo
- Departamento de Genética, Instituto Nacional de Rehabilitación (INR), Mexico City 014389, Mexico
| | - Berenice Rivera-Paredez
- Centro de Investigación en Políticas, Población y Salud, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Guadalupe León-Reyes
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - Nelly Patiño
- Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - Manuel Castillejos-López
- Departamento de Epidemiología, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City 14080, Mexico
| | - Jorge Salmerón
- Centro de Investigación en Políticas, Población y Salud, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
| | - Rafael Velázquez-Cruz
- Laboratorio de Genómica del Metabolismo Óseo, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
- Correspondence: ; Tel.: +52-(55)-5350-1900; Fax: +52-(55)-5350-1999
| |
Collapse
|
9
|
Association of Serum 25(OH)D with Metabolic Syndrome in Chinese Women of Childbearing Age. Nutrients 2022; 14:nu14112301. [PMID: 35684100 PMCID: PMC9182986 DOI: 10.3390/nu14112301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Objective: To analyze the associations between serum 25(OH)D levels and the risk of metabolic syndrome (MetS) and its components, and the related genetic and non-genetic factors in non-diabetic women of childbearing age in China. Methods: Subjects were randomly selected from the 2015 Chinese Adult Chronic Disease and Nutrition Surveillance. The data of sociodemographic characteristics and lifestyle factors were obtained through questionnaire survey. Anthropometry was measured by trained interviewers, and fasting blood was collected to test 25-hydroxyvitamin D [25(OH)D], total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), fasting blood glucose (FBG), and other related parameters. Generalized linear mode and multivariate logistic analysis were performed to analyze the associations between serum 25(OH)D and MetS and its components, adjusting for the possible confounders. Results: Body mass index (BMI), serum alanine aminotransferase (ALT), hypersensitive C-reactive protein (hs-CRP), 25(OH)D, phosphorus (P), and parathyroid hormone (PTH) levels were associated with the number of MetS’s components. G allele carriers of GC rs2282679 had higher diastolic blood pressure (DBP) and FBG levels compared with the TT genotypes, while higher genetic risk score (GRS) seemed to be associated with reduced HDL-C level. The odds ratio (OR) for MetS in lowest group of 25(OH)D was 1.533 (0.980−2.399) after adjusting for season, district, area type, latitude, age, BMI, PTH, P, ALT, CRE, interleukin-6 (IL-6), and hs-CRP, compared with the median group, but the association was not significant. An insufficient 25(OH)D concentration (<14.22 ng/mL) was significantly related to the risk of elevated waist circumference (WC) (OR = 1.612 (1.014−2.561)) and TG (OR = 2.210 (1.318−3.706)), and reduced HDL-C (OR = 1.639 (1.206−2.229)) after adjusting for the confounders among these women. Moreover, these relationships were not affected by vitamin D metabolism-related gene polymorphisms. Conclusion: After comprehensively considering various influencing factors, significant associations between insufficient serum 25(OH)D and MetS‘s components, including elevated WC, TG, and reduced HDL-C, were observed. However, MetS, hypertension, and hyperglycemia were not found independently associated with 25(OH)D levels.
Collapse
|
10
|
Zhao T, Zhang D, Liu Y, Feng M, Xu Z, Huang H, Zhang L, Li W, Li X. The Association Between GC Gene Polymorphisms and Metabolic Syndrome in Chinese Rural Population: A Case-Control Study. Diabetes Metab Syndr Obes 2022; 15:165-174. [PMID: 35058699 PMCID: PMC8765441 DOI: 10.2147/dmso.s346528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/21/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND GC (group-specific component globulin) encoding VDBP (Vitamin D binding protein) polymorphisms have been associated with susceptibility to some diseases such as diabetes, obesity, osteoporosis, and polycystic ovary syndrome, but the evidence for metabolic syndrome (MetS) in the Chinese rural population is inconclusive. Therefore, we investigated the relationship between GC variants (rs7041, rs4588, rs2282679, and rs705117) and MetS risk as well as VDBP levels in the Chinese rural population. PATIENTS AND METHODS The participants (range of age: 20-90 years) of this case-control study were recruited from the northern Chinese Han rural population. We matched 445 MetS cases with non-MetS controls in a 1:1 ratio by sex, age (within 5 years). Real-time PCR technology was carried out by TaqMan assays to examine the four variants of rs7041, rs4588, rs2282679, and rs705117 within the GC gene. To identify the association of GC gene polymorphisms with MetS, we calculated ORs using a conditional logistic regression model adjusted for potential confounding factors. RESULTS We observed inverse associations of CA and AA genotypes of rs4588 with risk of MetS (OR = 0.678, 95% CI 0.505-0.910, P = 0.010; 0.603, 95% CI 0.373-0.973, P = 0.039, respectively) compared with carriers of CC genotype. A similar relationship was also found between rs2282679 and MetS, showing that carrying AC genotype of rs2282679 can decrease the risk of MetS (OR = 0.683, 95% CI 0.509-0.917, P = 0.011) compared with carriers of AA genotype. The results of correlation analysis between MetS components and GC polymorphisms showed that the ORs of AA genotype of rs4588 with high level of TG (triglycerides) and low level of HDL-C (high-density lipoprotein cholesterol) were 0.473 (95% CI 0.245-0.911, P = 0.025) and 0.268 (95% CI 0.117-0.615, P = 0.002), respectively; the ORs of CC genotype of rs2282679 with high level of TG and low level of HDL-C were 0.428 (95% CI 0.217-0.842, P = 0.014) and 0.263 (95% CI 0.110-0.628, P = 0.003), respectively. However, there was no significant association between the concentration of VDBP and MetS risk. CONCLUSION Among the Chinese rural population, GC polymorphism was associated with lower metabolic syndrome susceptibility, which might be through affecting blood lipid levels (TG and HDL-C).
Collapse
Affiliation(s)
- Tong Zhao
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Dongdong Zhang
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Yiming Liu
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Mingming Feng
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Ze Xu
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Haoyue Huang
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Luoya Zhang
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Wenjie Li
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
| | - Xing Li
- Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People’s Republic of China
- Correspondence: Xing Li Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, People’s Republic of ChinaTel +86 371 6778 1305 Email
| |
Collapse
|
11
|
Bharti N, Banerjee R, Achalere A, Kasibhatla SM, Joshi R. Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations. PeerJ 2021; 9:e12294. [PMID: 34824904 PMCID: PMC8590392 DOI: 10.7717/peerj.12294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. METHODS Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni's multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. RESULTS Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be 'deleterious'. CONCLUSIONS Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.
Collapse
Affiliation(s)
- Neeraj Bharti
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Ruma Banerjee
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Archana Achalere
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Sunitha Manjari Kasibhatla
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Rajendra Joshi
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| |
Collapse
|
12
|
Xiao J, Lv J, Wang S, Zhou Y, Chen L, Lu J, Zhang X, Wang X, Gu Y, Lu Q. Association of serum 25-hydroxyvitamin D with metabolic syndrome and type 2 diabetes: a one sample Mendelian randomization study. BMC Geriatr 2021; 21:391. [PMID: 34187381 PMCID: PMC8244233 DOI: 10.1186/s12877-021-02307-6] [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: 02/04/2021] [Accepted: 05/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Vitamin D deficiency has been associated with type 2 diabetes (T2D) and metabolic syndrome (MS) and its components. However, it is unclear whether a low concentration of vitamin D is the cause or consequence of these health conditions. Thus, this study aimed to evaluate the association of vitamin D concentrations and its genetic risk scores (GRSs) with MS and its component diseases, such as T2D, in middle-aged and elderly participants from rural eastern China. Methods A subset of 2393 middle-aged and elderly individuals were selected from 70,458 participants of the Nantong Chronic Diseases Study of 2017–2018 in China. We used two 25-hydroxyvitamin D (25[OH]D) synthesis single-nucleotide polymorphisms (SNPs) (DHCR7-rs12785878 and CYP2R1-rs10741657) and two 25(OH) D metabolism SNPs (GC-rs2282679 and CYP24A1-rs6013897) for creating GRSs, which were used as instrumental variables to assess the effect of genetically lowered 25(OH) D concentrations on MS and T2D based on the Wald ratio. F statistics were used to validate that the four SNPs genetically determined 25(OH) D concentrations. Results Compared to vitamin D sufficient individuals, individuals with vitamin D insufficiency had an odds ratio (OR [95% confidence interval {CI}]) of MS of 1.30 (1.06–1.61) and of T2D of 1.32 (1.08–1.64), individuals with vitamin D deficiency had an ORs (95% CI) of MS of 1.50 (1.24–1.79) and of T2D of 1.47 (1.12–1.80), and those with vitamin D severe deficiency had an ORs (95% CI) of MS of 1.52 (1.29–1.85) and of T2D of 1.54 (1.27–1.85). Mendelian randomization analysis showed a 25-nmol/L decrease in genetically instrumented serum 25(OH) D concentrations using the two synthesis SNPs (DHCR7 and CYP2R1 genes) associated with the risk of T2D and abnormal diastolic blood pressure (DBP) with ORs of 1.10 (95%CI: 1.02–1.45) for T2D and 1.14 (95%CI: 1.03–1.43) for DBP. Conclusions This one sample Mendelian randomization analysis shows genetic evidence for a causal role of lower 25(OH) D concentrations in promoting of T2D and abnormal DBP in middle-aged and elderly participants from rural China. Supplementary Information The online version contains supplementary material available at 10.1186/s12877-021-02307-6.
Collapse
Affiliation(s)
- Jing Xiao
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019
| | - Jingyi Lv
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019
| | - Shiyu Wang
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019
| | - Yang Zhou
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019
| | - Lunwen Chen
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019
| | - Juying Lu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226001
| | - Xiaoyi Zhang
- Department of Endocrinology and Metabolism, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226001
| | - Xiaojian Wang
- Department of Chronic Disease and Prevention, Center for Disease Control and Prevention of Haian, Nantong, Jiangsu, P.R. China, 226600
| | - Yunjuan Gu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Nantong University, No.20 Xisi Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226001.
| | - Qingyun Lu
- Department of Epidemiology and Medical Statistics, School of Public Health, Nantong University, No.9 Seyuan Road, Chongchuan District, Nantong, Jiangsu, P.R. China, 226019.
| |
Collapse
|
13
|
Lu H, Zhang J, Chen YE, Garcia-Barrio MT. Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases. Cardiovasc Drugs Ther 2021; 35:637-654. [PMID: 33856594 PMCID: PMC8216854 DOI: 10.1007/s10557-021-07175-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2021] [Indexed: 12/11/2022]
Abstract
Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. Genome-wide association studies (GWAS) are powerful epidemiological tools to find genes and variants associated with cardiovascular diseases while follow-up biological studies allow to better understand the etiology and mechanisms of disease and assign causality. Improved methodologies and reduced costs have allowed wider use of bulk and single-cell RNA sequencing, human-induced pluripotent stem cells, organoids, metabolomics, epigenomics, and novel animal models in conjunction with GWAS. In this review, we feature recent advancements relevant to cardiovascular diseases arising from the integration of genetic findings with multiple enabling technologies within multidisciplinary teams to highlight the solidifying transformative potential of this approach. Well-designed workflows integrating different platforms are greatly improving and accelerating the unraveling and understanding of complex disease processes while promoting an effective way to find better drug targets, improve drug design and repurposing, and provide insight towards a more personalized clinical practice.
Collapse
Affiliation(s)
- Haocheng Lu
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA
| | - Jifeng Zhang
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA.
| | - Minerva T Garcia-Barrio
- Department of Internal Medicine, University of Michigan Medical Center, 2800 Plymouth Rd, Ann Arbor, MI, 48109-2800, USA.
| |
Collapse
|
14
|
Preguiça I, Alves A, Nunes S, Fernandes R, Gomes P, Viana SD, Reis F. Diet-induced rodent models of obesity-related metabolic disorders-A guide to a translational perspective. Obes Rev 2020; 21:e13081. [PMID: 32691524 DOI: 10.1111/obr.13081] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Diet is a critical element determining human health and diseases, and unbalanced food habits are major risk factors for the development of obesity and related metabolic disorders. Despite technological and pharmacological advances, as well as intensification of awareness campaigns, the prevalence of metabolic disorders worldwide is still increasing. Thus, novel therapeutic approaches with increased efficacy are urgently required, which often depends on cellular and molecular investigations using robust animal models. In the absence of perfect rodent models, those induced by excessive consumption of fat and sugars better replicate the key aspects that are the root causes of human metabolic diseases. However, the results obtained using these models cannot be directly compared, particularly because of the use of different dietary protocols, and animal species and strains, among other confounding factors. This review article revisits diet-induced models of obesity and related metabolic disorders, namely, metabolic syndrome, prediabetes, diabetes and nonalcoholic fatty liver disease. A critical analysis focused on the main pathophysiological features of rodent models, as opposed to the criteria defined for humans, is provided as a practical guide with a translational perspective for the establishment of animal models of obesity-related metabolic diseases.
Collapse
Affiliation(s)
- Inês Preguiça
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal
| | - André Alves
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal
| | - Sara Nunes
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal
| | - Rosa Fernandes
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal
| | - Pedro Gomes
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal.,Department of Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal.,Center for Health Technology and Services Research (CINTESIS), University of Porto, Porto, Portugal
| | - Sofia D Viana
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal.,ESTESC-Coimbra Health School, Pharmacy, Polytechnic Institute of Coimbra, Coimbra, Portugal
| | - Flávio Reis
- Institute of Pharmacology and Experimental Therapeutics, and Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), University of Coimbra, Coimbra, Portugal
| |
Collapse
|
15
|
Giri AK, Prasad G, Bandesh K, Parekatt V, Mahajan A, Banerjee P, Kauser Y, Chakraborty S, Rajashekar D, Sharma A, Mathur SK, Basu A, McCarthy MI, Tandon N, Bharadwaj D. Multifaceted genome-wide study identifies novel regulatory loci in SLC22A11 and ZNF45 for body mass index in Indians. Mol Genet Genomics 2020; 295:1013-1026. [PMID: 32363570 DOI: 10.1007/s00438-020-01678-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 04/11/2020] [Indexed: 12/22/2022]
Abstract
Obesity, a risk factor for multiple diseases (e.g. diabetes, hypertension, cancers) originates through complex interactions between genes and prevailing environment (food habit and lifestyle) that varies across populations. Indians exhibit a unique obesity phenotype with high abdominal adiposity for a given body weight compared to matched white populations suggesting presence of population-specific genetic and environmental factors influencing obesity. However, Indian population-specific genetic contributors for obesity have not been explored yet. Therefore, to identify potential genetic contributors, we performed a two-staged genome-wide association study (GWAS) for body mass index (BMI), a common measure to evaluate obesity in 5973 Indian adults and the lead findings were further replicated in 1286 Indian adolescents. Our study revealed novel association of variants-rs6913677 in BAI3 gene (p = 1.08 × 10-8) and rs2078267 in SLC22A11 gene (p = 4.62 × 10-8) at GWAS significance, and of rs8100011 in ZNF45 gene (p = 1.04 × 10-7) with near GWAS significance. As genetic loci may dictate the phenotype through modulation of epigenetic processes, we overlapped genetic data of identified signals with their DNA methylation patterns in 236 Indian individuals and performed methylation quantitative trait loci (meth-QTL) analysis. Further, functional roles of discovered variants and underlying genes were speculated using publicly available gene regulatory databases (ENCODE, JASPAR, GeneHancer, GTEx). The identified variants in BAI3 and SLC22A11 genes were found to dictate methylation patterns at unique CpGs harboring critical cis-regulatory elements. Further, BAI3, SLC22A11 and ZNF45 variants were located in repressive chromatin, active enhancer, and active chromatin regions, respectively, in human subcutaneous adipose tissue in ENCODE database. Additionally, these genomic regions represented potential binding sites for key transcription factors implicated in obesity and/or metabolic disorders. Interestingly, GTEx portal identify rs8100011 as a robust cis-expression quantitative trait locus (cis-eQTL) in subcutaneous adipose tissue (p = 1.6 × 10-7), and ZNF45 gene expression in skeletal muscle of Indian subjects showed an inverse correlation with BMI indicating its possible role in obesity. In conclusion, our study discovered 3 novel population-specific functional genetic variants (rs6913677, rs2078267, rs8100011) in 2 novel (SLC22A11 and ZNF45) and 1 earlier reported gene (BAI3) for BMI in Indians. Our study decodes key genomic loci underlying obesity phenotype in Indians that may serve as prospective drug targets in future.
Collapse
Affiliation(s)
- Anil K Giri
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Khushdeep Bandesh
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Vaisak Parekatt
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Priyanka Banerjee
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Yasmeen Kauser
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Shraddha Chakraborty
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Donaka Rajashekar
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Abhay Sharma
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India
| | - Sandeep Kumar Mathur
- Department of Endocrinology, Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi, India.
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, India. .,Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|