1
|
Jin H, Kim YA, Lee Y, Kwon SH, Do AR, Seo S, Won S, Seo JH. Identification of genetic variants associated with diabetic kidney disease in multiple Korean cohorts via a genome-wide association study mega-analysis. BMC Med 2023; 21:16. [PMID: 36627639 PMCID: PMC9832630 DOI: 10.1186/s12916-022-02723-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The pathogenesis of diabetic kidney disease (DKD) is complex, involving metabolic and hemodynamic factors. Although DKD has been established as a heritable disorder and several genetic studies have been conducted, the identification of unique genetic variants for DKD is limited by its multiplex classification based on the phenotypes of diabetes mellitus (DM) and chronic kidney disease (CKD). Thus, we aimed to identify the genetic variants related to DKD that differentiate it from type 2 DM and CKD. METHODS We conducted a large-scale genome-wide association study mega-analysis, combining Korean multi-cohorts using multinomial logistic regression. A total of 33,879 patients were classified into four groups-normal, DM without CKD, CKD without DM, and DKD-and were further analyzed to identify novel single-nucleotide polymorphisms (SNPs) associated with DKD. Additionally, fine-mapping analysis was conducted to investigate whether the variants of interest contribute to a trait. Conditional analyses adjusting for the effect of type 1 DM (T1D)-associated HLA variants were also performed to remove confounding factors of genetic association with T1D. Moreover, analysis of expression quantitative trait loci (eQTL) was performed using the Genotype-Tissue Expression project. Differentially expressed genes (DEGs) were analyzed using the Gene Expression Omnibus database (GSE30529). The significant eQTL DEGs were used to explore the predicted interaction networks using search tools for the retrieval of interacting genes and proteins. RESULTS We identified three novel SNPs [rs3128852 (P = 8.21×10-25), rs117744700 (P = 8.28×10-10), and rs28366355 (P = 2.04×10-8)] associated with DKD. Moreover, the fine-mapping study validated the causal relationship between rs3128852 and DKD. rs3128852 is an eQTL for TRIM27 in whole blood tissues and HLA-A in adipose-subcutaneous tissues. rs28366355 is an eQTL for HLA-group genes present in most tissues. CONCLUSIONS We successfully identified SNPs (rs3128852, rs117744700, and rs28366355) associated with DKD and verified the causal association between rs3128852 and DKD. According to the in silico analysis, TRIM27 and HLA-A can define DKD pathophysiology and are associated with immune response and autophagy. However, further research is necessary to understand the mechanism of immunity and autophagy in the pathophysiology of DKD and to prevent and treat DKD.
Collapse
Affiliation(s)
- Heejin Jin
- Institute of Health and Environment, Seoul National University, Seoul, Korea
| | - Ye An Kim
- Division of Endocrinology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Korea
| | - Young Lee
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea
| | - Seung-Hyun Kwon
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea
| | - Sujin Seo
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Sungho Won
- Institute of Health and Environment, Seoul National University, Seoul, Korea.,Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea.,RexSoft Corps, Seoul, Korea
| | - Je Hyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea.
| |
Collapse
|
2
|
Zeng WL, Yang SK, Song N, Chu FF. The impact of angiotensin converting enzyme insertion/deletion gene polymorphism on diabetic kidney disease: A debatable issue. Nefrologia 2022; 42:415-431. [PMID: 36460431 DOI: 10.1016/j.nefroe.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/21/2021] [Indexed: 06/17/2023] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the influence of ACE I/D gene polymorphisms on diabetic kidney disease (DKD) risk. METHODS All eligible investigations were identified, the number of various genotype in the case and control group were reviewed. The pooled analysis was performed using Stata software. RESULTS In overall subjects, 24,321 participants with 12,961 cases and 11,360 controls were included. the pooled analysis showed a significant link between D allele, DD or II genotype and DKD risk (D versus I: OR=1.316, 95% CI: 1.213-1.427, P=0.000; DD versus ID+II: OR=1.414, 95% CI: 1.253-1.595, P=0.000; II versus DD+ID: OR=0.750, 95% CI: 0.647-0.869, P=0.000). The subgroup pooled analysis showed that ACE I/D gene polymorphism was correlated with DKD both in Asian and in Chinese population. In addition, ACE I/D gene polymorphism was correlated with type 2 DKD (D versus I: OR=1.361, 95% CI: 1.243-1.490, P=0.000; DD versus ID+II: OR=1.503, 95% CI: 1.310-1.726, P=0.000; II versus DD+ID: OR=0.738, 95% CI: 0.626 -0.870, P=0.000). However, there was no obvious correlation in Caucasian subjects and type 1 diabetic patients. CONCLUSION ACE I/D polymorphisms were correlated with DKD in Asian and type 2 diabetic populations. ACE D allele/DD genotype might be a risk factor, while ACE II genotype might be a protective factor for DKD.
Collapse
Affiliation(s)
- Wen-Li Zeng
- Department of Nephrology, The First Affiliated Hospital of the University of South China, Hengyang 421001, Hunan Province, China
| | - Shi-Kun Yang
- Department of Nephrology, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan Province, China
| | - Na Song
- Department of Nephrology, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan Province, China
| | - Fen-Fen Chu
- Department of Nephrology, The First Affiliated Hospital of the University of South China, Hengyang 421001, Hunan Province, China.
| |
Collapse
|
3
|
ElHajj Chehadeh S, Sayed NS, Abdelsamad HS, Almahmeed W, Khandoker AH, Jelinek HF, Alsafar HS. Genetic Variants and Their Associations to Type 2 Diabetes Mellitus Complications in the United Arab Emirates. Front Endocrinol (Lausanne) 2022; 12:751885. [PMID: 35069435 PMCID: PMC8772337 DOI: 10.3389/fendo.2021.751885] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Aim Type 2 Diabetes Mellitus (T2DM) is associated with microvascular complications, including diabetic retinopathy (DR), diabetic nephropathy (DNp), and diabetic peripheral neuropathy (DPN). In this study, we investigated genetic variations and Single Nucleotide Polymorphisms (SNPs) associated with DR, DNp, DPN and their combinations among T2DM patients of Arab origin from the United Arab Emirates, to establish the role of genes in the progression of microvascular diabetes complications. Methods A total of 158 Emirati patients with T2DM were recruited in this study. The study population was divided into 8 groups based on the presence of single, dual, or all three complications. SNPs were selected for association analyses through a search of publicly available databases, specifically genome-wide association study (GWAS) catalog, infinome genome interpretation platform, and GWAS Central database. A multivariate logistic regression analysis and association test were performed to evaluate the association between 83 SNPs and DR, DNp, DPN, and their combinations. Results Eighty-three SNPs were identified as being associated with T2DM and 18 SNPs had significant associations to one or more diabetes complications. The most strongly significant association for DR was rs3024997 SNP in the VEGFA gene. The top-ranked SNP for DPN was rs4496877 in the NOS3 gene. A trend towards association was detected at rs833068 and rs3024998 in the VEGFA gene with DR and rs743507 and rs1808593 in the NOS3 gene with DNp. For dual complications, the rs833061, rs833068 and rs3024997 in the VEGFA gene and the rs4149263 SNP in the ABCA1 gene were also with borderline association with DR/DNp and DPN/DNp, respectively. Diabetic with all of the complications was significantly associated with rs2230806 in the ABCA1 gene. In addition, the highly associated SNPs rs3024997 of the VEGFA gene and rs4496877 of the NOS3 gene were linked to DR and DPN after adjusting for the effects of other associated markers, respectively. Conclusions The present study reports associations of different genetic polymorphisms with microvascular complications and their combinations in Emirati T2DM patients, reporting new associations, and corroborating previous findings. Of interest is that some SNPs/genes were only present if multiple comorbidities were present and not associated with any single complication.
Collapse
Affiliation(s)
| | - Noura S. Sayed
- Khalifa University Center of Biotechnology, Abu Dhabi, United Arab Emirates
| | - Hanin S. Abdelsamad
- Biomedical Engineering Department, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Wael Almahmeed
- Institute of Cardiac Science, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
- Heart and Vascular Institute, Cleveland Clinic, Abu Dhabi, United Arab Emirates
| | - Ahsan H. Khandoker
- Biomedical Engineering Department, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Herbert F. Jelinek
- Khalifa University Center of Biotechnology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering Department, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Healthcare Engineering Innovation Center (HEIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba S. Alsafar
- Khalifa University Center of Biotechnology, Abu Dhabi, United Arab Emirates
- Biomedical Engineering Department, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| |
Collapse
|
4
|
He X, Sun J, Liu C, Yu X, Li H, Zhang W, Li Y, Geng Y, Wang Z. Compositional Alterations of Gut Microbiota in Patients with Diabetic Kidney Disease and Type 2 Diabetes Mellitus. Diabetes Metab Syndr Obes 2022; 15:755-765. [PMID: 35280499 PMCID: PMC8911313 DOI: 10.2147/dmso.s347805] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Emerging evidence has revealed that gut microbiota plays a pivotal role in the pathogenesis of type 2 diabetes mellitus (T2DM) and diabetic kidney disease (DKD). However, few studies have used metagenomic sequencing to analyze the alterations of gut microbiota community in patients with early-stage DKD. METHODS We carried out metagenomic sequencing in fecal samples of 10 DKD patients (DKD group) and 10 T2DM patients who appeared to be less prone to DKD (non-DKD group), aiming to compare the composition and function of gut microbiota between the DKD and non-DKD groups. RESULTS The gut microbial community of the DKD group was significantly different from that of the non-DKD group, characterized by a marked increase in phylum Proteobacteria, genus Selenomonadales, Neosynechococcus, Shigella, Bilophila, Acidaminococcus, species, Escherichia coli, Bacteroides plebeius, Megasphaera elsdenii, Acidaminococcus unclassified, and Bilophila wadsworthia. The amounts of species Citrobacter farmeri and Syntrophaceticus schinkii were significantly and positively correlated with the urinary albumin creatinine ratio in the DKD group. Furthermore, functional analysis based on dbCAN and KEGG databases showed aberrant lipopolysaccharide (LPS) biosynthesis and carbohydrate metabolism in the gut microbiome of the DKD group. CONCLUSION Our findings provided evidence for alterations in the composition and function of gut microbiota in patients with DKD versus the non-DKD group. These data may contribute to a more comprehensive understanding of the pathological mechanisms of DKD.
Collapse
Affiliation(s)
- Xin He
- Dialysis Department of Nephrology Hospital, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Jiping Sun
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Chao Liu
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Xiaoyang Yu
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Huixian Li
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Wenjing Zhang
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Yan Li
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Yingzhou Geng
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
| | - Zhigang Wang
- Department of Nephrology, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, People’s Republic of China
- Correspondence: Zhigang Wang, First Affiliated Hospital of Xi’an Jiaotong University, West Yanta Road 277, Xi’an, 710061, People’s Republic of China, Email
| |
Collapse
|
5
|
Zeng WL, Yang SK, Song N, Chu FF. The impact of angiotensin converting enzyme insertion/deletion gene polymorphism on diabetic kidney disease: A debatable issue. Nefrologia 2021; 42:S0211-6995(21)00158-2. [PMID: 34503862 DOI: 10.1016/j.nefro.2021.07.008] [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: 03/06/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the influence of ACE I/D gene polymorphisms on diabetic kidney disease (DKD) risk. METHODS All eligible investigations were identified, the number of various genotype in the case and control group were reviewed. The pooled analysis was performed using Stata software. RESULTS In overall subjects, 24,321 participants with 12,961 cases and 11,360 controls were included. the pooled analysis showed a significant link between D allele, DD or II genotype and DKD risk (D versus I: OR=1.316, 95% CI: 1.213-1.427, P=0.000; DD versus ID+II: OR=1.414, 95% CI: 1.253-1.595, P=0.000; II versus DD+ID: OR=0.750, 95% CI: 0.647-0.869, P=0.000). The subgroup pooled analysis showed that ACE I/D gene polymorphism was correlated with DKD both in Asian and in Chinese population. In addition, ACE I/D gene polymorphism was correlated with type 2 DKD (D versus I: OR=1.361, 95% CI: 1.243-1.490, P=0.000; DD versus ID+II: OR=1.503, 95% CI: 1.310-1.726, P=0.000; II versus DD+ID: OR=0.738, 95% CI: 0.626 -0.870, P=0.000). However, there was no obvious correlation in Caucasian subjects and type 1 diabetic patients. CONCLUSION ACE I/D polymorphisms were correlated with DKD in Asian and type 2 diabetic populations. ACE D allele/DD genotype might be a risk factor, while ACE II genotype might be a protective factor for DKD.
Collapse
Affiliation(s)
- Wen-Li Zeng
- Department of Nephrology, The First Affiliated Hospital of the University of South China, Hengyang 421001, Hunan Province, China
| | - Shi-Kun Yang
- Department of Nephrology, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan Province, China
| | - Na Song
- Department of Nephrology, The Third Xiangya Hospital of Central South University, Changsha 410013, Hunan Province, China
| | - Fen-Fen Chu
- Department of Nephrology, The First Affiliated Hospital of the University of South China, Hengyang 421001, Hunan Province, China.
| |
Collapse
|
6
|
Koch PA, Dornan GL, Hessenberger M, Haucke V. The molecular mechanisms mediating class II PI 3-kinase function in cell physiology. FEBS J 2021; 288:7025-7042. [PMID: 33387369 DOI: 10.1111/febs.15692] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
The phosphoinositide 3-kinase (PI3K) family of lipid-modifying enzymes plays vital roles in cell signaling and membrane trafficking through the production of 3-phosphorylated phosphoinositides. Numerous studies have analyzed the structure and function of class I and class III PI3Ks. In contrast, we know comparably little about the structure and physiological functions of the class II enzymes. Only recent studies have begun to unravel their roles in development, endocytic and endolysosomal membrane dynamics, signal transduction, and cell migration, while the mechanisms that control their localization and enzymatic activity remain largely unknown. Here, we summarize our current knowledge of the class II PI3Ks and outline open questions related to their structure, enzymatic activity, and their physiological and pathophysiological functions.
Collapse
Affiliation(s)
- Philipp Alexander Koch
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Germany
| | | | - Manuel Hessenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.,Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Germany
| |
Collapse
|
7
|
Tziastoudi M, Stefanidis I, Zintzaras E. The genetic map of diabetic nephropathy: evidence from a systematic review and meta-analysis of genetic association studies. Clin Kidney J 2020; 13:768-781. [PMID: 33123356 PMCID: PMC7577775 DOI: 10.1093/ckj/sfaa077] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Despite the extensive efforts of scientists, the genetic background of diabetic nephropathy (DN) has not yet been clarified. To elucidate the genetic variants that predispose to the development of DN, we conducted a systematic review and meta-analysis of all available genetic association studies (GAS) of DN. We searched in the Human Genome Epidemiology Navigator (HuGE Navigator) and PubMed for available GAS of DN. The threshold for meta-analysis was three studies per genetic variant. The association between genotype distribution and DN was examined using the generalized linear odds ratio (ORG). For variants with available allele frequencies, the examined model was the allele contrast. The pooled OR was estimated using the DerSimonian and Laird random effects model. The publication bias was assessed with Egger’s test. We performed pathway analysis of significant genes with DAVID 6.7. Genetic data of 606 variants located in 228 genes were retrieved from 360 GASs and were synthesized with meta-analytic methods. ACACB, angiotensin I-converting enzyme (ACE), ADIPOQ, AGT, AGTR1, AKR1B1, APOC1, APOE, ATP1B2, ATP2A3, CARS, CCR5, CGNL1, Carnosine dipeptidase 1 (CNDP1), CYGB-PRCD, EDN1, Engulfment and cell motility 1 (ELMO1), ENPP1, EPO, FLT4, FTO, GLO1, HMGA2, IGF2/INS/TH cluster, interleukin 1B (IL1B), IL8, IL10, KCNQ1, KNG, LOC101927627, Methylenetetrahydrofolate reductase, nitric oxide synthase 3 (NOS3), SET domain containing seven, histone lysine methyltransferase (SETD7), Sirtuin 1 (SIRT1), SLC2A1, SLC2A2, SLC12A3, SLC19A3, TCF7L2, TGFB1, TIMP1, TTC39C, UNC13B, VEGFA, WTAPP1, WWC1 as well as XYLT1 and three intergenic polymorphisms showed significant association with DN. Pathway analysis revealed the overrepresentation of six signalling pathways. The significant findings provide further evidence for genetic factors implication in DN offering new perspectives in discovery of new therapies.
Collapse
Affiliation(s)
- Maria Tziastoudi
- Department of Biomathematics, University of Thessaly, School of Medicine, Larissa, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, University of Thessaly, School of Medicine, Larissa, Greece
| | - Elias Zintzaras
- Department of Biomathematics, University of Thessaly, School of Medicine, Larissa, Greece.,The Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| |
Collapse
|
8
|
Ren X, Li X. Advances in Research on Diabetes by Human Nutriomics. Int J Mol Sci 2019; 20:ijms20215375. [PMID: 31671732 PMCID: PMC6861882 DOI: 10.3390/ijms20215375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022] Open
Abstract
The incidence and prevalence of diabetes mellitus (DM) have increased rapidly worldwide over the last two decades. Because the pathogenic factors of DM are heterogeneous, determining clinically effective treatments for DM patients is difficult. Applying various nutrient analyses has yielded new insight and potential treatments for DM patients. In this review, we summarized the omics analysis methods, including nutrigenomics, nutritional-metabolomics, and foodomics. The list of the new targets of SNPs, genes, proteins, and gut microbiota associated with DM has been obtained by the analysis of nutrigenomics and microbiomics within last few years, which provides a reference for the diagnosis of DM. The use of nutrient metabolomics analysis can obtain new targets of amino acids, lipids, and metal elements, which provides a reference for the treatment of DM. Foodomics analysis can provide targeted dietary strategies for DM patients. This review summarizes the DM-associated molecular biomarkers in current applied omics analyses and may provide guidance for diagnosing and treating DM.
Collapse
Affiliation(s)
- Xinmin Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China.
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Xiangdong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China.
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
9
|
Otto GW, Kaisaki PJ, Brial F, Le Lay A, Cazier JB, Mott R, Gauguier D. Conserved properties of genetic architecture of renal and fat transcriptomes in rat models of insulin resistance. Dis Model Mech 2019; 12:dmm.038539. [PMID: 31213483 PMCID: PMC6679378 DOI: 10.1242/dmm.038539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
To define renal molecular mechanisms that are affected by permanent hyperglycaemia and might promote phenotypes relevant to diabetic nephropathy, we carried out linkage analysis of genome-wide gene transcription in the kidneys of F2 offspring from the Goto-Kakizaki (GK) rat model of type 2 diabetes and normoglycaemic Brown Norway (BN) rats. We mapped 2526 statistically significant expression quantitative trait loci (eQTLs) in the cross. More than 40% of eQTLs mapped in the close vicinity of the linked transcripts, underlying possible cis-regulatory mechanisms of gene expression. We identified eQTL hotspots on chromosomes 5 and 9 regulating the expression of 80-165 genes, sex or cross direction effects, and enriched metabolic and immunological processes by segregating GK alleles. Comparative analysis with adipose tissue eQTLs in the same cross showed that 496 eQTLs, in addition to the top enriched biological pathways, are conserved in the two tissues. Extensive similarities in eQTLs mapped in the GK rat and in the spontaneously hypertensive rat (SHR) suggest a common aetiology of disease phenotypes common to the two strains, including insulin resistance, which is a prominent pathophysiological feature in both GK rats and SHRs. Our data shed light on shared and tissue-specific molecular mechanisms that might underlie aetiological aspects of insulin resistance in the context of spontaneously occurring hyperglycaemia and hypertension. Summary: Kidney and fat expression QTL mapping in rat models of spontaneously occurring insulin resistance associated with either diabetes or hypertension reveals conserved gene expression regulation, suggesting shared aetiology of disease phenotypes.
Collapse
Affiliation(s)
- Georg W Otto
- Genetics and Genomic Medicine, University College London Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
| | - Pamela J Kaisaki
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, United Kingdom
| | - Francois Brial
- University Paris Descartes, INSERM UMR 1124, 45 rue des Saint-Pères, 75006 Paris, France
| | - Aurélie Le Lay
- University Paris Descartes, INSERM UMR 1124, 45 rue des Saint-Pères, 75006 Paris, France
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, Medical School, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Richard Mott
- University College London Genetics Institute, Gower Street, London WC1E 6BT, United Kingdom
| | - Dominique Gauguier
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, United Kingdom .,University Paris Descartes, INSERM UMR 1124, 45 rue des Saint-Pères, 75006 Paris, France.,McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC H3A 0G1, Canada
| |
Collapse
|