1
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Sonti S, Littleton SH, Pahl MC, Zimmerman AJ, Chesi A, Palermo J, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Pack AI, Gehrman PR, Keene AC, Grant SFA. Perturbation of the insomnia WDR90 genome-wide association studies locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q. Sleep 2024; 47:zsae085. [PMID: 38571402 PMCID: PMC11236950 DOI: 10.1093/sleep/zsae085] [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: 08/15/2023] [Revised: 01/28/2024] [Indexed: 04/05/2024] Open
Abstract
Although genome-wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated phosphatidyl inositol glycan (PIG)-Q as a functionally relevant gene at the insomnia "WDR90" GWAS locus. However, importantly that effort did not characterize the corresponding underlying causal variant. Specifically, our previous 3D genomic datasets nominated a shortlist of three neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium within an intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. We sought to investigate the influence of these SNPs collectively and then individually on PIG-Q modulation to pinpoint the causal "regulatory" variant. Starting with gross level perturbation, deletion of the entire region in NPCs via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from individual luciferase reporter assays for each SNP in iPSCs revealed that the region with the rs3752495 risk allele (RA) induced a ~2.5-fold increase in luciferase expression. Importantly, rs3752495 also exhibited an allele-specific effect, with the RA increasing the luciferase expression by ~2-fold versus the non-RA. In conclusion, our variant-to-function approach and in vitro validation implicate rs3752495 as a causal insomnia variant embedded within WDR90 while modulating the expression of the distally located PIG-Q.
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Affiliation(s)
- Shilpa Sonti
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber J Zimmerman
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory, Medicine University of Pennsylvania Perelman School of Medicine, Philadelphia PA, USA
| | - Justin Palermo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth B Brown
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phillip R Gehrman
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
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Tan X, Li G, Deng H, Xiao G, Wang Y, Zhang C, Chen Y. Obesity enhances the response to neoadjuvant anti-PD1 therapy in oral tongue squamous cell carcinoma. Cancer Med 2024; 13:e7346. [PMID: 38923758 PMCID: PMC11194614 DOI: 10.1002/cam4.7346] [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: 11/30/2023] [Revised: 03/29/2024] [Accepted: 05/18/2024] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVES Previous studies have demonstrated that obesity may impact the efficacy of anti-PD1 therapy, but the underlying mechanism remains unclear. In this study, our objective was to determine the prognostic value of obesity in patients with oral tongue squamous cell carcinoma (OTSCC) treated with pembrolizumab and establish a subtype based on fatty acid metabolism-related genes (FAMRGs) for immunotherapy. MATERIALS AND METHODS We enrolled a total of 56 patients with OTSCC who underwent neoadjuvant anti-PD1 therapy. Univariate and multivariate Cox regression analyses, Kaplan-Meier survival analysis, and immunohistochemistry staining were performed. Additionally, we acquired the gene expression profiles of pan-cancer samples and conducted GSEA and KEGG pathway analysis. Moreover, data from TCGA, MSigDB, UALCAN, GEPIA and TIMER were utilized to construct the FAMRGs subtype. RESULTS Our findings indicate that high Body Mass Index (BMI) was significantly associated with improved PFS (HR = 0.015; 95% CI, 0.001 to 0.477; p = 0.015), potentially attributed to increased infiltration of PD1 + T cells. A total of 91 differentially expressed FAMRGs were identified between the response and non-response groups in pan-cancer patients treated with immunotherapy. Of these, 6 hub FAMRGs (ACSL5, PLA2G2D, PROCA1, IL4I1, UBE2L6 and PSME1) were found to affect PD-1 expression and T cell infiltration in HNSCC, which may impact the efficacy of anti-PD1 therapy. CONCLUSION This study demonstrates that obesity serves as a robust prognostic predictor for patients with OTSCC undergoing neoadjuvant anti-PD1 therapy. Furthermore, the expression of 6 hub FAMRGs (ACSL5, PLA2G2D, PROCA1, IL4I1, UBE2L6 and PSME1) plays a pivotal role in the context of anti-PD1 therapy and deserves further investigation.
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Affiliation(s)
- Xiyan Tan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Head and Neck SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Guoli Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Head and Neck SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Honghao Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Head and Neck SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Guoming Xiao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Head and Neck SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Yaqin Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Chenzhi Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Colorectal SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
| | - Yanfeng Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhouP.R. China
- Department of Head and Neck SurgerySun Yat‐sen University Cancer CenterGuangzhouP.R. China
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Conery M, Pippin JA, Wagley Y, Trang K, Pahl MC, Villani DA, Favazzo LJ, Ackert-Bicknell CL, Zuscik MJ, Katsevich E, Wells AD, Zemel BS, Voight BF, Hankenson KD, Chesi A, Grant SF. GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585778. [PMID: 38562830 PMCID: PMC10983984 DOI: 10.1101/2024.03.19.585778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Over 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblast 1.19 cells (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from cross-cell type stratified LD-score regression involving 98 cell types grouped into 15 tissues. 24 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues that warrant attention in future screens.
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Affiliation(s)
- Mitchell Conery
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Khanh Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David A. Villani
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Cell Biology, Stems Cells and Development Ph.D. Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lacey J. Favazzo
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Cheryl L. Ackert-Bicknell
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael J. Zuscik
- Colorado Program for Musculoskeletal Research, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Orthopedics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
- University of Colorado Interdisciplinary Joint Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Malfait J, Wan J, Spicuglia S. Epromoters are new players in the regulatory landscape with potential pleiotropic roles. Bioessays 2023; 45:e2300012. [PMID: 37246247 DOI: 10.1002/bies.202300012] [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: 01/17/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Precise spatiotemporal control of gene expression during normal development and cell differentiation is achieved by the combined action of proximal (promoters) and distal (enhancers) cis-regulatory elements. Recent studies have reported that a subset of promoters, termed Epromoters, works also as enhancers to regulate distal genes. This new paradigm opened novel questions regarding the complexity of our genome and raises the possibility that genetic variation within Epromoters has pleiotropic effects on various physiological and pathological traits by differentially impacting multiple proximal and distal genes. Here, we discuss the different observations pointing to an important role of Epromoters in the regulatory landscape and summarize the evidence supporting a pleiotropic impact of these elements in disease. We further hypothesize that Epromoter might represent a major contributor to phenotypic variation and disease.
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Affiliation(s)
- Juliette Malfait
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Jing Wan
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
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5
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Sonti S, Littleton SH, Pahl MC, Zimmerman AJ, Chesi A, Palermo J, Lasconi C, Brown EB, Pippin JA, Wells AD, Doldur-Balli F, Pack AI, Gehrman PR, Keene AC, Grant SFA. Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553739. [PMID: 37645863 PMCID: PMC10462147 DOI: 10.1101/2023.08.17.553739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Although genome wide association studies (GWAS) have been crucial for the identification of loci associated with sleep traits and disorders, the method itself does not directly uncover the underlying causal variants and corresponding effector genes. The overwhelming majority of such variants reside in non-coding regions and are therefore presumed to impact the activity of cis-regulatory elements, such as enhancers. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' locus. However, importantly that effort did not characterize the corresponding underlying causal variant at this GWAS signal. Specifically, our genome-wide ATAC-seq and high-resolution promoter-focused Capture C datasets generated in this cell setting brought our attention to a shortlist of three tightly neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium in a candidate intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. The objective of this study was to investigate the influence of the proxy SNPs collectively and then individually on PIG-Q modulation and to pinpoint the causal "regulatory" variant among the three SNPs. Starting at a gross level perturbation, deletion of the entire region harboring all three SNPs in human iPSC-derived neural progenitor cells via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from more refined individual luciferase reporter assays for each of the three SNPs in iPSCs revealed that the intronic region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression (n=10). Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold compared to the non-risk allele. In conclusion, our variant-to-function approach and subsequent in vitro validation implicates rs3752495 as a causal insomnia risk variant embedded at the WDR90-PIG-Q locus.
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Affiliation(s)
- Shilpa Sonti
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Amber J Zimmerman
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Justin Palermo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Chiara Lasconi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Elizabeth B Brown
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fusun Doldur-Balli
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Allan I Pack
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Phillip R Gehrman
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - S F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
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Role of ACSL5 in fatty acid metabolism. Heliyon 2023; 9:e13316. [PMID: 36816310 PMCID: PMC9932481 DOI: 10.1016/j.heliyon.2023.e13316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/07/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Free fatty acids (FFAs) are essential energy sources for most body tissues. A fatty acid must be converted to fatty acyl-CoA to oxidize or be incorporated into new lipids. Acyl-CoA synthetase long-chain family member 5 (ACSL5) is localized in the endoplasmic reticulum and mitochondrial outer membrane, where it catalyzes the formation of fatty acyl-CoAs from long-chain fatty acids (C16-C20). Fatty acyl-CoAs are then used in lipid synthesis or β-oxidation mediated pathways. ACSL5 plays a pleiotropic role in lipid metabolism depending on substrate preferences, subcellular localization and tissue specificity. Here, we review the role of ACSL5 in fatty acid metabolism in multiple metabolic tissues, including the liver, small intestine, adipose tissue, and skeletal muscle. Given the increasing number of studies suggesting the role of ACSL5 in glucose and lipid metabolism, we also summarized the effects of ACSL5 on circulating lipids and insulin resistance.
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7
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Ganekal P, Vastrad B, Vastrad C, Kotrashetti S. Identification of biomarkers, pathways, and potential therapeutic targets for heart failure using next-generation sequencing data and bioinformatics analysis. Ther Adv Cardiovasc Dis 2023; 17:17539447231168471. [PMID: 37092838 PMCID: PMC10134165 DOI: 10.1177/17539447231168471] [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] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Heart failure (HF) is the most common cardiovascular diseases and the leading cause of cardiovascular diseases related deaths. Increasing molecular targets have been discovered for HF prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated biomarkers that might aid the diagnosis and treatment of HF. METHODS We searched next-generation sequencing (NGS) dataset (GSE161472) and identified differentially expressed genes (DEGs) by comparing 47 HF samples and 37 normal control samples using limma in R package. Gene ontology (GO) and pathway enrichment analyses of the DEGs were performed using the g: Profiler database. The protein-protein interaction (PPI) network was plotted with Human Integrated Protein-Protein Interaction rEference (HiPPIE) and visualized using Cytoscape. Module analysis of the PPI network was done using PEWCC1. Then, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed by Cytoscape software. Finally, we performed receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. RESULTS A total of 930 DEGs, 464 upregulated genes and 466 downregulated genes, were identified in HF. GO and REACTOME pathway enrichment results showed that DEGs mainly enriched in localization, small molecule metabolic process, SARS-CoV infections, and the citric acid tricarboxylic acid (TCA) cycle and respiratory electron transport. After combining the results of the PPI network miRNA-hub gene regulatory network and TF-hub gene regulatory network, 10 hub genes were selected, including heat shock protein 90 alpha family class A member 1 (HSP90AA1), arrestin beta 2 (ARRB2), myosin heavy chain 9 (MYH9), heat shock protein 90 alpha family class B member 1 (HSP90AB1), filamin A (FLNA), epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), cullin 4A (CUL4A), YEATS domain containing 4 (YEATS4), and lysine acetyltransferase 2B (KAT2B). CONCLUSIONS This discovery-driven study might be useful to provide a novel insight into the diagnosis and treatment of HF. However, more experiments are needed in the future to investigate the functional roles of these genes in HF.
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Affiliation(s)
- Prashanth Ganekal
- Department of General Medicine, Basaveshwara Medical College, Chitradurga, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, #253, Bharthinagar, Dharwad 580001, India
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8
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Hou T, Tian Y, Cao Z, Zhang J, Feng T, Tao W, Sun H, Wen H, Lu X, Zhu Q, Li M, Lu X, Liu B, Zhao Y, Yang Y, Zhu WG. Cytoplasmic SIRT6-mediated ACSL5 deacetylation impedes nonalcoholic fatty liver disease by facilitating hepatic fatty acid oxidation. Mol Cell 2022; 82:4099-4115.e9. [PMID: 36208627 DOI: 10.1016/j.molcel.2022.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/08/2022] [Accepted: 09/16/2022] [Indexed: 11/05/2022]
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9
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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10
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Limardi PC, Oktavianthi S, Priliani L, Lestari R, Saraswati MR, Suastika K, Malik SG. Transcription factor 7-like 2 single nucleotide polymorphisms rs290487 and rs290481 are associated with dyslipidemia in the Balinese population. PeerJ 2022; 10:e13149. [PMID: 35341056 PMCID: PMC8953500 DOI: 10.7717/peerj.13149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
Background Dyslipidemia is one of the major risks for the development of cardiovascular diseases which has been the leading cause of death in developing countries. Previously, common polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been associated with altered lipid profiles. In this study, we investigated the associations of TCF7L2 SNPs, rs290487 and rs290481, with dyslipidemia and altered lipid profile in the Balinese. Methods A total of 565 subjects from four locations in the Bali Province, Indonesia, were recruited. Serum lipid concentrations (triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC)) were measured using standard protocol. SNP genotyping was done using the amplification refractory system mutation polymerase chain reaction (ARMS-PCR) method. Results We found the shifted major/minor allele frequencies of both SNPs (0.56 for rs290487 T allele, 0.53 for rs290481 T allele) in the Balinese, as compared to dbSNP. The rs290487 and rs290481 C alleles were significantly associated with dyslipidemia, particularly high TC and high LDL-C. These associations were independent of age, sex, population, obesity, diabetes mellitus, and high TyG index as a proxy for insulin resistance. The haplotype CC also showed similar association with these traits. Our findings indicate that TCF7L2 polymorphisms are associated with dyslipidemia and altered lipid profile in the Balinese.
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Affiliation(s)
- Prisca C. Limardi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, DKI Jakarta, Indonesia,Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, West Java, Indonesia
| | - Sukma Oktavianthi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, DKI Jakarta, Indonesia
| | - Lidwina Priliani
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, DKI Jakarta, Indonesia
| | - Retno Lestari
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok, West Java, Indonesia
| | - Made Ratna Saraswati
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Ketut Suastika
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Safarina G. Malik
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, DKI Jakarta, Indonesia
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11
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Pippin JA, Chesi A, Wagley Y, Su C, Pahl MC, Hodge KM, Johnson ME, Wells AD, Hankenson KD, Grant SFA. CRISPR-Cas9-Mediated Genome Editing Confirms EPDR1 as an Effector Gene at the BMD GWAS-Implicated ' STARD3NL' Locus. JBMR Plus 2021; 5:e10531. [PMID: 34532616 PMCID: PMC8441377 DOI: 10.1002/jbm4.10531] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/02/2021] [Indexed: 11/12/2022] Open
Abstract
Genome-wide-association studies (GWASs) have discovered genetic signals robustly associated with BMD, but typically not the precise localization of effector genes. By intersecting genome-wide promoter-focused Capture C and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data generated in human mesenchymal progenitor cell (hMSC)-derived osteoblasts, consistent contacts were previously predicted between the EPDR1 promoter and multiple BMD-associated candidate causal variants at the 'STARD3NL' locus. RNAi knockdown of EPDR1 expression in hMSC-derived osteoblasts was shown to lead to inhibition of osteoblastogenesis. To fully characterize the physical connection between these putative noncoding causal variants at this locus and the EPDR1 gene, clustered regularly interspaced short-palindromic repeat Cas9 endonuclease (CRISPR-Cas9) genome editing was conducted in hFOB1.19 cells across the single open-chromatin region harboring candidates for the underlying causal variant, rs1524068, rs6975644, and rs940347, all in close proximity to each other. RT-qPCR and immunoblotting revealed dramatic and consistent downregulation of EPDR1 specifically in the edited differentiated osteoblast cells. Consistent with EPDR1 expression changes, alkaline phosphatase staining was also markedly reduced in the edited differentiated cells. Collectively, CRISPR-Cas9 genome editing in the hFOB1.19 cell model supports previous observations, where this regulatory region harboring GWAS-implicated variation operates through direct long-distance physical contact, further implicating a key role for EPDR1 in osteoblastogenesis and BMD determination. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- James A Pippin
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Alessandra Chesi
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Yadav Wagley
- Department of Orthopedic SurgeryUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Chun Su
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Matthew C Pahl
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Kenyaita M Hodge
- Genetics and Molecular Biology Graduate Program, Laney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Matthew E Johnson
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | - Andrew D Wells
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Kurt D Hankenson
- Department of Orthopedic SurgeryUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Struan F A Grant
- Center for Spatial and Functional GenomicsChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of PediatricsUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
- Divisions of Genetics and EndocrinologyChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
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12
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Huang X, Glessner JT, Huang J, Zhou D, March ME, Wang H, Xia Q, Hakonarson H, Li J. Discovery of Novel Host Molecular Factors Underlying HBV/HCV Infection. Front Cell Dev Biol 2021; 9:690882. [PMID: 34458256 PMCID: PMC8397444 DOI: 10.3389/fcell.2021.690882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Hepatitis is an inflammatory condition of the liver, which is frequently caused by the infection of hepatitis B virus (HBV) or hepatitis C virus (HCV). Hepatitis can lead to the development of chronic complications including cancer, making it a major public health burden. Co-infection of HBV and HCV can result in faster disease progression. Therefore, it is important to identify shared genetic susceptibility loci for HBV and HCV infection to further understand the underlying mechanism. Through a meta-analysis based on genome-wide association summary statistics of HBV and HCV infection, we found one novel locus in the Asian population and two novel loci in the European population. By functional annotation based on multi-omics data, we identified the likely target genes at each novel locus, such as HMGB1 and ATF3, which play a critical role in autophagy and immune response to virus. By re-analyzing a microarray dataset from Hmgb1–/– mice and RNA-seq data from mouse liver tissue overexpressing ATF3, we found that differential expression of autophagy and immune and metabolic gene pathways underlie these conditions. Our study reveals novel common susceptibility loci to HBV and HCV infection, supporting their role in linking autophagy signaling and immune response.
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Affiliation(s)
- Xubo Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jinxia Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
| | - Desheng Zhou
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hongna Wang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
| | - Qianghua Xia
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Human Genetics and Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jin Li
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, China
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13
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Untangling the genetic link between type 1 and type 2 diabetes using functional genomics. Sci Rep 2021; 11:13871. [PMID: 34230558 PMCID: PMC8260770 DOI: 10.1038/s41598-021-93346-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
There is evidence pointing towards shared etiological features between type 1 diabetes (T1D) and type 2 diabetes (T2D) despite both phenotypes being considered genetically distinct. However, the existence of shared genetic features for T1D and T2D remains complex and poorly defined. To better understand the link between T1D and T2D, we employed an integrated functional genomics approach involving extensive chromatin interaction data (Hi-C) and expression quantitative trait loci (eQTL) data to characterize the tissue-specific impacts of single nucleotide polymorphisms associated with T1D and T2D. We identified 195 pleiotropic genes that are modulated by tissue-specific spatial eQTLs associated with both T1D and T2D. The pleiotropic genes are enriched in inflammatory and metabolic pathways that include mitogen-activated protein kinase activity, pertussis toxin signaling, and the Parkinson's disease pathway. We identified 8 regulatory elements within the TCF7L2 locus that modulate transcript levels of genes involved in immune regulation as well as genes important in the etiology of T2D. Despite the observed gene and pathway overlaps, there was no significant genetic correlation between variant effects on T1D and T2D risk using European ancestral summary data. Collectively, our findings support the hypothesis that T1D and T2D specific genetic variants act through genetic regulatory mechanisms to alter the regulation of common genes, and genes that co-locate in biological pathways, to mediate pleiotropic effects on disease development. Crucially, a high risk genetic profile for T1D alters biological pathways that increase the risk of developing both T1D and T2D. The same is not true for genetic profiles that increase the risk of developing T2D. The conversion of information on genetic susceptibility to the protein pathways that are altered provides an important resource for repurposing or designing novel therapies for the management of diabetes.
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14
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Zhang Z, Xu L, Xu X. The role of transcription factor 7-like 2 in metabolic disorders. Obes Rev 2021; 22:e13166. [PMID: 33615650 DOI: 10.1111/obr.13166] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022]
Abstract
Transcription factor 7-like 2 (TCF7L2), a member of the T cell factor/lymphoid enhancer factor family, generally forms a complex with β-catenin to regulate the downstream target genes as an effector of the canonical Wnt signalling pathway. TCF7L2 plays a vital role in various biological processes and functions in many organs and tissues, including the liver, islet and adipose tissues. Further, TCF7L2 down-regulates hepatic gluconeogenesis and promotes lipid accumulation. In islets, TCF7L2 not only affects the insulin secretion of the β-cells but also has an impact on other cells. In addition, TCF7L2 influences adipogenesis in adipose tissues. Thus, an out-of-control TCF7L2 expression can result in metabolic disorders. The TCF7L2 gene is composed of 17 exons, generating 13 different transcripts, and has many single-nucleotide polymorphisms (SNPs). The discovery that these SNPs have an impact on the risk of type 2 diabetes (T2D) has attracted thorough investigations in the study of TCF7L2. Apart from T2D, TCF7L2 SNPs are also associated with type 1, posttransplant and other types of diabetes. Furthermore, TCF7L2 variants affect the progression of other disorders, such as obesity, cancers, metabolic syndrome and heart diseases. Finally, the interaction between TCF7L2 variants and diet also needs to be investigated.
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Affiliation(s)
- Zhensheng Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Zhejiang University School of Medicine, Hangzhou, China
| | - Li Xu
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University Cancer Center, Hangzhou, China.,NHC Key Laboratory of Combined Multi-organ Transplantation, Hangzhou, China.,Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang University Cancer Center, Hangzhou, China
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15
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Iafusco F, Maione G, Rosanio FM, Mozzillo E, Franzese A, Tinto N. Cystic Fibrosis-Related Diabetes (CFRD): Overview of Associated Genetic Factors. Diagnostics (Basel) 2021; 11:diagnostics11030572. [PMID: 33810109 PMCID: PMC8005125 DOI: 10.3390/diagnostics11030572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) is the most common autosomal recessive disease in the Caucasian population and is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene that encodes for a chloride/bicarbonate channel expressed on the membrane of epithelial cells of the airways and of the intestine, as well as in cells with exocrine and endocrine functions. A common nonpulmonary complication of CF is cystic fibrosis-related diabetes (CFRD), a distinct form of diabetes due to insulin insufficiency or malfunction secondary to destruction/derangement of pancreatic betacells, as well as to other factors that affect their function. The prevalence of CFRD increases with age, and 40–50% of CF adults develop the disease. Several proposed hypotheses on how CFRD develops have emerged, including exocrine-driven fibrosis and destruction of the entire pancreas, as well as contrasting theories on the direct or indirect impact of CFTR mutation on islet function. Among contributors to the development of CFRD, in addition to CFTR genotype, there are other genetic factors related and not related to type 2 diabetes. This review presents an overview of the current understanding on genetic factors associated with glucose metabolism abnormalities in CF.
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Affiliation(s)
- Fernanda Iafusco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy; (F.I.); (G.M.)
- CEINGE Advanced Biotechnology, 80131 Naples, Italy
| | - Giovanna Maione
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy; (F.I.); (G.M.)
- CEINGE Advanced Biotechnology, 80131 Naples, Italy
| | - Francesco Maria Rosanio
- Regional Center of Pediatric Diabetology, Department of Translational Medical Sciences, Section of Pediatrics, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.R.); (E.M.); (A.F.)
| | - Enza Mozzillo
- Regional Center of Pediatric Diabetology, Department of Translational Medical Sciences, Section of Pediatrics, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.R.); (E.M.); (A.F.)
| | - Adriana Franzese
- Regional Center of Pediatric Diabetology, Department of Translational Medical Sciences, Section of Pediatrics, University of Naples “Federico II”, 80131 Naples, Italy; (F.M.R.); (E.M.); (A.F.)
| | - Nadia Tinto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, 80131 Naples, Italy; (F.I.); (G.M.)
- CEINGE Advanced Biotechnology, 80131 Naples, Italy
- Correspondence:
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16
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Hou G, Harley ITW, Lu X, Zhou T, Xu N, Yao C, Qin Y, Ouyang Y, Ma J, Zhu X, Yu X, Xu H, Dai D, Ding H, Yin Z, Ye Z, Deng J, Zhou M, Tang Y, Namjou B, Guo Y, Weirauch MT, Kottyan LC, Harley JB, Shen N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nat Commun 2021; 12:135. [PMID: 33420081 PMCID: PMC7794586 DOI: 10.1038/s41467-020-20460-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Since most variants that impact polygenic disease phenotypes localize to non-coding genomic regions, understanding the consequences of regulatory element variants will advance understanding of human disease mechanisms. Here, we report that the systemic lupus erythematosus (SLE) risk variant rs2431697 as likely causal for SLE through disruption of a regulatory element, modulating miR-146a expression. Using epigenomic analysis, genome-editing and 3D chromatin structure analysis, we show that rs2431697 tags a cell-type dependent distal enhancer specific for miR-146a that physically interacts with the miR-146a promoter. NF-kB binds the disease protective allele in a sequence-specific manner, increasing expression of this immunoregulatory microRNA. Finally, CRISPR activation-based modulation of this enhancer in the PBMCs of SLE patients attenuates type I interferon pathway activation by increasing miR-146a expression. Our work provides a strategy to define non-coding RNA functional regulatory elements using disease-associated variants and provides mechanistic links between autoimmune disease risk genetic variation and disease etiology.
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Affiliation(s)
- Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Isaac T W Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ning Xu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Chao Yao
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences(SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031, China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Ye Ouyang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xinyi Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Hong Xu
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
- Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127, China
| | - Dai Dai
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China
| | - Jun Deng
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Mi Zhou
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Ya Guo
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Leah C Kottyan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - John B Harley
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, 45229, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032, China.
- Shanghai Institute of Rheumatology, China-Australia Centre for Personalized Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, China.
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45229, USA.
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Nguyen-Tu MS, Martinez-Sanchez A, Leclerc I, Rutter GA, da Silva Xavier G. Adipocyte-specific deletion of Tcf7l2 induces dysregulated lipid metabolism and impairs glucose tolerance in mice. Diabetologia 2021; 64:129-141. [PMID: 33068125 PMCID: PMC7567653 DOI: 10.1007/s00125-020-05292-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022]
Abstract
AIMS/HYPOTHESIS Transcription factor 7-like 2 (TCF7L2) is a downstream effector of the Wnt/β-catenin signalling pathway implicated in type 2 diabetes risk through genome-wide association studies. Although its expression is critical for adipocyte development, the potential roles of changes in adipose tissue TCF7L2 levels in diabetes risk are poorly defined. Here, we investigated whether forced changes in Tcf7l2 expression in adipocytes affect whole body glucose or lipid metabolism and crosstalk between disease-relevant tissues. METHODS Tcf7l2 was selectively ablated in mature adipocytes in C57BL/6J mice using Cre recombinase under Adipoq promoter control to recombine Tcf7l2 alleles floxed at exon 1 (referred to as aTCF7L2 mice). aTCF7L2 mice were fed normal chow or a high-fat diet for 12 weeks. Glucose and insulin sensitivity, as well as beta cell function, were assessed in vivo and in vitro. Levels of circulating NEFA, selected hormones and adipokines were measured using standard assays. RESULTS Reduced TCF7L2 expression in adipocytes altered glucose tolerance and insulin secretion in male but not in female mice. Thus, on a normal chow diet, male heterozygote knockout mice (aTCF7L2het) exhibited impaired glucose tolerance at 16 weeks (p = 0.03) and increased fat mass (1.4 ± 0.1-fold, p = 0.007) but no changes in insulin secretion. In contrast, male homozygote knockout (aTCF7L2hom) mice displayed normal body weight but impaired oral glucose tolerance at 16 weeks (p = 0.0001). These changes were mechanistically associated with impaired in vitro glucose-stimulated insulin secretion (decreased 0.5 ± 0.1-fold vs control mice, p = 0.02) and decreased levels of the incretins glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide (0.6 ± 0.1-fold and 0.4 ± 0.1-fold vs control mice, p = 0.04 and p < 0.0001, respectively). Circulating levels of plasma NEFA and fatty acid binding protein 4 were increased by 1.3 ± 0.1-fold and 1.8 ± 0.3-fold vs control mice (p = 0.03 and p = 0.05, respectively). Following exposure to a high-fat diet for 12 weeks, male aTCF7L2hom mice exhibited reduced in vivo glucose-stimulated insulin secretion (0.5 ± 0.1-fold vs control mice, p = 0.02). CONCLUSIONS/INTERPRETATION Loss of Tcf7l2 gene expression selectively in adipocytes leads to a sexually dimorphic phenotype, with impairments not only in adipocytes, but also in pancreatic islet and enteroendocrine cells in male mice only. Our findings suggest novel roles for adipokines and incretins in the effects of diabetes-associated variants in TCF7L2, and further illuminate the roles of TCF7L2 in glucose homeostasis and diabetes risk. Graphical abstract.
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Affiliation(s)
- Marie-Sophie Nguyen-Tu
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College Centre for Translational and Experimental Medicine, London, UK
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College Centre for Translational and Experimental Medicine, London, UK
| | - Isabelle Leclerc
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College Centre for Translational and Experimental Medicine, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College Centre for Translational and Experimental Medicine, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
| | - Gabriela da Silva Xavier
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Hammersmith Hospital, Imperial College Centre for Translational and Experimental Medicine, London, UK.
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK.
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18
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Mathiesen DS, Bagger JI, Hansen KB, Junker AE, Plamboeck A, Harring S, Idorn T, Hornum M, Holst JJ, Jonsson AE, Hansen T, Vilsbøll T, Lund A, Knop FK. No detectable effect of a type 2 diabetes-associated TCF7L2 genotype on the incretin effect. Endocr Connect 2020; 9:1221-1232. [PMID: 33252353 PMCID: PMC7774769 DOI: 10.1530/ec-20-0471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
The T allele of TCF7L2 rs7903146 is a common genetic variant associated with type 2 diabetes (T2D), possibly by modulation of incretin action. In this study, we evaluated the effect of the TCF7L2 rs7903146 T allele on the incretin effect and other glucometabolic parameters in normal glucose tolerant individuals (NGT) and participants with T2D. The rs7903146 variant was genotyped in cohorts of 61 NGT individuals (23 were heterozygous (CT) or homozygous (TT) T allele carriers) and 43 participants with T2D (20 with CT/TT). Participants were previously examined by an oral glucose tolerance test (OGTT) and a subsequent isoglycemic intravenous glucose infusion (IIGI). The incretin effect was assessed by quantification of the difference in integrated beta cell secretory responses during the OGTT and IIGI. Glucose and hormonal levels were measured during experimental days, and from these, indices of beta cell function and insulin sensitivity were calculated. No genotype-specific differences in the incretin effect were observed in the NGT group (P = 0.70) or the T2D group (P = 0.68). NGT T allele carriers displayed diminished glucose-dependent insulinotropic polypeptide response during OGTT (P = 0.01) while T allele carriers with T2D were characterized by lower C-peptide AUC after OGTT (P = 0.04) and elevated glucose AUC after OGTT (P = 0.04). In conclusion, our findings do not exclude that this specific TCF7L2 variant increases the risk of developing T2D via diminished incretin effect, but genotype-related defects were not detectable in these cohorts.
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Affiliation(s)
- David S Mathiesen
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Jonatan I Bagger
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Medicine, Gentofte and Herlev Hospital, University of Copenhagen, Denmark
| | - Katrine B Hansen
- Department of Medicine, Gentofte and Herlev Hospital, University of Copenhagen, Denmark
| | | | - Astrid Plamboeck
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Signe Harring
- Department of Gastroenterology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Thomas Idorn
- Center for Cancer and Organ Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mads Hornum
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Cancer and Organ Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Gentofte and Herlev Hospital, University of Copenhagen, Denmark
| | | | | | | | - Tina Vilsbøll
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Novartis Healthcare A/S, Copenhagen, Denmark
- Department of Nephrology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Asger Lund
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Filip K Knop
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Novartis Healthcare A/S, Copenhagen, Denmark
- Department of Nephrology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Gentofte and Herlev Hospital, University of Copenhagen, Denmark
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19
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Zhang X, Chen K, Chen X, Kourkoumelis N, Li G, Wang B, Zhu C. Integrative Analysis of Genomics and Transcriptome Data to Identify Regulation Networks in Female Osteoporosis. Front Genet 2020; 11:600097. [PMID: 33329745 PMCID: PMC7734180 DOI: 10.3389/fgene.2020.600097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Osteoporosis is a highly heritable skeletal muscle disease. However, the genetic mechanisms mediating the pathogenesis of osteoporosis remain unclear. Accordingly, in this study, we aimed to clarify the transcriptional regulation and heritability underlying the onset of osteoporosis. Methods: Transcriptome gene expression data were obtained from the Gene Expression Omnibus database. Microarray data from peripheral blood monocytes of 73 Caucasian women with high and low bone mineral density (BMD) were analyzed. Differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) were identified. Differences in BMD were then attributed to several gene modules using weighted gene co-expression network analysis (WGCNA). LncRNA/mRNA regulatory networks were constructed based on the WGCNA and subjected to functional enrichment analysis. Results: In total, 3,355 mRNAs and 999 lncRNAs were identified as differentially expressed genes between patients with high and low BMD. The WGCNA yielded three gene modules, including 26 lncRNAs and 55 mRNAs as hub genes in the blue module, 36 lncRNAs and 31 mRNAs as hub genes in the turquoise module, and 56 mRNAs and 30 lncRNAs as hub genes in the brown module. JUN and ACSL5 were subsequently identified in the modular gene network. After functional pathway enrichment, 40 lncRNAs and 16 mRNAs were found to be related to differences in BMD. All three modules were enriched in metabolic pathways. Finally, mRNA/lncRNA/pathway networks were constructed using the identified regulatory networks of lncRNAs/mRNAs and pathway enrichment relationships. Conclusion: The mRNAs and lncRNAs identified in this WGCNA could be novel clinical targets in the diagnosis and management of osteoporosis. Our findings may help elucidate the complex interactions between transcripts and non-coding RNAs and provide novel perspectives on the regulatory mechanisms of osteoporosis.
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Affiliation(s)
- Xianzuo Zhang
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Kun Chen
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoxuan Chen
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Nikolaos Kourkoumelis
- Department of Medical Physics, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Guoyuan Li
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bing Wang
- School of Electrical and Information Engineering, Anhui University of Technology, Ma'anshan, China
| | - Chen Zhu
- Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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20
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Grant SFA, Wells AD, Rich SS. Next steps in the identification of gene targets for type 1 diabetes. Diabetologia 2020; 63:2260-2269. [PMID: 32797243 PMCID: PMC7527360 DOI: 10.1007/s00125-020-05248-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022]
Abstract
The purpose of this review is to provide a view of the future of genomics and other omics approaches in defining the genetic contribution to all stages of risk of type 1 diabetes and the functional impact and clinical implementations of the associated variants. From the recognition nearly 50 years ago that genetics (in the form of HLA) distinguishes risk of type 1 diabetes from type 2 diabetes, advances in technology and sample acquisition through collaboration have identified over 60 loci harbouring SNPs associated with type 1 diabetes risk. Coupled with HLA region genes, these variants account for the majority of the genetic risk (~50% of the total risk); however, relatively few variants are located in coding regions of genes exerting a predicted protein change. The vast majority of genetic risk in type 1 diabetes appears to be attributed to regions of the genome involved in gene regulation, but the target effectors of those genetic variants are not readily identifiable. Although past genetic studies clearly implicated immune-relevant cell types involved in risk, the target organ (the beta cell) was left untouched. Through emergent technologies, using combinations of genetics, gene expression, epigenetics, chromosome conformation and gene editing, novel landscapes of how SNPs regulate genes have emerged. Furthermore, both the immune system and the beta cell and their biological pathways have been implicated in a context-specific manner. The use of variants from immune and beta cell studies distinguish type 1 diabetes from type 2 diabetes and, when they are combined in a genetic risk score, open new avenues for prediction and treatment. Graphical abstract.
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Affiliation(s)
- Struan F A Grant
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Departments of Pediatrics and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Divisions of Human Genetics and Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA.
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21
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Liu X, Xu W, Leng F, Hao C, Kolora SRR, Li W. Prioritizing long range interactions in noncoding regions using GWAS and deletions perturbed TADs. Comput Struct Biotechnol J 2020; 18:2945-2952. [PMID: 33209206 PMCID: PMC7642798 DOI: 10.1016/j.csbj.2020.10.014] [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: 07/28/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies (GWAS) have contributed significantly to predisposing the disease etiology by associating single nucleotide polymorphisms (SNPs) with complex diseases. However, most GWAS-SNPs are in the noncoding regions that may affect distal genes via long range enhancer-promoter interactions. Thus, the common practice on GWAS discoveries cannot fully reveal the molecular mechanisms underpinning complex diseases. It is known that perturbations of topological associated domains (TADs) lead to long range interactions which underlie disease etiology. To identify the probable long range interactions in noncoding regions via GWAS and TADs perturbed by deletions, we integrated datasets from GWAS-SNPs, enhancers, TADs, and deletions. After ranking and clustering, we prioritized 201,132 high confident pairs of GWAS-SNPs and target genes. In this study, we performed a systematic inference on noncoding regions via GWAS-SNPs and deletion-perturbed TADs to boost GWAS discovery power. The high confident pairs of GWAS-SNPs and target genes (SE-Gs) provide the promising candidates to understand the molecular mechanisms underlying complex diseases with emphasis on the three-dimensional genome.
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Affiliation(s)
- Xuanshi Liu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wenjian Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fei Leng
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Sree Rohit Raj Kolora
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China.,MOE Key Laboratory of Major Diseases in Children, Beijing, China.,Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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22
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Viñuela A, Varshney A, van de Bunt M, Prasad RB, Asplund O, Bennett A, Boehnke M, Brown AA, Erdos MR, Fadista J, Hansson O, Hatem G, Howald C, Iyengar AK, Johnson P, Krus U, MacDonald PE, Mahajan A, Manning Fox JE, Narisu N, Nylander V, Orchard P, Oskolkov N, Panousis NI, Payne A, Stitzel ML, Vadlamudi S, Welch R, Collins FS, Mohlke KL, Gloyn AL, Scott LJ, Dermitzakis ET, Groop L, Parker SCJ, McCarthy MI. Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. Nat Commun 2020; 11:4912. [PMID: 32999275 PMCID: PMC7528108 DOI: 10.1038/s41467-020-18581-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.
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Affiliation(s)
- Ana Viñuela
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland ,grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, NE1 4EP Newcastle, UK
| | - Arushi Varshney
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Martijn van de Bunt
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK
| | - Rashmi B. Prasad
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Olof Asplund
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Amanda Bennett
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Michael Boehnke
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Andrew A. Brown
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland ,grid.8241.f0000 0004 0397 2876Population Health and Genomics, University of Dundee, Dundee, Scotland, DD1 9SY UK
| | - Michael R. Erdos
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - João Fadista
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.6203.70000 0004 0417 4147Department of Epidemiology Research, Statens Serum Institut, Copenhagen, DK 2300 Denmark ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Ola Hansson
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Gad Hatem
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Cédric Howald
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Apoorva K. Iyengar
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Paul Johnson
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Ulrika Krus
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Patrick E. MacDonald
- grid.17089.37Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta Canada
| | - Anubha Mahajan
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.418158.10000 0004 0534 4718Present Address: Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Jocelyn E. Manning Fox
- grid.17089.37Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta Canada
| | - Narisu Narisu
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vibe Nylander
- grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK
| | - Peter Orchard
- grid.214458.e0000000086837370Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Nikolay Oskolkov
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Nikolaos I. Panousis
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Anthony Payne
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK
| | - Michael L. Stitzel
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.63054.340000 0001 0860 4915Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032 USA
| | - Swarooparani Vadlamudi
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Ryan Welch
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Francis S. Collins
- grid.280128.10000 0001 2233 9230Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Karen L. Mohlke
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Anna L. Gloyn
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK ,grid.168010.e0000000419368956Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford University, Stanford, CA USA
| | - Laura J. Scott
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Emmanouil T. Dermitzakis
- grid.8591.50000 0001 2322 4988Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden ,grid.7737.40000 0004 0410 2071Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Stephen C. J. Parker
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mark I. McCarthy
- grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE UK ,grid.410556.30000 0001 0440 1440Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE UK ,grid.418158.10000 0004 0534 4718Present Address: Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
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23
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Verma AK, Beg MMA, Saleem M, Al Reshidi F, Ahmad H, Alenazi F, Khan NA, Akther J, Joshi PC. Cell free TCF7L2 gene alteration and their association with Type 2 diabetes mellitus in North Indian population. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Nat Commun 2020; 11:3294. [PMID: 32620744 PMCID: PMC7335045 DOI: 10.1038/s41467-020-17089-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/02/2020] [Indexed: 01/14/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is mediated by autoreactive antibodies that damage multiple tissues. Genome-wide association studies (GWAS) link >60 loci with SLE risk, but the causal variants and effector genes are largely unknown. We generated high-resolution spatial maps of SLE variant accessibility and gene connectivity in human follicular helper T cells (TFH), a cell type required for anti-nuclear antibodies characteristic of SLE. Of the ~400 potential regulatory variants identified, 90% exhibit spatial proximity to genes distant in the 1D genome sequence, including variants that loop to regulate the canonical TFH genes BCL6 and CXCR5 as confirmed by genome editing. SLE ‘variant-to-gene’ maps also implicate genes with no known role in TFH/SLE disease biology, including the kinases HIPK1 and MINK1. Targeting these kinases in TFH inhibits production of IL-21, a cytokine crucial for class-switched B cell antibodies. These studies offer mechanistic insight into the SLE-associated regulatory architecture of the human genome. T cells are a major cell type involved in systemic lupus erythematosus (SLE). Here, the authors use promoter capture-C and ATAC-seq in human follicular T helper cells to identify SLE genes distant from GWAS loci (via 3D interaction) and validate the function of key regulatory elements and genes in vitro.
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25
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Aksit MA, Pace RG, Vecchio-Pagán B, Ling H, Rommens JM, Boelle PY, Guillot L, Raraigh KS, Pugh E, Zhang P, Strug LJ, Drumm ML, Knowles MR, Cutting GR, Corvol H, Blackman SM. Genetic Modifiers of Cystic Fibrosis-Related Diabetes Have Extensive Overlap With Type 2 Diabetes and Related Traits. J Clin Endocrinol Metab 2020; 105:5599821. [PMID: 31697830 PMCID: PMC7236628 DOI: 10.1210/clinem/dgz102] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
CONTEXT Individuals with cystic fibrosis (CF) develop a distinct form of diabetes characterized by β-cell dysfunction and islet amyloid accumulation similar to type 2 diabetes (T2D), but generally have normal insulin sensitivity. CF-related diabetes (CFRD) risk is determined by both CFTR, the gene responsible for CF, and other genetic variants. OBJECTIVE To identify genetic modifiers of CFRD and determine the genetic overlap with other types of diabetes. DESIGN AND PATIENTS A genome-wide association study was conducted for CFRD onset on 5740 individuals with CF. Weighted polygenic risk scores (PRSs) for type 1 diabetes (T1D), T2D, and diabetes endophenotypes were tested for association with CFRD. RESULTS Genome-wide significance was obtained for variants at a novel locus (PTMA) and 2 known CFRD genetic modifiers (TCF7L2 and SLC26A9). PTMA and SLC26A9 variants were CF-specific; TCF7L2 variants also associated with T2D. CFRD was strongly associated with PRSs for T2D, insulin secretion, postchallenge glucose concentration, and fasting plasma glucose, and less strongly with T1D PRSs. CFRD was inconsistently associated with PRSs for insulin sensitivity and was not associated with a PRS for islet autoimmunity. A CFRD PRS comprising variants selected from these PRSs (with a false discovery rate < 0.1) and the genome-wide significant variants was associated with CFRD in a replication population. CONCLUSIONS CFRD and T2D have more etiologic and mechanistic overlap than previously known, aligning along pathways involving β-cell function rather than insulin sensitivity. Two CFRD risk loci are unrelated to T2D and may affect multiple aspects of CF. An 18-variant PRS stratifies risk of CFRD in an independent population.
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Affiliation(s)
- Melis A Aksit
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rhonda G Pace
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Johanna M Rommens
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Pierre-Yves Boelle
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, iPLESP, AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Loic Guillot
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Karen S Raraigh
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Lisa J Strug
- The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | | | - Michael R Knowles
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Garry R Cutting
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Scott M Blackman
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Division of Pediatric Endocrinology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Correspondence and Reprint Requests: Scott M. Blackman, McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205. E-mail:
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26
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Laurenti MC, Dalla Man C, Varghese RT, Andrews JC, Rizza RA, Matveyenko A, De Nicolao G, Cobelli C, Vella A. Diabetes-associated genetic variation in TCF7L2 alters pulsatile insulin secretion in humans. JCI Insight 2020; 5:136136. [PMID: 32182220 DOI: 10.1172/jci.insight.136136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/05/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDMetabolic disorders such as type 2 diabetes have been associated with a decrease in insulin pulse frequency and amplitude. We hypothesized that the T allele at rs7903146 in TCF7L2, previously associated with β cell dysfunction, would be associated with changes in these insulin pulse characteristics.METHODSTwenty-nine nondiabetic subjects (age 46 ± 2, BMI 28 ± 1 kg/m2) participated in this study. Of these, 16 were homozygous for the C allele at rs7903146 and 13 were homozygous for the T allele. Deconvolution of peripheral C-peptide concentrations allowed the reconstruction of portal insulin secretion over time. These data were used for subsequent analyses. Pulse orderliness was assessed by approximate entropy (ApEn), and the dispersion of insulin pulses was measured by a frequency dispersion index (FDI) after a Fast Fourier Transform (FFT) of individual insulin secretion rates.RESULTSDuring fasting conditions, the CC genotype group exhibited decreased pulse disorderliness compared with the TT genotype group (1.10 ± 0.03 vs. 1.19 ± 0.04, P = 0.03). FDI decreased in response to hyperglycemia in the CC genotype group, perhaps reflecting less entrainment of insulin secretion during fasting.CONCLUSIONDiabetes-associated variation in TCF7L2 is associated with decreased orderliness and pulse dispersion, unchanged by hyperglycemia. Quantification of ApEn and FDI could represent novel markers of β cell health.FUNDINGThis work was funded by US NIH (DK78646, DK116231), University of Padova research grant CPDA145405, and Mayo Clinic General Clinical Research Center (UL1 TR000135).
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Affiliation(s)
- Marcello C Laurenti
- Division of Endocrinology, Diabetes & Metabolism, Mayo Clinic, Rochester, Minnesota, USA
| | - Chiara Dalla Man
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Ron T Varghese
- Division of Endocrinology, Diabetes & Metabolism, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Robert A Rizza
- Division of Endocrinology, Diabetes & Metabolism, Mayo Clinic, Rochester, Minnesota, USA
| | - Aleksey Matveyenko
- Division of Endocrinology, Diabetes & Metabolism, Mayo Clinic, Rochester, Minnesota, USA.,Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Giuseppe De Nicolao
- Department of Computer Engineering and Systems Science, University of Pavia, Pavia, Italy
| | - Claudio Cobelli
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Adrian Vella
- Division of Endocrinology, Diabetes & Metabolism, Mayo Clinic, Rochester, Minnesota, USA
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27
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Hemerich D, Pei J, Harakalova M, van Setten J, Boymans S, Boukens BJ, Efimov IR, Michels M, van der Velden J, Vink A, Cheng C, van der Harst P, Moore JH, Mokry M, Tragante V, Asselbergs FW. Integrative Functional Annotation of 52 Genetic Loci Influencing Myocardial Mass Identifies Candidate Regulatory Variants and Target Genes. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002328. [PMID: 30681347 DOI: 10.1161/circgen.118.002328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Regulatory elements may be involved in the mechanisms by which 52 loci influence myocardial mass, reflected by abnormal amplitude and duration of the QRS complex on the ECG. Functional annotation thus far did not take into account how these elements are affected in disease context. METHODS We generated maps of regulatory elements on hypertrophic cardiomyopathy patients (ChIP-seq N=14 and RNA-seq N=11) and nondiseased hearts (ChIP-seq N=4 and RNA-seq N=11). We tested enrichment of QRS-associated loci on elements differentially acetylated and directly regulating differentially expressed genes between hypertrophic cardiomyopathy patients and controls. We further performed functional annotation on QRS-associated loci using these maps of differentially active regulatory elements. RESULTS Regions differentially affected in disease showed a stronger enrichment ( P=8.6×10-5) for QRS-associated variants than those not showing differential activity ( P=0.01). Promoters of genes differentially regulated between hypertrophic cardiomyopathy patients and controls showed more enrichment ( P=0.001) than differentially acetylated enhancers ( P=0.8) and super-enhancers ( P=0.025). We also identified 74 potential causal variants overlapping these differential regulatory elements. Eighteen of the genes mapped confirmed previous findings, now also pinpointing the potentially affected regulatory elements and candidate causal variants. Fourteen new genes were also mapped. CONCLUSIONS Our results suggest differentially active regulatory elements between hypertrophic cardiomyopathy patients and controls can offer more insights into the mechanisms of QRS-associated loci than elements not affected by disease.
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Affiliation(s)
- Daiane Hemerich
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.)
| | - Jiayi Pei
- CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.).,Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | - Magdalena Harakalova
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Jessica van Setten
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Sander Boymans
- Department of Genetics, Center for Molecular Medicine, Cancer Genomics Netherlands (S.B.), UMC Utrecht
| | - Bas J Boukens
- Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.J.B.)
| | - Igor R Efimov
- Department of Biomedical Engineering, The George Washington University, Washington, DC (I.R.E.)
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands (M. Michels)
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center (J.v.d.V.)
| | - Aryan Vink
- Department of Pathology (A.V.), UMC Utrecht, Utrecht University, The Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | | | - Jason H Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, University of Pennsylvania, PA (J.H.M.)
| | - Michal Mokry
- Department of Pediatrics, Wilhelmina Children's Hospital, Utrecht (M. Mokry.)
| | - Vinicius Tragante
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,Durrer Center for Cardiogenetic Research, ICINNetherlands Heart Institute, Utrecht (F.W.A.).,Institute of Cardiovascular Science, Faculty of Population Health Sciences (F.W.A.), University College London, United Kingdom.,Health Data Research UK London, Institute of Health Informatics F.W.A.), University College London, United Kingdom
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28
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Tian L, Shao W, Ip W, Song Z, Badakhshi Y, Jin T. The developmental Wnt signaling pathway effector β-catenin/TCF mediates hepatic functions of the sex hormone estradiol in regulating lipid metabolism. PLoS Biol 2019; 17:e3000444. [PMID: 31589598 PMCID: PMC6797220 DOI: 10.1371/journal.pbio.3000444] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/17/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
The bipartite transcription factor β-catenin (β-cat)/T cell factor (TCF), formed by free β-cat and a given TCF family member, serves as the effector of the developmental Wnt signaling cascade. β-cat/TCFs also serve as effectors of certain peptide hormones or growth factors during adulthood. We reported that liver-specific expression of dominant-negative Transcription factor 7 like 2 (TCF7L2DN) led to impaired glucose disposal. Here we show that, in this LTCFDN transgenic mouse model, serum and hepatic lipid contents were elevated in male but not in female mice. In hepatocytes, TCF7L2DN adenovirus infection led to stimulated expression of genes that encode lipogenic transcription factors and lipogenic enzymes, while estradiol (E2) treatment attenuated the stimulation, associated with Wnt-target gene activation. Mechanistically, this E2-mediated activation can be attributed to elevated β-cat Ser675 phosphorylation and TCF expression. In wild-type female mice, ovariectomy (OVX) plus high-fat diet (HFD) challenge impaired glucose disposal and insulin tolerance, associated with increased hepatic lipogenic transcription factor sterol regulatory element-binding protein 1-c (SREBP-1c) expression. In wild-type mice with OVX, E2 reconstitution attenuated HFD-induced metabolic defects. Some of the attenuation effects, including insulin intolerance, elevated liver-weight gain, and hepatic SREBP-1c expression, were not affected by E2 reconstitution in HFD-fed LTCFDN mice with OVX. Finally, the effects of E2 in hepatocytes on β-cat/TCF activation can be attenuated by the G-protein-coupled estrogen receptor (GPER) antagonist G15. Our study thus expanded the scope of functions of the Wnt pathway effector β-cat/TCF, as it can also mediate hepatic functions of E2 during adulthood. This study also enriches our mechanistic understanding of gender differences in the risk and pathophysiology of metabolic diseases.
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Affiliation(s)
- Lili Tian
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Center, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Weijuan Shao
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Center, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Wilfred Ip
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Zhuolun Song
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Center, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Yasaman Badakhshi
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Center, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Tianru Jin
- Division of Advanced Diagnostics, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Center, Faculty of Medicine, University of Toronto, Toronto, Canada
- * E-mail:
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29
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Grant SFA. The TCF7L2 Locus: A Genetic Window Into the Pathogenesis of Type 1 and Type 2 Diabetes. Diabetes Care 2019; 42:1624-1629. [PMID: 31409726 PMCID: PMC6702598 DOI: 10.2337/dci19-0001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/12/2019] [Indexed: 02/03/2023]
Abstract
Over the past ∼15 years there has been great progress in our understanding of the genetics of both type 1 diabetes and type 2 diabetes. This has been driven principally by genome-wide association studies (GWAS) in increasingly larger sample sizes, where many distinct loci have now been reported for both traits. One of the loci that dominates these studies is the TCF7L2 locus for type 2 diabetes. This genetic signal has been leveraged to explore multiple aspects of disease risk, including developments in genetic risk scores, genetic commonalities with cancer, and for gaining insights into diabetes-related molecular pathways. Furthermore, the TCF7L2 locus has aided in providing insights into the genetics of both latent autoimmune diabetes in adults and various presentations of type 1 diabetes. This review outlines the knowledge gained to date and highlights how work with this locus leads the way in guiding how many other genetic loci could be similarly used to gain insights into the pathogenesis of diabetes.
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Affiliation(s)
- Struan F A Grant
- Divisions of Human Genetics and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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30
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Justesen L, Ribel-Madsen R, Gillberg L, Hansen NS, Wulff AL, Grunnet LG, Brøns C. TCF7L2 Expression Is Regulated by Cell Differentiation and Overfeeding in Human Adipose Tissue. Endocr Res 2019; 44:110-116. [PMID: 30721637 DOI: 10.1080/07435800.2019.1573827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aim: The TCF7L2 gene variant rs7903146 has the largest effect on type 2 diabetes risk reported in genome-wide association studies, however its role in adipose tissue development and function is unknown. We investigate the association between gene variant rs7903146 and metabolic parameters and examine in vitro and ex vivo gene expression of TCF7L2 in human adipose tissue and progenitor cells from two independent populations of young healthy men with increased risk of type 2 diabetes due to low birth weight (LBW). Design: Adipose tissue biopsies were excised from 40 healthy young men with low and normal birth weights (NBW) after a control and 5-day high-fat overfeeding diet. In another cohort including 13 LBW and 13 NBW men, adipocyte progenitor cells were isolated and cultivated. Transcriptome-wide expression was performed on RNA extracted from biopsies or cell cultures. Results: Diet-induced peripheral insulin resistance is more pronounced in carriers of the T-risk allele rs7903146, whereas no association with hepatic insulin resistance was shown. TCF7L2 expression increased during adipogenesis in isolated preadipocytes from both LBW and NBW men (p < 0.001) and correlated positively with markers of progenitor cell proliferation and maturation capacity. In the mature adipose tissue, LBW men had lower expression of TCF7L2 compared to NBW men at baseline (p = 0.03) and TCF7L2 expression was suppressed by short-term overfeeding in NBW men (p = 0.005). Conclusions: The results suggest a regulation of TCF7L2 expression during adipogenesis and in mature adipose tissue upon overfeeding, and further that young men exposed to an adverse intrauterine environment have reduced mature adipose tissue TCF7L2 expression.
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Affiliation(s)
- Louise Justesen
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
- b Laboratory of Molecular Medicine, Department of Clinical Immunology , Rigshospitalet , Copenhagen , Denmark
| | - Rasmus Ribel-Madsen
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
- c The Danish Diabetes Academy , Odense , Denmark
| | - Linn Gillberg
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
| | - Ninna S Hansen
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
- d Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen , Denmark
- e Danish PhD School of Molecular Metabolism , Odense , Denmark
| | - Anne Louise Wulff
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
| | - Louise G Grunnet
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
- c The Danish Diabetes Academy , Odense , Denmark
| | - Charlotte Brøns
- a Department of Endocrinology, Diabetes and Metabolism , Rigshospitalet , Copenhagen , Denmark
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31
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Redondo MJ, Evans-Molina C, Steck AK, Atkinson MA, Sosenko J. The Influence of Type 2 Diabetes-Associated Factors on Type 1 Diabetes. Diabetes Care 2019; 42:1357-1364. [PMID: 31167894 PMCID: PMC6647039 DOI: 10.2337/dc19-0102] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/27/2019] [Indexed: 02/03/2023]
Abstract
Current efforts to prevent progression from islet autoimmunity to type 1 diabetes largely focus on immunomodulatory approaches. However, emerging data suggest that the development of diabetes in islet autoantibody-positive individuals may also involve factors such as obesity and genetic variants associated with type 2 diabetes, and the influence of these factors increases with age at diagnosis. Although these factors have been linked with metabolic outcomes, particularly through their impact on β-cell function and insulin sensitivity, growing evidence suggests that they might also interact with the immune system to amplify the autoimmune response. The presence of factors shared by both forms of diabetes contributes to disease heterogeneity and thus has important implications. Characteristics that are typically considered to be nonimmune should be incorporated into predictive algorithms that seek to identify at-risk individuals and into the designs of trials for disease prevention. The heterogeneity of diabetes also poses a challenge in diagnostic classification. Finally, after clinically diagnosing type 1 diabetes, addressing nonimmune elements may help to prevent further deterioration of β-cell function and thus improve clinical outcomes. This Perspectives in Care article highlights the role of type 2 diabetes-associated genetic factors (e.g., gene variants at transcription factor 7-like 2 [TCF7L2]) and obesity (via insulin resistance, inflammation, β-cell stress, or all three) in the pathogenesis of type 1 diabetes and their impacts on age at diagnosis. Recognizing that type 1 diabetes might result from the sum of effects from islet autoimmunity and type 2 diabetes-associated factors, their interactions, or both affects disease prediction, prevention, diagnosis, and treatment.
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Affiliation(s)
- Maria J Redondo
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Carmella Evans-Molina
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN.,Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN.,Richard L. Roudebush VA Medical Center, Indianapolis, IN
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Mark A Atkinson
- Departments of Pathology and Pediatrics, University of Florida Diabetes Institute, Gainesville, FL
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32
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Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes. Nat Genet 2019; 51:1137-1148. [PMID: 31253982 DOI: 10.1038/s41588-019-0457-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023]
Abstract
Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clusters or super-enhancers. So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in three-dimensional (3D) space. Furthermore, their target genes are often unknown. We have created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers to their target genes, often located hundreds of kilobases away. It also revealed >1,300 groups of islet enhancers, super-enhancers and active promoters that form 3D hubs, some of which show coordinated glucose-dependent activity. We demonstrate that genetic variation in hubs impacts insulin secretion heritability, and show that hub annotations can be used for polygenic scores that predict T2D risk driven by islet regulatory variants. Human islet 3D chromatin architecture, therefore, provides a framework for interpretation of T2D genome-wide association study (GWAS) signals.
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33
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Takeuchi F, Kukimoto I, Li Z, Li S, Li N, Hu Z, Takahashi A, Inoue S, Yokoi S, Chen J, Hang D, Kuroda M, Matsuda F, Mizuno M, Mori S, Wu P, Tanaka N, Matsuo K, Kamatani Y, Kubo M, Ma D, Shi Y. Genome-wide association study of cervical cancer suggests a role for ARRDC3 gene in human papillomavirus infection. Hum Mol Genet 2019; 28:341-348. [PMID: 30412241 DOI: 10.1093/hmg/ddy390] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
The development of cervical cancer is initiated by human papillomavirus (HPV) infection and involves both viral and host genetic factors. Genome-wide association studies (GWAS) of cervical cancer have identified associations in the HLA locus and two loci outside HLA, but the principal genes that control infection and pathogenesis have not been identified. In the present study, we performed GWAS of cervical cancer in East Asian populations, involving 2609 cases and 4712 controls in the discovery stage and 1461 cases and 3295 controls in the follow-up stage. We identified novel-significant associations at 5q14 with the lead single nucleotide polymorphism (SNP) rs59661306 (P = 2.4 × 10-11) and at 7p11 with the lead SNP rs7457728 (P = 1.2 × 10-8). In 5q14, the chromatin region of the GWAS-significant SNPs was found to be in contact with the promoter of the ARRDC3 (arrestin domain-containing 3) gene. In our functional studies, ARRDC3 knockdown in HeLa cells caused significant reductions in both cell growth and susceptibility to HPV16 pseudovirion infection, suggesting that ARRDC3 is involved in the infectious entry of HPV into the cell. Our study advances the understanding of host genes that are responsible for cervical cancer susceptibility and guides future research on HPV infection and cancer development.
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Affiliation(s)
- Fumihiko Takeuchi
- Research Institute,National Center for Global Health and Medicine, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases,Musashimurayama-shi, Tokyo, Japan
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, P.R. China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, P.R. China.,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Shuang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Ni Li
- Program Office for Cancer Screening in Urban China, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, P.R. China
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Shusaku Inoue
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Sana Yokoi
- Cancer Genome Center, Chiba Cancer Center Research Institute, Chiba, Japan.,Division of Genetic Diagnostics, Chiba Cancer Center, Chiba, Japan
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Dong Hang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mika Mizuno
- Department of Gynecological Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Seiichiro Mori
- Pathogen Genomics Center, National Institute of Infectious Diseases,Musashimurayama-shi, Tokyo, Japan
| | - Peng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Naotake Tanaka
- Division of Gynecology, Chiba Cancer Center, Chiba, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan.,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University & The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, P.R. China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, P.R. China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, P.R. China.,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
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Pérez-Núñez I, Karaky M, Fedetz M, Barrionuevo C, Izquierdo G, Matesanz F, Alcina A. Splice-site variant in ACSL5: a marker promoting opposing effect on cell viability and protein expression. Eur J Hum Genet 2019; 27:1836-1844. [PMID: 31053784 PMCID: PMC6871522 DOI: 10.1038/s41431-019-0414-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/21/2019] [Accepted: 04/06/2019] [Indexed: 01/15/2023] Open
Abstract
Long-chain Acyl-CoA synthetases (ACSLs) activate fatty acids (FAs) by thioesterification with Coenzyme A (CoA), generating FA-CoAs. These products are essential for lipid metabolism and carcinogenesis. In previous study, we identified an intronic variant rs2256368:A>G, whose G allele promotes exon 20 skipping in up to 43% of ACSL5 transcripts but its functional relevance is unclear. Here, we compared the expression of splice (Spl) and nonsplice (NSpl) ACSL5 variants and the effect on cell viability under culture conditions that force cells to metabolize fatty acids. We found that lymphoblastoid cell lines from 1000 Genomes Project, bearing Spl genotypes, showed a reduced expression of total ACSL5 protein due to an inefficient translation of the Spl RNA. These cells impaired growth in cultures with phorbol myristate acetate-ionomycin (PMA-Io) or medium deprived of glucose, while production of reactive oxygen species increased in PMA-Io. Specific ACSL5-isoform transfection in HEK239T (kidney), U87 (astroglioma), and HOG (oligodendrocyte) cells showed the Spl protein to be the causal factor of cell-growth inhibition, despite its reduced protein expression. Our findings indicate that the variant rs2256368:A>G can predict a growth inhibitory activity, caused by the Spl isoform of ACSL5 protein, opposed to the activity of the NSpl. Deep understanding of its functioning might have application in metabolic diseases and cancer.
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Affiliation(s)
- Iván Pérez-Núñez
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Mohamad Karaky
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - María Fedetz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Cristina Barrionuevo
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Guillermo Izquierdo
- Unidad de Esclerosis Múltiple, Hospital Universitario Virgen Macarena, 41009, Sevilla, Spain
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain.
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain.
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35
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Chesi A, Wagley Y, Johnson ME, Manduchi E, Su C, Lu S, Leonard ME, Hodge KM, Pippin JA, Hankenson KD, Wells AD, Grant SFA. Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density. Nat Commun 2019; 10:1260. [PMID: 30890710 PMCID: PMC6425012 DOI: 10.1038/s41467-019-09302-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 03/05/2019] [Indexed: 12/21/2022] Open
Abstract
Osteoporosis is a devastating disease with an essential genetic component. GWAS have discovered genetic signals robustly associated with bone mineral density (BMD), but not the precise localization of effector genes. Here, we carry out physical and direct variant to gene mapping in human mesenchymal progenitor cell-derived osteoblasts employing a massively parallel, high resolution Capture C based method in order to simultaneously characterize the genome-wide interactions of all human promoters. By intersecting our Capture C and ATAC-seq data, we observe consistent contacts between candidate causal variants and putative target gene promoters in open chromatin for ~ 17% of the 273 BMD loci investigated. Knockdown of two novel implicated genes, ING3 at ‘CPED1-WNT16’ and EPDR1 at ‘STARD3NL’, inhibits osteoblastogenesis, while promoting adipogenesis. This approach therefore aids target discovery in osteoporosis, here on the example of two relevant genes involved in the fate determination of mesenchymal progenitors, and can be applied to other common genetic diseases. GWAS have identified numerous genetic loci for bone mineral density (BMD) and fracture risk. Here, the authors map these variants to putative target genes using ATAC-seq and Capture C of human osteoblasts and confirm ING3 and EPDR1 as BMD genes in in vitro osteoblast differentiation experiments.
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Affiliation(s)
- Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Yadav Wagley
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.,Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA
| | - Kurt D Hankenson
- Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA. .,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA. .,Divisions of Genetics and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, 19104, PA, USA.
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36
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Redondo MJ, Steck AK, Sosenko J, Anderson M, Antinozzi P, Michels A, Wentworth JM, Atkinson MA, Pugliese A, Geyer S. Transcription Factor 7-Like 2 ( TCF7L2) Gene Polymorphism and Progression From Single to Multiple Autoantibody Positivity in Individuals at Risk for Type 1 Diabetes. Diabetes Care 2018; 41:2480-2486. [PMID: 30275285 PMCID: PMC6245213 DOI: 10.2337/dc18-0861] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/10/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The type 2 diabetes-associated alleles at the TCF7L2 locus mark a type 1 diabetes phenotype characterized by single islet autoantibody positivity as well as lower glucose and higher C-peptide measures. Here, we studied whether the TCF7L2 locus influences progression of islet autoimmunity, from single to multiple (≥2) autoantibody positivity, in relatives of patients with type 1 diabetes. RESEARCH DESIGN AND METHODS We evaluated 244 participants in the Type 1 Diabetes TrialNet Pathway to Prevention study with confirmed single autoantibody positivity at screening and Immunochip single nucleotide polymorphism data (47.5% male; median age 12.8 years, range 1.2-45.9; 90.2% white). We analyzed risk allele frequency at TCF7L2 rs4506565 (in linkage disequilibrium with rs7903146). Altogether, 62.6% participants carried ≥1 risk allele. Univariate and multivariable Cox proportional hazards models and Kaplan-Meier statistical methods were used. RESULTS During follow-up (median 5.2 years, range 0.2-12.6), 62% of the single autoantibody-positive participants developed multiple autoantibody positivity. In the overall cohort, the TCF7L2 locus did not significantly predict progression to multiple autoantibody positivity. However, among single GAD65 autoantibody-positive participants (n = 158), those who carried ≥1 risk allele had a lower rate of progression to multiple autoantibody positivity (hazard ratio [HR] 0.65, P = 0.033) than those who did not, after adjustment for HLA risk haplotypes and age. Among subjects who were either IA-2 or insulin autoantibody positive only, carrying ≥1 TCF7L2 risk allele was not a significant factor overall, but in overweight or obese participants, it increased the risk of progression to multiple autoantibody positivity (HR 3.02, P = 0.016) even with adjustment for age. CONCLUSIONS The type 2 diabetes-associated TCF7L2 locus influences progression of islet autoimmunity, with differential effects by autoantibody specificity and interaction by obesity/overweight.
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Affiliation(s)
- Maria J Redondo
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | | | - Mark Anderson
- University of California San Francisco, San Francisco, CA
| | | | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - John M Wentworth
- Walter and Eliza Hall Institute and Royal Melbourne Hospital, Parkville, Australia
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Abstract
Complexity in genome architecture determines how gene expression programs are established, maintained, and modified from early developmental stages to normal adult phenotypes. Large scale and hierarchical organization of the genome impacts various aspects of cell functions, ranging from X-chromosome inactivation, stem-cell fate determination to transcription, DNA replication, and cellular repair. While chromatin loops and topologically-associated domains represent a basic structural or fundamental unit of chromatin organization, spatio-temporal organization of the genome further creates a complex network of interacting genome patterns, forming chromosomal compartments and chromosome territories. The understanding of human diseases, including cancers, auto-immune disorders, Alzheimer's, and cardiovascular diseases, relies on the associated molecular and epigenetic mechanisms. There is a growing interest in the impact of three-dimensional chromatin folding upon the genome structure and function, which gives rise to the question "What's in the fold?" and is the main focus of this review. Here we discuss the principles determining the spatial and regulatory relationships between gene regulation and three-dimensional chromatin landscapes, and how changes in chromatin-folding could influence the outcome of genome function in healthy and disease states.
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38
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Adams JD, Vella A. What Can Diabetes-Associated Genetic Variation in TCF7L2 Teach Us About the Pathogenesis of Type 2 Diabetes? Metab Syndr Relat Disord 2018; 16:383-389. [PMID: 29993315 DOI: 10.1089/met.2018.0024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a polygenic metabolic disorder characterized by hyperglycemia occurring as a result of impaired insulin secretion and/or insulin resistance. Among the various genetic factors associated with T2DM, a common genetic variant within the transcription factor 7-like 2 locus (TCF7L2) confers the greatest genetic risk for development of the disease. However, the mechanism(s) by which TCF7L2 predisposes to diabetes remain uncertain. Here we review the current literature pertaining to the potential mechanisms by which TCF7L2 confers risk of T2DM, using genetic variation as a probe to understand the pathogenesis of the disease.
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Affiliation(s)
- J D Adams
- Endocrine Research Unit, Department of Endocrinology, Diabetes and Nutrition, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Adrian Vella
- Endocrine Research Unit, Department of Endocrinology, Diabetes and Nutrition, Mayo Clinic College of Medicine , Rochester, Minnesota
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39
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Huang ZQ, Liao YQ, Huang RZ, Chen JP, Sun HL. Possible role of TCF7L2 in the pathogenesis of type 2 diabetes mellitus. BIOTECHNOL BIOTEC EQ 2018; 32:830-834. [DOI: 10.1080/13102818.2018.1438211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 02/05/2018] [Indexed: 01/17/2023] Open
Affiliation(s)
- Zhi-qiu Huang
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Yao-qi Liao
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Run-ze Huang
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Jin-peng Chen
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Hui-lin Sun
- Department of Endocrinology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, PR China
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40
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Manduchi E, Williams SM, Chesi A, Johnson ME, Wells AD, Grant SFA, Moore JH. Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS. Hum Genet 2018; 137:413-425. [PMID: 29797095 PMCID: PMC5996751 DOI: 10.1007/s00439-018-1893-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/20/2018] [Indexed: 12/29/2022]
Abstract
Although Genome Wide Association Studies (GWAS) have led to many valuable insights into the genetic bases of common diseases over the past decade, the issue of missing heritability has surfaced, as the discovered main effect genetic variants found to date do not account for much of a trait's predicted genetic component. We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.
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Affiliation(s)
- Elisabetta Manduchi
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Alessandra Chesi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew E Johnson
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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41
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Smith AJP, Deloukas P, Munroe PB. Emerging applications of genome-editing technology to examine functionality of GWAS-associated variants for complex traits. Physiol Genomics 2018; 50:510-522. [PMID: 29652634 DOI: 10.1152/physiolgenomics.00028.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Over the last decade, genome-wide association studies (GWAS) have propelled the discovery of thousands of loci associated with complex diseases. The focus is now turning toward the function of these association signals, determining the causal variant(s) among those in strong linkage disequilibrium, and identifying their underlying mechanisms, such as long-range gene regulation. Genome-editing techniques utilizing zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and clustered regularly-interspaced short palindromic repeats with Cas9 nuclease (CRISPR-Cas9) are becoming the tools of choice to establish functionality for these variants, due to the ability to assess effects of single variants in vivo. This review will discuss examples of how these technologies have begun to aid functional analysis of GWAS loci for complex traits such as cardiovascular disease, Type 2 diabetes, cancer, obesity, and autoimmune disease. We focus on analysis of variants occurring within noncoding genomic regions, as these comprise the majority of GWAS variants, providing the greatest challenges to determining functionality, and compare editing strategies that provide different levels of evidence for variant functionality. The review describes molecular insights into some of these potentially causal variants and how these may relate to the pathology of the trait and look toward future directions for these technologies in post-GWAS analysis, such as base-editing.
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Affiliation(s)
- Andrew J P Smith
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London , United Kingdom.,NIHR Barts Biomedical Research Centre, Queen Mary University of London , London , United Kingdom
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London , United Kingdom.,NIHR Barts Biomedical Research Centre, Queen Mary University of London , London , United Kingdom
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London , United Kingdom.,NIHR Barts Biomedical Research Centre, Queen Mary University of London , London , United Kingdom
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42
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CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control. Mamm Genome 2018; 29:205-228. [PMID: 29196861 PMCID: PMC9881389 DOI: 10.1007/s00335-017-9727-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/31/2023]
Abstract
The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. With the advent of genome- and epigenome-editing tools based on the CRISPR technology, it is now possible to test the functional relevance of the regulatory elements and alterations on a genomic scale. Here, we review the various CRISPR-based strategies that have been developed to functionally validate the candidate regulatory elements in mammals as well as the non-coding genetic variants found to be associated with human disease. We also discuss how these synthetic biology tools have helped to elucidate the role of three-dimensional nuclear architecture and higher-order chromatin organization in shaping functional genome and controlling gene expression.
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43
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Song C, Yan H, Wang H, Zhang Y, Cao H, Wan Y, Kong L, Chen S, Xu H, Pan B, Zhang J, Fan G, Xin H, Liang Z, Jia W, Tian XL. AQR is a novel type 2 diabetes-associated gene that regulates signaling pathways critical for glucose metabolism. J Genet Genomics 2018; 45:111-120. [PMID: 29502958 DOI: 10.1016/j.jgg.2017.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 12/19/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a common metabolic disease influenced by both genetic and environmental factors. In this study, we performed an in-house genotyping and meta-analysis study using three independent GWAS datasets of T2DM and found that rs3743121, located 1 kb downstream of AQR, was a novel susceptibility SNP associated with T2DM. The risk allele C of rs3743121 was correlated with the increased expression of AQR in white blood cells, similar to that observed in T2DM models. The knockdown of AQR in HepG2 facilitated the glucose uptake, decreased the expression level of PCK2, increased the phosphorylation of GSK-3β, and restored the insulin sensitivity. Furthermore, the suppression of AQR inhibited the mTOR pathway and the protein ubiquitination process. Our study suggests that AQR is a novel type 2 diabetes-associated gene that regulates signaling pathways critical for glucose metabolism.
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Affiliation(s)
- Chun Song
- Laboratory of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Han Yan
- Laboratory of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Hanming Wang
- Laboratory of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yan Zhang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing 100871, China; Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Huiqing Cao
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yiqi Wan
- Human Population Genetics, Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang 330006, China
| | - Lingbao Kong
- Human Population Genetics, Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang 330006, China
| | - Shenghan Chen
- Human Population Genetics, Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang 330006, China
| | - Hong Xu
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China
| | - Bingxing Pan
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang 330031, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330006, China
| | - Guohuang Fan
- Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Hongbo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang 330031, China
| | - Zicai Liang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Weiping Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Xiao-Li Tian
- Laboratory of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing 100871, China; Human Population Genetics, Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang 330006, China.
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44
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Xia Q, Lu S, Ostrovsky J, McCormack SE, Falk MJ, Grant SFA. PARP-1 Inhibition Rescues Short Lifespan in Hyperglycemic C. Elegans And Improves GLP-1 Secretion in Human Cells. Aging Dis 2018; 9:17-30. [PMID: 29392078 PMCID: PMC5772855 DOI: 10.14336/ad.2017.0230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/02/2017] [Indexed: 01/12/2023] Open
Abstract
TCF7L2 is located at one of the most strongly associated type 2 diabetes loci reported to date. We previously reported that the most abundant member of a specific protein complex to bind across the presumed causal variant at this locus, rs7903146, was poly [ADP-ribose] polymerase type 1 (PARP-1). We analyzed the impact of PARP-1 inhibition on C. elegans health in the setting of hyperglycemia and on glucose-stimulated GLP-1 secretion in human intestinal cells. Given that high glucose concentrations progressively shorten the lifespan of C. elegans, in part by impacting key well-conserved insulin-modulated signaling pathways, we investigated the effect of PARP-1 inhibition with Olaparib on the lifespan of C. elegans nematodes under varying hyperglycemic conditions. Subsequently, we investigated whether Olaparib treatment had any effect on glucose-stimulated GLP-1 secretion in the human NCI-H716 intestinal cell line, a model system for the investigation of enteroendocrine function. Treatment with 100uM Olaparib in nematodes exposed to high concentrations of glucose led to significant lifespan rescue. The beneficial lifespan effect of Olaparib appeared to require both PARP-1 and TCF7L2, since treatment had no effect in hyperglycemic conditions in knock-out worm strains for either of these homologs. Further investigation using the NCI-H716 cells revealed that Olaparib significantly enhanced secretion of the incretin, GLP-1, plus the gene expression of TCF7L2, GCG and PC1. These data from studies in both C. elegans and a human cell line suggest that PARP-1 inhibition offers a novel therapeutic avenue to treat type 2 diabetes.
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Affiliation(s)
- Qianghua Xia
- 1Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sumei Lu
- 1Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julian Ostrovsky
- 1Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shana E McCormack
- 2Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,3Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,4Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marni J Falk
- 1Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,3Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- 1Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,2Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,3Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,4Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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45
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Redondo MJ, Geyer S, Steck AK, Sosenko J, Anderson M, Antinozzi P, Michels A, Wentworth J, Xu P, Pugliese A. TCF7L2 Genetic Variants Contribute to Phenotypic Heterogeneity of Type 1 Diabetes. Diabetes Care 2018; 41:311-317. [PMID: 29025879 PMCID: PMC5780048 DOI: 10.2337/dc17-0961] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/17/2017] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The phenotypic diversity of type 1 diabetes suggests heterogeneous etiopathogenesis. We investigated the relationship of type 2 diabetes-associated transcription factor 7 like 2 (TCF7L2) single nucleotide polymorphisms (SNPs) with immunologic and metabolic characteristics at type 1 diabetes diagnosis. RESEARCH DESIGN AND METHODS We studied TrialNet participants with newly diagnosed autoimmune type 1 diabetes with available TCF7L2 rs4506565 and rs7901695 SNP data (n = 810; median age 13.6 years; range 3.3-58.6). We modeled the influence of carrying a TCF7L2 variant (i.e., having 1 or 2 minor alleles) on the number of islet autoantibodies and oral glucose tolerance test (OGTT)-stimulated C-peptide and glucose measures at diabetes diagnosis. All analyses were adjusted for known confounders. RESULTS The rs4506565 variant was a significant independent factor of expressing a single autoantibody, instead of multiple autoantibodies, at diagnosis (odds ratio [OR] 1.66 [95% CI 1.07, 2.57], P = 0.024). Interaction analysis demonstrated that this association was only significant in participants ≥12 years old (n = 504; OR 2.12 [1.29, 3.47], P = 0.003) but not younger ones (n = 306, P = 0.73). The rs4506565 variant was independently associated with higher C-peptide area under the curve (AUC) (P = 0.008) and lower mean glucose AUC (P = 0.0127). The results were similar for the rs7901695 SNP. CONCLUSIONS In this cohort of individuals with new-onset type 1 diabetes, type 2 diabetes-linked TCF7L2 variants were associated with single autoantibody (among those ≥12 years old), higher C-peptide AUC, and lower glucose AUC levels during an OGTT. Thus, carriers of the TCF7L2 variant had a milder immunologic and metabolic phenotype at type 1 diabetes diagnosis, which could be partly driven by type 2 diabetes-like pathogenic mechanisms.
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Affiliation(s)
- Maria J Redondo
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX
| | | | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | | | - Mark Anderson
- University of California, San Francisco, San Francisco, CA
| | | | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - John Wentworth
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Ping Xu
- University of South Florida, Tampa, FL
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46
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Noordam R, Zwetsloot CPA, de Mutsert R, Mook-Kanamori DO, Lamb HJ, de Roos A, de Koning EJP, Rosendaal FR, Willems van Dijk K, van Heemst D. Interrelationship of the rs7903146 TCF7L2 gene variant with measures of glucose metabolism and adiposity: The NEO study. Nutr Metab Cardiovasc Dis 2018; 28:150-157. [PMID: 29174029 DOI: 10.1016/j.numecd.2017.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS We investigated the interrelationship of rs7903146-T in TCF7L2 with measures of glucose metabolism and measures of adiposity. METHODS AND RESULTS This cross-sectional analysis was conducted in 5744 middle-aged participants (mean (standard deviation [SD]) age is 55.9 (6.0) years) from the Netherlands Epidemiology of Obesity (NEO) Study. Associations between rs7903146-T and Type 2 diabetes mellitus (T2D) were assessed with logistic regression. Additive (per-allele) associations with measures of glucose metabolism (e.g., fasting insulin) and adiposity (e.g., body mass index [BMI]) were examined with multivariable linear regression. In the total study population, rs7903146-T was associated with a higher risk of T2D (additive odds ratio: 1.42; 95% confidence interval: 1.17; 1.72), and specifically with T2D treated with insulin analogs (2.31 [1.19; 4.46]). After exclusion of participants treated with glucose-lowering medication, rs7903146-T was associated with lower mean insulin concentration (additive mean difference: -0.07 SD [-0.14; 0.00]), but not with higher mean glucose concentration (0.03 SD [-0.01; 0.07]). Furthermore, rs7903146-T was associated with, among other measures of adiposity, a lower mean BMI (-0.04 SD [-0.09; -0.00]), and a lower mean total body fat (-0.04 SD [-0.08; -0.00]). The association between rs7903146-T and T2D increased after adjustment for BMI (odds ratio: 1.51 [1.24; 1.86]); the association between rs7903146-T and fasting insulin diminished after adjustment (-0.05 SD [-0.11; 0.02]). CONCLUSION rs7903146-T is associated with a decreased insulin concentration and increased risk of T2D with opposing effects of adjustment for adiposity.
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Affiliation(s)
- R Noordam
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands.
| | - C P A Zwetsloot
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - R de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - D O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands; Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - H J Lamb
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - A de Roos
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - E J P de Koning
- Department of Internal Medicine, Section Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - F R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - K Willems van Dijk
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands; Department of Internal Medicine, division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - D van Heemst
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
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47
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Affiliation(s)
- R David Leslie
- Department of Immunobiology, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K.
| | - Struan F A Grant
- Divisions of Human Genetics and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA .,Departments of Pediatrics and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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48
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Lu M, Li C. Nutrient sensing in pancreatic islets: lessons from congenital hyperinsulinism and monogenic diabetes. Ann N Y Acad Sci 2017; 1411:65-82. [PMID: 29044608 DOI: 10.1111/nyas.13448] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/05/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022]
Abstract
Pancreatic beta cells sense changes in nutrients during the cycles of fasting and feeding and release insulin accordingly to maintain glucose homeostasis. Abnormal beta cell nutrient sensing resulting from gene mutations leads to hypoglycemia or diabetes. Glucokinase (GCK) plays a key role in beta cell glucose sensing. As one form of congenital hyperinsulinism (CHI), activating mutations of GCK result in a decreased threshold for glucose-stimulated insulin secretion and hypoglycemia. In contrast, inactivating mutations of GCK result in diabetes, including a mild form (MODY2) and a severe form (permanent neonatal diabetes mellitus (PNDM)). Mutations of beta cell ion channels involved in insulin secretion regulation also alter glucose sensing. Activating or inactivating mutations of ATP-dependent potassium (KATP ) channel genes result in severe but completely opposite clinical phenotypes, including PNDM and CHI. Mutations of the other ion channels, including voltage-gated potassium channels (Kv 7.1) and voltage-gated calcium channels, also lead to abnormal glucose sensing and CHI. Furthermore, amino acids can stimulate insulin secretion in a glucose-independent manner in some forms of CHI, including activating mutations of the glutamate dehydrogenase gene, HDAH deficiency, and inactivating mutations of KATP channel genes. These genetic defects have provided insight into a better understanding of the complicated nature of beta cell fuel-sensing mechanisms.
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Affiliation(s)
- Ming Lu
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics & Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Endocrinology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China
| | - Changhong Li
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics & Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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49
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Abstract
PURPOSE OF REVIEW Deciphering the mechanisms of type 2 diabetes (T2DM) risk loci can greatly inform on disease pathology. This review discusses current knowledge of mechanisms through which genetic variants influence T2DM risk and considerations for future studies. RECENT FINDINGS Over 100 T2DM risk loci to date have been identified. Candidate causal variants at risk loci map predominantly to non-coding sequence. Physiological, epigenomic and gene expression data suggest that variants at many known T2DM risk loci affect pancreatic islet regulation, although variants at other loci also affect protein function and regulatory processes in adipose, pre-adipose, liver, skeletal muscle and brain. The effects of T2DM variants on regulatory activity in these tissues appear largely, but not exclusively, due to altered transcription factor binding. Putative target genes of T2DM variants have been defined at an increasing number of loci and some, such as FTO, may entail several genes and multiple tissues. Gene networks in islets and adipocytes have been implicated in T2DM risk, although the molecular pathways of risk genes remain largely undefined. Efforts to fully define the mechanisms of T2DM risk loci are just beginning. Continued identification of risk mechanisms will benefit from combining genetic fine-mapping with detailed phenotypic association data, high-throughput epigenomics data from diabetes-relevant tissue, functional screening of candidate genes and genome editing of cellular and animal models.
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Affiliation(s)
- Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA.
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50
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Zhou W, Anderson AL, Turner AP, De Iuliis GN, McCluskey A, McLaughlin EA, Nixon B. Characterization of a novel role for the dynamin mechanoenzymes in the regulation of human sperm acrosomal exocytosis. Mol Hum Reprod 2017; 23:657-673. [DOI: 10.1093/molehr/gax044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/27/2017] [Indexed: 12/16/2022] Open
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