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Lou J, Chu X, Yang X, Jamil M, Zhu H. Deciphering DNA repair gene mutational landscape in uterine corpus endometrial carcinoma patients using next generation sequencing. Am J Cancer Res 2024; 14:210-226. [PMID: 38323278 PMCID: PMC10839304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC) is a significant health concern with a complex genetic landscape impacting disease susceptibility and progression. This study aimed to unravel the spectrum of DNA repair gene mutations in Pakistani UCEC patients through Next Generation Sequencing (NGS) and explore their potential functional consequences via downstream analyses. NGS analysis of genomic DNA from 30 UCEC patients was conducted to identify clinically significant pathogenic mutations in DNA repair genes. This analysis revealed mutations in 4 key DNA repair genes: BRCA1, BRCA2, APC, and CDH1. Kaplan-Meier (KM) analysis was employed to assess the prognostic value of these mutations on patient overall survival (OS) in UCEC. To delve into the functional impact of these mutations, we performed RT-qPCR, immunohistochemistry (IHC), and western blot analyses on the mutated UCEC samples compared to their non-mutated counterparts. These results unveiled the up-regulation in the expression of the mutated genes, suggesting a potential association between the identified mutations and enhanced gene activity. Additionally, targeted bisulfite sequencing analysis was utilized to evaluate DNA methylation patterns in the promoters of the mutated genes. Strikingly, hypomethylation in the promoters of BRCA1, BRCA2, APC, and CDH1 was observed in the mutated UCEC samples relative to the non-mutated, indicating the involvement of epigenetic mechanisms in the altered gene expression. In conclusion, this study offers insights into the genetic landscape of DNA repair gene mutations in Pakistani UCEC patients. The presence of pathogenic mutations in BRCA1, BRCA2, APC, and CDH1, coupled with their down-regulation and hypermethylation, suggests a convergence of genetic and epigenetic factors contributing to genomic instability in UCEC cells. These findings enhance our understanding of UCEC susceptibility and provide potential avenues for targeted therapeutic interventions in Pakistani UCEC patients.
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Affiliation(s)
- Jun Lou
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Key Laboratory of Translational Research for CancerNanchang 330029, Jiangxi, China
| | - Xiaoyan Chu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Xiaorong Yang
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Hong Zhu
- Department of Gynecological Oncology, Jiangxi Cancer HospitalNanchang 330029, Jiangxi, China
- The Second Affiliated Hospital of Nanchang Medical CollegeNanchang 330029, Jiangxi, China
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2
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Chattopadhyay A, Lee CY, Shen YC, Lu KC, Hsiao TH, Lin CH, La LC, Tsai MH, Lu TP, Chuang EY. Multi-ethnic imputation system (MI-System): a genotype imputation server for high-dimensional data. J Biomed Inform 2023:104423. [PMID: 37308034 DOI: 10.1016/j.jbi.2023.104423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/11/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
OBJECTIVE Genotype imputation is a commonly used technique that infers un-typed variants into a study's genotype data, allowing better identification of causal variants in disease studies. However, due to overrepresentation of Caucasian studies, there's a lack of understanding of genetic basis of health-outcomes in other ethnic populations. Therefore, facilitating imputation of missing key-predictor-variants that can potentially improve a risk health-outcome prediction model, specifically for Asian ancestry, is of utmost relevance. METHODS We aimed to construct an imputation and analysis web-platform, that primarily facilitates, but is not limited to, genotype imputation on East-Asians. The goal is to provide a collaborative imputation platform for researchers in the public domain, towards rapidly and efficiently conducting accurate genotype imputation. RESULTS We present an online genotype imputation platform, Multi-ethnic Imputation System (MI-System) (https://misystem.cgm.ntu.edu.tw/), that offers users 3 established pipelines, SHAPEIT2-IMPUTE2, SHAPEIT4-IMPUTE5, and Beagle5.1 for conducting imputation analyses. In addition to 1000 Genomes and Hapmap3, a new customized Taiwan Biobank (TWB) reference panel, specifically created for Taiwanese-Chinese ancestry is provided. MI-System further offers functions to create customized reference panels to be used for imputation, conduct quality control, split whole genome data into chromosomes, and convert genome builds. CONCLUSION Users can upload their genotype data and perform imputation with minimum effort and resources. The utility functions further can be utilized to preprocess user uploaded data with easy clicks. MI-System potentially contributes to Asian-population genetics research, while eliminating the requirement for high performing computational resources and bioinformatics expertise. It will enable an increased pace of research and provide a knowledge-base for genetic carriers of complex diseases, therefore greatly enhancing patient-driven research. STATEMENT OF SIGNIFICANCE Multi-ethnic Imputation System (MI-System), primarily facilitates, but is not limited to, imputation on East-Asians, through 3 established prephasing-imputation pipelines, SHAPEIT2-IMPUTE2, SHAPEIT4-IMPUTE5, and Beagle5.1, where users can upload their genotype data and perform imputation and other utility functions with minimum effort and resources. A new customized Taiwan Biobank (TWB) reference panel, specifically created for Taiwanese-Chinese ancestry is provided. Utility functions include (a) create customized reference panels, (b) conduct quality control, (c) split whole genome data into chromosomes, and (d) convert genome builds. Users can also combine 2 reference panels using the system and use combined panels as reference to conduct imputation using MI-System.
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Affiliation(s)
- Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Chien-Yueh Lee
- Master Program for Biomedical Engineering, College of Biomedical Engineering, China Medical University, Taichung 40402, Taiwan
| | - Ying-Cheng Shen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Kuan-Chen Lu
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taiwan
| | - Liang-Chuan La
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan; Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan; Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan; Center of Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan; Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan; Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan.
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3
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Perry DJ, Shapiro MR, Chamberlain SW, Kusmartseva I, Chamala S, Balzano-Nogueira L, Yang M, Brant JO, Brusko M, Williams MD, McGrail KM, McNichols J, Peters LD, Posgai AL, Kaddis JS, Mathews CE, Wasserfall CH, Webb-Robertson BJM, Campbell-Thompson M, Schatz D, Evans-Molina C, Pugliese A, Concannon P, Anderson MS, German MS, Chamberlain CE, Atkinson MA, Brusko TM. A genomic data archive from the Network for Pancreatic Organ donors with Diabetes. Sci Data 2023; 10:323. [PMID: 37237059 PMCID: PMC10219990 DOI: 10.1038/s41597-023-02244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Network for Pancreatic Organ donors with Diabetes (nPOD) is the largest biorepository of human pancreata and associated immune organs from donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, islet autoantibody positivity (AAb+), and without diabetes. nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating procedures, and associated de-identified data/metadata to researchers around the world. Herein describes the release of high-parameter genotyping data from this collection. 372 donors were genotyped using a custom precision medicine single nucleotide polymorphism (SNP) microarray. Data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). These data are publicly-available to enable genotype-specific sample requests and the study of novel genotype:phenotype associations, aiding in the mission of nPOD to enhance understanding of diabetes pathogenesis to promote the development of novel therapies.
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Affiliation(s)
- Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Melanie R Shapiro
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Sonya W Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Irina Kusmartseva
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leandro Balzano-Nogueira
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Mingder Yang
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jason O Brant
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - MacKenzie D Williams
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Kieran M McGrail
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - James McNichols
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leeana D Peters
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Bobbie-Jo M Webb-Robertson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biomedical Engineering, College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Desmond Schatz
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, 33021, USA
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32601, USA
| | - Mark S Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael S German
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Chester E Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Huang M, Chen W, Wang M, Huang Y, Liu H, Ming Y, Chen Y, Tang Z, Jia B. Advanced Delivery Strategies for Immunotherapy in Type I Diabetes Mellitus. BioDrugs 2023; 37:331-352. [PMID: 37178431 PMCID: PMC10182560 DOI: 10.1007/s40259-023-00594-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2023] [Indexed: 05/15/2023]
Abstract
Type 1 diabetes mellitus (T1DM) has been defined as an autoimmune disease characterised by immune-mediated destruction of the pancreatic β cells, leading to absolute insulin deficiency and hyperglycaemia. Current research has increasingly focused on immunotherapy based on immunosuppression and regulation to rescue T-cell-mediated β-cell destruction. Although T1DM immunotherapeutic drugs are constantly under clinical and preclinical development, several key challenges remain, including low response rates and difficulty in maintaining therapeutic effects. Advanced drug delivery strategies can effectively harness immunotherapies and improve their potency while reducing their adverse effects. In this review, we briefly introduce the mechanisms of T1DM immunotherapy and focus on the current research status of the integration of the delivery techniques in T1DM immunotherapy. Furthermore, we critically analyse the challenges and future directions of T1DM immunotherapy.
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Affiliation(s)
- Mingshu Huang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Weixing Chen
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Min Wang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yisheng Huang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Hongyu Liu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yue Ming
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yuanxin Chen
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Zhengming Tang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Bo Jia
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China.
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5
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Fan W, Pang H, Li X, Xie Z, Huang G, Zhou Z. Plasma-derived exosomal miRNAs as potentially novel biomarkers for latent autoimmune diabetes in adults. Diabetes Res Clin Pract 2023; 197:110570. [PMID: 36746199 DOI: 10.1016/j.diabres.2023.110570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/06/2023]
Abstract
AIM To characterize the exosomal miRNA profiles of latent autoimmune diabetes in adults (LADA) and evaluate the biomarker potential of selected miRNAs to distinguish LADA from type 2 diabetes (T2D). METHODS Plasma-derived exosomal miRNA expression profiles were measured in patients with LADA (N = 5) and control subjects (N = 5). Five differentially expressed miRNAs were selected to validate their expression levels and assess their diagnostic potential by quantitative real-time PCR (qRT-PCR) in a larger cohort. RESULTS Seventy-five differentially expressed plasma-derived exosomal miRNAs were identified in LADA patients compared to healthy subjects. The expression levels of three exosomal miRNAs (hsa-miR-146a-5p, hsa-miR-223-3p and hsa-miR-21-5p) were significantly different between the LADA group and the T2D group. The three miRNAs exhibited areas under the receiver operating characteristic curves of 0.978, 0.96 and 0.809, respectively. CONCLUSIONS This study uncovers the miRNA profiles of plasma-derived exosomes from LADA patients and identifies exosomal miRNAs as potential biomarkers to discriminate LADA from T2D for the first time. Our data demonstrate the function of exosomal miRNAs in the development of LADA and contribute to an in-depth understanding of the precise mechanisms underlying the pathogenesis of LADA.
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Affiliation(s)
- Wenqi Fan
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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6
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Pang H, Lin J, Luo S, Huang G, Li X, Xie Z, Zhou Z. The missing heritability in type 1 diabetes. Diabetes Obes Metab 2022; 24:1901-1911. [PMID: 35603907 PMCID: PMC9545639 DOI: 10.1111/dom.14777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022]
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disease characterized by an absolute deficiency of insulin. It affects more than 20 million people worldwide and imposes an enormous financial burden on patients. The underlying pathogenic mechanisms of T1D are still obscure, but it is widely accepted that both genetics and the environment play an important role in its onset and development. Previous studies have identified more than 60 susceptible loci associated with T1D, explaining approximately 80%-85% of the heritability. However, most identified variants confer only small increases in risk, which restricts their potential clinical application. In addition, there is still a so-called 'missing heritability' phenomenon. While the gap between known heritability and true heritability in T1D is small compared with that in other complex traits and disorders, further elucidation of T1D genetics has the potential to bring novel insights into its aetiology and provide new therapeutic targets. Many hypotheses have been proposed to explain the missing heritability, including variants remaining to be found (variants with small effect sizes, rare variants and structural variants) and interactions (gene-gene and gene-environment interactions; e.g. epigenetic effects). In the following review, we introduce the possible sources of missing heritability and discuss the existing related knowledge in the context of T1D.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
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7
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Zajec A, Trebušak Podkrajšek K, Tesovnik T, Šket R, Čugalj Kern B, Jenko Bizjan B, Šmigoc Schweiger D, Battelino T, Kovač J. Pathogenesis of Type 1 Diabetes: Established Facts and New Insights. Genes (Basel) 2022; 13:genes13040706. [PMID: 35456512 PMCID: PMC9032728 DOI: 10.3390/genes13040706] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 01/08/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the T-cell-mediated destruction of insulin-producing β-cells in pancreatic islets. It generally occurs in genetically susceptible individuals, and genetics plays a major role in the development of islet autoimmunity. Furthermore, these processes are heterogeneous among individuals; hence, different endotypes have been proposed. In this review, we highlight the interplay between genetic predisposition and other non-genetic factors, such as viral infections, diet, and gut biome, which all potentially contribute to the aetiology of T1D. We also discuss a possible active role for β-cells in initiating the pathological processes. Another component in T1D predisposition is epigenetic influences, which represent a link between genetic susceptibility and environmental factors and may account for some of the disease heterogeneity. Accordingly, a shift towards personalized therapies may improve the treatment results and, therefore, result in better outcomes for individuals in the long-run. There is also a clear need for a better understanding of the preclinical phases of T1D and finding new predictive biomarkers for earlier diagnosis and therapy, with the final goal of reverting or even preventing the development of the disease.
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Affiliation(s)
- Ana Zajec
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Robert Šket
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Barbara Čugalj Kern
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Darja Šmigoc Schweiger
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Battelino
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Kovač
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Pang H, Luo S, Huang G, Li X, Xie Z, Zhou Z. The Association of CTLA-4 rs231775 and rs3087243 Polymorphisms with Latent Autoimmune Diabetes in Adults: A Meta-Analysis. Biochem Genet 2021; 60:1222-1235. [PMID: 34822071 DOI: 10.1007/s10528-021-10152-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022]
Abstract
Polymorphisms rs231775 and rs3087243 of cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) gene have been associated with risk of latent autoimmune diabetes in adults (LADA). However, the results were inconsistent. The purpose of this study was to quantitatively assess the relationship between polymorphisms rs231775 and rs3087243 of CTLA-4 and LADA in a larger pooled population by performing a meta-analysis. Systematic search for eligible studies was conducted in PubMed, Web of Science, and Embase. Case-control studies containing genotype frequencies of polymorphisms rs231775 or rs3087243 were selected, and pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the associations between polymorphisms of CTLA-4 and LADA in allelic, dominant and recessive genetic model. A total of eleven studies, in which five studies reported rs231775, two studies reported rs3087342, and four studies reported both rs231775 and rs3087243, were identified. Among them, one study wasn't included in the following meta-analysis because the distribution of genotypes in the control group didn't comply with Hardy-Weinberg equilibrium. Significant associations with susceptibility to LADA were detected for rs231775 (785 cases and 3435 controls) and for rs3087243 (820 cases and 4824 controls) in overall population. Further subgroup analyses for ethnicity (Asian, Caucasian, and African) have also indicated the positive association between rs231775 and LADA. As for rs3087243, subgroup analyses detected the association between polymorphism and LADA in Caucasian population under recessive model. Polymorphisms rs231775 and rs3087243 of CTLA-4 gene are potential risk factors for LADA and may serve as novel genetic biomarkers of LADA.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China
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Jabalameli MR, Fitzpatrick FM, Colombo R, Howles SA, Leggatt G, Walker V, Wiberg A, Kunji ERS, Ennis S. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones. Mol Genet Genomic Med 2021; 9:e1749. [PMID: 34346195 PMCID: PMC8683635 DOI: 10.1002/mgg3.1749] [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: 07/22/2020] [Revised: 05/13/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Calcium kidney stones are common and recurrences are often not preventable by available empiric remedies. Their etiology is multifactorial and polygenic, and an increasing number of genes are implicated. Their identification will enable improved management. METHODS DNA from three stone-formers in a Southampton family (UK) and two from an Italian family were analyzed independently by whole exome sequencing and selected variants were genotyped across all available members of both pedigrees. A disease variant of SLC25A25 (OMIM 608745), encoding the mitochondrial ATP-Mg/Pi carrier 3 (APC3) was identified, and analyzed structurally and functionally with respect to its calcium-regulated transport activity. RESULTS All five patients had a heterozygous dominant SLC25A25 variant (rs140777921; GRCh37.p13: chr 9 130868670 G>C; p.Gln349His; Reference Sequence NM_001006641.3). Non-stone formers also carried the variant indicating incomplete penetrance. Modeling suggests that the variant lacks a conserved polar interaction, which may cause structural instability. Calcium-regulated ATP transport was reduced to ~20% of the wild type, showing a large reduction in function. CONCLUSION The transporter is important in regulating mitochondrial ATP production. This rare variant may increase urine lithogenicity through impaired provision of ATP for solute transport processes in the kidney, and/or for purinergic signaling. Variants found in other genes may compound this abnormality.
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Affiliation(s)
- M Reza Jabalameli
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Fiona M Fitzpatrick
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Roberto Colombo
- Faculty of Medicine 'Agostino Gemelli', Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases, Niguarda Ca´Granda Metropolitan Hospital, Milan, Italy
| | - Sarah A Howles
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Gary Leggatt
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth, UK
| | - Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton, Southampton, UK
| | - Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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