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Zhou J, Xu B, He F, Shu Y, Chen X, Liu Z, Sun B, Zhang W. Association of RASGRP1 polymorphism with vascular complications in Chinese diabetic patients with glycemic control and antihypertensive treatment. Cardiovasc Diabetol 2024; 23:166. [PMID: 38730425 PMCID: PMC11088008 DOI: 10.1186/s12933-024-02267-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Studies have shown that RASGRP1 was potently associated with the onset of type 2 diabetes mellitus (T2DM), and RASGRP1 rs7403531 was significantly correlated with islet function in T2DM patients. However, the effect of RASGRP1 polymorphism on blood glucose and blood pressure in T2DM patients after continuous treatment has yet to be fully elucidated. OBJECTIVE This study aimed to explore the association between RASGRP1 genetic polymorphism and cardiovascular complications in T2DM patients, so as to provide more evidence for the individualized treatment of T2DM patients. METHODS We retrospectively analyzed a large-scale multicenter drug clinical study cohort that based on a 2 × 2 factorial (glucose control axis and blood pressure lowering axis) randomized controlled design, with follow-up for 5 years. The major vascular endpoint events included cardiovascular death, non-fatal stroke, coronary heart disease, new-onset or worsening renal disease, and diabetic retinopathy. RASGRP1 rs12593201, rs56254815 and rs7403531 were finally selected as candidate single nucleotide polymorphisms. Mixed linear model and Cox hazard ratio (HR) model were used for data analysis with IBM SPSS (version 20.0 for windows; Chicago, IL). RESULTS Our study enrolled 1357 patients with high-risk diabetes, with a mean follow-up duration of 4.8 years. RASGRP1 rs7403531 was associated with vascular events in hypoglycemic and antihypertensive therapy. Specifically, compared with CC carriers, patients with CT/TT genotype had fewer major microvascular events (HR = 0.41, 95% confidence interval (CI) 0.21-0.80, P = 0.009), and reduced the risk of major eye disease events (HR = 0.44, 95% CI 0.20-0.94, P = 0.03). For glucose lowering axis, CT/TT carriers had a lower risk of secondary nephropathy (HR = 0.48, 95% CI 0.25-0.92, P = 0.03) in patients with standard glycemic control. For blood pressure lowering axis, all cerebrovascular events (HR = 2.24, 95% CI 1.11-4.51, P = 0.025) and stroke events (HR = 2.07, 95% CI 1.03-4.15, P = 0.04) were increased in patients with CC genotype compared to those with CT/TT genotype in the placebo group, respectively. Furthermore, patients with CC genotype showed a reduced risk of major cerebrovascular events in antihypertensive group (HR = 0.36, 95% CI 0.15-0.86, P = 0.021). For RASGRP1 rs56254815, compared with the AA genotype carriers, the systolic blood pressure of AG/GG carriers in the antihypertensive group decreased by 1.5mmhg on average (P = 0.04). In the placebo group, the blood pressure of AG/GG carriers was 1.7mmHg higher than that of AA carriers (P = 0.02). CONCLUSION We found that patients with G allele of RASGRP1 (rs56254815) showed a better antihypertensive therapy efficacy in T2DM patients. The rs7403531 T allele could reduce the risk of major microvascular events and major eye diseases in T2DM patients receiving either hypoglycemic or antihypertensive therapy. Our findings suggest that RASGRP1 genetic polymorphism might predict the cardiovascular complications in T2DM patients.
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Affiliation(s)
- Jiecan Zhou
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China.
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China.
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China.
| | - Bo Xu
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China
| | - Fazhong He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 410078, Changsha, Hunan, China
- Department of Pharmacy-Quality control section of medical department, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, China
| | - Yan Shu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Xiaoping Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 410078, Changsha, Hunan, China
| | - Zhaoqian Liu
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 410078, Changsha, Hunan, China
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China.
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 410078, Changsha, Hunan, China.
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, People's Middle Street, Changsha, 410011, Hunan , P. R. China.
| | - Wei Zhang
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, China.
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 110 Xiangya Rode, Kaifu district, 410008, Changsha, Hunan, P.R. China.
- Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 410078, Changsha, Hunan, China.
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Tsygankov AY. Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges. Int J Mol Sci 2024; 25:4434. [PMID: 38674019 PMCID: PMC11050124 DOI: 10.3390/ijms25084434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
This Special Issue entitled "Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges" is focused on a relatively novel vertebrate gene/protein family termed alternatively TULA, UBASH3, or STS [...].
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases. HGG ADVANCES 2024; 5:100279. [PMID: 38389303 PMCID: PMC10943488 DOI: 10.1016/j.xhgg.2024.100279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Li J, Yang Y, Xia Y, Luo S, Lin J, Xiao Y, Li X, Huang G, Yang L, Xie Z, Zhou Z. Effect of SIRT1 gene single-nucleotide polymorphisms on susceptibility to type 1 diabetes in a Han Chinese population. J Endocrinol Invest 2024; 47:819-826. [PMID: 37695462 DOI: 10.1007/s40618-023-02190-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
AIMS SIRT1 deficiency has been associated with diabetes, and a variant of the SIRT1 gene has been found to be involved in human autoimmune diabetes; however, it is unclear whether this genetic variation exists in Han Chinese with type 1 diabetes (T1D) and whether it contributes to development of T1D. Therefore, we aimed to explore the association of the SIRT1 gene single-nucleotide polymorphisms (SNPs) rs10997866 and rs3818292 in a Han Chinese population with T1D. METHODS This study recruited 2653 unrelated Han Chinese individuals, of whom 1289 had T1D and 1364 were healthy controls. Allelic and genotypic distributions of SIRT1 polymorphisms (rs10997866 and rs3818292) were determined by MassARRAY. Basic characteristics, genotype and allele frequencies of selected SNPs were compared between the T1D patients and healthy controls. Further genotype-phenotype association analysis of the SNPs was performed on the T1D patients divided into three groups according to genotype. Statistical analyses included the chi-square test, Mann‒Whitney U test, Kruskal‒Wallis H test and logistic regression. RESULTS The allelic (G vs. A) and genotypic (GA vs. AA) distributions of SIRT1 rs10997866 were significantly different in T1D patients and healthy controls (P = 0.039, P = 0.027), and rs10997866 was associated with T1D susceptibility under dominant, overdominant and additive models (P = 0.026, P = 0.030 and P = 0.027, respectively). Moreover, genotype-phenotype association analysis showed the GG genotype of rs10997866 and the GG genotype of rs3818292 to be associated with higher titers of IA-2A (P = 0.013 and P = 0.038, respectively). CONCLUSION SIRT1 rs10997866 is significantly associated with T1D susceptibility, with the minor allele G conferring a higher risk of T1D. Moreover, SIRT1 gene rs10997866 and rs3818292 correlate with the titer of IA-2A in Han Chinese individuals with T1D.
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Affiliation(s)
- J 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
| | - Y Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Y Xia
- 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
| | - S 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
| | - J Lin
- 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
| | - Y Xiao
- 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
| | - X 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
| | - G 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
| | - L Yang
- 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
| | - Z 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.
| | - Z 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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Xiao L, Qiao J, Huang Y, Tan B, Hong L, Li Z, Cai G, Wu Z, Zheng E, Wang S, Gu T. RASGRP1 targeted by H3K27me3 regulates myoblast proliferation and differentiation in mice and pigs. Acta Biochim Biophys Sin (Shanghai) 2024; 56:452-461. [PMID: 38419500 PMCID: PMC10984873 DOI: 10.3724/abbs.2024011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/14/2023] [Indexed: 03/02/2024] Open
Abstract
Skeletal muscle is not only the largest organ in the body that is responsible for locomotion and exercise but also crucial for maintaining the body's energy metabolism and endocrine secretion. The trimethylation of histone H3 lysine 27 (H3K27me3) is one of the most important histone modifications that participates in muscle development regulation by repressing the transcription of genes. Previous studies indicate that the RASGRP1 gene is regulated by H3K27me3 in embryonic muscle development in pigs, but its function and regulatory role in myogenesis are still unclear. In this study, we verify the crucial role of H3K27me3 in RASGRP1 regulation. The gain/loss function of RASGRP1 in myogenesis regulation is performed using mouse myoblast C2C12 cells and primarily isolated porcine skeletal muscle satellite cells (PSCs). The results of qPCR, western blot analysis, EdU staining, CCK-8 assay and immunofluorescence staining show that overexpression of RASGRP1 promotes cell proliferation and differentiation in both skeletal muscle cell models, while knockdown of RASGRP1 leads to the opposite results. These findings indicate that RASGRP1 plays an important regulatory role in myogenesis in both mice and pigs.
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Affiliation(s)
- Liyao Xiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Jiaxin Qiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Yiyang Huang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Baohua Tan
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Shanshan Wang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- College of Life ScienceHubei UniversityWuhan430000China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
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Fan S, Kang B, Li S, Li W, Chen C, Chen J, Deng L, Chen D, Zhou J. Exploring the multifaceted role of RASGRP1 in disease: immune, neural, metabolic, and oncogenic perspectives. Cell Cycle 2024; 23:722-746. [PMID: 38865342 PMCID: PMC11229727 DOI: 10.1080/15384101.2024.2366009] [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: 05/02/2023] [Accepted: 11/25/2023] [Indexed: 06/14/2024] Open
Abstract
RAS guanyl releasing protein 1 (RASGRP1) is a guanine nucleotide exchange factor (GEF) characterized by the presence of a RAS superfamily GEF domain. It functions as a diacylglycerol (DAG)-regulated nucleotide exchange factor, specifically activating RAS through the exchange of bound GDP for GTP. Activation of RAS by RASGRP1 has a wide range of downstream effects at the cellular level. Thus, it is not surprising that many diseases are associated with RASGRP1 disorders. Here, we present an overview of the structure and function of RASGRP1, its crucial role in the development, expression, and regulation of immune cells, and its involvement in various signaling pathways. This review comprehensively explores the relationship between RASGRP1 and various diseases, elucidates the underlying molecular mechanisms of RASGRP1 in each disease, and identifies potential therapeutic targets. This study provides novel insights into the role of RASGRP1 in insulin secretion and highlights its potential as a therapeutic target for diabetes. The limitations and challenges associated with studying RASGRP1 in disease are also discussed.
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Affiliation(s)
- Shangzhi Fan
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Bo Kang
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shaoqian Li
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weiyi Li
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Canyu Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jixiang Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lijing Deng
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Danjun Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jiecan Zhou
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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Vukojević K, Šoljić V, Martinović V, Raguž F, Filipović N. The Ubiquitin-Associated and SH3 Domain-Containing Proteins (UBASH3) Family in Mammalian Development and Immune Response. Int J Mol Sci 2024; 25:1932. [PMID: 38339213 PMCID: PMC10855836 DOI: 10.3390/ijms25031932] [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: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
UBASH3A and UBASH3B are protein families of atypical protein tyrosine phosphatases that function as regulators of various cellular processes during mammalian development. As UBASH3A has only mild phosphatase activity, its regulatory effects are based on the phosphatase-independent mechanisms. On the contrary, UBASH3B has strong phosphatase activity, and the suppression of its receptor signalling is mediated by Syk and Zap-70 kinases. The regulatory functions of UBASH3A and UBASH3B are particularly evident in the lymphoid tissues and kidney development. These tyrosine phosphatases are also known to play key roles in autoimmunity and neoplasms. However, their involvement in mammalian development and its regulatory functions are largely unknown and are discussed in this review.
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Affiliation(s)
- Katarina Vukojević
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia;
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Department of Histology and Embryology, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
- Faculty of Health Studies, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Center for Translational Research in Biomedicine, University of Split School of Medicine, 21000 Split, Croatia
| | - Violeta Šoljić
- Department of Histology and Embryology, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
- Faculty of Health Studies, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
| | - Vlatka Martinović
- Department of Surgery, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Fila Raguž
- Department of Internal Medicine, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Natalija Filipović
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia;
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Center for Translational Research in Biomedicine, University of Split School of Medicine, 21000 Split, Croatia
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Pandey R, Bakay M, Hakonarson H. SOCS-JAK-STAT inhibitors and SOCS mimetics as treatment options for autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis. Front Immunol 2023; 14:1271102. [PMID: 38022642 PMCID: PMC10643230 DOI: 10.3389/fimmu.2023.1271102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmune diseases arise from atypical immune responses that attack self-tissue epitopes, and their development is intricately connected to the disruption of the JAK-STAT signaling pathway, where SOCS proteins play crucial roles. Conditions such as autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis exhibit immune system dysfunctions associated with JAK-STAT signaling dysregulation. Emerging therapeutic strategies utilize JAK-STAT inhibitors and SOCS mimetics to modulate immune responses and alleviate autoimmune manifestations. Although more research and clinical studies are required to assess their effectiveness, safety profiles, and potential for personalized therapeutic approaches in autoimmune conditions, JAK-STAT inhibitors and SOCS mimetics show promise as potential treatment options. This review explores the action, effectiveness, safety profiles, and future prospects of JAK inhibitors and SOCS mimetics as therapeutic agents for psoriasis, autoimmune uveitis, systemic lupus erythematosus, and autoimmune encephalitis. The findings underscore the importance of investigating these targeted therapies to advance treatment options for individuals suffering from autoimmune diseases.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA, United States
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9
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Urrutia I, Martínez R, Calvo B, Saso-Jiménez L, González P, Fernández-Rubio E, Martín-Nieto A, Aguayo A, Rica I, Gaztambide S, Castano L. Autoimmune Diabetes From Childhood to Adulthood: The Role of Pancreatic Autoantibodies and HLA-DRB1 Genotype. J Clin Endocrinol Metab 2023; 108:e1341-e1346. [PMID: 37207452 DOI: 10.1210/clinem/dgad277] [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: 02/18/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
CONTEXT Autoimmune diabetes can develop at any age, but unlike early-onset diabetes, adult onset is less well documented. We aimed to compare, over a wide age range, the most reliable predictive biomarkers for this pathology: pancreatic-autoantibodies and HLA-DRB1 genotype. METHODS A retrospective study of 802 patients with diabetes (aged 11 months to 66 years) was conducted. Pancreatic autoantibodies at diagnosis: insulin autoantibodies (IAA), glutamate decarboxylase autoantibodies (GADA), islet tyrosine phosphatase 2 autoantibodies (IA2A), and zinc transporter-8 autoantibodies (ZnT8A) and HLA-DRB1 genotype were analyzed. RESULTS Compared with early-onset patients, adults had a lower frequency of multiple autoantibodies, with GADA being the most common. At early onset, IAA was the most frequent in those younger than 6 years and correlated inversely with age; GADA and ZnT8A correlated directly and IA2A remained stable.The absence of HLA-DRB1 risk genotype was associated with higher age at diabetes onset (27.5 years; interquartile range [IQR], 14.3-35.7), whereas the high-risk HLA-DR3/DR4 was significantly more common at lower age (11.9 years; IQR, 7.1-21.6). ZnT8A was associated with DR4/non-DR3 (odds ratio [OR], 1.91; 95% CI, 1.15-3.17), GADA with DR3/non-DR4 (OR, 2.97; 95% CI, 1.55-5.71), and IA2A with DR4/non-DR3 and DR3/DR4 (OR, 3.89; 95% CI, 2.28-6.64, and OR, 3.08; 95% CI, 1.83-5.18, respectively). No association of IAA with HLA-DRB1 was found. CONCLUSION Autoimmunity and HLA-DRB1 genotype are age-dependent biomarkers. Adult-onset autoimmune diabetes is associated with lower genetic risk and lower immune response to pancreatic islet cells compared with early-onset diabetes.
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Affiliation(s)
- Inés Urrutia
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
| | - Rosa Martínez
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
| | - Begona Calvo
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Medical Oncology, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Laura Saso-Jiménez
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
| | - Pedro González
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Endocrinology and Nutrition, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Elsa Fernández-Rubio
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Endocrinology and Nutrition, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Alicia Martín-Nieto
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Endocrinology and Nutrition, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Anibal Aguayo
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
| | - Itxaso Rica
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
- Department of Pediatric Endocrinology, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Sonia Gaztambide
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
- Department of Endocrinology and Nutrition, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Luis Castano
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- CIBERDEM, CIBERER, UPV-EHU, Endo-ERN, 48903 Barakaldo, Spain
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553722. [PMID: 37645944 PMCID: PMC10462090 DOI: 10.1101/2023.08.17.553722] [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
Objective To systematically characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate gene expression in an allele dependent manner. Methods We designed a massively parallel reporter assay (MPRA) containing ~32K variants and transfected it into an Epstein-Barr virus transformed B cell line generated from an SLE case. Results Our study expands our understanding of hQTLs, illustrating that epigenetic QTLs are more likely to contribute to functional mechanisms than eQTLs and other variant types, and a large proportion of hQTLs overlap transcription start sites (TSS) of noncoding RNAs. In addition, we nominate 17 variants (including 11 novel) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells. Conclusion We uncover important insights into the mechanistic relationships between genotype, epigenetics, gene expression, and SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
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11
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Fichna M, Małecki PP, Żurawek M, Furman K, Gębarski B, Fichna P, Ruchała M. Genetic variants and risk of endocrine autoimmunity in relatives of patients with Addison's disease. Endocr Connect 2023; 12:e230008. [PMID: 37010089 PMCID: PMC10235924 DOI: 10.1530/ec-23-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 04/04/2023]
Abstract
Since individuals with Addison's disease (AD) present considerable co-occurrence of additional autoimmune conditions, clustering of autoimmunity was also predicted among their relatives. The study was aimed to assess circulating autoantibodies in first-degree relatives of patients with AD and to correlate them with the established genetic risk factors (PTPN22 rs2476601, CTLA4 rs231775, and BACH2 rs3757247). Antibodies were evaluated using validated commercial assays, and genotyping was performed using TaqMan chemistry. The studied cohort comprised 112 female and 75 male relatives. Circulating autoantibodies were found in 69 relatives (36.9%). Thyroid autoantibodies, that is antibodies to thyroid peroxidase (aTPO) and thyroglobulin (aTg), were detectable in 25.1 and 17.1% relatives, respectively. Antibodies to 21-hydroxylase (a21OH) were found in 5.8% individuals, and beta cell-specific antibodies to ZnT8, GAD, and IA2 were found in 7.5, 8.0, and 2.7%, respectively. The prevalence of a21OH (P = 0.0075; odds ratio (OR) 7.68; 95% CI 1.903-36.0), aTPO (P < 0.0001; OR 3.85; 95% CI 1.873-7.495), and aTg (P < 0.0001; OR 7.73; 95% CI 3.112-19.65), as well as aGAD (P = 0.0303; OR 3.38; 95% CI 1.180-9.123) and aZnT8 (P = 0.032; OR 6.40; 95% CI 1.846-21.91), was significantly increased in carriers of rs2476601 T allele. Moreover, T allele appeared to be a risk factor for multiple circulating autoantibody specificities (P = 0.0009; OR 5.79; 95% CI 1.962-15.81). None of the studied autoantibodies demonstrated significant association with rs231775 in CTLA4 (P > 0.05), and only weak association was detected between BACH2 rs3757247 and circulating aTPO (P = 0.0336; OR 2.12; 95%CI 1.019-4.228). In conclusion, first-degree relatives of patients with AD, carriers of the PTPN22 rs2476601 T allele, are at particular risk of developing autoantibodies to endocrine antigens.
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Affiliation(s)
- Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr P Małecki
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Piotr Fichna
- Department of Paediatric Diabetes and Obesity, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
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12
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Shi FY, Wang Y, Huang D, Liang Y, Liang N, Chen XW, Gao G. Computational Assessment of the Expression-modulating Potential for Non-coding Variants. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:662-673. [PMID: 34890839 PMCID: PMC10787178 DOI: 10.1016/j.gpb.2021.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Large-scale genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression. However, pinpointing causal variants effectively and efficiently remains a serious challenge. Here, we developed CARMEN, a novel algorithm to identify functional non-coding expression-modulating variants. Multiple evaluations demonstrated CARMEN's superior performance over state-of-the-art tools. Applying CARMEN to GWAS and eQTL datasets further pinpointed several causal variants other than the reported lead single-nucleotide polymorphisms (SNPs). CARMEN scales well with the massive datasets, and is available online as a web server at http://carmen.gao-lab.org.
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Affiliation(s)
- Fang-Yuan Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Yu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Dong Huang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yu Liang
- Human Aging Research Institute, School of Life Science, Nanchang University, Nanchang 330031, China
| | - Nan Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China
| | - Xiao-Wei Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Biomedical Pioneering Innovative Center (BIOPIC) & Beijing Advanced Innovation Center for Genomics (ICG), Center for Bioinformatics (CBI), Peking University, Beijing 100871, China.
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13
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Tsygankov AY. TULA Proteins in Men, Mice, Hens, and Lice: Welcome to the Family. Int J Mol Sci 2023; 24:ijms24119126. [PMID: 37298079 DOI: 10.3390/ijms24119126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The two members of the UBASH3/STS/TULA protein family have been shown to critically regulate key biological functions, including immunity and hemostasis, in mammalian biological systems. Negative regulation of signaling through immune receptor tyrosine-based activation motif (ITAM)- and hemITAM-bearing receptors mediated by Syk-family protein tyrosine kinases appears to be a major molecular mechanism of the down-regulatory effect of TULA-family proteins, which possess protein tyrosine phosphatase (PTP) activity. However, these proteins are likely to carry out some PTP-independent functions as well. Whereas the effects of TULA-family proteins overlap, their characteristics and their individual contributions to cellular regulation also demonstrate clearly distinct features. Protein structure, enzymatic activity, molecular mechanisms of regulation, and biological functions of TULA-family proteins are discussed in this review. In particular, the usefulness of the comparative analysis of TULA proteins in various metazoan taxa, for identifying potential roles of TULA-family proteins outside of their functions already established in mammalian systems, is examined.
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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14
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Newman JRB, Concannon P, Ge Y. UBASH3A Interacts with PTPN22 to Regulate IL2 Expression and Risk for Type 1 Diabetes. Int J Mol Sci 2023; 24:ijms24108671. [PMID: 37240014 DOI: 10.3390/ijms24108671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
UBASH3A is a negative regulator of T cell activation and IL-2 production and plays key roles in autoimmunity. Although previous studies revealed the individual effects of UBASH3A on risk for type 1 diabetes (T1D; a common autoimmune disease), the relationship of UBASH3A with other T1D risk factors remains largely unknown. Given that another well-known T1D risk factor, PTPN22, also inhibits T cell activation and IL-2 production, we investigated the relationship between UBASH3A and PTPN22. We found that UBASH3A, via its Src homology 3 (SH3) domain, physically interacts with PTPN22 in T cells, and that this interaction is not altered by the T1D risk coding variant rs2476601 in PTPN22. Furthermore, our analysis of RNA-seq data from T1D cases showed that the amounts of UBASH3A and PTPN22 transcripts exert a cooperative effect on IL2 expression in human primary CD8+ T cells. Finally, our genetic association analyses revealed that two independent T1D risk variants, rs11203203 in UBASH3A and rs2476601 in PTPN22, interact statistically, jointly affecting risk for T1D. In summary, our study reveals novel interactions, both biochemical and statistical, between two independent T1D risk loci, and suggests how these interactions may affect T cell function and increase risk for T1D.
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Affiliation(s)
- Jeremy R B Newman
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yan Ge
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
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15
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Pandey R, Bakay M, Hakonarson H. CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration. Int J Mol Sci 2023; 24:ijms24098224. [PMID: 37175930 PMCID: PMC10179542 DOI: 10.3390/ijms24098224] [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: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
CLEC16A is emerging as an important genetic risk factor for several autoimmune disorders and for Parkinson disease (PD), opening new avenues for translational research and therapeutic development. While the exact role of CLEC16A in health and disease is still being elucidated, the gene plays a critical role in the regulation of autophagy, mitophagy, endocytosis, intracellular trafficking, immune function, and in biological processes such as insulin secretion and others that are important to cellular homeostasis. As shown in both human and animal modeling studies, CLEC16A hypofunction predisposes to both autoinflammatory phenotype and neurodegeneration. While the two are clearly related, further functional studies are needed to fully understand the mechanisms involved for optimized therapeutic interventions. Based on recent data, mitophagy-inducing drugs may be warranted, and such therapy should be tested in clinical trials as these drugs would tackle the underlying pathogenic mechanism (s) and could treat or prevent symptoms of autoimmunity and neurodegeneration in individuals with CLEC16A risk variants. Accordingly, interventions directed at reversing the dysregulated mitophagy and the consequences of loss of function of CLEC16A without activating other detrimental cellular pathways could present an effective therapy. This review presents the emerging role of CLEC16A in health and disease and provides an update on the disease processes that are attributed to variants located in the CLEC16A gene, which are responsible for autoimmune disorders and neurodegeneration with emphasis on how this information is being translated into practical and effective applications in the clinic.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104-4318, USA
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Mousa M, Albarguthi S, Albreiki M, Farooq Z, Sajid S, El Hajj Chehadeh S, ElBait GD, Tay G, Deeb AA, Alsafar H. Whole-Exome Sequencing in Family Trios Reveals De Novo Mutations Associated with Type 1 Diabetes Mellitus. BIOLOGY 2023; 12:biology12030413. [PMID: 36979105 PMCID: PMC10044903 DOI: 10.3390/biology12030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease characterized by insulin deficiency and loss of pancreatic islet β-cells. The objective of this study is to identify de novo mutations in 13 trios from singleton families that contribute to the genetic basis of T1DM through the application of whole-exome sequencing (WES). Of the 13 families sampled for this project, 12 had de novo variants, with Family 7 having the highest number (nine) of variants linked to T1DM/autoimmune pathways, whilst Family 4 did not have any variants past the filtering steps. There were 10 variants of 7 genes reportedly associated with T1DM (MST1; TDG; TYRO3; IFIHI; GLIS3; VEGFA; TYK2). There were 20 variants of 13 genes that were linked to endocrine, metabolic, or autoimmune diseases. Our findings demonstrate that trio-based WES is a powerful approach for identifying new candidate genes for the pathogenesis of T1D. Genotyping and functional annotation of the discovered de novo variants in a large cohort is recommended to ascertain their association with disease pathogenesis.
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Affiliation(s)
- Mira Mousa
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Sara Albarguthi
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Mohammed Albreiki
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Zenab Farooq
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sameeha Sajid
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sarah El Hajj Chehadeh
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Gihan Daw ElBait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Guan Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Asma Al Deeb
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Department of Endocrinology, Mafraq Hospital, Abu Dhabi 127788, United Arab Emirates
| | - Habiba Alsafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Correspondence:
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17
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Yuan Y, Zhu Q, Yao X, Shi Z, Wen J. Maternal circulating metabolic biomarkers and their prediction performance for gestational diabetes mellitus related macrosomia. BMC Pregnancy Childbirth 2023; 23:113. [PMID: 36788507 PMCID: PMC9926775 DOI: 10.1186/s12884-023-05440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
INTRODUCTION Gestational diabetes mellitus (GDM), a metabolism-related pregnancy complication, is significantly associated with an increased risk of macrosomia. We hypothesized that maternal circulating metabolic biomarkers differed between women with GDM and macrosomia (GDM-M) and women with GDM and normal neonatal weight (GDM-N), and had good prediction performance for GDM-M. METHODS Plasma samples from 44 GDM-M and 44 GDM-N were analyzed using Olink Proseek multiplex metabolism assay targeting 92 biomarkers. Combined different clinical characteristics and Olink markers, LASSO regression was used to optimize variable selection, and Logistic regression was applied to build a predictive model. Nomogram was developed based on the selected variables visually. Receiver operating characteristic (ROC) curve, calibration plot, and clinical impact curve were used to validate the model. RESULTS We found 4 metabolism-related biomarkers differing between groups [CLUL1 (Clusterin-like protein 1), VCAN (Versican core protein), FCRL1 (Fc receptor-like protein 1), RNASE3 (Eosinophil cationic protein), FDR < 0.05]. Based on the different clinical characteristics and Olink markers, a total of nine predictors, namely pre-pregnancy body mass index (BMI), weight gain at 24 gestational weeks (gw), parity, oral glucose tolerance test (OGTT) 2 h glucose at 24 gw, high-density lipoprotein (HDL) and low-density lipoprotein (LDL) at 24 gw, and plasma expression of CLUL1, VCAN and RNASE3 at 24 gw, were identified by LASSO regression. The model constructed using these 9 predictors displayed good prediction performance for GDM-M, with an area under the ROC of 0.970 (sensitivity = 0.955, specificity = 0.886), and was well calibrated (P Hosmer-Lemeshow test = 0.897). CONCLUSION The Model included pre-pregnancy BMI, weight gain at 24 gw, parity, OGTT 2 h glucose at 24 gw, HDL and LDL at 24 gw, and plasma expression of CLUL1, VCAN and RNASE3 at 24 gw had good prediction performance for predicting macrosomia in women with GDM.
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Affiliation(s)
- Yingdi Yuan
- grid.460072.7Department of Pediatrics, The First People’s Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital of Lianyungang (Lianyungang Clinical College of Nanjing Medical University), Lianyungang, China ,grid.459791.70000 0004 1757 7869Nanjing Maternity and Child Health Care Institute, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qingyi Zhu
- grid.459791.70000 0004 1757 7869Nanjing Maternity and Child Health Care Institute, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China ,grid.459791.70000 0004 1757 7869Department of Obstetrics, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiaodie Yao
- grid.459791.70000 0004 1757 7869Nanjing Maternity and Child Health Care Institute, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhonghua Shi
- Department of Obstetrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
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18
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Khunsriraksakul C, Li Q, Markus H, Patrick MT, Sauteraud R, McGuire D, Wang X, Wang C, Wang L, Chen S, Shenoy G, Li B, Zhong X, Olsen NJ, Carrel L, Tsoi LC, Jiang B, Liu DJ. Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus. Nat Commun 2023; 14:668. [PMID: 36750564 PMCID: PMC9905560 DOI: 10.1038/s41467-023-36306-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Systemic lupus erythematosus is a heritable autoimmune disease that predominantly affects young women. To improve our understanding of genetic etiology, we conduct multi-ancestry and multi-trait meta-analysis of genome-wide association studies, encompassing 12 systemic lupus erythematosus cohorts from 3 different ancestries and 10 genetically correlated autoimmune diseases, and identify 16 novel loci. We also perform transcriptome-wide association studies, computational drug repurposing analysis, and cell type enrichment analysis. We discover putative drug classes, including a histone deacetylase inhibitor that could be repurposed to treat lupus. We also identify multiple cell types enriched with putative target genes, such as non-classical monocytes and B cells, which may be targeted for future therapeutics. Using this newly assembled result, we further construct polygenic risk score models and demonstrate that integrating polygenic risk score with clinical lab biomarkers improves the diagnostic accuracy of systemic lupus erythematosus using the Vanderbilt BioVU and Michigan Genomics Initiative biobanks.
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Affiliation(s)
- Chachrit Khunsriraksakul
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Qinmengge Li
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Havell Markus
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Daniel McGuire
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Chen Wang
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lida Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Siyuan Chen
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ganesh Shenoy
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Nancy J Olsen
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Dajiang J Liu
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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19
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Cook TW, Wilstermann AM, Mitchell JT, Arnold NE, Rajasekaran S, Bupp CP, Prokop JW. Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics. Biomolecules 2023; 13:257. [PMID: 36830626 PMCID: PMC9953665 DOI: 10.3390/biom13020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Insulin is amongst the human genome's most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS-IGF2. This INS-IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS-IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3'UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.
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Affiliation(s)
- Taylor W. Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jackson T. Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Nicholas E. Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
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20
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Meng Z, Ma Y, Li W, Deng X. Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study. PeerJ 2023; 11:e14595. [PMID: 36718446 PMCID: PMC9884046 DOI: 10.7717/peerj.14595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/28/2022] [Indexed: 01/26/2023] Open
Abstract
Background and Objective Epidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses. Methods A two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10-8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger. Results Inverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00-1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00-1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01-1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02-1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-GCST010776: P = 0.7660; ebi-a-GCST010777: P = 0.6017). Conclusions The findings suggests that periodontitis and the higher GCF IL-1β levels is causally related to increase susceptibility of COVID-19. However, given the limitations of our study, the well-designed randomized controlled trials are needed to confirm its findings, which may represent a new non-pharmaceutical intervention for preventing COVID-19.
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Affiliation(s)
- Zhaoqiang Meng
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yujia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, P. R. China
| | - Wenjing Li
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China,Peking University Health Science Center, Institute of Medical Technology, Beijing, P. R. China,Key Laboratory of Dental Material, National Medical Products Administration, Beijing, China
| | - Xuliang Deng
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China,Key Laboratory of Dental Material, National Medical Products Administration, Beijing, China
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21
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Seviiri M, Law MH, Ong JS, Gharahkhani P, Fontanillas P, Olsen CM, Whiteman DC, MacGregor S. A multi-phenotype analysis reveals 19 susceptibility loci for basal cell carcinoma and 15 for squamous cell carcinoma. Nat Commun 2022; 13:7650. [PMID: 36496446 PMCID: PMC9741635 DOI: 10.1038/s41467-022-35345-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Basal cell carcinoma and squamous cell carcinoma are the most common skin cancers, and have genetic overlap with melanoma, pigmentation traits, autoimmune diseases, and blood biochemistry biomarkers. In this multi-trait genetic analysis of over 300,000 participants from Europe, Australia and the United States, we reveal 78 risk loci for basal cell carcinoma (19 previously unknown and replicated) and 69 for squamous cell carcinoma (15 previously unknown and replicated). The previously unknown risk loci are implicated in cancer development and progression (e.g. CDKL1), pigmentation (e.g. TPCN2), cardiometabolic (e.g. FADS2), and immune-regulatory pathways for innate immunity (e.g. IFIH1), and HIV-1 viral load modulation (e.g. CCR5). We also report an optimised polygenic risk score for effective risk stratification for keratinocyte cancer in the Canadian Longitudinal Study of Aging (794 cases and 18139 controls), which could facilitate skin cancer surveillance e.g. in high risk subpopulations such as transplantees.
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Affiliation(s)
- Mathias Seviiri
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.
- Center for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Matthew H Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jue-Sheng Ong
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Puya Gharahkhani
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - David C Whiteman
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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22
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Williams CL, Fareed R, Mortimer GLM, Aitken RJ, Wilson IV, George G, Gillespie KM, Williams AJK, Long AE. The longitudinal loss of islet autoantibody responses from diagnosis of type 1 diabetes occurs progressively over follow-up and is determined by low autoantibody titres, early-onset, and genetic variants. Clin Exp Immunol 2022; 210:151-162. [PMID: 36181724 PMCID: PMC9750828 DOI: 10.1093/cei/uxac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/03/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2023] Open
Abstract
The clinical usefulness of post-diagnosis islet autoantibody levels is unclear and factors that drive autoantibody persistence are poorly defined in type 1 diabetes (T1D). Our aim was to characterise the longitudinal loss of islet autoantibody responses after diagnosis in a large, prospectively sampled UK cohort. Participants with T1D [n = 577] providing a diagnosis sample [range -1.0 to 2.0 years] and at least one post-diagnosis sample (<32.0 years) were tested for autoantibodies to glutamate decarboxylase 65 (GADA), islet antigen-2 (IA-2A), and zinc transporter 8 (ZnT8A). Select HLA and non-HLA SNPs were considered. Non-genetic and genetic factors were assessed by multivariable logistic regression models for autoantibody positivity at initial sampling and autoantibody loss at final sampling. For GADA, IA-2A, and ZnT8A, 70.8%, 76.8%, and 40.1%, respectively, remained positive at the final sampling. Non-genetic predictors of autoantibody loss were low baseline autoantibody titres (P < 0.0001), longer diabetes duration (P < 0.0001), and age-at-onset under 8 years (P < 0.01--0.05). Adjusting for non-genetic covariates, GADA loss was associated with low-risk HLA class II genotypes (P = 0.005), and SNPs associated with autoimmunity RELA/11q13 (P = 0.017), LPP/3q28 (P = 0.004), and negatively with IFIH1/2q24 (P = 0.018). IA-2A loss was not associated with genetic factors independent of other covariates, while ZnT8A loss was associated with the presence of HLA A*24 (P = 0.019) and weakly negatively with RELA/11q13 (P = 0.049). The largest longitudinal study of islet autoantibody responses from diagnosis of T1D shows that autoantibody loss is heterogeneous and influenced by low titres at onset, longer duration, earlier age-at-onset, and genetic variants. These data may inform clinical trials where post-diagnosis participants are recruited.
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Affiliation(s)
- C L Williams
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - R Fareed
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - G L M Mortimer
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - R J Aitken
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - I V Wilson
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - G George
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - K M Gillespie
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - A J K Williams
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - The BOX Study Group
BallavChitrabhanuDrBucks Healthcare Trust, UKDuttaAtanuDrBucks Healthcare Trust, UKRussell-TaylorMichelleDrBucks Healthcare Trust, UKBesserRachelDrOxford University Hospitals Trust UK, UKBursellJamesDrMilton Keynes University Hospital, UKChandranShanthiDrMilton Keynes University Hospital, UKPatelSejalDrWexham Park Hospital, UKSmithAnneDrNorthampton General Hospital, UKKenchaiahManoharaDrNorthampton General Hospital, UKMargabanthuGomathiDrKettering General Hospital, UKKavvouraFoteiniDrRoyal Berkshire Hospital, UKYaliwalChandanDrRoyal Berkshire Hospital, UK
| | - A E Long
- Correspondence: Dr Anna. E. Long. Diabetes and Metabolism, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK.
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23
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The relationship between GAD65 autoantibody and the risk of T1DM onset. J Diabetes Metab Disord 2022. [PMID: 36404832 PMCID: PMC9672278 DOI: 10.1007/s40200-022-01098-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objectives Type 1 diabetes mellitus (T1DM) is a well-known autoimmune disease, characterized by β-cell destruction in pancreas islet cells, which results insulin deficiency and subsequent hyperglycemic sequelae. While there is screening for type 2 DM that leads to better glycemic control and outcome, the majority of T1DM patients are diagnosed when much of the pancreatic cells and their function are disturbed. The aim of this article is to present an overview of the effective factors in the positivity of Glutamic acid decarboxylase antibody )GADA( and identifying the high-risk individuals for T1DM. Methods We searched English literature available at National Library of Medicine via PubMed, and Google Scholar through December 2020. Finally, 79 papers have been included in the study. Studies were summarized based on the number of positive autoantibodies and onset of T1DM over time and GADA correlation with different variables. Conclusions GADA is an easy marker to measure that can be detected many months prior to the clinical presentation and remains positive even after early childhood.
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24
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Ferjeni Z, Raouia F, Abida O, Penha-Gonçalves C, Masmoudi H. Association of IGHM polymorphisms with susceptibility to type 1 diabetes. Immunol Res 2022; 70:325-330. [PMID: 35048256 DOI: 10.1007/s12026-021-09252-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/04/2021] [Indexed: 01/15/2023]
Abstract
Differentiation of B lymphocytes is accompanied by a regulated switch in the expression pattern and stability of surface and secretory immunoglobulins (Igs). Several lines of evidence show that autoimmune responses evolving in much autoimmune pathologies were associated with a high level of humoral Ig, but their pathogenic role remains elusive. The aim of this study was to test the hypothesis that variants at the immunoglobulin heavy-chain IGH locus are genetic determinants to T1D susceptibility. Here, we tested the genetic association of the variants of the immunoglobulin heavy-chain IGH locus as a genetic determinant to T1D susceptibility. A total of 255 subjects from 59 Tunisian families were genotyped for 15 SNPs mapping in 4 regions in IGH locus. We found that rs1950942, rs2180790, rs1808152, and rs1956596 of IGHM and rs2516751 variant located in the IGHA1/IGHG2 region were significantly associated with a risk for T1D p = 7E-3; p = 0.03; p = 0.02; p = 0.043; and p = 3.65E-5, respectively. The TATGG haplotype derived from LD across three SNPs from IGHM gene and two SNPs from IGHD gene was significantly over-transmitted from parents to affect offspring. Our results suggest that genetic variants at the IGH locus are associated with T1D susceptibility. These variations may predispose to IgG AutoAbs production against pancreatic antigens and AutoAbs multi-reactivity, leading to T1D development.
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Affiliation(s)
- Zouidi Ferjeni
- Biology Department, Faculty of Arts and Sciences of Muhayil Aseer, King Khalid University, Abha, Saudi Arabia.
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia.
| | - Fakhfakh Raouia
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - O Abida
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | | | - H Masmoudi
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
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25
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Gootjes C, Zwaginga JJ, Roep BO, Nikolic T. Functional Impact of Risk Gene Variants on the Autoimmune Responses in Type 1 Diabetes. Front Immunol 2022; 13:886736. [PMID: 35603161 PMCID: PMC9114814 DOI: 10.3389/fimmu.2022.886736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that develops in the interplay between genetic and environmental factors. A majority of individuals who develop T1D have a HLA make up, that accounts for 50% of the genetic risk of disease. Besides these HLA haplotypes and the insulin region that importantly contribute to the heritable component, genome-wide association studies have identified many polymorphisms in over 60 non-HLA gene regions that also contribute to T1D susceptibility. Combining the risk genes in a score (T1D-GRS), significantly improved the prediction of disease progression in autoantibody positive individuals. Many of these minor-risk SNPs are associated with immune genes but how they influence the gene and protein expression and whether they cause functional changes on a cellular level remains a subject of investigation. A positive correlation between the genetic risk and the intensity of the peripheral autoimmune response was demonstrated both for HLA and non-HLA genetic risk variants. We also observed epigenetic and genetic modulation of several of these T1D susceptibility genes in dendritic cells (DCs) treated with vitamin D3 and dexamethasone to acquire tolerogenic properties as compared to immune activating DCs (mDC) illustrating the interaction between genes and environment that collectively determines risk for T1D. A notion that targeting such genes for therapeutic modulation could be compatible with correction of the impaired immune response, inspired us to review the current knowledge on the immune-related minor risk genes, their expression and function in immune cells, and how they may contribute to activation of autoreactive T cells, Treg function or β-cell apoptosis, thus contributing to development of the autoimmune disease.
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Affiliation(s)
- Chelsea Gootjes
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Jaap Jan Zwaginga
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Bart O Roep
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Tatjana Nikolic
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
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26
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Genetic Variants Associated with Neuropeptide Y Autoantibody Levels in Newly Diagnosed Individuals with Type 1 Diabetes. Genes (Basel) 2022; 13:genes13050869. [PMID: 35627254 PMCID: PMC9142038 DOI: 10.3390/genes13050869] [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: 03/10/2022] [Revised: 04/30/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
(1) Autoantibodies to the leucine variant of neuropeptide Y (NPY-LA) have been found in individuals with type 1 diabetes (T1D). We investigated the association between the levels of NPY-LA and single nucleotide polymorphisms (SNP) to better understand the genetic regulatory mechanisms of autoimmunity in T1D and the functional impacts of increased NPY-LA levels. (2) NPY-LA measurements from serum and SNP genotyping were done on 560 newly diagnosed individuals with T1D. SNP imputation with the 1000 Genomes reference panel was followed by an association analysis between the SNPs and measured NPY-LA levels. Additionally, functional enrichment and pathway analyses were done. (3) Three loci (DGKH, DCAF5, and LINC02261) were associated with NPY-LA levels (p-value < 1.5 × 10−6), which indicates an association with neurologic and vascular disorders. SNPs associated with variations in expression levels were found in six genes (including DCAF5). The pathway analysis showed that NPY-LA was associated with changes in gene transcription, protein modification, immunological functions, and the MAPK pathway. (4) Conclusively, we found NPY-LA to be significantly associated with three loci (DGKH, DCAF5, and LINC02261), and based on our findings we hypothesize that the presence of NPY-LA is associated with the regulation of the immune system and possibly neurologic and vascular disorders.
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27
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Qu HQ, Qu J, Glessner J, Liu Y, Mentch F, Chang X, March M, Li J, Roizen JD, Connolly JJ, Sleiman P, Hakonarson H. Improved genetic risk scoring algorithm for type 1 diabetes prediction. Pediatr Diabetes 2022; 23:320-323. [PMID: 34997821 PMCID: PMC8983464 DOI: 10.1111/pedi.13310] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Precise risk prediction of type 1 diabetes (T1D) facilitates early intervention and identification of risk factors prior to irreversible beta-islet cell destruction, and can significantly improve T1D prevention and clinical care. Sharp et al. developed a genetic risk scoring (GRS) system for T1D (T1D-GRS2) capable of predicting T1D risk in children of European ancestry. The T1D-GRS2 was developed on the basis of causal genetic variants, thus may be applicable to minor populations, while a trans-ethnic GRS for T1D may avoid the exacerbation of health disparities due to the lack of genomic information in minorities. METHODS Here, we describe a T1D-GRS2 calculator validated in two independent cohorts, including African American children and European American children. Participants were recruited by the Center for Applied Genomics at the Children's Hospital of Philadelphia. RESULTS It demonstrates that GRS2 is applicable to the T1D risk prediction in the AA cohort, while population-specific thresholds are needed for different populations. CONCLUSIONS The study highlights the potential to further improve T1D-GRS2 performance with the inclusion of additional genetic markers.
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Affiliation(s)
- Hui-Qi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Jingchun Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joseph Glessner
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Yichuan Liu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Xiao Chang
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Michael March
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Jin Li
- Department of Cell Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Jeffrey D Roizen
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - John J Connolly
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Patrick Sleiman
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA., Corresponding author and reprint requests should be addressed to: Dr. Hakon Hakonarson, Center for Applied Genomics, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104, United States of America, Telephone: 267-426-0088, Fax: 267-426-0363,
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Verma A, Tsao NL, Thomann LO, Ho YL, Iyengar SK, Luoh SW, Carr R, Crawford DC, Efird JT, Huffman JE, Hung A, Ivey KL, Levin MG, Lynch J, Natarajan P, Pyarajan S, Bick AG, Costa L, Genovese G, Hauger R, Madduri R, Pathak GA, Polimanti R, Voight B, Vujkovic M, Zekavat SM, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O’Donnell C, Damrauer SM, Liao KP. A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program. PLoS Genet 2022; 18:e1010113. [PMID: 35482673 PMCID: PMC9049369 DOI: 10.1371/journal.pgen.1010113] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/20/2022] [Indexed: 12/14/2022] Open
Abstract
The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n = 35) or hospitalization (n = 42) due to severe COVID-19 using genome-wide association summary data from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828 = 53 and nrs505922 = 59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p = 1.32 x 10-199), and thrombosis ORrs505922 1.33, p = 2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p = 4.12 × 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p = 2.26× 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p = 6.48 x10-23, lupus OR 0.84, p = 3.97 x 10-06. PheWAS stratified by ancestry demonstrated differences in genotype-phenotype associations. LMNA (rs581342) associated with neutropenia OR 1.29 p = 4.1 x 10-13 among Veterans of African and Hispanic ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.
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Affiliation(s)
- Anurag Verma
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Noah L. Tsao
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lauren O. Thomann
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Sudha K. Iyengar
- Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, Oregon, United States of America
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Rotonya Carr
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- University of Washington, Division of Gastroenterology, Seattle, Washington, United States of America
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jimmy T. Efird
- Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, United States of America
| | - Jennifer E. Huffman
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Adriana Hung
- Tennessee Valley Healthcare System (Nashville VA) & Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kerry L. Ivey
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- South Australian Health and Medical Research Institute, Infection and Immunity Theme, Adelaide, South Australia, Australia
- Harvard T.H. Chan School of Public Health, Department of Nutrition, Cambridge, Massachusetts, United States of America
| | - Michael G. Levin
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, United States of America
| | - Pradeep Natarajan
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexander G. Bick
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lauren Costa
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Giulio Genovese
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Hauger
- Department of Psychiatry, University of California, San Diego, La Jolla, California; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, California, United States of America
| | - Ravi Madduri
- University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, United States of America
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Gita A. Pathak
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Benjamin Voight
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marijana Vujkovic
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Seyedeh Maryam Zekavat
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- Yale School of Medicine New Haven, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Yale School of Medicine New Haven, New Haven, Connecticut, United States of America
- Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
| | - Juan P. Casas
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Philip S. Tsao
- VA Palo Alto Health Care System, Palo Alto, California, United States of America
- Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, California, United States of America
| | - J. Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Christopher O’Donnell
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Scott M. Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katherine P. Liao
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
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Dai H, Qian Y, Lv H, Jiang L, Jiang H, Shen M, Chen H, Chen Y, Zheng S, Fu Q, Yang T, Xu K. Rs864745 in JAZF1, an Islet Function Associated Variant, Correlates With Plasma Lipid Levels in Both Type 1 and Type 2 Diabetes Status, but Not Healthy Subjects. Front Endocrinol (Lausanne) 2022; 13:898893. [PMID: 35846288 PMCID: PMC9283698 DOI: 10.3389/fendo.2022.898893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE This study aims to reveal the association between JAZF1 rs864745 A>G variant and type 2 diabetes (T2D), type 1 diabetes (T1D) risk, and their correlation with clinical features, including islet function, islet autoimmunity, and plasma lipid levels. METHODS We included 2505 healthy controls based on oral glucose tolerance test (OGTT), 1736 unrelated T2D, and 1003 unrelated autoantibody-positive T1D individuals. Binary logistic regression was performed to evaluate the relationships between rs864745 in JAZF1 and T2D, T1D, and islet-specific autoantibody status under the additive model, while multiple linear regression was used to assess its effect on glycemic-related quantitative traits and plasma lipid levels. RESULTS We did not find any association between rs864745 in JAZF1 and T2D, T1D, or their subgroups (All P > 0.05). For glycemic traits, we found that the G allele of this variant was significantly associated with higher 120 min insulin level, insulinogenic index (IGI), corrected insulin response (CIR), and acute insulin response (BIGTT-AIR) (P = 0.033, 0.006, 0.009, and 0.016, respectively) in healthy individuals. Similar associations were observed in newly diagnosed T2D but not T1D individuals. Although this variant had no impact on islet autoimmunity (All P > 0.05), significant associations with plasma total cholesterol (TC) and low-density lipoprotein (LDL) level stratified by JAZF1 rs864745 variant were observed in the disease status of T2D (P = 0.002 and 0.003) and T1D (P = 0.024 and 0.009), with significant heterogeneity to healthy individuals. CONCLUSIONS The common JAZF1 rs864745 variant contributes to islet function and lipid metabolism, which might be put into genetic risk scores to assess the risk of related clinical features.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Tao Yang
- *Correspondence: Tao Yang, ; Kuanfeng Xu,
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30
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Chen Y, Shen M, Ji C, Huang Y, Shi Y, Ji L, Qin Y, Gu Y, Fu Q, Chen H, Xu K, Yang T. Genome-Wide Identification of N6-Methyladenosine Associated SNPs as Potential Functional Variants for Type 1 Diabetes. Front Endocrinol (Lausanne) 2022; 13:913345. [PMID: 35784577 PMCID: PMC9243540 DOI: 10.3389/fendo.2022.913345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES N6-methyladenosine (m6A) is essential in the regulation of the immune system, but the role that its single nucleotide polymorphisms (SNPs) play in the pathogenesis of type 1 diabetes (T1D) remains unknown. This study demonstrated the association between genetic variants in m6A regulators and T1D risk based on a case-control study in a Chinese population. METHODS The tagging SNPs in m6A regulators were genotyped in 1005 autoantibody-positive patients with T1D and 1257 controls using the Illumina Human OmniZhongHua-8 platform. Islet-specific autoantibodies were examined by radioimmunoprecipitation in all the patients. The mixed-meal glucose tolerance test was performed on 355 newly diagnosed patients to evaluate their residual islet function. The functional annotations for the identified SNPs were performed in silico. Using 102 samples from a whole-genome expression microarray, key signaling pathways associated with m6A regulators in T1D were comprehendingly evaluated. RESULTS Under the additive model, we observed three tag SNPs in the noncoding region of the PRRC2A (rs2260051, rs3130623) and YTHDC2 (rs1862315) gene are associated with T1D risk. Although no association was found between these SNPs and islet function, patients carrying risk variants had a higher positive rate for ZnT8A, GADA, and IA-2A. Further analyses showed that rs2260051[T] was associated with increased expression of PRRC2A mRNA (P = 7.0E-13), and PRRC2A mRNA was significantly higher in peripheral blood mononuclear cell samples from patients with T1D compared to normal samples (P = 0.022). Enrichment analyses indicated that increased PRRC2A expression engages in the most significant hallmarks of cytokine-cytokine receptor interaction, cell adhesion and chemotaxis, and neurotransmitter regulation pathways. The potential role of increased PRRC2A in disrupting immune homeostasis is through the PI3K/AKT pathway and neuro-immune interactions. CONCLUSION This study found intronic variants in PRRC2A and YTHDC2 associated with T1D risk in a Chinese Han population. PRRC2A rs2260051[T] may be implicated in unbalanced immune homeostasis by affecting the expression of PRRC2A mRNA. These findings enriched our understanding of m6A regulators and their intronic SNPs that underlie the pathogenesis of T1D.
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Affiliation(s)
- Yang Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Shen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen Ji
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yanqian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun Shi
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Ji
- Department of Emergency Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Qin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Gu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Fu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuanfeng Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Yang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Tao Yang,
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Qi YY, Zhao XY, Liu XR, Wang YN, Zhai YL, Zhang XX, Wang XY, Zhang LJ, Zhao YF, Cui Y, Ning XH, Zhou XJ. Lupus susceptibility region containing CTLA4 rs17268364 functionally reduces CTLA4 expression by binding EWSR1 and correlates IFN-α signature. Arthritis Res Ther 2021; 23:279. [PMID: 34736521 PMCID: PMC8567630 DOI: 10.1186/s13075-021-02664-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Dysregulation of T cells mediated immune responses is a hallmark in the development of systemic lupus erythematosus (SLE). Recent genome wide association study (GWAS) revealed the genetic contribution of variants located in the cytotoxic T lymphocyte-associated protein-4 (CTLA4)-inducible T cell co-stimulator (ICOS) intergenic region to SLE susceptibility. Our aim is to find a functional variant in this region. Methods The genetic association results in the CTLA4-ICOS region from previous GWAS were adopted to select the potential variant which was further replicated in two independent cohorts (Henan cohort 2053 SLE patients and 1845 healthy controls, Beijing cohort 2303 SLE patients and 19,262 healthy). In order to explore the functional significance in SLE, bioinformatics with validation experiments (including electrophoretic mobility shift assay and luciferase reporter assay) and mRNA expression analysis were also performed. Results A variant located in the CTLA4-ICOS intergenic region, rs17268364, was associated with susceptibility to SLE patients in Chinese populations (risk allele, pmeta = 7.02×10−11, OR 1.19, 95%CI 1.13–1.26). The bioinformatics suggested that rs17268364 might affect the expression of CTLA4, not ICOS. The rs17268364 risk G allele containing sequence reduced the expression of the reporter gene by binding transcriptional repressor Ewing sarcoma breakpoint region 1 (EWSR1). Following genotype-mRNA expression, the analysis also showed the risk allele of rs17268364 was associated with low CTLA4 expression in lupus nephritis (LN) patients. Healthy individuals carrying rs17268364 risk G allele was significantly correlated with higher levels of IFN-α signature including increased lymphocyte antigen 6E (LY6E) (p=0.031), interferon-stimulated gene 15 (ISG15) (p=0.038), interferon regulatory factor 9 (IRF9) (p=0.028), and interferon regulatory factor 5 (IRF5) (p=0.040) mRNA expression. Conclusions The present study confirmed the functional role of rs17268364 in the CTLA4-ICOS intergenic region that increased SLE susceptibility in the Chinese population. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02664-y.
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Affiliation(s)
- Yuan-Yuan Qi
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China. .,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.
| | - Xin-Yu Zhao
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xin-Ran Liu
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Yan-Na Wang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Ya-Ling Zhai
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiao-Xue Zhang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiao-Yang Wang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Li-Jie Zhang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Ya-Fei Zhao
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Yan Cui
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiang-Hui Ning
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 4500052, Henan, China
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China. .,Key Laboratory of Renal Disease, Ministry of Health of China, No.8 Xi Shi Ku Street, Xi Cheng District, Beijing, 100034, China. .,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, No.8 Xi Shi Ku Street, Xi Cheng District, Beijing, 100034, China.
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Verma A, Tsao N, Thomann L, Ho YL, Iyengar S, Luoh SW, Carr R, Crawford D, Efird JT, Huffman J, Hung A, Ivey K, Levin M, Lynch J, Natarajan P, Pyarajan S, Bick A, Costa L, Genovese G, Hauger R, Madduri R, Pathak G, Polimanti R, Voight B, Vujkovic M, Zekavat M, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O'Donnell C, Damrauer S, Liao K. A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34642702 PMCID: PMC8509103 DOI: 10.1101/2021.05.18.21257396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828=53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 × 10-199), and thrombosis ORrs505922 1.33, p=2.2 × 10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 × 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26 × 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 × 10-23, lupus OR 0.84, p=3.97 × 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 × 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.
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Affiliation(s)
- Anurag Verma
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Noah Tsao
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Yuk-Lam Ho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Sudha Iyengar
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland OR, USA.,Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rotonya Carr
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,University of Washington, Division of Gastroenterology Seattle, WA USA
| | - Dana Crawford
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jimmy T Efird
- Cardiovascular Medicine Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Adriana Hung
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA.,Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA
| | - Kerry Ivey
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Tennessee Valley Healthcare System (Nashville VA) & Vanderbilt University, Nashville, Tennessee, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Michael Levin
- VA Portland Health Care System, Portland OR, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Julie Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA
| | - Pradeep Natarajan
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, USA
| | - Saiju Pyarajan
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Alexander Bick
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Vanderbilt University, Nashville, Tennessee, USA
| | - Lauren Costa
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Richard Hauger
- Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, USA
| | - Ravi Madduri
- University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA.,Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois
| | - Gita Pathak
- VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, Connecticut, USA
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Psychiatry, Yale School of Medicine, Connecticut, USA
| | - Benjamin Voight
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marijana Vujkovic
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maryam Zekavat
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Broad Institute of MIT & Harvard, Cambridge, MA, USA.,Yale School of Medicine New Haven, CT, USA
| | - Hongyu Zhao
- VA Connecticut Healthcare System, West Haven, CT, USA.,Yale School of Medicine New Haven, CT, USA.,Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | | | | | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Juan P Casas
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, California, USA.,Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Christopher O'Donnell
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA.,Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katherine Liao
- VA Boston Healthcare System, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Boston, Massachusetts, USA
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33
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Fichna M, Żurawek M, Słomiński B, Sumińska M, Czarnywojtek A, Rozwadowska N, Fichna P, Myśliwiec M, Ruchała M. Polymorphism in BACH2 gene is a marker of polyglandular autoimmunity. Endocrine 2021; 74:72-79. [PMID: 33966174 PMCID: PMC8440266 DOI: 10.1007/s12020-021-02743-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 11/06/2022]
Abstract
PURPOSE Genetically predisposed individuals may develop several autoimmune diseases-autoimmune polyendocrine syndromes (APS). APS types 2-4, are complex disorders, which combine various organ-specific autoimmune conditions. Recent reports support the considerable role of the BACH2 gene in immune cell differentiation and shifting the T-cell balance towards regulatory T-cells. BACH2 polymorphisms are associated with autoimmune disorders, including Addison's disease (AD), Graves' disease (GD), and probably type 1 diabetes (T1D). Our study was aimed to investigate the BACH2 variant, rs3757247, in endocrine autoimmunity in the Polish population. METHODS The analysis comprised 346 individuals with APS, 387 with T1D only, and 568 controls. Genotyping was performed using TaqMan chemistry. RESULTS APS type 2 was found in 219 individuals, type 3 in 102, and type 4 in 25 subjects. Overall, AD was diagnosed in 244 subjects, Hashimoto's thyroiditis-in 238, T1D-in 127, GD-in 58, vitiligo and chronic gastritis each in 40 patients, celiac disease-in 28, premature menopause in 18, and alopecia in 4 patients. Minor T allele at rs3757247 was found in 56.4% APS vs. 44.1% control alleles (OR 1.59; 95%CI: 1.30-1.95, p < 0.0001). The distribution of genotypes revealed excess TT homozygotes in the APS cohort (33.2 vs. 20.1% in controls, p < 0.0001). The frequencies of rs3757247 alleles and genotypes in T1D patients did not present significant differences vs. controls (p-values > 0.05). CONCLUSIONS These results provide evidence of the association between BACH2 polymorphism and polyglandular autoimmunity. Since carriers of rs3757247 display increased risk for additional autoimmune conditions, this variant could identify individuals prone to develop APS.
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Affiliation(s)
- Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland.
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Bartosz Słomiński
- Department of Medical Immunology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Marta Sumińska
- Department of Paediatric Diabetes and Obesity, Poznan University of Medical Sciences, Poznan, Poland
| | - Agata Czarnywojtek
- Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Piotr Fichna
- Department of Paediatric Diabetes and Obesity, Poznan University of Medical Sciences, Poznan, Poland
| | - Małgorzata Myśliwiec
- Department of Paediatrics, Diabetology and Endocrinology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
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Qu J, Qu HQ, Bradfield JP, Glessner JT, Chang X, Tian L, March M, Connolly JJ, Roizen JD, Sleiman PMA, Hakonarson H. Insights into non-autoimmune type 1 diabetes with 13 novel loci in low polygenic risk score patients. Sci Rep 2021; 11:16013. [PMID: 34362956 PMCID: PMC8346538 DOI: 10.1038/s41598-021-94994-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 01/21/2023] Open
Abstract
With polygenic risk score (PRS) for autoimmune type 1 diabetes (T1D), this study identified T1D cases with low T1D PRS and searched for susceptibility loci in these cases. Our hypothesis is that genetic effects (likely mediated by relatively rare genetic variants) of non-mainstream (or non-autoimmune) T1D might have been diluted in the previous studies on T1D cases in general. Two cohorts for the PRS modeling and testing respectively were included. The first cohort consisted of 3302 T1D cases and 6181 controls, and the independent second cohort consisted of 3297 T1D cases and 6169 controls. Cases with low T1D PRS were identified using PRSice-2 and compared to controls with low T1D PRS by genome-wide association (GWA) test. Thirteen novel genetic loci with high imputation quality (Quality Score r2 > 0.91) were identified of SNPs/SNVs associated with low PRS T1D at genome-wide significance (P ≤ 5.0 × E-08), in addition to 4 established T1D loci, 3 reported loci by our previous study, as well as 9 potential novel loci represented by rare SNVs, but with relatively low imputation quality (Quality Score r2 < 0.90). For the 13 novel loci, 9 regions have been reported of association with obesity related traits by previous GWA studies. Three loci encoding long intergenic non-protein coding RNAs (lncRNA), and 2 loci involved in N-linked glycosylation are also highlighted in this study.
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Affiliation(s)
- Jingchun Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Hui-Qi Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | | | - Joseph T. Glessner
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Xiao Chang
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Lifeng Tian
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Michael March
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - John J. Connolly
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Jeffrey D. Roizen
- grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Patrick M. A. Sleiman
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Hakon Hakonarson
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
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35
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Laisk T, Lepamets M, Koel M, Abner E, Mägi R. Genome-wide association study identifies five risk loci for pernicious anemia. Nat Commun 2021; 12:3761. [PMID: 34145262 PMCID: PMC8213695 DOI: 10.1038/s41467-021-24051-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
Pernicious anemia is a rare condition characterized by vitamin B12 deficiency anemia due to lack of intrinsic factor, often caused by autoimmune gastritis. Patients with pernicious anemia have a higher incidence of other autoimmune disorders, such as type 1 diabetes, vitiligo, and autoimmune thyroid issues. Therefore, the disease has a clear autoimmune basis, although the genetic susceptibility factors have thus far remained poorly studied. We conduct a genome-wide association study meta-analysis in 2166 cases and 659,516 European controls from population-based biobanks and identify genome-wide significant signals in or near the PTPN22 (rs6679677, p = 1.91 × 10-24, OR = 1.63), PNPT1 (rs12616502, p = 3.14 × 10-8, OR = 1.70), HLA-DQB1 (rs28414666, p = 1.40 × 10-16, OR = 1.38), IL2RA (rs2476491, p = 1.90 × 10-8, OR = 1.22) and AIRE (rs74203920, p = 2.33 × 10-9, OR = 1.83) genes, thus providing robust associations between pernicious anemia and genetic risk factors.
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Affiliation(s)
- Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mariann Koel
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Erik Abner
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
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36
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Armitage LH, Wallet MA, Mathews CE. Influence of PTPN22 Allotypes on Innate and Adaptive Immune Function in Health and Disease. Front Immunol 2021; 12:636618. [PMID: 33717184 PMCID: PMC7946861 DOI: 10.3389/fimmu.2021.636618] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Protein tyrosine phosphatase, non-receptor type 22 (PTPN22) regulates a panoply of leukocyte signaling pathways. A single nucleotide polymorphism (SNP) in PTPN22, rs2476601, is associated with increased risk of Type 1 Diabetes (T1D) and other autoimmune diseases. Over the past decade PTPN22 has been studied intensely in T cell receptor (TCR) and B cell receptor (BCR) signaling. However, the effect of the minor allele on PTPN22 function in TCR signaling is controversial with some reports concluding it has enhanced function and blunts TCR signaling and others reporting it has reduced function and increases TCR signaling. More recently, the core function of PTPN22 as well as functional derangements imparted by the autoimmunity-associated variant allele of PTPN22 have been examined in monocytes, macrophages, dendritic cells, and neutrophils. In this review we will discuss the known functions of PTPN22 in human cells, and we will elaborate on how autoimmunity-associated variants influence these functions across the panoply of immune cells that express PTPN22. Further, we consider currently unresolved questions that require clarification on the role of PTPN22 in immune cell function.
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Affiliation(s)
- Lucas H. Armitage
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Mark A. Wallet
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
- Immuno-Oncology at Century Therapeutics, LLC, Philadelphia, PA, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
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37
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Type 1 diabetes: genes associated with disease development. Cent Eur J Immunol 2021; 45:439-453. [PMID: 33658892 PMCID: PMC7882399 DOI: 10.5114/ceji.2020.103386] [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: 03/27/2019] [Accepted: 01/02/2020] [Indexed: 11/17/2022] Open
Abstract
Type 1 diabetes (T1D) is the third most common autoimmune disease which develops due to genetic and environmental risk factors. Based on the World Health Organization (WHO) report from 2014 the number of people suffering from all types of diabetes ascended to 422 million, compared to 108 million in 1980. It was calculated that this number will double by the end of 2030. In 2015 American Diabetes Association (ADA) announced that 30.3 million Americans (that is 9.4% of the overall population) had diabetes of which only approximately 1.25 million had T1D. Nowadays, T1D represents roughly 10% of adult diabetes cases total. Multiple genetic abnormalities at different loci have been found to contribute to type 1 diabetes development. The analysis of genome-wide association studies (GWAS) of T1D has identified over 50 susceptible regions (and genes within these regions). Many of these regions are defined by single nucleotide polymorphisms (SNPs) but molecular mechanisms through which they increase or lower the risk of diabetes remain unknown. Genetic factors (in existence since birth) can be detected long before the emergence of immunological or clinical markers. Therefore, a comprehensive understanding of the multiple genetic factors underlying T1D is extremely important for further clinical trials and development of personalized medicine for diabetic patients. We present an overview of current studies and information about regions in the human genome associated with T1D. Moreover, we also put forward information about epigenetic modifications, non-coding RNAs and environmental factors involved in T1D development and onset.
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38
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Giampaoli O, Conta G, Calvani R, Miccheli A. Can the FUT2 Non-secretor Phenotype Associated With Gut Microbiota Increase the Children Susceptibility for Type 1 Diabetes? A Mini Review. Front Nutr 2020; 7:606171. [PMID: 33425974 PMCID: PMC7785815 DOI: 10.3389/fnut.2020.606171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
The global toll of type 1 diabetes (T1D) has steadily increased over the last decades. It is now widely acknowledged that T1D pathophysiology is more complex than expected. Indeed, a multifaceted interplay between genetic, metabolic, inflammatory and environmental factors exists that leads to heterogeneous clinical manifestations across individuals. Children with non-secretor phenotype and those affected by T1D share low abundance of bifidobacteria, low content of short-chain fatty acids, intestinal phosphatase alkaline and a high incidence of inflammatory bowel diseases. In this context, host-gut microbiota dyad may represent a relevant contributor to T1D development and progression due to its crucial role in shaping host immunity and susceptibility to autoimmune conditions. The FUT2 gene is responsible for the composition and functional properties of glycans in mucosal tissues and bodily secretions, including human milk. FUT2 polymorphisms may profoundly influence gut microbiota composition and host susceptibility to viral infections and chronic inflammatory disease. In this minireview, the possible interplay between mothers' phenotype, host FUT2 genetic background and gut microbiota composition will be discussed in perspective of the T1D onset. The study of FUT2-gut microbiota interaction may add a new piece on the puzzling T1D etiology and unveil novel targets of intervention to contrast T1D development and progression. Dietary interventions, including the intake of α-(1, 2)-fucosyl oligosaccharides in formula milk and the use of specific prebiotics and probiotics, could be hypothesized.
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Affiliation(s)
- Ottavia Giampaoli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Giorgia Conta
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Riccardo Calvani
- Fondazione Policlinico Universitario 'Agostino Gemelli' IRCCS, Rome, Italy
| | - Alfredo Miccheli
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy.,Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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39
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Gurlin RE, Giraldo JA, Latres E. 3D Bioprinting and Translation of Beta Cell Replacement Therapies for Type 1 Diabetes. TISSUE ENGINEERING PART B-REVIEWS 2020; 27:238-252. [PMID: 32907514 DOI: 10.1089/ten.teb.2020.0192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disorder in which the body's own immune system selectively attacks beta cells within pancreatic islets resulting in insufficient insulin production and loss of the ability to regulate blood glucose (BG) levels. Currently, the standard of care consists of BG level monitoring and insulin administration, which are essential to avoid the consequences of dysglycemia and long-term complications. Although recent advances in continuous glucose monitoring and automated insulin delivery systems have resulted in improved clinical outcomes for users, nearly 80% of people with T1D fail to achieve their target hemoglobin A1c (HbA1c) levels defined by the American Diabetes Association. Intraportal islet transplantation into immunosuppressed individuals with T1D suffering from impaired awareness of hypoglycemia has resulted in lower HbA1c, elimination of severe hypoglycemic events, and insulin independence, demonstrating the unique potential of beta cell replacement therapy (BCRT) in providing optimal glycemic control and a functional cure for T1D. BCRTs need to maximize cell engraftment, long-term survival, and function in the absence of immunosuppression to provide meaningful clinical outcomes to all people living with T1D. One innovative technology that could enable widespread translation of this approach into the clinic is three-dimensional (3D) bioprinting. Herein, we review how bioprinting could facilitate translation of BCRTs as well as the current and forthcoming techniques used for bioprinting of a BCRT product. We discuss the strengths and weaknesses of 3D bioprinting in this context in addition to the road ahead for the development of BCRTs. Impact statement Significant research developments in beta cell replacement therapies show its promise in providing a functional cure for type 1 diabetes (T1D); yet, their widespread clinical use has been difficult to achieve. This review provides a brief overview of the requirements for a beta cell replacement product followed by a discussion on both the promise and limitations of three-dimensional bioprinting in facilitating the fabrication of such products to enable translation into the clinic. Advancements in this area could be a key component to unlocking the safety and effectiveness of beta cell therapy for T1D.
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Affiliation(s)
- Rachel E Gurlin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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Timasheva YR, Nasibullin TR, Tuktarova IA, Erdman VV, Galiullin TR, Zaplakhova OV, Bakhtiiarova KZ, Mustafina OE. [The analysis of association between multiple sclerosis and genetic markers identified in genome-wide association studies]. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:54-60. [PMID: 32844631 DOI: 10.17116/jnevro202012007254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Our aim was to analyse the association with multiple sclerosis of the genetic markers of autoimmune disorders identified in genome-wide association studies in ethnically homogenous groups of Russians and Tatars residing in the Republic of Bashkortostan. MATERIAL AND METHODS We performed genotyping of the genetic variants rs2069762 in IL2 gene, rs759648 in PVT1 gene, rs1800682 in FAS gene and rs12708716 in CLEC16A gene in the study group consisting of 1724 people (547 patients with multiple sclerosis, 1177 representatives of the control group). We analysed the association of the studied genetic markers with multiple sclerosis using logistic regression under additive genetic model implemented in PLINK program with sex a covariate. RESULTS In the group of Tatars, we detected an association of PVT1 rs759648*Callele with multiple sclerosis (OR=1.42, p=0,023). Meta-analysis of the study results in the two ethnic groups we confirmed the association of the PVT1 rs759648*C allele with the disease (random effects model and fixed effect model: OR=1.29, p=0,018). CONCLUSION Our results provide an evidence of an association between multiple sclerosis and the PVT1 rs759648 allele in the populations of Russian and Tatars from the Republic of Bashkortostan. No association with any other studied polymorphic variant was found in the two ethnic groups.
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Affiliation(s)
- Y R Timasheva
- Institute of Biochemistry and Genetics of Ufa Federal Research Centre of Russian Academy of Sciences, Ufa, Russia.,Bashkir State Medical University, Ufa, Russia
| | - T R Nasibullin
- Institute of Biochemistry and Genetics of Ufa Federal Research Centre of Russian Academy of Sciences, Ufa, Russia
| | - I A Tuktarova
- Institute of Biochemistry and Genetics of Ufa Federal Research Centre of Russian Academy of Sciences, Ufa, Russia
| | - V V Erdman
- Institute of Biochemistry and Genetics of Ufa Federal Research Centre of Russian Academy of Sciences, Ufa, Russia
| | - T R Galiullin
- G.G. Kuvatov Republic Clinical Hospital, Ufa, Russia
| | | | | | - O E Mustafina
- Institute of Biochemistry and Genetics of Ufa Federal Research Centre of Russian Academy of Sciences, Ufa, Russia
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Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways. J Allergy Clin Immunol 2020; 147:894-909. [PMID: 32795586 DOI: 10.1016/j.jaci.2020.07.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Chr17q12-21.2 region is the strongest and most consistently associated region with asthma susceptibility. The functional genes or single nucleotide polymorphisms (SNPs) are not obvious due to linkage disequilibrium. OBJECTIVES We sought to comprehensively investigate whole-genome sequence and RNA sequence from human bronchial epithelial cells to dissect functional genes/SNPs for asthma severity in the Severe Asthma Research Program. METHODS Expression quantitative trait loci analysis (n = 114), correlation analysis (n = 156) of gene expression and asthma phenotypes, and pathway analysis were performed in bronchial epithelial cells and replicated. Genetic association for asthma severity (426 severe vs 531 nonsevere asthma) and longitudinal asthma exacerbations (n = 273) was performed. RESULTS Multiple SNPs in gasdermin B (GSDMB) associated with asthma severity (odds ratio, >1.25) and longitudinal asthma exacerbations (P < .05). Expression quantitative trait loci analyses identified multiple SNPs associated with expression levels of post-GPI attachment to proteins 3, GSDMB, or gasdermin A (3.1 × 10-9 <P < 1.8 × 10-4). Higher expression levels of GSDMB correlated with asthma and greater number of exacerbations (P < .05). Expression levels of GSDMB correlated with genes involved in IFN signaling, MHC class I antigen presentation, and immune system pathways (false-discovery rate-adjusted P < .05). rs1031458 and rs3902920 in GSDMB colocalized with IFN regulatory factor binding sites and associated with GSDMB expression, asthma severity, and asthma exacerbations (P < .05). CONCLUSIONS By using a unique set of gene expression data from lung cells obtained using bronchoscopy from comprehensively characterized subjects with asthma, we show that SNPs in GSDMB associated with asthma severity, exacerbations, and GSDMB expression levels. Furthermore, its expression levels correlated with asthma exacerbations and antiviral pathways. Thus, GSDMB is a functional gene for both asthma susceptibility and severity.
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Myers DR, Norlin E, Vercoulen Y, Roose JP. Active Tonic mTORC1 Signals Shape Baseline Translation in Naive T Cells. Cell Rep 2020; 27:1858-1874.e6. [PMID: 31067469 PMCID: PMC6593126 DOI: 10.1016/j.celrep.2019.04.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Naive CD4+ T cells are an example of dynamic cell homeostasis: T cells need to avoid autoreactivity while constantly seeing self-peptides, yet they must be primed to react to foreign antigens during infection. The instructive signals that balance this primed yet quiescent state are unknown. Interactions with self-peptides result in membrane-proximal, tonic signals in resting T cells. Here we reveal selective and robust tonic mTORC1 signals in CD4+ T cells that influence T cell fate decisions. We find that the Ras exchange factor Rasgrp1 is necessary to generate tonic mTORC1 signals. Genome-wide ribosome profiling of resting, primary CD4+ T cells uncovers a baseline translational landscape rich in mTOR targets linked to mitochondria, oxidative phosphorylation, and splicing. Aberrantly increased tonic mTORC1 signals from a Rasgrp1Anaef allele result in immunopathology with spontaneous appearance of T peripheral helper cells, follicular helper T cells, and anti-nuclear antibodies that are preceded by subtle alterations in the translational landscape. Myers et al. evaluate a mouse model of autoimmunity, Rasgrp1Anaef. They find that T cells with the Rasgrp1Anaef allele exhibit altered signaling from Rasgrp1 to the mTORC1 pathway in the basal state. They show that increased basal Rasgrp1Anaef-mTORC1 signals lead to an altered translational landscape in T cells and immunopathology.
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Affiliation(s)
- Darienne R Myers
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emilia Norlin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yvonne Vercoulen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
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Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR. Genome Res 2020; 30:724-735. [PMID: 32424072 PMCID: PMC7263195 DOI: 10.1101/gr.255273.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
Despite the interest in characterizing genomic variation, the presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, since there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different genome-wide techniques. In addition, we obtained new experimental human population information across 95 African, European, and East Asian individuals for 16 inversions, including four already validated variants without high-throughput genotyping methods. Through comparison with previous data, independent replicates and both inversion breakpoints, we demonstrate that the technique is highly accurate and reproducible. Most studied inversions are widespread across continents, and their frequency is negatively correlated with genetic length. Moreover, all except two show clear signs of being recurrent, and we could better define the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, the generated genotypes have allowed us to check inversion functional effects, validating gene expression differences reported before for two inversions and finding new candidate associations. Therefore, the developed methodology makes it possible to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
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Myers DR, Wheeler B, Roose JP. mTOR and other effector kinase signals that impact T cell function and activity. Immunol Rev 2020; 291:134-153. [PMID: 31402496 DOI: 10.1111/imr.12796] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 07/11/2019] [Indexed: 12/27/2022]
Abstract
T cells play important roles in autoimmune diseases and cancer. Following the cloning of the T cell receptor (TCR), the race was on to map signaling proteins that contributed to T cell activation downstream of the TCR as well as co-stimulatory molecules such as CD28. We term this "canonical TCR signaling" here. More recently, it has been appreciated that T cells need to accommodate increased metabolic needs that stem from T cell activation in order to function properly. A central role herein has emerged for mechanistic/mammalian target of rapamycin (mTOR). In this review we briefly cover canonical TCR signaling to set the stage for discussion on mTOR signaling, mRNA translation, and metabolic adaptation in T cells. We also discuss the role of mTOR in follicular helper T cells, regulatory T cells, and other T cell subsets. Our lab recently uncovered that "tonic signals", which pass through proximal TCR signaling components, are robustly and selectively transduced to mTOR to promote baseline translation of various mRNA targets. We discuss insights on (tonic) mTOR signaling in the context of T cell function in autoimmune diseases such as lupus as well as in cancer immunotherapy through CAR-T cell or checkpoint blockade approaches.
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Affiliation(s)
- Darienne R Myers
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Wheeler
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
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Luo S, Li X, Huang G, Xie Z, Xiang Y, Dai Z, Lin J, Zhou Z. Distinct two different ages associated with clinical profiles of acute onset type 1 diabetes in Chinese patients. Diabetes Metab Res Rev 2020; 36:e3209. [PMID: 31343818 DOI: 10.1002/dmrr.3209] [Citation(s) in RCA: 6] [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: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND There are abundant variations in the phenotypes and genetics of type 1 diabetes (T1D) patients across different races. This study aimed to assess differences between juvenile acute onset (JAO) and adult acute onset in Chinese T1D patients. METHODS Seven hundred and fifty-one acute onset T1D patients were divided into two groups by the patient onset age as follows: the juvenile acute onset group (≤20 years, JAO group) and the adult acute onset group (>20 years, AAO group). Clinical characteristics, islet autoantibodies, and HLA class II haplotypes and genotypes were compared between these two groups. RESULTS In comparison with AAO patients, JAO patients had significantly lower relative weights and lower triglyceride levels (P < .001, P < .01, respectively) but higher frequency of ketoacidosis (P < .001), higher daily insulin dosage (Pc < .001), higher HbA1c (Pc < .05), and higher HDL-cholesterol levels (Pc < .01). The JAO group showed a higher prevalence of IA-2A, ZnT8A, and multiple autoantibodies than that in the AAO group (P < .001, P < .01, P < .001, respectively). Haplotypes for DRB1*0301-DQA1*03-DQB1*0201, DR3, DR4, DR9, and DR3/DR9 genotypes are highly associated with JAO susceptibility, whereas only DR3 and DR9 genotypes confer risk for AAO. In the JAO group but not the AAO group, DR3 is related to ZnT8A, and DR3/DR9 is related to IA-2A and multiple autoantibodies. CONCLUSIONS These observations suggest that JAO patients markedly differ from AAO patients in their clinical manifestations and genetics in the Chinese T1D population. Notably, the DR3/DR9 genotype can facilitate the appearance of IA-2A or multiple autoantibodies in JAO patients.
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Affiliation(s)
- Shuoming Luo
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Xia Li
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Gan Huang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Zhiguo Xie
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Yufei Xiang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Zhijie Dai
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Jian Lin
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
| | - Zhiguang Zhou
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, National Clinical Research Center for Metabolic Disease, Changsha, China
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Renaux C, Buzdugan L, Kalisch M, Bühlmann P. Hierarchical inference for genome-wide association studies: a view on methodology with software. Comput Stat 2020. [DOI: 10.1007/s00180-019-00939-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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STAT4 sequence variant and elevated gene expression are associated with type 1 diabetes in Polish children. Cent Eur J Immunol 2020; 45:22-28. [PMID: 32425676 PMCID: PMC7226553 DOI: 10.5114/ceji.2019.92492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/23/2019] [Indexed: 12/23/2022] Open
Abstract
Introduction Type 1 diabetes (T1D) is caused by the autoimmune destruction of pancreatic β cells, resulting from coincident genetic predisposition and some environmental triggers. Signal transducer and activator of transcription 4 (STAT4) gene encodes a transcription factor, which promotes Th1 cell differentiation, interferon γ production, and development of Th17 cells. Polymorphisms of STAT4 are associated with several autoimmune conditions, while studies in T1D provided inconsistent results. This analysis was designed to investigate the association of STAT4 rs7574865 with T1D in Polish children and to assess STAT4 expression in newly diagnosed subjects. Material and methods Rs7574865 was genotyped in 656 T1D children and 782 healthy individuals. STAT4 mRNA expression was analyzed in peripheral blood mononuclear cells (PBMCs) from 29 children with T1D and 27 age-matched controls. β-cell and thyroid-specific serum autoantibodies were assessed with radioimmunoassays. Results The distribution of rs7574865 genotypes and alleles demonstrated significant difference (p = 0.002, p < 0.001, respectively) between patients vs. controls. Carriers of the minor T allele presented earlier T1D onset (p = 0.017). No differences were found in γ-cell autoantibody in genotype-stratified patients (p > 0.050), while anti-thyroid antibodies were more frequent in carriers of the minor allele(p = 0.039 for anti-thyroperoxidase, p = 0.007 for anti-thyroglobulin antibodies, respectively). STAT4 was overexpressed in PBMCs from T1D patients (p = 0.008), especially subjects with two/three circulating β-cell antibodies (p < 0.001). Conclusions The study confirms an association of STAT4 rs7574865 with T1D in Polish patients, and provides an evidence for its relationship with an earlier disease onset and concomitant thyroid autoimmunity. STAT4 expression appears elevated in T1D, especially with more severe reaction against β-cell antigens.
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Colli ML, Szymczak F, Eizirik DL. Molecular Footprints of the Immune Assault on Pancreatic Beta Cells in Type 1 Diabetes. Front Endocrinol (Lausanne) 2020; 11:568446. [PMID: 33042023 PMCID: PMC7522353 DOI: 10.3389/fendo.2020.568446] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/17/2020] [Indexed: 12/25/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic disease caused by the selective destruction of the insulin-producing pancreatic beta cells by infiltrating immune cells. We presently evaluated the transcriptomic signature observed in beta cells in early T1D and compared it with the signatures observed following in vitro exposure of human islets to inflammatory or metabolic stresses, with the aim of identifying "footprints" of the immune assault in the target beta cells. We detected similarities between the beta cell signatures induced by cytokines present at different moments of the disease, i.e., interferon-α (early disease) and interleukin-1β plus interferon-γ (later stages) and the beta cells from T1D patients, identifying biological process and signaling pathways activated during early and late stages of the disease. Among the first responses triggered on beta cells was an enrichment in antiviral responses, pattern recognition receptors activation, protein modification and MHC class I antigen presentation. During putative later stages of insulitis the processes were dominated by T-cell recruitment and activation and attempts of beta cells to defend themselves through the activation of anti-inflammatory pathways (i.e., IL10, IL4/13) and immune check-point proteins (i.e., PDL1 and HLA-E). Finally, we mined the beta cell signature in islets from T1D patients using the Connectivity Map, a large database of chemical compounds/drugs, and identified interesting candidates to potentially revert the effects of insulitis on beta cells.
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Affiliation(s)
- Maikel L. Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- *Correspondence: Maikel L. Colli
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, United States
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The Critical Role of Bach2 in Shaping the Balance between CD4 + T Cell Subsets in Immune-Mediated Diseases. Mediators Inflamm 2019; 2019:2609737. [PMID: 32082072 PMCID: PMC7012215 DOI: 10.1155/2019/2609737] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 01/12/2023] Open
Abstract
The transcription factor Bach2 which is predominantly expressed in B and T lymphocytes represses the expression of genes by forming heterodimers with small Maf and Batf proteins and binding to the corresponding sequence on the DNA. In this way, Bach2 serves as a highly conserved repressor which controls the terminal differentiation and maturation of both B and T lymphocytes. It is required for class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes in activated B cells, and its function in B cell differentiation has been well-described. Furthermore, emerging data show that Bach2 regulates transcriptional activity in T cells at super enhancers or regions of high transcriptional activity, thus stabilizing immunoregulatory capacity and maintaining T cell homeostasis. Bach2 is also critical for the formation and function of CD4+ T cell lineages (Th1, Th2, Th9, Th17, T follicular helper (Tfh), and regulatory T (Treg) cells). Genetic variations within Bach2 locus are associated with numerous immune-mediated diseases including multiple sclerosis (MS), rheumatoid arthritis (RA), chronic pancreatitis (CP), type 2 chronic airway inflammation, inflammatory bowel disease (IBD), and type 1 diabetes. Here, we reveal a critical role of Bach2 in regulating T cell biology and the correlation with these immune-mediated diseases.
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Feng Y, Zhang Y, Chen Y, Chen S, Shen M, Fu Q, He Y, Liu Y, Hsu HT, Xu X, Chen H, Yang T, Xu K. The associations between three genome-wide risk variants for serum C-peptide of T1D and autoantibody-positive T1D risk, and clinical characteristics in Chinese population. J Hum Genet 2019; 65:297-303. [PMID: 31827251 DOI: 10.1038/s10038-019-0705-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 01/12/2023]
Abstract
AIMS Recent meta-genome-wide association studies identified several genetic variants associated with beta-cell function in type 1 diabetes (T1D). The aim of this study was to investigate the associations between these variants and T1D risk, C-peptide levels, islet-specific autoantibodies, and lipid levels in Chinese Han population. METHODS A total of 1005 unrelated autoantibody-positive T1D cases and 1417 healthy controls were included, which were genotyped for rs559047, rs9260151, and rs3135002. T1D individuals were measured for both C-peptide and lipid levels. Logistic regression models were used to examine these associations. RESULTS We found that rs3135002 A allele showed a genome-wide significant association with T1D risk (OR = 0.22, 95% CI = 0.17-0.30; P = 7.49 × 10-27), and significant heterogeneity of effect size was observed between early-onset and later-onset T1D subgroups (I2 = 80% and P = 0.026). Rs559047 had a nominal association with fasting C-peptide levels in newly diagnosed T1D individuals (P = 0.036). Moreover, rs3135002 A allele was significantly associated with GADA positivity (OR = 0.52, 95% CI = 0.30-0.91, P = 0.02). In addition, nominal correlations were observed with HDL levels for rs559047 (P = 0.042), while LDL levels for rs9260151 (P = 0.032) in T1D individuals. CONCLUSIONS Our results indicate that there are both similarities and differences for the associations of genetic variants among T1D development, progression, and related autoimmunity, metabolic traits.
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Affiliation(s)
- Yingjie Feng
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Yuyue Zhang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Yang Chen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Shu Chen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China.,Department of Endocrinology, Affiliated Hospital 2 of Nantong University, Nantong, Jiangsu, 226001, China
| | - Min Shen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Qi Fu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Yunqiang He
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Yuwei Liu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Hsiang-Ting Hsu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Xinyu Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Heng Chen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Tao Yang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Kuanfeng Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China.
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