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Hrovatin K, Bastidas-Ponce A, Bakhti M, Zappia L, Büttner M, Salinno C, Sterr M, Böttcher A, Migliorini A, Lickert H, Theis FJ. Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas. Nat Metab 2023; 5:1615-1637. [PMID: 37697055 PMCID: PMC10513934 DOI: 10.1038/s42255-023-00876-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/26/2023] [Indexed: 09/13/2023]
Abstract
Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have been generated, a consensus on pancreatic cell states in development, homeostasis and diabetes as well as the value of preclinical animal models is missing. Here, we present an scRNA-seq cross-condition mouse islet atlas (MIA), a curated resource for interactive exploration and computational querying. We integrate over 300,000 cells from nine scRNA-seq datasets consisting of 56 samples, varying in age, sex and diabetes models, including an autoimmune type 1 diabetes model (NOD), a glucotoxicity/lipotoxicity type 2 diabetes model (db/db) and a chemical streptozotocin β-cell ablation model. The β-cell landscape of MIA reveals new cell states during disease progression and cross-publication differences between previously suggested marker genes. We show that β-cells in the streptozotocin model transcriptionally correlate with those in human type 2 diabetes and mouse db/db models, but are less similar to human type 1 diabetes and mouse NOD β-cells. We also report pathways that are shared between β-cells in immature, aged and diabetes models. MIA enables a comprehensive analysis of β-cell responses to different stressors, providing a roadmap for the understanding of β-cell plasticity, compensation and demise.
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Affiliation(s)
- Karin Hrovatin
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medical Faculty, Technical University of Munich, Munich, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Luke Zappia
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Maren Büttner
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Ciro Salinno
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Medical Faculty, Technical University of Munich, Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Adriana Migliorini
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- McEwen Stem Cell Institute, University Health Network (UHN), Toronto, Ontario, Canada
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Medical Faculty, Technical University of Munich, Munich, Germany.
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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2
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Ćwilichowska N, Świderska KW, Dobrzyń A, Drąg M, Poręba M. Diagnostic and therapeutic potential of protease inhibition. Mol Aspects Med 2022; 88:101144. [PMID: 36174281 DOI: 10.1016/j.mam.2022.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Proteases are enzymes that hydrolyze peptide bonds in proteins and peptides; thus, they control virtually all biological processes. Our understanding of protease function has advanced considerably from nonselective digestive enzymes to highly specialized molecular scissors that orchestrate complex signaling networks through a limited proteolysis. The catalytic activity of proteases is tightly regulated at several levels, ranging from gene expression through trafficking and maturation to posttranslational modifications. However, when this delicate balance is disturbed, many diseases develop, including cancer, inflammatory disorders, diabetes, and neurodegenerative diseases. This new understanding of the role of proteases in pathologic physiology indicates that these enzymes represent excellent molecular targets for the development of therapeutic inhibitors, as well as for the design of chemical probes to visualize their redundant activity. Recently, numerous platform technologies have been developed to identify and optimize protease substrates and inhibitors, which were further used as lead structures for the development of chemical probes and therapeutic drugs. Due to this considerable success, the clinical potential of proteases in therapeutics and diagnostics is rapidly growing and is still not completely explored. Therefore, small molecules that can selectively target aberrant protease activity are emerging in diseases cells. In this review, we describe modern trends in the design of protease drugs as well as small molecule activity-based probes to visualize selected proteases in clinical settings.
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Affiliation(s)
- Natalia Ćwilichowska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina W Świderska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Dobrzyń
- Nencki Institute of Experimental Biology, Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
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3
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Association between type 2 diabetes mellitus and TCF7L2 gene variant in the Pakistani cohort. Int J Diabetes Dev Ctries 2022. [DOI: 10.1007/s13410-022-01138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Diniz IG, Noce RRD, Pereira AP, Silva ANLMD, Sacuena ERP, Lemes RB, Cardoso-Costa GDL, Araújo GS, Machado JLP, Figueiredo FADPL, Hümemeier T, Guerreiro JF. Common BMI and diabetes-related genetic variants: A pilot study among indigenous people in the Brazilian Amazon. Genet Mol Biol 2022; 45:e20210153. [PMID: 35560161 PMCID: PMC9104643 DOI: 10.1590/1678-4685-gmb-2021-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022] Open
Abstract
This study was carried out to investigate the frequency of genetic variants related to body mass index (BMI) and type 2 diabetes (T2D) and evaluating the potential impact of risk alleles on susceptibility to these disorders in six indigenous peoples from Brazilian Amazon region. The majority of Fst values for pairwise population comparisons among the indigenous groups are low or moderate. The indigenous people show high values of differentiation with Africans, Europeans and Southeast Asians and moderate values with East Asian and American populations, as expected. The allelic frequencies among indigenous indicate that the majority of associations observed with T2D in continental populations can be replicated in native Amazonians. The genetic risk scores calculated for T2D in indigenous are high and similar to those calculated for Americans and East Asians, while the estimates obtained for obesity are low, probably due to the low frequencies of the risk allele of the FTO gene found in our samples. ADRB3-rs4994 and ABCC8-rs1799854 genes showed a significant association with BMI and waist circumference, and the KCNJ11-rs5219 gene with hyperglycemia. These results emphasize the importance of knowing the genetic variability underlying complex genetic diseases in indigenous peoples and the search for particular or rare variants.
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Affiliation(s)
- Isabela Guerreiro Diniz
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Belém, PA, Brazil
| | - Rosilene Reis Della Noce
- Universidade Federal do Pará, Instituto de Ciências da Saúde, Faculdade de Nutrição, Belém, PA, Brazil
| | - Ana Paula Pereira
- Universidade Federal do Pará, Instituto de Ciências da Saúde, Faculdade de Nutrição, Belém, PA, Brazil
| | | | | | - Renan Barbosa Lemes
- Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Greice de Lemos Cardoso-Costa
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Belém, PA, Brazil
| | - Gilderlânio Santana Araújo
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Belém, PA, Brazil
| | - Jéssica Lígia Picanço Machado
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Belém, PA, Brazil
| | | | - Tábita Hümemeier
- Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - João Farias Guerreiro
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Genética Humana e Médica, Belém, PA, Brazil
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Mahnam K, Shakhsi-Niaei M, Ziaei M, Sweazea KL. In silico evaluation of the downstream effect of mutated glucagon is consistent with higher blood glucose homeostasis in Galliformes and Strigiformes. Gen Comp Endocrinol 2021; 314:113925. [PMID: 34624309 DOI: 10.1016/j.ygcen.2021.113925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
In contrast to mammals, glucagon is reported as a much more potent blood glucose modulator in birds. Interestingly, we have found p.Thr16Ser mutation, a variation in the highly conserved glucagon hormone, in Galliformes as well as Strigiformes. To check the effect of this mutation on the receptor binding of glucagon, we predicted the ancestral glucagon receptor sequence of all available Galliformes and Strigiformes species. Subsequently, we analysed their binding to the mutated and wild type glucagon (ancestral) by molecular dynamics simulation. At first, we made a model of ancestral glucagon receptor and ancestral mutated, and wild type glucagon in the order Galliformes and Strigiformes. Then we performed molecular dynamics for each Galliformes and Strigiformes receptor as well as each glucagon peptide, respectively. The final structures were used for docking simulation of glucagon to their receptors. The results of the docking simulations showed a stronger binding affinity of mutated glucagon to glucagon receptors. Afterward, we obtained blood glucose concentrations of all available Galliformes members, as well as all available members of its only taxonomic neighbour (order Anseriformes) in superorder Galloanserae. Interestingly the p.Thr16Ser mutation could finely cluster these two orders into two groups: higher blood glucose concentration (order Galliformes, 17.64 ± 1.66 mMol/L) and lower blood glucose concentration (order Anseriformes, 11.34 ± 1.11 mMol/L). Strigiformes which carry the mutated glucagon peptide show also high blood glucose concentrations (17.40 ± 1.51 mMol/L). Therefore, the results suggest this mutation, which leads to stronger binding affinity of mutated glucagon to its receptor, may be a driving force for higher blood glucose homeostasis in the related birds.
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Affiliation(s)
- Karim Mahnam
- Department of Biology, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Mostafa Shakhsi-Niaei
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
| | - Maryam Ziaei
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
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Liu C, Sun YV. Anticipation of Precision Diabetes and Promise of Integrative Multi-Omics. Endocrinol Metab Clin North Am 2021; 50:559-574. [PMID: 34399961 DOI: 10.1016/j.ecl.2021.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Precision diabetes is a concept of customizing delivery of health practices based on variability of diabetes. The authors reviewed recent research on type 2 diabetes heterogeneity and -omic biomarkers, including genomic, epigenomic, and metabolomic markers associated with type 2 diabetes. The emerging multiomics approach integrates complementary and interconnected molecular layers to provide systems level understanding of disease mechanisms and subtypes. Although the multiomic approach is not currently ready for routine clinical applications, future studies in the context of precision diabetes, particular in populations from diverse ethnic and demographic groups, may lead to improved diagnosis, treatment, and management of diabetes and diabetic complications.
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Affiliation(s)
- Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road Northeast, Atlanta, GA 30322, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Road Northeast, Atlanta, GA 30322, USA; Atlanta VA Healthcare System, 1670 Clairmont Road, Decatur, GA 30033, USA.
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Korivi M, Huang YW, Liu BR. Cell-Penetrating Peptides as a Potential Drug Delivery System for Effective Treatment of Diabetes. Curr Pharm Des 2021; 27:816-825. [PMID: 33076803 DOI: 10.2174/1381612826666201019102640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND/PURPOSE Type 2 diabetes (T2D) is characterized by hyperglycemia resulting from the body's inability to produce and/or use insulin. Patients with T2D often have hyperinsulinemia, dyslipidemia, inflammation, and oxidative stress, which then lead to hypertension, chronic kidney disease, cardiovascular disease, and increased risk of morbidity and mortality (9th leading cause globally). Insulin and related pharmacological therapies are widely used to manage T2D, despite their limitations. Efficient drug delivery systems (DDS) that control drug kinetics may decrease side effects, allow for efficient targeting, and increase the bioavailability of drugs to achieve maximum therapeutic benefits. Thus, the development of effective DDS is crucial to beat diabetes. METHODS Here, we introduced a highly bioavailable vector, cell-penetrating peptides (CPPs), as a powerful DDS to overcome limitations of free drug administration. RESULTS CPPs are short peptides that serve as a potent tool for delivering therapeutic agents across cell membranes. Various cargoes, including proteins, DNA, RNA, liposomes, therapeutic molecules, and nanomaterials, generally retain their bioactivity upon entering cells. The mechanisms of CPPs/cargoes intracellular entry are classified into two parts: endocytic pathways and direct membrane translocation. In this article, we focus on the applications of CPPs/therapeutic agents in the treatment of diabetes. Hypoglycemic drugs with CPPs intervention can enhance therapeutic effectiveness, and CPP-mediated drug delivery can facilitate the actions of insulin. Numerous studies indicate that CPPs can effectively deliver insulin, produce synergistic effects with immunosuppressants for successful pancreatic islet xenotransplantation, prolong pharmacokinetics, and retard diabetic nephropathy. CONCLUSION We suggest that CPPs can be a new generation of drug delivery systems for effective treatment and management of diabetes and diabetes-associated complications.
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Affiliation(s)
- Mallikarjuna Korivi
- Exercise and Metabolism Research Center, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Yue-Wern Huang
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65409-1120, United States
| | - Betty R Liu
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan
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Xia C, Zhang X, Cao T, Wang J, Li C, Yue L, Niu K, Shen Y, Ma G, Chen F. Hepatic Transcriptome Analysis Revealing the Molecular Pathogenesis of Type 2 Diabetes Mellitus in Zucker Diabetic Fatty Rats. Front Endocrinol (Lausanne) 2020; 11:565858. [PMID: 33329383 PMCID: PMC7732450 DOI: 10.3389/fendo.2020.565858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
Around 9% of the adult population in the world (463 million) suffer from diabetes mellitus. Most of them (~90%) belong to type 2 diabetes mellitus (T2DM), which is a common chronic metabolic disorder, and the number of cases has been reported to increase each year. Zucker diabetic fatty (ZDF) rat provides a successful animal model to study the pathogenesis of T2DM. Although previous hepatic transcriptome studies revealed some novel genes associated with the occurrence and development of T2DM, there still lacks the comprehensive transcriptomic analysis for the liver tissues of ZDF rats. We performed comparative transcriptome analyses between the liver tissues of ZDF rats and healthy ZCL rats and also evaluated several clinical indices. We could identify 214 and 104 differentially expressed genes (DEGs) and lncRNAs in ZDF rats, respectively. Pathway and biofunction analyses showed a synergistic effect between mRNAs and lncRNAs. By comprehensively analyzing transcriptomic data and clinical indices, we detected some typical features of T2DM in ZDF rats, such as upregulated metabolism (significant increased lipid absorption/transport/utilization, gluconeogenesis, and protein hydrolysis), increased inflammation, liver injury and increased endoplasmic reticulum (ER) stress. In addition, of the 214 DEGs, 114 were known and 100 were putative T2DM-related genes, most of which have been associated with substance metabolism (particularly degradation), inflammation, liver injury and ER stress biofunctions. Our study provides an important reference and improves understanding of molecular pathogenesis of obesity-associated T2DM. Our data can also be used to identify potential diagnostic markers and therapeutic targets, which should strengthen the prevention and treatment of T2DM.
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Affiliation(s)
- Chengdong Xia
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiuli Zhang
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianshu Cao
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiannong Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cuidan Li
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Liya Yue
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Kaifeng Niu
- China National Center for Bioinformation, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yicheng Shen
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guannan Ma
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- China National Center for Bioinformation, Beijing, China
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Lee K, Moon S, Park MJ, Koh IU, Choi NH, Yu HY, Kim YJ, Kong J, Kang HG, Kim SC, Kim BJ. Integrated Analysis of Tissue-Specific Promoter Methylation and Gene Expression Profile in Complex Diseases. Int J Mol Sci 2020; 21:E5056. [PMID: 32709145 PMCID: PMC7404266 DOI: 10.3390/ijms21145056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
This study investigated whether the promoter region of DNA methylation positively or negatively regulates tissue-specific genes (TSGs) and if it correlates with disease pathophysiology. We assessed tissue specificity metrics in five human tissues, using sequencing-based approaches, including 52 whole genome bisulfite sequencing (WGBS), 52 RNA-seq, and 144 chromatin immunoprecipitation sequencing (ChIP-seq) data. A correlation analysis was performed between the gene expression and DNA methylation levels of the TSG promoter region. The TSG enrichment analyses were conducted in the gene-disease association network (DisGeNET). The epigenomic association analyses of CpGs in enriched TSG promoters were performed using 1986 Infinium MethylationEPIC array data. A correlation analysis showed significant associations between the promoter methylation and 449 TSGs' expression. A disease enrichment analysis showed that diabetes- and obesity-related diseases were high-ranked. In an epigenomic association analysis based on obesity, 62 CpGs showed statistical significance. Among them, three obesity-related CpGs were newly identified and replicated with statistical significance in independent data. In particular, a CpG (cg17075888 of PDK4), considered as potential therapeutic targets, were associated with complex diseases, including obesity and type 2 diabetes. The methylation changes in a substantial number of the TSG promoters showed a significant association with metabolic diseases. Collectively, our findings provided strong evidence of the relationship between tissue-specific patterns of epigenetic changes and metabolic diseases.
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Affiliation(s)
- Kibaick Lee
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Sanghoon Moon
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Mi-Jin Park
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - In-Uk Koh
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Nak-Hyeon Choi
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Ho-Yeong Yu
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Young Jin Kim
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Jinhwa Kong
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Song Cheol Kim
- Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do 28519, Korea; (K.L.); (S.M.); (M.-J.P.); (I.-U.K.); (N.-H.C.); (H.-Y.Y.); (Y.J.K.); (J.K.)
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Nasykhova YA, Barbitoff YA, Serebryakova EA, Katserov DS, Glotov AS. Recent advances and perspectives in next generation sequencing application to the genetic research of type 2 diabetes. World J Diabetes 2019; 10:376-395. [PMID: 31363385 PMCID: PMC6656706 DOI: 10.4239/wjd.v10.i7.376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/23/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes (T2D) mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem. High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D. Recent advances in the application of sequencing technologies to T2D research include, but are not limited to: (1) Fine mapping of causal rare and common genetic variants; (2) Identification of confident gene-level associations; (3) Identification of novel candidate genes by specific scoring approaches; (4) Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques; and (5) Investigation of microbial community alterations in patients with T2D. In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis, as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis, prevention, and treatment of the disease.
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Affiliation(s)
- Yulia A Nasykhova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
| | - Yury A Barbitoff
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Bioinformatics Institute, St. Petersburg 194021, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Elena A Serebryakova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
| | - Dmitry S Katserov
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
| | - Andrey S Glotov
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
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Zhang T, Qi Z, Wang H, Ding S. Adeno-Associated Virus-Mediated Knockdown of SLC16A11 Improves Glucose Tolerance and Hepatic Insulin Signaling in High Fat Diet-Fed Mice. Exp Clin Endocrinol Diabetes 2019; 129:104-111. [PMID: 31185508 DOI: 10.1055/a-0840-3330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND SLC16A11, a member of the SLC16 family, is associated with lipid metabolism, causing increased intracellular triacylglycerol (TAG) levels. In the current study, our primary goal was to determine if an SLC16A11 knockdown would improve glucose tolerance and hepatic insulin signaling in high fat diet (HFD)-fed mice. Additionally, the mechanism for exercise-improved insulin sensitivity remains unclear, and there is no mechanistic insight into SLC16A11's role in insulin sensitivity under exercise stress. Therefore, we also examined the impact of endurance exercise on the abundance of SLC16A11. METHODS C57BL/6 J male mice were fed either regular chow (Control) or HFD for 8 weeks and then injected with adeno-associated virus (AAV). Plasma parameters, tissue lipid contents, glucose tolerance, and expression profiles of hepatic insulin signaling were detected. Also, other mice were divided randomly into sedentary and exercise groups. We assessed hepatic expression of SLC16A11 after 8 weeks of endurance exercise. RESULTS 1) Hepatic SLC16A11 expression was greater in HFD-fed mice compared to Control mice. 2) AAV-mediated knockdown of SLC16A11 improved glucose tolerance, prevented TAG accumulation in serum and liver, and increased phosphorylation of protein kinase B (Akt) and glycogen synthesis kinase-3β (GSK3β) in HFD-fed mice. 3) Endurance exercise decreased hepatic SLC16A11 expression. CONCLUSIONS Inactivation of SLC16A11, which is robustly induced by HFD, improved glucose tolerance and hepatic insulin signaling, independent of body weight, but related to TAG. Additionally, SLC16A11 might mediate the health benefits of endurance exercise.
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Affiliation(s)
- Tan Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China.,College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Zhengtang Qi
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China.,College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Haiyan Wang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China.,College of Physical Education and Health, East China Normal University, Shanghai, China
| | - Shuzhe Ding
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China.,College of Physical Education and Health, East China Normal University, Shanghai, China
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Grabherr MG, Kaminska B, Komorowski J. Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal. Genes (Basel) 2018; 9:genes9100505. [PMID: 30340386 PMCID: PMC6210603 DOI: 10.3390/genes9100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Manfred G Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden.
- National Bioinformatics Infrastructure Sweden, Uppsala University, 752 36 Uppsala, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Bozena Kaminska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland.
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China.
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden.
- Institute of Computer Science of the Polish Academy of Sciences, 02-093 Warsaw, Poland.
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Willmer T, Johnson R, Louw J, Pheiffer C. Blood-Based DNA Methylation Biomarkers for Type 2 Diabetes: Potential for Clinical Applications. Front Endocrinol (Lausanne) 2018; 9:744. [PMID: 30564199 PMCID: PMC6288427 DOI: 10.3389/fendo.2018.00744] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) is a leading cause of death and disability worldwide. It is a chronic metabolic disorder that develops due to an interplay of genetic, lifestyle, and environmental factors. The biological onset of the disease occurs long before clinical symptoms develop, thus the search for early diagnostic and prognostic biomarkers, which could facilitate intervention strategies to prevent or delay disease progression, has increased considerably in recent years. Epigenetic modifications represent important links between genetic, environmental and lifestyle cues and increasing evidence implicate altered epigenetic marks such as DNA methylation, the most characterized and widely studied epigenetic mechanism, in the pathogenesis of T2D. This review provides an update of the current status of DNA methylation as a biomarker for T2D. Four databases, Scopus, Pubmed, Cochrane Central, and Google Scholar were searched for studies investigating DNA methylation in blood. Thirty-seven studies were identified, and are summarized with respect to population characteristics, biological source, and method of DNA methylation quantification (global, candidate gene or genome-wide). We highlight that differential methylation of the TCF7L2, KCNQ1, ABCG1, TXNIP, PHOSPHO1, SREBF1, SLC30A8, and FTO genes in blood are reproducibly associated with T2D in different population groups. These genes should be prioritized and replicated in longitudinal studies across more populations in future studies. Finally, we discuss the limitations faced by DNA methylation studies, which include including interpatient variability, cellular heterogeneity, and lack of accounting for study confounders. These limitations and challenges must be overcome before the implementation of blood-based DNA methylation biomarkers into a clinical setting. We emphasize the need for longitudinal prospective studies to support the robustness of the current findings of this review.
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Affiliation(s)
- Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- *Correspondence: Tarryn Willmer
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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