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Yang K, Zhang Y, Ding J, Li Z, Zhang H, Zou F. Autoimmune CD8+ T cells in type 1 diabetes: from single-cell RNA sequencing to T-cell receptor redirection. Front Endocrinol (Lausanne) 2024; 15:1377322. [PMID: 38800484 PMCID: PMC11116783 DOI: 10.3389/fendo.2024.1377322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by pancreatic β cell destruction and mediated primarily by autoreactive CD8+ T cells. It has been shown that only a small number of stem cell-like β cell-specific CD8+ T cells are needed to convert normal mice into T1D mice; thus, it is likely that T1D can be cured or significantly improved by modulating or altering self-reactive CD8+ T cells. However, stem cell-type, effector and exhausted CD8+ T cells play intricate and important roles in T1D. The highly diverse T-cell receptors (TCRs) also make precise and stable targeted therapy more difficult. Therefore, this review will investigate the mechanisms of autoimmune CD8+ T cells and TCRs in T1D, as well as the related single-cell RNA sequencing (ScRNA-Seq), CRISPR/Cas9, chimeric antigen receptor T-cell (CAR-T) and T-cell receptor-gene engineered T cells (TCR-T), for a detailed and clear overview. This review highlights that targeting CD8+ T cells and their TCRs may be a potential strategy for predicting or treating T1D.
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Affiliation(s)
- Kangping Yang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yihan Zhang
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Jiatong Ding
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Zelin Li
- The First Clinical Medicine School, Nanchang University, Nanchang, China
| | - Hejin Zhang
- The Second Clinical Medicine School, Nanchang University, Nanchang, China
| | - Fang Zou
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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2
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Starskaia I, Valta M, Pietilä S, Suomi T, Pahkuri S, Kalim UU, Rasool O, Rydgren E, Hyöty H, Knip M, Veijola R, Ilonen J, Toppari J, Lempainen J, Elo LL, Lahesmaa R. Distinct cellular immune responses in children en route to type 1 diabetes with different first-appearing autoantibodies. Nat Commun 2024; 15:3810. [PMID: 38714671 PMCID: PMC11076468 DOI: 10.1038/s41467-024-47918-w] [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: 07/17/2023] [Accepted: 04/12/2024] [Indexed: 05/10/2024] Open
Abstract
Previous studies have revealed heterogeneity in the progression to clinical type 1 diabetes in children who develop islet-specific antibodies either to insulin (IAA) or glutamic acid decarboxylase (GADA) as the first autoantibodies. Here, we test the hypothesis that children who later develop clinical disease have different early immune responses, depending on the type of the first autoantibody to appear (GADA-first or IAA-first). We use mass cytometry for deep immune profiling of peripheral blood mononuclear cell samples longitudinally collected from children who later progressed to clinical disease (IAA-first, GADA-first, ≥2 autoantibodies first groups) and matched for age, sex, and HLA controls who did not, as part of the Type 1 Diabetes Prediction and Prevention study. We identify differences in immune cell composition of children who later develop disease depending on the type of autoantibodies that appear first. Notably, we observe an increase in CD161 expression in natural killer cells of children with ≥2 autoantibodies and validate this in an independent cohort. The results highlight the importance of endotype-specific analyses and are likely to contribute to our understanding of pathogenic mechanisms underlying type 1 diabetes development.
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Grants
- 1-SRA-2016-342-M-R, 1-SRA-2019-732-M-B, 3-SRA-2020-955-S-B JDRF
- BMH4-CT98-3314 European Commission (EC)
- Academy of Finland (292538, 292335, 294337, 319280, 31444, 319280, 329277, 331790, 310561, 314443, 329278, 335434, 335611 and 341342), Novo Nordisk Foundation, Centre of Excellence in Molecular Systems Immunology and Physiology Research 2012-2017 [Decision No 250114]; Special Research Funds for University Hospitals in Finland; Diabetes Research Foundation, Finland; European Foundation for the Study of Diabetes; Päivikki and Sakari Sohlberg Foundation; Pediatric Research Foundation. Business Finland, the Sigrid Jusélius Foundation, Jane and Aatos Erkko Foundation, the Finnish Cancer Foundation, InFLAMES Flagship Programme of the Academy of Finland, Diabetes Wellness Suomi, the Finnish cultural foundation. the European Research Council ERC (677943), the Finnish Medical Foundation, the Finnish Pediatric Research Foundation and the Hospital Districht of South-West Finland.
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Affiliation(s)
- Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Milla Valta
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Sirpa Pahkuri
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Emilie Rydgren
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, and Fimlab Laboratories, Tampere, Finland
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riitta Veijola
- Department of Pediatrics, Research Unit of Clinical Medicine, Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Toppari
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Johanna Lempainen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland.
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland.
- Clinical Microbiology, Turku University Hospital, Turku, Finland.
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
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3
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Frost B, Schmidt M, Klein B, Loeffler-Wirth H, Krohn K, Reidenbach T, Binder H, Stubenvoll A, Simon JC, Saalbach A, Kunz M. Single-cell transcriptomics reveals prominent expression of IL-14, IL-18, and IL-32 in psoriasis. Eur J Immunol 2023; 53:e2250354. [PMID: 37540729 DOI: 10.1002/eji.202250354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/21/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
RATIONALE Psoriasis is a chronic inflammatory skin disease involving different cytokines and chemokines. OBJECTIVES Here we use single-cell transcriptomic analyses to identify relevant immune cell and nonimmune cell populations for an in-depth characterization of cell types and inflammatory mediators in this disease. METHODS Psoriasis skin lesions of eight patients are analyzed using single-cell technology. Data are further validated by in situ hybridization (ISH) of human tissues, serum analyses of human samples and tissues of a murine model of psoriasis, and by in vitro cell culture experiments. RESULTS Several different immune-activated cell types with particular cytokine patterns are identified such as keratinocytes, T-helper cells, dendritic cells, macrophages, and fibroblasts. Apart from well-known factors, IL-14 (TXLNA), IL-18, and IL-32 are identified with prominent expression in individual cell types in psoriasis. The percentage of inflammatory cellular subtypes expressing IL-14, IL-18, and IL-32 was significantly higher in psoriatic skin compared with healthy control skin. These findings were confirmed by ISH of human skin samples, in a murine model of psoriasis, in human serum samples, and in in vitro experiments. CONCLUSIONS Taken together, we provide a differentiated view of psoriasis immune-cell phenotypes that support the role of IL-14, IL-18, and IL-32 in psoriasis pathogenesis.
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Affiliation(s)
- Bennet Frost
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Maria Schmidt
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Benjamin Klein
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Knuth Krohn
- Medical Faculty, Center for DNA Technologies, University of Leipzig, Leipzig, Germany
| | - Timo Reidenbach
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Antonia Stubenvoll
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jan C Simon
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Anja Saalbach
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
| | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
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Lernmark Å, Akolkar B, Hagopian W, Krischer J, McIndoe R, Rewers M, Toppari J, Vehik K, Ziegler AG. Possible heterogeneity of initial pancreatic islet beta-cell autoimmunity heralding type 1 diabetes. J Intern Med 2023; 294:145-158. [PMID: 37143363 PMCID: PMC10524683 DOI: 10.1111/joim.13648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The etiology of type 1 diabetes (T1D) foreshadows the pancreatic islet beta-cell autoimmune pathogenesis that heralds the clinical onset of T1D. Standardized and harmonized tests of autoantibodies against insulin (IAA), glutamic acid decarboxylase (GADA), islet antigen-2 (IA-2A), and ZnT8 transporter (ZnT8A) allowed children to be followed from birth until the appearance of a first islet autoantibody. In the Environmental Determinants of Diabetes in the Young (TEDDY) study, a multicenter (Finland, Germany, Sweden, and the United States) observational study, children were identified at birth for the T1D high-risk HLA haploid genotypes DQ2/DQ8, DQ2/DQ2, DQ8/DQ8, and DQ4/DQ8. The TEDDY study was preceded by smaller studies in Finland, Germany, Colorado, Washington, and Sweden. The aims were to follow children at increased genetic risk to identify environmental factors that trigger the first-appearing autoantibody (etiology) and progress to T1D (pathogenesis). The larger TEDDY study found that the incidence rate of the first-appearing autoantibody was split into two patterns. IAA first peaked already during the first year of life and tapered off by 3-4 years of age. GADA first appeared by 2-3 years of age to reach a plateau by about 4 years. Prior to the first-appearing autoantibody, genetic variants were either common or unique to either pattern. A split was also observed in whole blood transcriptomics, metabolomics, dietary factors, and exposures such as gestational life events and early infections associated with prolonged shedding of virus. An innate immune reaction prior to the adaptive response cannot be excluded. Clarifying the mechanisms by which autoimmunity is triggered to either insulin or GAD65 is key to uncovering the etiology of autoimmune T1D.
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Affiliation(s)
- Åke Lernmark
- Department of Clinical Sciences, Lund University CRC, Skåne University Hospital, Malmö, Sweden
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD USA
| | | | - Jeffrey Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Richard McIndoe
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, Colorado USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, and Institute of Biomedicine, Research Centre for Integrated Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL USA
| | - Anette-G. Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische Universität München, and Forschergruppe Diabetes e.V., Neuherberg, Germany
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5
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Suomi T, Starskaia I, Kalim UU, Rasool O, Jaakkola MK, Grönroos T, Välikangas T, Brorsson C, Mazzoni G, Bruggraber S, Overbergh L, Dunger D, Peakman M, Chmura P, Brunak S, Schulte AM, Mathieu C, Knip M, Lahesmaa R, Elo LL. Gene expression signature predicts rate of type 1 diabetes progression. EBioMedicine 2023; 92:104625. [PMID: 37224769 DOI: 10.1016/j.ebiom.2023.104625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Type 1 diabetes is a complex heterogenous autoimmune disease without therapeutic interventions available to prevent or reverse the disease. This study aimed to identify transcriptional changes associated with the disease progression in patients with recent-onset type 1 diabetes. METHODS Whole-blood samples were collected as part of the INNODIA study at baseline and 12 months after diagnosis of type 1 diabetes. We used linear mixed-effects modelling on RNA-seq data to identify genes associated with age, sex, or disease progression. Cell-type proportions were estimated from the RNA-seq data using computational deconvolution. Associations to clinical variables were estimated using Pearson's or point-biserial correlation for continuous and dichotomous variables, respectively, using only complete pairs of observations. FINDINGS We found that genes and pathways related to innate immunity were downregulated during the first year after diagnosis. Significant associations of the gene expression changes were found with ZnT8A autoantibody positivity. Rate of change in the expression of 16 genes between baseline and 12 months was found to predict the decline in C-peptide at 24 months. Interestingly and consistent with earlier reports, increased B cell levels and decreased neutrophil levels were associated with the rapid progression. INTERPRETATION There is considerable individual variation in the rate of progression from appearance of type 1 diabetes-specific autoantibodies to clinical disease. Patient stratification and prediction of disease progression can help in developing more personalised therapeutic strategies for different disease endotypes. FUNDING A full list of funding bodies can be found under Acknowledgments.
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Affiliation(s)
- Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland; Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Maria K Jaakkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Tommi Välikangas
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Caroline Brorsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gianluca Mazzoni
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Lut Overbergh
- Katholieke Universiteit Leuven/Universitaire Ziekenhuizen, Leuven, Belgium
| | - David Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, England, UK
| | - Mark Peakman
- Immunology & Inflammation Research Therapeutic Area, Sanofi, MA, USA
| | - Piotr Chmura
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Chantal Mathieu
- Katholieke Universiteit Leuven/Universitaire Ziekenhuizen, Leuven, Belgium
| | - Mikael Knip
- Paediatric Research Centre, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Tampere Centre for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland; Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland.
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku, Finland; Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland.
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6
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Derr AG, Arowosegbe A, Satish B, Redick SD, Qaisar N, Guo Z, Vanderleeden E, Trombly MI, Baer CE, Harlan DM, Greiner DL, Garber M, Wang JP. An Early Islet Transcriptional Signature Is Associated With Local Inflammation in Autoimmune Diabetes. Diabetes 2023; 72:261-274. [PMID: 36346618 PMCID: PMC9871196 DOI: 10.2337/db22-0521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Identifying the early islet cellular processes of autoimmune type 1 diabetes (T1D) in humans is challenging given the absence of symptoms during this period and the inaccessibility of the pancreas for sampling. In this article, we study temporal events in pancreatic islets in LEW.1WR1 rats, in which autoimmune diabetes can be induced with virus infection, by performing transcriptional analysis of islets harvested during the prediabetic period. Single-cell RNA-sequencing and differential expression analyses of islets from prediabetic rats reveal subsets of β- and α-cells under stress as evidenced by heightened expression, over time, of a transcriptional signature characterized by interferon-stimulated genes, chemokines including Cxcl10, major histocompatibility class I, and genes for the ubiquitin-proteasome system. Mononuclear phagocytes show increased expression of inflammatory markers. RNA-in situ hybridization of rat pancreatic tissue defines the spatial distribution of Cxcl10+ β- and α-cells and their association with CD8+ T cell infiltration, a hallmark of insulitis and islet destruction. Our studies define early islet transcriptional events during immune cell recruitment to islets and reveal spatial associations between stressed β- and α-cells and immune cells. Insights into such early processes can assist in the development of therapeutic and prevention strategies for T1D.
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Affiliation(s)
- Alan G. Derr
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
| | - Adediwura Arowosegbe
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Basanthi Satish
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Sambra D. Redick
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Natasha Qaisar
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Zhiru Guo
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Emma Vanderleeden
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Melanie I. Trombly
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Christina E. Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA
| | - David M. Harlan
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Dale L. Greiner
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA
- Program in Bioinformatics and Integrative Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Jennifer P. Wang
- Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
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7
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Borzouei S, Gholamian-Hamadan M, Behzad M. Impact of interleukin-32α on T helper cell-related cytokines, transcription factors, and proliferation in patients with type 2 diabetes mellitus. Immunopharmacol Immunotoxicol 2022; 45:268-276. [PMID: 36263937 DOI: 10.1080/08923973.2022.2138430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE The ability of interleukin (IL)-32α to induce T helper (Th) 1, Th17, and Treg cytokines (IFN-γ, IL-17, and IL-10, respectively), and transcription factors [(signal transducer and activator of transcription (STAT) 1 and T-box (T-bet) for Th1, STAT3 and retinoid-related orphan receptor (ROR)-γt for Th17, and STAT5 and forkhead box P3 (Foxp3) for Treg)] were investigated in type 2 diabetes mellitus (T2DM). IL-32α effects on Th cell proliferation and related factors including IL-2 and NF-κB were also explored. METHODS Serum levels of IL-32α in 31 patients and 31 healthy controls (HCs) were determined by ELISA assay. CD4+ T cells cultured with polyclonal activators in the presence and absence of recombinant IL-32α (rIL-32α). Gene expressions in cultured Th cells were assessed with real-time PCR. Cytokines in supernatants were measured with ELISA. Proliferation experiments were assessed by flow cytometry. RESULTS The patients showed significant increase in IL-32α levels compared with HCs and its levels were positively correlated with fasting plasma glucose and hemoglobin A1c. rIL-32α enhanced IL-17 and IL-2 production, increased ROR-γt and NF-κB expression, and enhanced Th proliferation in both patients and HCs. In patients, IL-17, ROR-γt, NF-κB, and proliferation levels were higher than those in HCs, in cultures with and without rIL-32α (rIL-32α+ and rIL-32α-). IL-2 levels in rIL-32α+cultures of patients were significantly higher than the HCs, and it was positively correlated with proliferation rate and NF-κB expression. CONCLUSIONS Aberrant IL-32α levels are participated in T2DM pathogenesis. IL-32α potently induces Th17-related factors and amplifies the proliferative function of T cells.
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Affiliation(s)
- Shiva Borzouei
- Department of Internal Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Mahdi Behzad
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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8
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Junttila S, Smolander J, Elo LL. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data. Brief Bioinform 2022; 23:6649780. [PMID: 35880426 PMCID: PMC9487674 DOI: 10.1093/bib/bbac286] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, multicondition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudoreplicate bias. While several methods have already been introduced to carry out the statistical testing in multisubject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multisubject scRNA-seq data. Our results suggest that the pseudobulk methods performed generally best. Both pseudobulks and mixed models that model the subjects as a random effect were superior compared with the naïve single-cell methods that do not model the subjects in any way. While the naïve models achieved higher sensitivity than the pseudobulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naïve methods.
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Affiliation(s)
| | | | - Laura L Elo
- Corresponding author: Laura L. Elo, Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland. Tel.: +358504680795; E-mail:
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9
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Niinistö S, Miettinen ME, Cuthbertson D, Honkanen J, Hakola L, Autio R, Erlund I, Arohonka P, Vuorela A, Härkönen T, Hyöty H, Krischer JP, Vaarala O, Knip M, Virtanen SM. Associations Between Serum Fatty Acids and Immunological Markers in Children Developing Islet Autoimmunity-The TRIGR Nested Case-Control Study. Front Immunol 2022; 13:858875. [PMID: 35693790 PMCID: PMC9175567 DOI: 10.3389/fimmu.2022.858875] [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] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/27/2022] [Indexed: 12/03/2022] Open
Abstract
Aims Altered immune functions as well as fatty acid intake and status have been associated with the development of type 1 diabetes. We aimed to study the relationship between fatty acids and immunological markers in young children with increased genetic risk for type 1 diabetes in order to define putative mechanisms related to development of islet autoimmunity. Methods Serum samples for fatty acid and immunological marker measurements were obtained in the Trial to Reduce IDDM in the Genetically at Risk (TRIGR) ancillary study (Divia) from children born between 2002 and 2007 in 15 countries. Case children (n = 95) were defined as having repeated positivity for at least two out of four diabetes-associated autoantibodies. For each case child, control children were selected matched for country and date of birth (n = 173). Serum fatty acids and immunological markers were measured from cord serum and at the age of 6 and 12 months. Spearman correlation coefficients were calculated between fatty acids and immunological markers. Results Correlations between circulating fatty acids and immunological markers were different in case children who developed islet autoimmunity than in control children already at birth continuing across the first year of life. In case children, saturated fatty acids (SFAs) showed stronger correlations with immunological markers, while in controls, polyunsaturated fatty acids (PUFAs) showed stronger correlations. Conclusions In cases, SFAs were associated with several immunological markers (CXCL10, IL-6, IL-9, IL-17, and CM-CSF) previously linked to the type 1 diabetes disease process. Findings indicate that fatty acids could have immunomodulatory potential in the early phase of the disease development, although causality between fatty acids and the immunological pathways remains to be explored. Trial registry number NCT00179777.
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Affiliation(s)
- Sari Niinistö
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Maija E. Miettinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - David Cuthbertson
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Jarno Honkanen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Leena Hakola
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
- Tampere University Hospital, Research, Development and Innovation Center, Tampere, Finland
| | - Reija Autio
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Iris Erlund
- Department of Government Services, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Petra Arohonka
- Department of Government Services, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Arja Vuorela
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taina Härkönen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Jeffrey P. Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Outi Vaarala
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Knip
- Pediatric Research Center, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Suvi M. Virtanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Unit of Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
- Tampere University Hospital, Research, Development and Innovation Center, Tampere, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
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10
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Starskaia I, Laajala E, Grönroos T, Härkönen T, Junttila S, Kattelus R, Kallionpää H, Laiho A, Suni V, Tillmann V, Lund R, Elo LL, Lähdesmäki H, Knip M, Kalim UU, Lahesmaa R. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia 2022; 65:844-860. [PMID: 35142878 PMCID: PMC8960578 DOI: 10.1007/s00125-022-05657-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. METHODS Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4-CD8- cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. RESULTS We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. CONCLUSIONS/INTERPRETATION These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.
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Affiliation(s)
- Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Roosa Kattelus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Veronika Suni
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vallo Tillmann
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
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11
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Dettmer R, Niwolik I, Cirksena K, Yoshimoto T, Tang Y, Mehmeti I, Gurgul-Convey E, Naujok O. Proinflammatory cytokines induce rapid, NO-independent apoptosis, expression of chemotactic mediators and interleukin-32 secretion in human pluripotent stem cell-derived beta cells. Diabetologia 2022; 65:829-843. [PMID: 35122482 PMCID: PMC8960637 DOI: 10.1007/s00125-022-05654-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS The aim of this study was to examine the effects of proinflammatory cytokines on cells of different developmental stages during the generation of stem cell-derived beta cells (SC-beta cells) from human pluripotent stem cells (hPSCs). We wanted to find out to what extent human SC-beta cells are suitable as an experimental cellular model and, with regard to a possible therapeutic use, whether SC-beta cells have a comparable vulnerability to cytokines as bona fide beta cells. METHODS hPSCs were differentiated towards pancreatic organoids (SC-organoids) using a 3D production protocol. SC-beta cells and non-insulin-producing cells were separated by FACS and differential gene expression profiles of purified human SC-beta cells, progenitor stages and the human beta cell line EndoC-βH1, as a reference, were determined after 24 h incubation with the proinflammatory cytokines IL-1β, TNF-α and IFN-γ via a transcriptome microarray. Furthermore, we investigated apoptosis based on caspase cleavage, the generation of reactive oxygen species and activation of mitogen-activated protein-kinase (MAPK) stress-signalling pathways. RESULTS A 24 h exposure of SC-beta cells to proinflammatory cytokines resulted in significant activation of caspase 3/7 and apoptosis via the extrinsic and intrinsic apoptosis signalling pathways. At this time point, SC-beta cells showed a markedly higher sensitivity towards proinflammatory cytokines than non-insulin-producing cells and EndoC-βH1 cells. Furthermore, we were able to demonstrate the generation of reactive oxygen species and rule out the involvement of NO-mediated stress. A transient activation of stress-signalling pathways p38 mitogen-activated protein kinases (p38) and c-Jun N-terminal kinase (JNK) was already observed after 10 min of cytokine exposure. The transcriptome analysis revealed that the cellular response to proinflammatory cytokines increased with the degree of differentiation of the cells. Cytokines induced the expression of multiple inflammatory mediators including IL-32, CXCL9 and CXCL10 in SC-beta cells and in non-insulin-producing cells. CONCLUSIONS/INTERPRETATION Our results indicate that human SC-beta cells respond to proinflammatory cytokines very similarly to human islets. Due to the fast and fulminant cellular response of SC-beta cells, we conclude that SC-beta cells represent a suitable model for diabetes research. In light of the immaturity of SC-beta cells, they may be an attractive model for developmentally young beta cells as they are, for example, present in patients with early-onset type 1 diabetes. The secretion of chemotactic signals may promote communication between SC-beta cells and immune cells, and non-insulin-producing cells possibly participate in the overall immune response and are thus capable of amplifying the immune response and further stimulating inflammation. We demonstrated that cytokine-treated SC-organoids secrete IL-32, which is considered a promising candidate for type 1 diabetes onset. This underlines the need to ensure the survival of SC-beta cells in an autoimmune environment such as that found in type 1 diabetes.
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Affiliation(s)
- Rabea Dettmer
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Isabell Niwolik
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Karsten Cirksena
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Toshiaki Yoshimoto
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Department of Digestive and Transplant Surgery, Tokushima University, Tokushima, Japan
| | - Yadi Tang
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Ilir Mehmeti
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Ewa Gurgul-Convey
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Ortwin Naujok
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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12
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Extracellular vesicle IL-32 promotes the M2 macrophage polarization and metastasis of esophageal squamous cell carcinoma via FAK/STAT3 pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:145. [PMID: 35428295 PMCID: PMC9013041 DOI: 10.1186/s13046-022-02348-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/26/2022] [Indexed: 01/02/2023]
Abstract
Background Metastasis is the leading cause of mortality in human cancers, including esophageal squamous cell carcinoma (ESCC). As a pro-inflammatory cytokine, IL-32 was reported to be a poor prognostic factor in many cancers. However, the role of IL-32 in ESCC metastasis remains unknown. Methods ESCC cells with ectopic expression or knockdown of IL-32 were established and their effects on cell motility were detected. Ultracentrifugation, Transmission electron microscopy and Western blot were used to verify the existence of extracellular vesicle IL-32 (EV-IL-32). Coculture assay, immunofluorescence, flow cytometry, and in vivo lung metastasis model were performed to identify how EV-IL-32 regulated the crosstalk between ESCC cells and macrophages. Results Here, we found that IL-32 was overexpressed and positively correlated to lymph node metastasis of ESCC. IL-32 was significantly higher in the tumor nest compared with the non-cancerous tissue. We found that IL-32β was the main isoform and loaded in EV derived from ESCC cells. The shuttling of EV-IL-32 derived from ESCC cells into macrophages could promote the polarization of M2 macrophages via FAK-STAT3 pathway. IL-32 overexpression facilitated lung metastasis and was positively correlated with the proportion of M2 macrophages in tumor microenvironment. Conclusions Taken together, our results indicated that EV-IL-32 derived from ESCC cell line could be internalized by macrophages and lead to M2 macrophage polarization via FAK-STAT3 pathway, thus promoting the metastasis of ESCC. These findings indicated that IL-32 could serve as a potential therapeutic target in patients with ESCC. Supplementary information The online version contains supplementary material available at 10.1186/s13046-022-02348-8.
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13
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Mohamed MS, Ghaly S, Azmy KH, Mohamed GA. Assessment of interleukin 32 as a novel biomarker for non-alcoholic fatty liver disease. EGYPTIAN LIVER JOURNAL 2022. [DOI: 10.1186/s43066-022-00189-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Non-alcoholic fatty liver disease (NAFLD) is a metabolic disorder characterised by enhanced hepatic fat deposition and inflammation. Efforts to manage NAFLD are limited by the poorly characterised pathological processes and the lack of precise non-invasive markers, thus, proving the need to further study the involved cytokines, which, in turn, may represent novel molecular targets with possible diagnostic and therapeutic applications. Hence, we aimed to assess the diagnostic utility of serum interleukin 32 (IL-32) in NAFLD cases. This case-control study included 40 NAFLD patients and 40 healthy controls. The serum IL-32 concentrations were assessed by the enzyme-linked immunosorbent assay (ELISA).
Results
The serum IL-32 concentrations were significantly higher in NAFLD cases than controls (76 [45.5–111.125] vs. 13 [8–15] pg/mL, P < 0.001, respectively). IL-32 at a cut-off point > 22.5 pg/mL had 100% sensitivity, 87.50% specificity, 88.9% positive predictive value, 100% negative predictive value, and 98.2% accuracy in detecting the NAFLD cases.
Conclusion
Serum IL-32 could be considered a novel non-invasive marker for NAFLD. Further investigations are warranted to verify the potential utility of IL-32 in the clinical setting.
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14
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Xu G, Grimes TD, Grayson TB, Chen J, Thielen LA, Tse HM, Li P, Kanke M, Lin TT, Schepmoes AA, Swensen AC, Petyuk VA, Ovalle F, Sethupathy P, Qian WJ, Shalev A. Exploratory study reveals far reaching systemic and cellular effects of verapamil treatment in subjects with type 1 diabetes. Nat Commun 2022; 13:1159. [PMID: 35241690 PMCID: PMC8894430 DOI: 10.1038/s41467-022-28826-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Currently, no oral medications are available for type 1 diabetes (T1D). While our recent randomized placebo-controlled T1D trial revealed that oral verapamil had short-term beneficial effects, their duration and underlying mechanisms remained elusive. Now, our global T1D serum proteomics analysis identified chromogranin A (CHGA), a T1D-autoantigen, as the top protein altered by verapamil and as a potential therapeutic marker and revealed that verapamil normalizes serum CHGA levels and reverses T1D-induced elevations in circulating proinflammatory T-follicular-helper cell markers. RNA-sequencing further confirmed that verapamil regulates the thioredoxin system and promotes an anti-oxidative, anti-apoptotic and immunomodulatory gene expression profile in human islets. Moreover, continuous use of oral verapamil delayed T1D progression, promoted endogenous beta-cell function and lowered insulin requirements and serum CHGA levels for at least 2 years and these benefits were lost upon discontinuation. Thus, the current studies provide crucial mechanistic and clinical insight into the beneficial effects of verapamil in T1D.
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Affiliation(s)
- Guanlan Xu
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Tiffany D Grimes
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Truman B Grayson
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Junqin Chen
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Lance A Thielen
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Hubert M Tse
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Peng Li
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,School of Nursing, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Fernando Ovalle
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anath Shalev
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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15
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Bediaga NG, Garnham AL, Naselli G, Bandala-Sanchez E, Stone NL, Cobb J, Harbison JE, Wentworth JM, Ziegler AG, Couper JJ, Smyth GK, Harrison LC. Cytotoxicity-Related Gene Expression and Chromatin Accessibility Define a Subset of CD4+ T Cells That Mark Progression to Type 1 Diabetes. Diabetes 2022; 71:566-577. [PMID: 35007320 PMCID: PMC8893947 DOI: 10.2337/db21-0612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/12/2021] [Indexed: 11/13/2022]
Abstract
Type 1 diabetes in children is heralded by a preclinical phase defined by circulating autoantibodies to pancreatic islet antigens. How islet autoimmunity is initiated and then progresses to clinical diabetes remains poorly understood. Only one study has reported gene expression in specific immune cells of children at risk associated with progression to islet autoimmunity. We analyzed gene expression with RNA sequencing in CD4+ and CD8+ T cells, natural killer (NK) cells, and B cells, and chromatin accessibility by assay for transposase-accessible chromatin sequencing (ATAC-seq) in CD4+ T cells, in five genetically at risk children with islet autoantibodies who progressed to diabetes over a median of 3 years ("progressors") compared with five children matched for sex, age, and HLA-DR who had not progressed ("nonprogressors"). In progressors, differentially expressed genes (DEGs) were largely confined to CD4+ T cells and enriched for cytotoxicity-related genes/pathways. Several top-ranked DEGs were validated in a semi-independent cohort of 13 progressors and 11 nonprogressors. Flow cytometry confirmed that progression was associated with expansion of CD4+ cells with a cytotoxic phenotype. By ATAC-seq, progression was associated with reconfiguration of regulatory chromatin regions in CD4+ cells, some linked to differentially expressed cytotoxicity-related genes. Our findings suggest that cytotoxic CD4+ T cells play a role in promoting progression to type 1 diabetes.
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Affiliation(s)
- Naiara G. Bediaga
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Alexandra L. Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Gaetano Naselli
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Esther Bandala-Sanchez
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Natalie L. Stone
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Joanna Cobb
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Jessica E. Harbison
- Department of Endocrinology and Diabetes, Women’s and Children’s Hospital, North Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John M. Wentworth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, Australia
| | - Annette-G. Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jennifer J. Couper
- Department of Endocrinology and Diabetes, Women’s and Children’s Hospital, North Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Leonard C. Harrison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Corresponding author: Leonard C. Harrison,
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16
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Shim S, Lee S, Hisham Y, Kim S, Nguyen TT, Taitt AS, Hwang J, Jhun H, Park HY, Lee Y, Yeom SC, Kim SY, Kim YG, Kim S. Comparison of the Seven Interleukin-32 Isoforms’ Biological Activities: IL-32θ Possesses the Most Dominant Biological Activity. Front Immunol 2022; 13:837588. [PMID: 35281066 PMCID: PMC8914309 DOI: 10.3389/fimmu.2022.837588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Cytokines are significantly associated with the homeostasis of immune responses in health and disease. Interleukin-32 (IL-32) is a cytokine originally discovered in natural killer cell transcript 4. IL-32 with different disorders has been described in terms of pathogenesis and the progression of diseases. Clinical studies have investigated IL-32 under various conditions, such as viral infection, autoimmune diseases, inflammatory diseases, certain types of cancer, vascular disease, and pulmonary diseases. The high expression of IL-32 was identified in different tissues with various diseases and found to have multiple transcripts of up to seven isoforms. However, the purification and biological activities of these isoforms have not been investigated yet. Therefore, in this study, we purified and compared the biological activity of recombinant IL-32 (rIL-32) isoforms. This is the first time for seven rIL-32 isoforms (α, β, δ, γ, ϵ, ζ, and θ) to be cloned and purified using an Escherichia coli expression system. Next, we evaluate the biological activities of these seven rIL-32 isoforms, which were used to treat different types of cells by assessing the levels of inflammatory cytokine production. The results revealed that rIL-32θ possessed the most dominant biological activity in both immune and non-immune cells.
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Affiliation(s)
- Saerok Shim
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Siyoung Lee
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Yasmin Hisham
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Sinae Kim
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Tam T. Nguyen
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Afeisha S. Taitt
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Jihyeong Hwang
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Hyunjhung Jhun
- Technical Assistance Center, Korea Food Research Institute, Wanju, South Korea
| | - Ho-Young Park
- Research Group of Functional Food Materials, Korea Food Research Institute, Wanju, South Korea
| | - Youngmin Lee
- Department of Medicine, Pusan Paik Hospital, Collage of Medicine, Inje University, Busan, South Korea
| | - Su Cheong Yeom
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, South Korea
| | - Sang-Yeob Kim
- Convergence Medicine Research Center, Asan Institute for Life Science, Asan Medical Center, Seoul, South Korea
| | - Yong-Gil Kim
- Division of Rheumatology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
- *Correspondence: Yong-Gil Kim, ; Soohyun Kim,
| | - Soohyun Kim
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea
- *Correspondence: Yong-Gil Kim, ; Soohyun Kim,
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17
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Kraus G, Weigelt M, Reinhardt S, Petzold A, Dahl A, Bonifacio E. Reproducibility of 10x Genomics single cell RNA sequencing method in the immune cell environment. J Immunol Methods 2022; 502:113227. [PMID: 35031279 DOI: 10.1016/j.jim.2022.113227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/04/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
10x Genomics is a highly accessible single cell RNA sequencing platform that allows for simultaneous gene expression analysis and identification of receptor chain combinations in cells of the adaptive immune system. Here, we asked whether the gene and receptor expression measurements in peripheral blood mononuclear cells (PBMC) are influenced by technical, cell freezing, FACS-processing, and day to day biological variation. No differentially expressed gene was observed between 1. triplicates aliquots taken from the same vial of frozen PBMC; 2. triplicate vials of frozen PBMC; and 3. triplicate aliquots taken from the same vial of frozen PBMC and processed separately for FACS staining and sorting of different PBMC populations. A small number of differentially expressed genes were observed between PBMC sampled, isolated and frozen from the same donor on different days, and these differences were more pronounced in the memory B cells than other cell populations. T cell receptors were recovered in all replicates when at least 5 cells per clonotype were identified. These findings show high reproducibility of 10x Genomics single cell RNA sequencing data in the immune cell context.
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Affiliation(s)
- Gloria Kraus
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Marc Weigelt
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Ezio Bonifacio
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany,; German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden, Dresden, Germany,; Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
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18
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Sudhir PR, Lin TD, Zhang Q. HLA Allele-Specific Quantitative Profiling of Type 1 Diabetic B Lymphocyte Immunopeptidome. J Proteome Res 2022; 21:250-264. [PMID: 34932366 PMCID: PMC8742597 DOI: 10.1021/acs.jproteome.1c00842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptide ligands presented by human leukocyte antigen (HLA) molecules on the cell surface represent the immunopeptidome that could be utilized for identification of antigenic peptides for immunotherapy and prevention of autoimmune diseases. Although T-cells are well-known key players in the destruction of pancreatic beta-cells in type 1 diabetes (T1D), increasing evidence points toward a role for B-cells in disease pathogenesis. However, as antigen presenting cells, little is known about the comprehensive immunopeptidome of B cells and their changes in the context of T1D. We performed HLA allele-specific quantitative immunopeptidomics using B lymphocytes derived from T1D patients and healthy controls. Hundreds of HLA-I and HLA-II immunopeptides were identified as differentially regulated in T1D per HLA allele for B cells sharing identical HLA alleles. The results were further validated using additional T1D and healthy B cells with partially overlapped HLA alleles. Differentially expressed immunopeptides were confirmed with targeted proteomics and for reactivity using known T-cell assays in the immune epitope database. Considering samples with identical HLA alleles are difficult to obtain for T1D and other similar HLA-restricted diseases, our work represents a viable approach to better understand HLA allele-specific antigen presentation and may facilitate identification of immunopeptides for therapeutic applications in autoimmune diseases. Data are available via ProteomeXchange with identifier PXD026184.
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Affiliation(s)
- Putty-Reddy Sudhir
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Tai-Du Lin
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA,Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA,Corresponding author: Qibin Zhang ()
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19
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Sen P, Andrabi SBA, Buchacher T, Khan MM, Kalim UU, Lindeman TM, Alves MA, Hinkkanen V, Kemppainen E, Dickens AM, Rasool O, Hyötyläinen T, Lahesmaa R, Orešič M. Quantitative genome-scale metabolic modeling of human CD4 + T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways. Cell Rep 2021; 37:109973. [PMID: 34758307 DOI: 10.1016/j.celrep.2021.109973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/26/2021] [Accepted: 10/19/2021] [Indexed: 02/04/2023] Open
Abstract
T cell activation, proliferation, and differentiation involve metabolic reprogramming resulting from the interplay of genes, proteins, and metabolites. Here, we aim to understand the metabolic pathways involved in the activation and functional differentiation of human CD4+ T cell subsets (T helper [Th]1, Th2, Th17, and induced regulatory T [iTreg] cells). Here, we combine genome-scale metabolic modeling, gene expression data, and targeted and non-targeted lipidomics experiments, together with in vitro gene knockdown experiments, and show that human CD4+ T cells undergo specific metabolic changes during activation and functional differentiation. In addition, we confirm the importance of ceramide and glycosphingolipid biosynthesis pathways in Th17 differentiation and effector functions. Through in vitro gene knockdown experiments, we substantiate the requirement of serine palmitoyltransferase (SPT), a de novo sphingolipid pathway in the expression of proinflammatory cytokines (interleukin [IL]-17A and IL17F) by Th17 cells. Our findings provide a comprehensive resource for selective manipulation of CD4+ T cells under disease conditions characterized by an imbalance of Th17/natural Treg (nTreg) cells.
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Affiliation(s)
- Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
| | | | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Tuomas Mikael Lindeman
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Victoria Hinkkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Esko Kemppainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Alex M Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Chemistry, University of Turku, 20520 Turku, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland.
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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20
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Ma P, Zhang P, Chen S, Shi W, Ye J, Chen S, Ju R, Liu B, Zheng Y, Liu Y. Immune Cell Landscape of Patients With Diabetic Macular Edema by Single-Cell RNA Analysis. Front Pharmacol 2021; 12:754933. [PMID: 34594230 PMCID: PMC8476792 DOI: 10.3389/fphar.2021.754933] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Purpose: We performed single-cell RNA sequencing (scRNA-seq), an unbiased and high-throughput single cell technology, to determine phenotype and function of peripheral immune cells in patients with diabetic macular edema (DME). Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from DME patients and healthy controls (HC). The single-cell samples were loaded on the Chromium platform (10x Genomics) for sequencing. R package Seurat v3 was used for data normalizing, clustering, dimensionality reduction, differential expression analysis, and visualization. Results: We constructed a single-cell RNA atlas comprising 57,650 PBMCs (24,919 HC, 32,731 DME). We divided all immune cells into five major immune cell lineages, including monocytes (MC), T cells (TC), NK cells (NK), B cells (BC), and dendritic cells (DC). Our differential expression gene (DEG) analysis showed that MC was enriched of genes participating in the cytokine pathway and inflammation activation. We further subdivided MC into five subsets: resting CD14++ MC, proinflammatory CD14++ MC, intermediate MC, resting CD16++ MC and pro-inflammatory CD16++ MC. Remarkably, we revealed that the proinflammatory CD14++ monocytes predominated in promoting inflammation, mainly by increasingly production of inflammatory cytokines (TNF, IL1B, and NFKBIA) and chemokines (CCL3, CCL3L1, CCL4L2, CXCL2, and CXCL8). Gene Ontology (GO) and pathway analysis of the DEGs demonstrated that the proinflammatory CD14++ monocytes, especially in DME patients, upregulated inflammatory pathways including tumor necrosis factor-mediated signaling pathway, I-kappaB kinase/NF-kappaB signaling, and toll-like receptor signaling pathway. Conclusion: In this study, we construct the first immune landscape of DME patients with T2D and confirmed innate immune dysregulation in peripheral blood based on an unbiased scRNA-seq approach. And these results demonstrate potential target cell population for anti-inflammation treatments.
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Affiliation(s)
- Pengjuan Ma
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Ping Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuxia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Shida Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Rong Ju
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bingqian Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Guangzhou, China
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21
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Hanna SJ, Tatovic D, Thayer TC, Dayan CM. Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. Front Immunol 2021; 12:751701. [PMID: 34659258 PMCID: PMC8519581 DOI: 10.3389/fimmu.2021.751701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/14/2021] [Indexed: 01/10/2023] Open
Abstract
In the past few years, huge advances have been made in techniques to analyse cells at an individual level using RNA sequencing, and many of these have precipitated exciting discoveries in the immunology of type 1 diabetes (T1D). This review will cover the first papers to use scRNAseq to characterise human lymphocyte phenotypes in T1D in the peripheral blood, pancreatic lymph nodes and islets. These have revealed specific genes such as IL-32 that are differentially expressed in islet -specific T cells in T1D. scRNAseq has also revealed wider gene expression patterns that are involved in T1D and can predict its development even predating autoantibody production. Single cell sequencing of TCRs has revealed V genes and CDR3 motifs that are commonly used to target islet autoantigens, although truly public TCRs remain elusive. Little is known about BCR repertoires in T1D, but scRNAseq approaches have revealed that insulin binding BCRs commonly use specific J genes, share motifs between donors and frequently demonstrate poly-reactivity. This review will also summarise new developments in scRNAseq technology, the insights they have given into other diseases and how they could be leveraged to advance research in the type 1 diabetes field to identify novel biomarkers and targets for immunotherapy.
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Affiliation(s)
- Stephanie J. Hanna
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Danijela Tatovic
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Terri C. Thayer
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Department of Biological and Chemical Sciences, School of Natural and Social Sciences, Roberts Wesleyan College, Rochester, NY, United States
| | - Colin M. Dayan
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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22
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Impact of interleukin-32 germ-line rs28372698 and intronic rs12934561 polymorphisms on cancer development: A systematic review and meta-analysis. Int Immunopharmacol 2021; 99:107964. [PMID: 34271417 DOI: 10.1016/j.intimp.2021.107964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/21/2021] [Accepted: 07/05/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE The pro-inflammatory cytokine IL-32 has high susceptibility to develop cancer. But no previous meta-analysis was done to provide firm evidence. This systematic review and meta-analysis was designed to evaluate the association of IL-32 gene polymorphisms (rs28372698 and rs12934561) with cancer. METHOD Eligible studies were selected using authentic databases searching from January 2013 to January 2021. Demographic data and genotypic information were extracted and organized from the selected studies. Review Manager (RevMan) version 5.4 was used to perform data analysis and data arrangement for meta-analysis. RESULTS A total of seven studies with 3395 patients and 3781 controls were included in this study. IL-32 rs28372698 polymorphism implied that mutant allele (TT) carriers had a significantly higher risk of cancer (OR = 1.43, p = 0.032). Codominant 3, recessive and allele models also showed 1.36-, 1.38- and 1.11-fold increased risk, respectively (p < 0.05). Besides, the Asian population showed a significantly increased risk in codominant 2 (OR = 1.74), codominant 3 (OR = 1.78), recessive (OR = 1.76) and allele model (OR = 1.16). IL-32 rs12934561 showed significantly reduced cancer risk in codominant 1 (OR = 0.66. p = 0.035), codominant 2 (OR = 0.76, p = 0.007), and dominant model (OR = 0.72, p = 0.012). After subgroup analysis, an association of rs12934561 was found in Asians (codominant 1: OR = 0.54, p = 7.28 × 10-8; codominant 2: OR = 1.40, p = 0.019; codominant 3: OR = 0.76, p = 0.0006; dominant model: OR = 0.64, p = 1.12 × 10-5; overdominant model: OR = 0.64, p = 3.92 × 10-7) but not in Caucasians. After stratifying with the control source, a significant (p < 0.05) association of rs28372698 and rs12934561 was found with cancer in population-based controls. No publication bias was found, and the outcome of this meta-analysis was not influenced by any individual study confirmed from sensitivity analysis. Moreover, trial sequential analysis (TSA) established a link between rs28372698 and rs12934561 polymorphisms and cancer. CONCLUSION The outcome of this meta-analysis revealed that IL-32 rs28372698 and rs12934561 polymorphisms are associated with cancer. Moreover, the Asian dynasty had a significant association compared to Caucasians.
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23
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Wesley JD, Pfeiffer S, Schneider D, Friedrich D, Perdue N, Sehested-Hansen B, Hagopian W, von Herrath MG. Peripheral autoreactive CD8 T-cell frequencies are too variable to be a reliable predictor of disease progression of human type 1 diabetes. Clin Transl Immunology 2021; 10:e1309. [PMID: 34267894 PMCID: PMC8273427 DOI: 10.1002/cti2.1309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022] Open
Abstract
Objectives The detection of a peripheral immune cell signature that specifically reflects autoimmunity in type 1 diabetes would enable the prediction and staging of disease on an individual basis. However, defining such a signature is technically challenging. Reliable interpretation of immune cell‐related biomarkers depends on their inherent variability and, to understand this variability, longitudinal analyses are required. Methods We performed a longitudinal observational study in which 40 individuals with elevated genetic risk of type 1 diabetes and persistent islet autoantibodies provided a blood sample every 4–6 weeks for > 1 year. Results Peripheral immune cell composition (T cells, NK cells and monocytes) was assessed using well‐validated flow cytometry panels and demonstrated that, while non‐antigen‐specific immune cell subsets were stable over time, autoantigen‐reactive T‐cell frequencies were highly variable in and between individuals. Neither the frequency nor phenotype of non‐antigen‐specific subsets or autoreactive CD8+ T cells associated with clinical onset of T1D. Conclusion The findings from the Type 1 Diabetes Longitudinal BIomarker Trial underscore the inherent challenge of evaluating changes in peripheral immune cell populations as surrogates of organ‐specific disease activity. The variability of peripheral antigen‐specific T cells precludes their use as a prognostic marker and clearly demonstrates that a reliable prognostic cell signature remains elusive.
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Affiliation(s)
| | | | | | | | - Nikole Perdue
- Novo Nordisk Research Center Seattle, Inc. Seattle WA USA
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24
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Arif S, Pujol-Autonell I, Kamra Y, Williams E, Yusuf N, Domingo-Vila C, Shahrabi Y, Pollock E, Khatri L, Peakman M, Tree T, Lorenc A. Mapping T Cell Responses to Native and Neo-Islet Antigen Epitopes in at Risk and Type 1 Diabetes Subjects. Front Immunol 2021; 12:675746. [PMID: 34262563 PMCID: PMC8274489 DOI: 10.3389/fimmu.2021.675746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022] Open
Abstract
Aims Recent studies highlight the potentially important role of neoepitopes in breaking immune tolerance in type 1 diabetes. T cell reactivity to these neoepitopes has been reported, but how this response compares quantitatively and phenotypically with previous reports on native epitopes is not known. Thus, an understanding of the relationship between native and neoepitopes and their role as tolerance breakers or disease drivers in type 1 diabetes is required. We set out to compare T cell reactivity and phenotype against a panel of neo- and native islet autoantigenic epitopes to examine how this relates to stages of type 1 diabetes development. Methods Fifty-four subjects comprising patients with T1D, and autoantibody-positive unaffected family members were tested against a panel of neo- and native epitopes by ELISPOT (IFN-γ, IL-10, and IL-17). A further subset of two patients was analyzed by Single Cell Immune Profiling (RNAseq and TCR α/β) after stimulation with pools of native and neoepitope peptides. Results T cell responses to native and neoepitopes were present in patients with type 1 diabetes and at-risk subjects, and overall, there were no significant differences in the frequency, magnitude, or phenotype between the two sets of peptide stimuli. Single cell RNAseq on responder T cells revealed a similar profile in T1D patients stimulated with either neo- or native epitopes. A pro-inflammatory gene expression profile (TNF-α, IFN-γ) was dominant in both native and neoepitope stimulated T cells. TCRs with identical clonotypes were found in T cell responding to both native and neoepitopes. Conclusion/Interpretation These data suggest that in peripheral blood, T cell responses to both native and neoepitopes are similar in terms of frequency and phenotype in patients with type 1 diabetes and high-risk unaffected family members. Furthermore, using a combination of transcriptomic and clonotypic analyses, albeit using a limited panel of peptides, we show that neoepitopes are comparable to native epitopes currently in use for immune-monitoring studies.
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Affiliation(s)
- Sefina Arif
- Department of Immunobiology, King’s College London, Guy’s Hospital, London, United Kingdom
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25
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Patel SK, Ma CS, Fourlanos S, Greenfield JR. Autoantibody-Negative Type 1 Diabetes: A Neglected Subtype. Trends Endocrinol Metab 2021; 32:295-305. [PMID: 33712367 DOI: 10.1016/j.tem.2021.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022]
Abstract
Up to 15% of individuals with a clinical phenotype of type 1 diabetes (T1D) do not have evidence of seropositivity for pancreatic islet autoantibodies. On this basis, they are classified as nonimmune or idiopathic, and remain an understudied population, as they are excluded from T1D immunomodulatory trials. Our limited understanding of the disease aetiopathogenesis in autoantibody-negative T1D hinders our ability to improve diagnostic pathways and discover novel therapeutic agents; particularly as we progress towards an era of precision medicine. This review summarises the current understanding and challenges in studying autoantibody-negative T1D. We review the literature regarding T1D classification, and the role of autoimmunity and defects in the immunogenic pathway that may distinguish autoantibody-positive and -negative T1D.
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Affiliation(s)
- Shivani K Patel
- Diabetes and Metabolism, Garvan Institute of Medical Research, Sydney, NSW, Australia; Department of Diabetes and Endocrinology, St. Vincent's Hospital, Sydney, NSW, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Cindy S Ma
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia; Human Immune Disorders, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Spiros Fourlanos
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Jerry R Greenfield
- Diabetes and Metabolism, Garvan Institute of Medical Research, Sydney, NSW, Australia; Department of Diabetes and Endocrinology, St. Vincent's Hospital, Sydney, NSW, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia.
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26
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Kucuksezer UC, Aktas Cetin E, Esen F, Tahrali I, Akdeniz N, Gelmez MY, Deniz G. The Role of Natural Killer Cells in Autoimmune Diseases. Front Immunol 2021; 12:622306. [PMID: 33717125 PMCID: PMC7947192 DOI: 10.3389/fimmu.2021.622306] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
Natural killer (NK) cells, the large granular lymphocytes differentiated from the common lymphoid progenitors, were discovered in early 1970’s. They are members of innate immunity and were initially defined by their strong cytotoxicity against virus-infected cells and by their important effector functions in anti-tumoral immune responses. Nowadays, NK cells are classified among the recently discovered innate lymphoid cell subsets and have capacity to influence both innate and adaptive immune responses. Therefore, they can be considered as innate immune cells that stands between the innate and adaptive arms of immunity. NK cells don’t express T or B cell receptors and are recognized by absence of CD3. There are two major subgroups of NK cells according to their differential expression of CD16 and CD56. While CD16+CD56dim subset is best-known by their cytotoxic functions, CD16-CD56bright NK cell subset produces a bunch of cytokines comparable to CD4+ T helper cell subsets. Another subset of NK cells with production of interleukin (IL)-10 was named as NK regulatory cells, which has suppressive properties and could take part in immune-regulatory responses. Activation of NK cells is determined by a delicate balance of cell-surface receptors that have either activating or inhibitory properties. On the other hand, a variety of cytokines including IL-2, IL-12, IL-15, and IL-18 influence NK cell activity. NK-derived cytokines and their cytotoxic functions through induction of apoptosis take part in regulation of the immune responses and could contribute to the pathogenesis of many immune mediated diseases including ankylosing spondylitis, Behçet’s disease, multiple sclerosis, rheumatoid arthritis, psoriasis, systemic lupus erythematosus and type-1 diabetes. Dysregulation of NK cells in autoimmune disorders may occur through multiple mechanisms. Thanks to the rapid developments in biotechnology, progressive research in immunology enables better characterization of cells and their delicate roles in the complex network of immunity. As NK cells stand in between innate and adaptive arms of immunity and “bridge” them, their contribution in inflammation and immune regulation deserves intense investigations. Better understanding of NK-cell biology and their contribution in both exacerbation and regulation of inflammatory disorders is a requisite for possible utilization of these multi-faceted cells in novel therapeutic interventions.
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Affiliation(s)
- Umut Can Kucuksezer
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Esin Aktas Cetin
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Fehim Esen
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.,Department of Ophthalmology, Medical Faculty, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ilhan Tahrali
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Nilgun Akdeniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Metin Yusuf Gelmez
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Gunnur Deniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
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27
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Gianchecchi E, Delfino DV, Fierabracci A. Natural Killer Cells: Potential Biomarkers and Therapeutic Target in Autoimmune Diseases? Front Immunol 2021; 12:616853. [PMID: 33679757 PMCID: PMC7933577 DOI: 10.3389/fimmu.2021.616853] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Autoimmune diseases recognize a multifactorial pathogenesis, although the exact mechanism responsible for their onset remains to be fully elucidated. Over the past few years, the role of natural killer (NK) cells in shaping immune responses has been highlighted even though their involvement is profoundly linked to the subpopulation involved and to the site where such interaction takes place. The aberrant number and functionality of NK cells have been reported in several different autoimmune disorders. In the present review, we report the most recent findings regarding the involvement of NK cells in both systemic and organ-specific autoimmune diseases, including type 1 diabetes (T1D), primary biliary cholangitis (PBC), systemic sclerosis, systemic lupus erythematosus (SLE), primary Sjögren syndrome, rheumatoid arthritis, and multiple sclerosis. In T1D, innate inflammation induces NK cell activation, disrupting the Treg function. In addition, certain genetic variants identified as risk factors for T1D influenced the activation of NK cells promoting their cytotoxic activity. The role of NK cells has also been demonstrated in the pathogenesis of PBC mediating direct or indirect biliary epithelial cell destruction. NK cell frequency and number were enhanced in both the peripheral blood and the liver of patients and associated with increased NK cell cytotoxic activity and perforin expression levels. NK cells were also involved in the perpetuation of disease through autoreactive CD4 T cell activation in the presence of antigen-presenting cells. In systemic sclerosis (SSc), in addition to phenotypic abnormalities, patients presented a reduction in CD56hi NK-cells. Moreover, NK cells presented a deficient killing activity. The influence of the activating and inhibitory killer cell immunoglobulin-like receptors (KIRs) has been investigated in SSc and SLE susceptibility. Furthermore, autoantibodies to KIRs have been identified in different systemic autoimmune conditions. Because of its role in modulating the immune-mediated pathology, NK subpopulation could represent a potential marker for disease activity and target for therapeutic intervention.
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Affiliation(s)
- Elena Gianchecchi
- VisMederi srl, Siena, Italy.,Infectivology and Clinical Trials Research Area, Primary Immunodeficiencies Research Unit, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Domenico V Delfino
- Section of Pharmacology, Department of Medicine, University of Perugia, Perugia, Italy
| | - Alessandra Fierabracci
- Infectivology and Clinical Trials Research Area, Primary Immunodeficiencies Research Unit, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
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28
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Timonen J, Mannerström H, Vehtari A, Lähdesmäki H. lgpr: An interpretable nonparametric method for inferring covariate effects from longitudinal Data. Bioinformatics 2021; 37:1860-1867. [PMID: 33471072 PMCID: PMC8317115 DOI: 10.1093/bioinformatics/btab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/14/2020] [Accepted: 01/08/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Longitudinal study designs are indispensable for studying disease progression. Inferring covariate effects from longitudinal data, however, requires interpretable methods that can model complicated covariance structures and detect nonlinear effects of both categorical and continuous covariates, as well as their interactions. Detecting disease effects is hindered by the fact that they often occur rapidly near the disease initiation time, and this time point cannot be exactly observed. An additional challenge is that the effect magnitude can be heterogeneous over the subjects. RESULTS We present lgpr, a widely applicable and interpretable method for nonparametric analysis of longitudinal data using additive Gaussian processes. We demonstrate that it outperforms previous approaches in identifying the relevant categorical and continuous covariates in various settings. Furthermore, it implements important novel features, including the ability to account for the heterogeneity of covariate effects, their temporal uncertainty, and appropriate observation models for different types of biomedical data. The lgpr tool is implemented as a comprehensive and user-friendly R-package. AVAILABILITY lgpr is available at jtimonen.github.io/lgpr-usage with documentation, tutorials, test data, and code for reproducing the experiments of this paper. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juho Timonen
- Department of Computer Science, Aalto University, Espoo, 00076, Finland
| | | | - Aki Vehtari
- Department of Computer Science, Aalto University, Espoo, 00076, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, 00076, Finland
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29
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de Albuquerque R, Komsi E, Starskaia I, Ullah U, Lahesmaa R. The role of Interleukin-32 in autoimmunity. Scand J Immunol 2021; 93:e13012. [PMID: 33336406 DOI: 10.1111/sji.13012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/28/2020] [Accepted: 12/12/2020] [Indexed: 01/10/2023]
Abstract
Interleukin-32 (IL-32) is a pro-inflammatory cytokine that induces other cytokines involved in inflammation, including tumour necrosis factor (TNF)-α, IL-6 and IL-1β. Recent evidence suggests that IL-32 has a crucial role in host defence against pathogens, as well as in the pathogenesis of chronic inflammation. Abnormal IL-32 expression has been linked to several autoimmune diseases, such as rheumatoid arthritis and inflammatory bowel diseases, and a recent study suggested the importance of IL-32 in the pathogenesis of type 1 diabetes. However, despite accumulating evidence, many molecular characteristics of this cytokine, including the secretory route and the receptor for IL-32, remain largely unknown. In addition, the IL-32 gene is found in higher mammals but not in rodents. In this review, we outline the current knowledge of IL-32 biological functions, properties, and its role in autoimmune diseases. We particularly highlight the role of IL-32 in rheumatoid arthritis and type 1 diabetes.
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Affiliation(s)
- Rafael de Albuquerque
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elina Komsi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ubaid Ullah
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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30
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Zhao M, Jiang J, Zhao M, Chang C, Wu H, Lu Q. The Application of Single-Cell RNA Sequencing in Studies of Autoimmune Diseases: a Comprehensive Review. Clin Rev Allergy Immunol 2020; 60:68-86. [PMID: 33236283 DOI: 10.1007/s12016-020-08813-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 01/15/2023]
Abstract
Complex composition is one of the most important features of the immune system, involving many types of organs, tissues, cells, and molecules that perform immune functions. The normal function of each component of the immune system is the guarantee for maintaining the relatively stable immune function of the body. When the self-immune tolerance mechanism of the body is unregulated or destroyed, the immune system reacts to autoantigens, resulting in damage to self-tissues and organs or an immunopathological state with abnormal functions. Autoimmune diseases are diverse, and their pathogenesis is complicated. Various immune cells and their interactions play significant roles in the occurrence and development of diseases. The solution to heterogeneity of immune cells is the basic science and translational understanding of how genes and the environment interact to induce disease so that we can develop personalized medicine, a goal that has to this point eluded scientists. Single-cell RNA sequencing (scRNA-Seq) refers to a new technique allowing high-throughput sequencing analysis of the whole transcriptome to reveal the gene expression status of individual cells. It has emerged as an indispensable tool in the field of life science research, and can help identify the complex mechanism of cell heterogeneity, discover new cell subsets, and help uncover the molecular mechanisms of pathogenesis, the evolution of disorders, and drug resistance. This information can provide us with new strategies for diagnosis and prognostic evaluation, as well as monitoring treatment responses. In this review, we summarize the crucial experimental procedures used for single-cell RNA sequencing, and the current applications of this technique to study autoimmune diseases are described in detail. This technique will be widely used in more in-depth studies of autoimmune diseases and will contribute to the diagnosis and therapies of these disorders.
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Affiliation(s)
- Mingming Zhao
- Department of Dermatology, the Second Xiangya Hospital, Central South University, 410011, Changsha, Hunan, People's Republic of China.,Hunan Key Laboratory of Medical Epigenomics, 410011, Changsha, Hunan, People's Republic of China
| | - Jiao Jiang
- Department of Dermatology, the Second Xiangya Hospital, Central South University, 410011, Changsha, Hunan, People's Republic of China.,Hunan Key Laboratory of Medical Epigenomics, 410011, Changsha, Hunan, People's Republic of China
| | - Ming Zhao
- Department of Dermatology, the Second Xiangya Hospital, Central South University, 410011, Changsha, Hunan, People's Republic of China.,Hunan Key Laboratory of Medical Epigenomics, 410011, Changsha, Hunan, People's Republic of China
| | - Christopher Chang
- Division of Pediatric Immunology and Allergy, Joe DiMaggio Children's Hospital, Hollywood, FL, 33021, USA.,Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, 95616, USA
| | - Haijing Wu
- Department of Dermatology, the Second Xiangya Hospital, Central South University, 410011, Changsha, Hunan, People's Republic of China. .,Hunan Key Laboratory of Medical Epigenomics, 410011, Changsha, Hunan, People's Republic of China.
| | - Qianjin Lu
- Department of Dermatology, the Second Xiangya Hospital, Central South University, 410011, Changsha, Hunan, People's Republic of China. .,Hunan Key Laboratory of Medical Epigenomics, 410011, Changsha, Hunan, People's Republic of China.
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31
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Akhbari P, Richardson SJ, Morgan NG. Type 1 Diabetes: Interferons and the Aftermath of Pancreatic Beta-Cell Enteroviral Infection. Microorganisms 2020; 8:microorganisms8091419. [PMID: 32942706 PMCID: PMC7565444 DOI: 10.3390/microorganisms8091419] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) have long been implicated in the pathogenesis of type 1 diabetes (T1D), and accumulating evidence has associated virus-induced autoimmunity with the loss of pancreatic beta cells in T1D. Inflammatory cytokines including interferons (IFN) form a primary line of defence against viral infections, and their chronic elevation is a hallmark feature of many autoimmune diseases. IFNs play a key role in activating and regulating innate and adaptive immune responses, and to do so they modulate the expression of networks of genes and transcription factors known generically as IFN stimulated genes (ISGs). ISGs in turn modulate critical cellular processes ranging from cellular metabolism and growth regulation to endoplasmic reticulum (ER) stress and apoptosis. More recent studies have revealed that IFNs also modulate gene expression at an epigenetic as well as post-transcriptional and post-translational levels. As such, IFNs form a key link connecting the various genetic, environmental and immunological factors involved in the initiation and progression of T1D. Therefore, gaining an improved understanding of the mechanisms by which IFNs modulate beta cell function and survival is crucial in explaining the pathogenesis of virally-induced T1D. This should provide the means to prevent, decelerate or even reverse beta cell impairment.
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32
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Aass KR, Kastnes MH, Standal T. Molecular interactions and functions of IL-32. J Leukoc Biol 2020; 109:143-159. [PMID: 32869391 DOI: 10.1002/jlb.3mr0620-550r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
IL-32 is a multifaceted cytokine associated with several diseases and inflammatory conditions. Its expression is induced in response to cellular stress such as hypoxia, infections, and pro-inflammatory cytokines. IL-32 can be secreted from cells and can induce the production of pro-inflammatory cytokines from several cell types but are also described to have anti-inflammatory functions. The intracellular form of IL-32 is shown to play an important role in various cellular processes, including the defense against intracellular bacteria and viruses and in modulation of cell metabolism. In this review, we discuss current literature on molecular interactions of IL-32 with other proteins. We also review data on the role of intracellular IL-32 as a metabolic regulator and its role in antimicrobial host defense.
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Affiliation(s)
- Kristin Roseth Aass
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway
| | - Martin H Kastnes
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway
| | - Therese Standal
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway.,Department of Hematology, St. Olavs Hospital, Trondheim, Norway
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33
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Rahman AH, Homann D. Mass cytometry and type 1 diabetes research in the age of single-cell data science. Curr Opin Endocrinol Diabetes Obes 2020; 27:231-239. [PMID: 32618635 PMCID: PMC7596883 DOI: 10.1097/med.0000000000000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW New single-cell tec. hnologies developed over the past decade have considerably reshaped the biomedical research landscape, and more recently have found their way into studies probing the pathogenesis of type 1 diabetes (T1D). In this context, the emergence of mass cytometry in 2009 revolutionized immunological research in two fundamental ways that also affect the T1D world: first, its ready embrace by the community and rapid dissemination across academic and private science centers alike established a new standard of analytical complexity for the high-dimensional proteomic stratification of single-cell populations; and second, the somewhat unexpected arrival of mass cytometry awoke the flow cytometry field from its seeming sleeping beauty stupor and precipitated substantial technological advances that by now approach a degree of analytical dimensionality comparable to mass cytometry. RECENT FINDINGS Here, we summarize in detail how mass cytometry has thus far been harnessed for the pursuit of discovery studies in T1D science; we provide a succinct overview of other single-cell analysis platforms that already have been or soon will be integrated into various T1D investigations; and we briefly consider how effective adoption of these technologies requires an adjusted model for expense allocation, prioritization of experimental questions, division of labor, and recognition of scientific contributions. SUMMARY The introduction of contemporary single-cell technologies in general, and of mass cytometry, in particular, provides important new opportunities for current and future T1D research; the necessary reconfiguration of research strategies to accommodate implementation of these technologies, however, may both broaden research endeavors by fostering genuine team science, and constrain their actual practice because of the need for considerable investments into infrastructure and technical expertise.
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Affiliation(s)
| | - Dirk Homann
- Precision Immunology Institute
- Diabetes, Obesity & Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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34
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Poma AM, Genoni A, Broccolo F, Denaro M, Pugliese A, Basolo F, Toniolo A. Immune Transcriptome of Cells Infected with Enterovirus Strains Obtained from Cases of Type 1 Diabetes. Microorganisms 2020; 8:microorganisms8071031. [PMID: 32664675 PMCID: PMC7409211 DOI: 10.3390/microorganisms8071031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
Enterovirus (EV) infection of insulin-producing pancreatic beta cells is associated with type 1 diabetes (T1D), but little is known about the mechanisms that lead the virus to cause a persistent infection and, possibly, to induce beta cell autoimmunity. A cell line susceptible to most enterovirus types was infected with EV isolates from cases of T1D and, for comparison, with a replication-competent strain of coxsackievirus B3. The transcription of immune-related genes and secretion of cytokines was evaluated in infected vs. uninfected cells. Acutely infected cells showed the preserved transcription of type I interferon (IFN) pathways and the enhanced transcription/secretion of IL6, IL8, LIF, MCP1, and TGFB1. On the other hand, infection by defective EV strains obtained from diabetic subjects suppressed IFN pathways and the transcription of most cytokines, while enhancing the expression of IL8, IL18, IL32, and MCP1. IL18 and IL32 are known for their pathogenic role in autoimmune diabetes. Thus, the cytokine profile of AV3 cells infected by diabetes-derived EV strains closely matches that observed in patients at the early stages of T1D. The concordance of our results with clinically verified information reinforces the hypothesis that the immune changes observed in type 1 diabetic patients are due to a hardly noticeable virus infection.
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Affiliation(s)
- Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
- Correspondence:
| | - Angelo Genoni
- Medical Microbiology, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.G.); (A.T.)
| | - Francesco Broccolo
- Medical Microbiology, Department of Medical Sciences, University Milano Bicocca, 20126 Milano, Italy;
| | - Maria Denaro
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
| | - Alberto Pugliese
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA;
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Clinical Area, University of Pisa, 56126 Pisa, Italy; (M.D.); (F.B.)
| | - Antonio Toniolo
- Medical Microbiology, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy; (A.G.); (A.T.)
- Global Virus Network, 21100 Varese, Italy
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35
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Liu Y, Du X, Cui J, Li C, Guo M, Lv J, Liu X, Dou J, Du X, Fang H, Chen Z. A Genome-Wide Analysis of Long Noncoding RNAs in Circulating Leukocytes and Their Differential Expression in Type 1 Diabetes Patients. J Diabetes Res 2020; 2020:9010314. [PMID: 33299893 PMCID: PMC7710437 DOI: 10.1155/2020/9010314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 11/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression at different levels in various diseases, including type 1 diabetes (T1D). However, the expression of circulating lncRNAs in leukocytes in T1D has not been well documented. To identify differentially expressed lncRNAs between T1D patients and healthy controls, RNA sequencing was performed on samples of leukocytes collected from both healthy persons and T1D patients. The categories, enriched pathways, coexpression networks, and the characteristics of novel lncRNAs were analyzed to provide an extensive profile. qPCR was adopted to validate the differential expression of lncRNAs in the validation cohort. A total of 14,930 lncRNAs and 16,063 mRNAs were identified in the peripheral blood leukocyte of T1D patients. After optimization using an adjusted p value (threshold of <0.05), 393 circulating lncRNAs were identified, of which 69 were downregulated and 324 were upregulated in T1D patients. Gene Ontology analysis indicated that these lncRNAs and mRNAs were enriched in the immune system category. Further analysis showed that 61.28% of the novel lncRNAs were conserved in humans. A set of 12 lncRNAs were selected for qPCR validation, and 9 of 12 lncRNAs were confirmed to show significant differential expression between the T1D and control validation cohorts. Among the 9 confirmed lncRNAs, lncRNA MSTRG.128697 and lncRNA MSTRG.128958 were novel and human-specific; however, further validation is required. lncRNA MSTRG.63013 has orthologous sequences in the mouse genome and was identified as a key node for etiology and pathophysiology in animal studies, which will help understand the epigenetic mechanisms of T1D complications.
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Affiliation(s)
- Yihan Liu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaoming Du
- Tianjin Stomatological Hospital, Tianjin Key Laboratory of Oral Function Reconstruction, Hospital of Stomatology, Nankai University, Tianjin 300041, China
| | - Jia Cui
- Department of Endocrinology, Chinese PLA General Hospital, Beijing 100853, China
| | - Changlong Li
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Meng Guo
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jianyi Lv
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xin Liu
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jingtao Dou
- Department of Endocrinology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaoyan Du
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Hongjuan Fang
- Department of Endocrinology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Zhenwen Chen
- School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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36
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Starling S. Blood signature for β-cell autoimmunity. Nat Rev Endocrinol 2019; 15:564-565. [PMID: 31391570 DOI: 10.1038/s41574-019-0251-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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