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Brozzi F, Jacovetti C, Cosentino C, Menoud V, Wu K, Bayazit MB, Abdulkarim B, Iseli C, Guex N, Guay C, Regazzi R. tRNA-derived fragments in T lymphocyte-beta cell crosstalk and in type 1 diabetes pathogenesis in NOD mice. Diabetologia 2024; 67:2260-2274. [PMID: 38967669 PMCID: PMC11446995 DOI: 10.1007/s00125-024-06207-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/02/2024] [Indexed: 07/06/2024]
Abstract
AIMS/HYPOTHESIS tRNAs play a central role in protein synthesis. Besides this canonical function, they were recently found to generate non-coding RNA fragments (tRFs) regulating different cellular activities. The aim of this study was to assess the involvement of tRFs in the crosstalk between immune cells and beta cells and to investigate their contribution to the development of type 1 diabetes. METHODS Global profiling of the tRFs present in pancreatic islets of 4- and 8-week-old NOD mice and in extracellular vesicles released by activated CD4+ T lymphocytes was performed by small RNA-seq. Changes in the level of specific fragments were confirmed by quantitative PCR. The transfer of tRFs from immune cells to beta cells occurring during insulitis was assessed using an RNA-tagging approach. The functional role of tRFs increasing in beta cells during the initial phases of type 1 diabetes was determined by overexpressing them in dissociated islet cells and by determining the impact on gene expression and beta cell apoptosis. RESULTS We found that the tRF pool was altered in the islets of NOD mice during the initial phases of type 1 diabetes. Part of these changes were triggered by prolonged exposure of beta cells to proinflammatory cytokines (IL-1β, TNF-α and IFN-γ) while others resulted from the delivery of tRFs produced by CD4+ T lymphocytes infiltrating the islets. Indeed, we identified several tRFs that were enriched in extracellular vesicles from CD4+/CD25- T cells and were transferred to beta cells upon adoptive transfer of these immune cells in NOD.SCID mice. The tRFs delivered to beta cells during the autoimmune reaction triggered gene expression changes that affected the immune regulatory capacity of insulin-secreting cells and rendered the cells more prone to apoptosis. CONCLUSIONS/INTERPRETATION Our data point to tRFs as novel players in the crosstalk between the immune system and insulin-secreting cells and suggest a potential involvement of this novel class of non-coding RNAs in type 1 diabetes pathogenesis. DATA AVAILABILITY Sequences are available from the Gene Expression Omnibus (GEO) with accession numbers GSE242568 and GSE256343.
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Affiliation(s)
- Flora Brozzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Cristina Cosentino
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Véronique Menoud
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | | | - Christian Iseli
- Bioinformatics Competence Centre, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Centre, EPFL, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Centre, University of Lausanne, Lausanne, Switzerland
- Bioinformatics Competence Centre, EPFL, Lausanne, Switzerland
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland.
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2
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Zdinak PM, Trivedi N, Grebinoski S, Torrey J, Martinez EZ, Martinez S, Hicks L, Ranjan R, Makani VKK, Roland MM, Kublo L, Arshad S, Anderson MS, Vignali DAA, Joglekar AV. De novo identification of CD4 + T cell epitopes. Nat Methods 2024; 21:846-856. [PMID: 38658646 PMCID: PMC11093748 DOI: 10.1038/s41592-024-02255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.
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Affiliation(s)
- Paul M Zdinak
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nishtha Trivedi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jessica Torrey
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Eduardo Zarate Martinez
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbiology and Immunology Diversity Scholars Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Salome Martinez
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Louise Hicks
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rashi Ranjan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Venkata Krishna Kanth Makani
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mary Melissa Roland
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lyubov Kublo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sanya Arshad
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mark S Anderson
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Alok V Joglekar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Systems Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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3
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Álvarez K, Rojas M. Nanoparticles targeting monocytes and macrophages as diagnostic and therapeutic tools for autoimmune diseases. Heliyon 2023; 9:e19861. [PMID: 37810138 PMCID: PMC10559248 DOI: 10.1016/j.heliyon.2023.e19861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/16/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Autoimmune diseases are chronic conditions that result from an inadequate immune response to self-antigens and affect many people worldwide. Their signs, symptoms, and clinical severity change throughout the course of the disease, therefore the diagnosis and treatment of autoimmune diseases are major challenges. Current diagnostic tools are often invasive and tend to identify the issue at advanced stages. Moreover, the available treatments for autoimmune diseases do not typically lead to complete remission and are associated with numerous side effects upon long-term usage. A promising strategy is the use of nanoparticles that can be used as contrast agents in diagnostic imaging techniques to detect specific cells present at the inflammatory infiltrates in tissues that are not easily accessible by biopsy. In addition, NPs can be designed to deliver drugs to a cell population or tissue. Considering the significant role played by monocytes in the development of chronic inflammatory conditions and their emergence as a target for extracorporeal monitoring and precise interventions, this review focuses on recent advancements in nanoparticle-based strategies for diagnosing and treating autoimmune diseases, with a particular emphasis on targeting monocyte populations.
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Affiliation(s)
- Karen Álvarez
- Grupo de Inmunología Celular e Inmunogenética, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UDEA), Colombia
| | - Mauricio Rojas
- Grupo de Inmunología Celular e Inmunogenética, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UDEA), Colombia
- Unidad de Citometría de Flujo, Sede de Investigación Universitaria (SIU), Universidad de Antioquia (UDEA), Colombia
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Mannering SI, Rubin AF, Wang R, Bhattacharjee P. Identifying New Hybrid Insulin Peptides (HIPs) in Type 1 Diabetes. Front Immunol 2021; 12:667870. [PMID: 33995402 PMCID: PMC8120023 DOI: 10.3389/fimmu.2021.667870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
In 2016 Delong et al. discovered a new type of neoepitope formed by the fusion of two unrelated peptide fragments. Remarkably these neoepitopes, called hybrid insulin peptides, or HIPs, are recognized by pathogenic CD4+ T cells in the NOD mouse and human pancreatic islet-infiltrating T cells in people with type 1 diabetes. Current data implicates CD4+ T-cell responses to HIPs in the immune pathogenesis of human T1D. Because of their role in the immune pathogenesis of human T1D it is important to identify new HIPs that are recognized by CD4+ T cells in people at risk of, or with, T1D. A detailed knowledge of T1D-associated HIPs will allow HIPs to be used in assays to monitor changes in T cell mediated beta-cell autoimmunity. They will also provide new targets for antigen-specific therapies for T1D. However, because HIPs are formed by the fusion of two unrelated peptides there are an enormous number of potential HIPs which makes it technically challenging to identify them. Here we review the discovery of HIPs, how they form and discuss approaches to identifying new HIPs relevant to the immune pathogenesis of human type 1 diabetes.
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Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Alan F Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ruike Wang
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
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5
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Sinha S, Renavikar PS, Crawford MP, Steward-Tharp SM, Brate A, Tsalikian E, Tansey M, Shivapour ET, Cho T, Kamholz J, Karandikar NJ. Altered expression of SIRPγ on the T-cells of relapsing remitting multiple sclerosis and type 1 diabetes patients could potentiate effector responses from T-cells. PLoS One 2020; 15:e0238070. [PMID: 32853219 PMCID: PMC7451561 DOI: 10.1371/journal.pone.0238070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/08/2020] [Indexed: 11/19/2022] Open
Abstract
Factors regulating self-antigen directed immune-responses in autoimmunity are poorly understood. Signal regulatory protein gamma (SIRPγ) is a human T-cell specific protein with genetic variants associated with type 1 diabetes (T1D). SIRPγ's function in the immune system remains unclear. We show that T1D and relapsing remitting multiple sclerosis (RRMS) subjects have significantly greater frequency of rs2281808 T genetic variant, that correlates with reduced SIRPγ-expression in T-cells. Importantly, reduced SIRPγ-expression in RRMS and T1D subjects was not restricted to T variant, suggesting SIRPγ-expression is also regulated by disease specific factors in autoimmunity. Interestingly, increased frequencies of SIRPγlow T-cells in RRMS and T1D positively correlated with proinflammatory molecules from T-cells. Finally, we show that SIRPγlow T-cells have enhanced pathogenecity in vivo in a GVHD model. These findings suggest that decreased-SIRPγ expression, either determined by genetic variants or through peripherally acquired processes, may have a mechanistic link to autoimmunity through induction of hyperactive T-cells.
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Affiliation(s)
- Sushmita Sinha
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Pranav S. Renavikar
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Michael P. Crawford
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Scott M. Steward-Tharp
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, Iowa, United States of America
| | - Ashley Brate
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Eva Tsalikian
- Department of Pediatrics, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Michael Tansey
- Department of Pediatrics, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Ezzatollah T. Shivapour
- Department of Neurology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Tracey Cho
- Department of Neurology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - John Kamholz
- Department of Neurology, University of Iowa Health Care, Iowa City, Iowa, United States of America
| | - Nitin J. Karandikar
- Department of Pathology, University of Iowa Health Care, Iowa City, Iowa, United States of America
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6
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Murfitt SA, Zaccone P, Wang X, Acharjee A, Sawyer Y, Koulman A, Roberts LD, Cooke A, Griffin JL. Metabolomics and Lipidomics Study of Mouse Models of Type 1 Diabetes Highlights Divergent Metabolism in Purine and Tryptophan Metabolism Prior to Disease Onset. J Proteome Res 2018; 17:946-960. [PMID: 28994599 DOI: 10.1021/acs.jproteome.7b00489] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the increase in incidence of type 1 diabetes (T1DM), there is an urgent need to understand the early molecular and metabolic alterations that accompany the autoimmune disease. This is not least because in murine models early intervention can prevent the development of disease. We have applied a liquid chromatography (LC-) and gas chromatography (GC-) mass spectrometry (MS) metabolomics and lipidomics analysis of blood plasma and pancreas tissue to follow the progression of disease in three models related to autoimmune diabetes: the nonobese diabetic (NOD) mouse, susceptible to the development of autoimmune diabetes, and the NOD-E (transgenic NOD mice that express the I-E heterodimer of the major histocompatibility complex II) and NOD-severe combined immunodeficiency (SCID) mouse strains, two models protected from the development of diabetes. All three analyses highlighted the metabolic differences between the NOD-SCID mouse and the other two strains, regardless of diabetic status indicating that NOD-SCID mice are poor controls for metabolic changes in NOD mice. By comparing NOD and NOD-E mice, we show the development of T1DM in NOD mice is associated with changes in lipid, purine, and tryptophan metabolism, including an increase in kynurenic acid and a decrease in lysophospholipids, metabolites previously associated with inflammation.
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Affiliation(s)
- Steven A Murfitt
- Department of Biochemistry, University of Cambridge , The Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Paola Zaccone
- Department of Pathology, University of Cambridge , Tennis Court Road, Cambridge CB2 1QP, U.K
| | - Xinzhu Wang
- Department of Biochemistry, University of Cambridge , The Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Animesh Acharjee
- Medical Research Council Human Nutrition Research, The Elsie Widdowson Laboratory , 120 Fulbourn Road, Cambridge CB1 9NL, U.K
| | - Yvonne Sawyer
- Department of Pathology, University of Cambridge , Tennis Court Road, Cambridge CB2 1QP, U.K
| | - Albert Koulman
- Medical Research Council Human Nutrition Research, The Elsie Widdowson Laboratory , 120 Fulbourn Road, Cambridge CB1 9NL, U.K
| | - Lee D Roberts
- Medical Research Council Human Nutrition Research, The Elsie Widdowson Laboratory , 120 Fulbourn Road, Cambridge CB1 9NL, U.K
| | - Anne Cooke
- Department of Pathology, University of Cambridge , Tennis Court Road, Cambridge CB2 1QP, U.K
| | - Julian Leether Griffin
- Department of Biochemistry, University of Cambridge , The Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.,Medical Research Council Human Nutrition Research, The Elsie Widdowson Laboratory , 120 Fulbourn Road, Cambridge CB1 9NL, U.K
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