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De George DJ, Jhala G, Selck C, Trivedi P, Brodnicki TC, Mackin L, Kay TW, Thomas HE, Krishnamurthy B. Altering β Cell Antigen Exposure to Exhausted CD8+ T Cells Prevents Autoimmune Diabetes in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1658-1669. [PMID: 38587315 DOI: 10.4049/jimmunol.2300785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
Chronic destruction of insulin-producing pancreatic β cells by T cells results in autoimmune diabetes. Similar to other chronic T cell-mediated pathologies, a role for T cell exhaustion has been identified in diabetes in humans and NOD mice. The development and differentiation of exhausted T cells depends on exposure to Ag. In this study, we manipulated β cell Ag presentation to target exhausted autoreactive T cells by inhibiting IFN-γ-mediated MHC class I upregulation or by ectopically expressing the β cell Ag IGRP under the MHC class II promotor in the NOD8.3 model. Islet PD-1+TIM3+CD8+ (terminally exhausted [TEX]) cells were primary producers of islet granzyme B and CD107a, suggestive of cells that have entered the exhaustion program yet maintained cytotoxic capacity. Loss of IFN-γ-mediated β cell MHC class I upregulation correlated with a significant reduction in islet TEX cells and diabetes protection in NOD8.3 mice. In NOD.TII/8.3 mice with IGRP expression induced in APCs, IGRP-reactive T cells remained exposed to high levels of IGRP in the islets and periphery. Consequently, functionally exhausted TEX cells, with reduced granzyme B expression, were significantly increased in these mice and this correlated with diabetes protection. These results indicate that intermediate Ag exposure in wild-type NOD8.3 islets allows T cells to enter the exhaustion program without becoming functionally exhausted. Moreover, Ag exposure can be manipulated to target this key cytotoxic population either by limiting the generation of cytotoxic TIM3+ cells or by driving their functional exhaustion, with both resulting in diabetes protection.
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Affiliation(s)
- David J De George
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Gaurang Jhala
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Claudia Selck
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Prerak Trivedi
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Thomas C Brodnicki
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Leanne Mackin
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
| | - Thomas W Kay
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Helen E Thomas
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
| | - Balasubramanian Krishnamurthy
- Immunology and Diabetes Unit, St Vincent's Institute, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria, Australia
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2
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Srivastava N, Hu H, Peterson OJ, Vomund AN, Stremska M, Zaman M, Giri S, Li T, Lichti CF, Zakharov PN, Zhang B, Abumrad NA, Chen YG, Ravichandran KS, Unanue ER, Wan X. CXCL16-dependent scavenging of oxidized lipids by islet macrophages promotes differentiation of pathogenic CD8 + T cells in diabetic autoimmunity. Immunity 2024:S1074-7613(24)00222-X. [PMID: 38754432 DOI: 10.1016/j.immuni.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/18/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
The pancreatic islet microenvironment is highly oxidative, rendering β cells vulnerable to autoinflammatory insults. Here, we examined the role of islet resident macrophages in the autoimmune attack that initiates type 1 diabetes. Islet macrophages highly expressed CXCL16, a chemokine and scavenger receptor for oxidized low-density lipoproteins (OxLDLs), regardless of autoimmune predisposition. Deletion of Cxcl16 in nonobese diabetic (NOD) mice suppressed the development of autoimmune diabetes. Mechanistically, Cxcl16 deficiency impaired clearance of OxLDL by islet macrophages, leading to OxLDL accumulation in pancreatic islets and a substantial reduction in intra-islet transitory (Texint) CD8+ T cells displaying proliferative and effector signatures. Texint cells were vulnerable to oxidative stress and diminished by ferroptosis; PD-1 blockade rescued this population and reversed diabetes resistance in NOD.Cxcl16-/- mice. Thus, OxLDL scavenging in pancreatic islets inadvertently promotes differentiation of pathogenic CD8+ T cells, presenting a paradigm wherein tissue homeostasis processes can facilitate autoimmune pathogenesis in predisposed individuals.
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Affiliation(s)
- Neetu Srivastava
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Hao Hu
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Orion J Peterson
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Anthony N Vomund
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Marta Stremska
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mohammad Zaman
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Shilpi Giri
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiandao Li
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Pavel N Zakharov
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nada A Abumrad
- Center for Human Nutrition, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kodi S Ravichandran
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; VIB/UGent Inflammation Research Centre and Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Emil R Unanue
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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3
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Rahimikollu J, Xiao H, Rosengart A, Rosen ABI, Tabib T, Zdinak PM, He K, Bing X, Bunea F, Wegkamp M, Poholek AC, Joglekar AV, Lafyatis RA, Das J. SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains. Nat Methods 2024; 21:835-845. [PMID: 38374265 DOI: 10.1038/s41592-024-02175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
Modern multiomic technologies can generate deep multiscale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make analyses and integration of high-dimensional omic datasets challenging. Here we present Significant Latent Factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, and has rigorous false discovery rate control. Using SLIDE on single-cell and spatial omic datasets, we uncovered significant interacting latent factors underlying a range of molecular, cellular and organismal phenotypes. SLIDE outperforms/performs at least as well as a wide range of state-of-the-art approaches, including other latent factor approaches. More importantly, it provides biological inference beyond prediction that other methods do not afford. Thus, SLIDE is a versatile engine for biological discovery from modern multiomic datasets.
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Affiliation(s)
- Javad Rahimikollu
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - AnnaElaine Rosengart
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron B I Rosen
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul M Zdinak
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kun He
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xin Bing
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Florentina Bunea
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Marten Wegkamp
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
- Department of Mathematics, Cornell University, Ithaca, NY, USA
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Alok V Joglekar
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Robert A Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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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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5
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Yang H, Luo J, Liu X, Luo Y, Lai X, Zou F. Unveiling cell subpopulations in T1D mouse islets using single-cell RNA sequencing. Am J Physiol Endocrinol Metab 2024; 326:E723-E734. [PMID: 38506753 DOI: 10.1152/ajpendo.00323.2023] [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: 09/29/2023] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of beta cells by immune cells. The interactions among cells within the islets may be closely linked to the pathogenesis of T1D. In this study, we used single-cell RNA sequencing (scRNA-Seq) to analyze the cellular heterogeneity within the islets of a T1D mouse model. We established a T1D mouse model induced by streptozotocin and identified cell subpopulations using scRNA-Seq technology. Our results revealed 11 major cell types in the pancreatic islets of T1D mice, with heterogeneity observed in the alpha and beta cell subgroups, which may play a crucial role in the progression of T1D. Flow cytometry further confirmed a mature alpha and beta cell reduction in T1D mice. Overall, our scRNA-Seq analysis provided insights into the cellular heterogeneity of T1D islet tissue and highlighted the potential importance of alpha and beta cells in developing T1D.NEW & NOTEWORTHY In this study, we created a comprehensive single-cell atlas of pancreatic islets in a T1D mouse model using scRNA-Seq and identified 11 major cell types in the islets, highlighting the role of alpha and beta cells in T1D. This study revealed a significant reduction in the maturity alpha and beta cells in T1D mice through flow cytometry. It also demonstrated the heterogeneity of alpha and beta cells, potentially crucial for T1D progression. Overall, our scRNA-Seq analysis provided new insights for understanding and treating T1D by studying cell subtype changes and functions.
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Affiliation(s)
- Huan Yang
- Department of Endocrinology, Jiujiang University Affiliated Hospital, Jiujiang, People's Republic of China
| | - Junming Luo
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Xuyang Liu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yue Luo
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Xiaoyang Lai
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Fang Zou
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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Maddaloni E, Amendolara R, Balena A, Latino A, Sessa RL, Buzzetti R. Immune checkpoint modulators in early clinical development for the treatment of type 1 diabetes. Expert Opin Investig Drugs 2024; 33:303-318. [PMID: 38427915 DOI: 10.1080/13543784.2024.2326036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
INTRODUCTION Despite the improvements of insulin therapy, people with type 1 diabetes (T1D) still suffer from a decreased quality of life and life expectancy. The search toward a cure for T1D is therefore still a scorching open field of research. AREAS COVERED Tackling the immune checkpoint signaling pathways has gained importance in the field of cancer immunotherapy. The same pathways can be targeted in autoimmunity with an opposite principle: to dampen the exaggerated immune response. In this review, we report a comprehensive excursus on the cellular and molecular mechanisms that lead to loss of immunological tolerance, and recent evidence on the role of immune checkpoint molecules in the development of T1D and their potential application for the mitigation of autoimmune diabetes. EXPERT OPINION Contrasting results about the efficacy of immune checkpoint modulators for T1D have been published, with very few molecules from preclinical studies eligible for use in humans. The heterogeneous and complex pathophysiology of T1D may explain the conflicting evidence. Designing clinical trials that acknowledge the pathophysiological and clinical complexity of T1D and that forecast the need of simultaneously tackling different disease pathways will be crucial to enhance the benefits which may be gained by such compounds.
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Affiliation(s)
- Ernesto Maddaloni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Rocco Amendolara
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Angela Balena
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Latino
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Rosario Luigi Sessa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Raffaella Buzzetti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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Wenzlau JM, Peterson OJ, Vomund AN, DiLisio JE, Hohenstein A, Haskins K, Wan X. Mapping of a hybrid insulin peptide in the inflamed islet β-cells from NOD mice. Front Immunol 2024; 15:1348131. [PMID: 38455055 PMCID: PMC10917911 DOI: 10.3389/fimmu.2024.1348131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
There is accumulating evidence that pathogenic T cells in T1D recognize epitopes formed by post-translational modifications of β-cell antigens, including hybrid insulin peptides (HIPs). The ligands for several CD4 T-cell clones derived from the NOD mouse are HIPs composed of a fragment of proinsulin joined to peptides from endogenous β-cell granule proteins. The diabetogenic T-cell clone BDC-6.9 reacts to a fragment of C-peptide fused to a cleavage product of pro-islet amyloid polypeptide (6.9HIP). In this study, we used a monoclonal antibody (MAb) to the 6.9HIP to determine when and where HIP antigens are present in NOD islets during disease progression and with which immune cells they associate. Immunogold labeling of the 6.9HIP MAb and organelle-specific markers for electron microscopy were employed to map the subcellular compartment(s) in which the HIP is localized within β-cells. While the insulin B9-23 peptide was present in nearly all islets, the 6.9HIP MAb stained infiltrated islets only in NOD mice at advanced stages of T1D development. Islets co-stained with the 6.9HIP MAb and antibodies to mark insulin, macrophages, and dendritic cells indicate that 6.9HIP co-localizes within insulin-positive β-cells as well as intra-islet antigen-presenting cells (APCs). In electron micrographs, the 6.9HIP co-localized with granule structures containing insulin alone or both insulin and LAMP1 within β-cells. Exposing NOD islets to the endoplasmic reticulum (ER) stress inducer tunicamycin significantly increased levels of 6.9HIP in subcellular fractions containing crinosomes and dense-core granules (DCGs). This work demonstrates that the 6.9HIP can be visualized in the infiltrated islets and suggests that intra-islet APCs may acquire and present HIP antigens within islets.
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Affiliation(s)
- Janet M. Wenzlau
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Orion J. Peterson
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, United States
| | - Anthony N. Vomund
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, United States
| | - James E. DiLisio
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Anita Hohenstein
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kathryn Haskins
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Xiaoxiao Wan
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, United States
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8
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Selck C, Jhala G, De George DJ, Kwong CTJ, Christensen MK, Pappas EG, Liu X, Ge T, Trivedi P, Kallies A, Thomas HE, Kay TWH, Krishnamurthy B. Extraislet expression of islet antigen boosts T cell exhaustion to partially prevent autoimmune diabetes. Proc Natl Acad Sci U S A 2024; 121:e2315419121. [PMID: 38285952 PMCID: PMC10861925 DOI: 10.1073/pnas.2315419121] [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: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024] Open
Abstract
Persistent antigen exposure results in the differentiation of functionally impaired, also termed exhausted, T cells which are maintained by a distinct population of precursors of exhausted T (TPEX) cells. T cell exhaustion is well studied in the context of chronic viral infections and cancer, but it is unclear whether and how antigen-driven T cell exhaustion controls progression of autoimmune diabetes and whether this process can be harnessed to prevent diabetes. Using nonobese diabetic (NOD) mice, we show that some CD8+ T cells specific for the islet antigen, islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) displayed terminal exhaustion characteristics within pancreatic islets but were maintained in the TPEX cell state in peripheral lymphoid organs (PLO). More IGRP-specific T cells resided in the PLO than in islets. To examine the impact of extraislet antigen exposure on T cell exhaustion in diabetes, we generated transgenic NOD mice with inducible IGRP expression in peripheral antigen-presenting cells. Antigen exposure in the extraislet environment induced severely exhausted IGRP-specific T cells with reduced ability to produce interferon (IFN)γ, which protected these mice from diabetes. Our data demonstrate that T cell exhaustion induced by delivery of antigen can be harnessed to prevent autoimmune diabetes.
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Affiliation(s)
- Claudia Selck
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Gaurang Jhala
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
| | - David J. De George
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Chun-Ting J. Kwong
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Marie K. Christensen
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Evan G. Pappas
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
| | - Xin Liu
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Tingting Ge
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Prerak Trivedi
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC3000, Australia
| | - Helen E. Thomas
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Thomas W. H. Kay
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
| | - Balasubramanian Krishnamurthy
- Immunology and Diabetes Unit, St. Vincent’s Institute, Fitzroy, VIC3065, Australia
- Department of Medicine, St. Vincent’s Hospital, University of Melbourne, Fitzroy, VIC3065, Australia
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9
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Herold KC, Delong T, Perdigoto AL, Biru N, Brusko TM, Walker LSK. The immunology of type 1 diabetes. Nat Rev Immunol 2024:10.1038/s41577-023-00985-4. [PMID: 38308004 DOI: 10.1038/s41577-023-00985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2023] [Indexed: 02/04/2024]
Abstract
Following the seminal discovery of insulin a century ago, treatment of individuals with type 1 diabetes (T1D) has been largely restricted to efforts to monitor and treat metabolic glucose dysregulation. The recent regulatory approval of the first immunotherapy that targets T cells as a means to delay the autoimmune destruction of pancreatic β-cells highlights the critical role of the immune system in disease pathogenesis and tends to pave the way for other immune-targeted interventions for T1D. Improving the efficacy of such interventions across the natural history of the disease will probably require a more detailed understanding of the immunobiology of T1D, as well as technologies to monitor residual β-cell mass and function. Here we provide an overview of the immune mechanisms that underpin the pathogenesis of T1D, with a particular emphasis on T cells.
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Affiliation(s)
- Kevan C Herold
- Department of Immunobiology, Yale University, New Haven, CT, USA.
- Department of Internal Medicine, Yale University, New Haven, CT, USA.
| | - Thomas Delong
- Anschutz Medical Campus, University of Colorado, Denver, CO, USA
| | - Ana Luisa Perdigoto
- Department of Internal Medicine, Yale University, New Haven, CT, USA
- Internal Medicine, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Noah Biru
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Lucy S K Walker
- Institute of Immunity & Transplantation, University College London, London, UK.
- Division of Infection & Immunity, University College London, London, UK.
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10
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Vandenbempt V, Eski SE, Brahma MK, Li A, Negueruela J, Bruggeman Y, Demine S, Xiao P, Cardozo AK, Baeyens N, Martelotto LG, Singh SP, Mariño E, Gysemans C, Gurzov EN. HAMSAB diet ameliorates dysfunctional signaling in pancreatic islets in autoimmune diabetes. iScience 2024; 27:108694. [PMID: 38213620 PMCID: PMC10783594 DOI: 10.1016/j.isci.2023.108694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/23/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
An altered gut microbiota is associated with type 1 diabetes (T1D), affecting the production of short-chain fatty acids (SCFA) and glucose homeostasis. We previously demonstrated that enhancing serum acetate and butyrate using a dietary supplement (HAMSAB) improved glycemia in non-obese diabetic (NOD) mice and patients with established T1D. The effects of SCFA on immune-infiltrated islet cells remain to be clarified. Here, we performed single-cell RNA sequencing on islet cells from NOD mice fed an HAMSAB or control diet. HAMSAB induced a regulatory gene expression profile in pancreas-infiltrated immune cells. Moreover, HAMSAB maintained the expression of β-cell functional genes and decreased cellular stress. HAMSAB-fed mice showed preserved pancreatic endocrine cell identity, evaluated by decreased numbers of poly-hormonal cells. Finally, SCFA increased insulin levels in human β-like cells and improved transplantation outcome in NOD/SCID mice. Our findings support the use of metabolite-based diet as attractive approach to improve glucose control in T1D.
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Affiliation(s)
- Valerie Vandenbempt
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Sema Elif Eski
- IRIBHM, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Manoja K. Brahma
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Ao Li
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Javier Negueruela
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Ylke Bruggeman
- Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Campus Gasthuisberg O&N 1, KU Leuven, 3000 Leuven, Belgium
| | - Stéphane Demine
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Peng Xiao
- Inflammatory and Cell Death Signaling in Diabetes group, Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Alessandra K. Cardozo
- Inflammatory and Cell Death Signaling in Diabetes group, Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Nicolas Baeyens
- Laboratoire de Physiologie et de Pharmacologie, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Luciano G. Martelotto
- Single Cell and Spatial-Omics Laboratory, Adelaide Centre of Epigenetics, University of Adelaide, Adelaide, SA 5005, Australia
| | | | - Eliana Mariño
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, VIC 3800, Australia
- ImmunoBiota Therapeutics Pty Ltd, Melbourne, VIC 3187, Australia
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Campus Gasthuisberg O&N 1, KU Leuven, 3000 Leuven, Belgium
| | - Esteban N. Gurzov
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
- WELBIO Department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium
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11
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Duan K, Liu J, Zhang J, Chu T, Liu H, Lou F, Liu Z, Gao B, Wei S, Wei F. Advancements in innate immune regulation strategies in islet transplantation. Front Immunol 2024; 14:1341314. [PMID: 38288129 PMCID: PMC10823010 DOI: 10.3389/fimmu.2023.1341314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/28/2023] [Indexed: 01/31/2024] Open
Abstract
As a newly emerging organ transplantation technique, islet transplantation has shown the advantages of minimal trauma and high safety since it was first carried out. The proposal of the Edmonton protocol, which has been widely applied, was a breakthrough in this method. However, direct contact between islets and portal vein blood will cause a robust innate immune response leading to massive apoptosis of the graft, and macrophages play an essential role in the innate immune response. Therefore, therapeutic strategies targeting macrophages in the innate immune response have become a popular research topic in recent years. This paper will summarize and analyze recent research on strategies for regulating innate immunity, primarily focusing on macrophages, in the field of islet transplantation, including drug therapy, optimization of islet preparation process, islet engineering and Mesenchymal stem cells cotransplantation. We also expounded the heterogeneity, plasticity and activation mechanism of macrophages in islet transplantation, providing a theoretical basis for further research.
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Affiliation(s)
- Kehang Duan
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiao Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Jian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Tongjia Chu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Huan Liu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Fengxiang Lou
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ziyu Liu
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Bing Gao
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Shixiong Wei
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Feng Wei
- Department of Hepatobiliary and Pancreatic Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
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12
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Jamison BL, Lawrance M, Wang CJ, DeBerg HA, Sansom DM, Gavin MA, Walker LS, Campbell DJ. An IL-2 mutein increases IL-10 and CTLA-4-dependent suppression of dendritic cells by regulatory T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569613. [PMID: 38106196 PMCID: PMC10723345 DOI: 10.1101/2023.12.01.569613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Interleukin-2 (IL-2) variants with increased CD25 dependence that selectively expand Foxp3+ regulatory T (TR) cells are in clinical trials for treating inflammatory diseases. Using an Fc-fused IL-2 mutein (Fc.IL-2 mutein) we developed that prevents diabetes in non-obese diabetic (NOD) mice, we show that Fc.IL-2 mutein induced an activated TR population with elevated proliferation, a transcriptional program associated with Stat5- and TCR-dependent gene modules, and high IL-10 and CTLA-4 expression. Increased IL-10 signaling limited surface MHC class II upregulation during conventional dendritic cell (cDC) maturation, while increased CTLA-4-dependent transendocytosis led to the transfer of CD80 and CD86 costimulatory ligands from maturing cDCs to TR cells. In NOD mice, Fc.IL-2 mutein treatment promoted the suppression of cDCs in the inflamed pancreas and pancreatic lymph nodes resulting in T cell anergy. Thus, IL-2 mutein-expanded TR cells have enhanced functional properties and restrict cDC function, offering promise for targeted immunotherapy use in autoimmune disease.
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Affiliation(s)
- Braxton L. Jamison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA
| | | | - Chun Jing Wang
- Institute of Immunity & Transplantation, Pears Building, University College London Division of Infection & Immunity, London, UK
| | | | - David M. Sansom
- Institute of Immunity & Transplantation, Pears Building, University College London Division of Infection & Immunity, London, UK
| | | | - Lucy S.K. Walker
- Institute of Immunity & Transplantation, Pears Building, University College London Division of Infection & Immunity, London, UK
| | - Daniel J. Campbell
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
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13
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James EA, Joglekar AV, Linnemann AK, Russ HA, Kent SC. The beta cell-immune cell interface in type 1 diabetes (T1D). Mol Metab 2023; 78:101809. [PMID: 37734713 PMCID: PMC10622886 DOI: 10.1016/j.molmet.2023.101809] [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] [Received: 07/01/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND T1D is an autoimmune disease in which pancreatic islets of Langerhans are infiltrated by immune cells resulting in the specific destruction of insulin-producing islet beta cells. Our understanding of the factors leading to islet infiltration and the interplay of the immune cells with target beta cells is incomplete, especially in human disease. While murine models of T1D have provided crucial information for both beta cell and autoimmune cell function, the translation of successful therapies in the murine model to human disease has been a challenge. SCOPE OF REVIEW Here, we discuss current state of the art and consider knowledge gaps concerning the interface of the islet beta cell with immune infiltrates, with a focus on T cells. We discuss pancreatic and immune cell phenotypes and their impact on cell function in health and disease, which we deem important to investigate further to attain a more comprehensive understanding of human T1D disease etiology. MAJOR CONCLUSIONS The last years have seen accelerated development of approaches that allow comprehensive study of human T1D. Critically, recent studies have contributed to our revised understanding that the pancreatic beta cell assumes an active role, rather than a passive position, during autoimmune disease progression. The T cell-beta cell interface is a critical axis that dictates beta cell fate and shapes autoimmune responses. This includes the state of the beta cell after processing internal and external cues (e.g., stress, inflammation, genetic risk) that that contributes to the breaking of tolerance by hyperexpression of human leukocyte antigen (HLA) class I with presentation of native and neoepitopes and secretion of chemotactic factors to attract immune cells. We anticipate that emerging insights about the molecular and cellular aspects of disease initiation and progression processes will catalyze the development of novel and innovative intervention points to provide additional therapies to individuals affected by T1D.
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Affiliation(s)
- Eddie A James
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Alok V Joglekar
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amelia K Linnemann
- Center for Diabetes and Metabolic Diseases, and Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holger A Russ
- Diabetes Institute, University of Florida, Gainesville, FL, USA; Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Sally C Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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14
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Bruggeman Y, Martens PJ, Sassi G, Viaene M, Wasserfall CH, Mathieu C, Gysemans C. Footprint of pancreas infiltrating and circulating immune cells throughout type 1 diabetes development. Front Endocrinol (Lausanne) 2023; 14:1275316. [PMID: 38027120 PMCID: PMC10667927 DOI: 10.3389/fendo.2023.1275316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Type 1 diabetes (T1D) is defined by immune cell infiltration of the pancreas, in particular the islets of Langerhans, referred to as insulitis, which is especially prominent during the early disease stages in association with decreased beta cell mass. An in-depth understanding of the dynamics and phenotype of the immune cells infiltrating the pancreas and the accompanying changes in their profiles in peripheral blood during T1D development is critical to generate novel preventive and therapeutic approaches, as well as to find biomarkers for the disease process. Methods Using multi-parameter flow cytometry, we explored the dynamic changes of immune cells infiltrating the pancreas and the pancreatic draining lymph nodes (PLN), compared to those in peripheral blood in female and male non-obese diabetic (NOD) mice during T1D progression. Results The early stages of T1D development were characterized by an influx of innate dendritic cells and neutrophils in the pancreas. While dendritic cells seemed to move in and out (to the PLN), neutrophils accumulated during the pre-symptomatic phase and reached a maximum at 8 weeks of age, after which their numbers declined. During disease progression, CD4+ and CD8+ T cells appeared to continuously migrate from the PLN to the pancreas, which coincided with an increase in beta cell autoimmunity and insulitis severity, and a decline in insulin content. At 12 weeks of age, CD4+ and especially CD8+ T cells in the pancreas showed a dramatic shift from naïve to effector memory phenotype, in contrast to the PLN, where most of these cells remained naïve. A large proportion of pancreas infiltrating CD4+ T cells were naïve, indicating that antigenic stimulation was not necessary to traffic and invade the pancreas. Interestingly, a pre-effector-like T cell dominated the peripheral blood. These cells were intermediates between naïve and effector memory cells as identified by single cell RNA sequencing and might be a potential novel therapeutic target. Conclusion These time- and tissue-dependent changes in the dynamics and functional states of CD4+ and CD8+ T cells are essential steps in our understanding of the disease process in NOD mice and need to be considered for the interpretation and design of disease-modifying therapies.
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Affiliation(s)
- Ylke Bruggeman
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Pieter-Jan Martens
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Gabriele Sassi
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Marijke Viaene
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Clive H. Wasserfall
- Diabetes Institute, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Chantal Mathieu
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Conny Gysemans
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
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15
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Pöysti S, Silojärvi S, Brodnicki TC, Catterall T, Liu X, Mackin L, Luster AD, Kay TWH, Christen U, Thomas HE, Hänninen A. Gut dysbiosis promotes islet-autoimmunity by increasing T-cell attraction in islets via CXCL10 chemokine. J Autoimmun 2023; 140:103090. [PMID: 37572540 DOI: 10.1016/j.jaut.2023.103090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 08/14/2023]
Abstract
CXCL10 is an IFNγ-inducible chemokine implicated in the pathogenesis of type 1 diabetes. T-cells attracted to pancreatic islets produce IFNγ, but it is unclear what attracts the first IFNγ -producing T-cells in islets. Gut dysbiosis following administration of pathobionts induced CXCL10 expression in pancreatic islets of healthy non-diabetes-prone (C57BL/6) mice and depended on TLR4-signaling, and in non-obese diabetic (NOD) mice, gut dysbiosis induced also CXCR3 chemokine receptor in IGRP-reactive islet-specific T-cells in pancreatic lymph node. In amounts typical to low-grade endotoxemia, bacterial lipopolysaccharide induced CXCL10 production in isolated islets of wild type and RAG1 or IFNG-receptor-deficient but not type-I-IFN-receptor-deficient NOD mice, dissociating lipopolysaccharide-induced CXCL10 production from T-cells and IFNγ. Although mostly myeloid-cell dependent, also β-cells showed activation of innate immune signaling pathways and Cxcl10 expression in response to lipopolysaccharide indicating their independent sensitivity to dysbiosis. Thus, CXCL10 induction in response to low levels of lipopolysaccharide may allow islet-specific T-cells imprinted in pancreatic lymph node to enter in healthy islets independently of IFN-g, and thus link gut dysbiosis to early islet-autoimmunity via dysbiosis-associated low-grade endotoxemia.
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MESH Headings
- Animals
- Mice
- Chemokine CXCL10/metabolism
- Chemokine CXCL10/immunology
- Islets of Langerhans/immunology
- Islets of Langerhans/metabolism
- Dysbiosis/immunology
- Autoimmunity
- Gastrointestinal Microbiome/immunology
- Mice, Inbred NOD
- Mice, Knockout
- Mice, Inbred C57BL
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Receptors, CXCR3/metabolism
- Receptors, CXCR3/genetics
- Receptors, CXCR3/immunology
- Lipopolysaccharides/immunology
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/etiology
- Interferon-gamma/metabolism
- Signal Transduction
- Toll-Like Receptor 4/metabolism
- Disease Models, Animal
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Affiliation(s)
- Sakari Pöysti
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Satu Silojärvi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Tara Catterall
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Xin Liu
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Leanne Mackin
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Andrew D Luster
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas W H Kay
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Urs Christen
- Klinikum der Goethe Universität Frankfurt, Frankfurt Am Main, Germany
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Arno Hänninen
- Institute of Biomedicine, University of Turku, Turku, Finland; Turku University Hospital Laboratory Division, Turku, Finland.
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16
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Collier JL, Pauken KE, Lee CA, Patterson DG, Markson SC, Conway TS, Fung ME, France JA, Mucciarone KN, Lian CG, Murphy GF, Sharpe AH. Single-cell profiling reveals unique features of diabetogenic T cells in anti-PD-1-induced type 1 diabetes mice. J Exp Med 2023; 220:e20221920. [PMID: 37432393 PMCID: PMC10336233 DOI: 10.1084/jem.20221920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/28/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Immune-related adverse events (irAEs) are a notable complication of PD-1 cancer immunotherapy. A better understanding of how these iatrogenic diseases compare with naturally arising autoimmune diseases is needed for treatment and monitoring of irAEs. We identified differences in anti-PD-1-induced type 1 diabetes (T1D) and spontaneous T1D in non-obese diabetic (NOD) mice by performing single-cell RNA-seq and TCR-seq on T cells from the pancreas, pancreas-draining lymph node (pLN), and blood of mice with PD-1-induced T1D or spontaneous T1D. In the pancreas, anti-PD-1 resulted in expansion of terminally exhausted/effector-like CD8+ T cells, an increase in T-bethi CD4+FoxP3- T cells, and a decrease in memory CD4+FoxP3- and CD8+ T cells in contrast to spontaneous T1D. Notably, anti-PD-1 caused increased TCR sharing between the pancreas and the periphery. Moreover, T cells in the blood of anti-PD-1-treated mice expressed markers that differed from spontaneous T1D, suggesting that the blood may provide a window to monitor irAEs rather than relying exclusively on the autoimmune target organ.
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Affiliation(s)
- Jenna L. Collier
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Kristen E. Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Dillon G. Patterson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Samuel C. Markson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Thomas S. Conway
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Megan E. Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Joshua A. France
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Christine G. Lian
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - George F. Murphy
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Arlene H. Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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17
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Martin TM, Burke SJ, Wasserfall CH, Collier JJ. Islet beta-cells and intercellular adhesion molecule-1 (ICAM-1): Integrating immune responses that influence autoimmunity and graft rejection. Autoimmun Rev 2023; 22:103414. [PMID: 37619906 PMCID: PMC10543623 DOI: 10.1016/j.autrev.2023.103414] [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: 07/16/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Type 1 diabetes (T1D) develops due to autoimmune targeting of the pancreatic islet β-cells. Clinical symptoms arise from reduced insulin in circulation. The molecular events and interactions between discrete immune cell populations, infiltration of such leukocytes into pancreatic and islet tissue, and selective targeting of the islet β-cells during autoimmunity and graft rejection are not entirely understood. One protein central to antigen presentation, priming of immune cells, trafficking of leukocytes, and vital for leukocyte effector function is the intercellular adhesion molecule-1 (ICAM-1). The gene encoding ICAM-1 is transcriptionally regulated and rapidly responsive (i.e., within hours) to pro-inflammatory cytokines. ICAM-1 is a transmembrane protein that can be glycosylated; its presence on the cell surface provides co-stimulatory functions for immune cell activation and stabilization of cell-cell contacts. ICAM-1 interacts with the β2-integrins, CD11a/CD18 (LFA-1) and CD11b/CD18 (Mac-1), which are present on discrete immune cell populations. A whole-body ICAM-1 deletion protects NOD mice from diabetes onset, strongly implicating this protein in autoimmune responses. Since several different cell types express ICAM-1, its biology is fundamentally essential for various physiological and pathological outcomes. Herein, we review the role of ICAM-1 during both autoimmunity and islet graft rejection to understand the mechanism(s) leading to islet β-cell death and dysfunction that results in insufficient circulating quantities of insulin to control glucose homeostasis.
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Affiliation(s)
- Thomas M Martin
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, LA 70808, United States of America; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Susan J Burke
- Laboratory of Immunogenetics, Pennington Biomedical Research Center, Baton Rouge, LA 70808, United States of America
| | - Clive H Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, United States of America
| | - J Jason Collier
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, LA 70808, United States of America; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States of America.
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18
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Yang X, Hou X, Zhang J, Liu Z, Wang G. Research progress on the application of single-cell sequencing in autoimmune diseases. Genes Immun 2023; 24:220-235. [PMID: 37550409 DOI: 10.1038/s41435-023-00216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Autoimmune diseases (AIDs) are caused by immune tolerance deficiency or abnormal immune regulation, leading to damage to host organs. The complicated pathogenesis and varied clinical symptoms of AIDs pose great challenges in diagnosing and monitoring this disease. Regrettably, the etiological factors and pathogenesis of AIDs are still not completely understood. It is noteworthy that the development of single-cell RNA sequencing (scRNA-seq) technology provides a new tool for analyzing the transcriptome of AIDs. In this essay, we have summarized the development of scRNA-seq technology, and made a relatively systematic review of the current research progress of scRNA-seq technology in the field of AIDs, providing a reference to preferably understand the pathogenesis, diagnosis, and treatment of AIDs.
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Affiliation(s)
- Xueli Yang
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| | - Junning Zhang
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Zhenyu Liu
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Guangyu Wang
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
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19
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Batdorf HM, Lawes LDL, Richardson JT, Burk DH, Dupuy SD, Karlstad MD, Noland RC, Burke SJ, Collier JJ. NOD mice have distinct metabolic and immunologic profiles when compared with genetically similar MHC-matched ICR mice. Am J Physiol Endocrinol Metab 2023; 325:E336-E345. [PMID: 37610410 PMCID: PMC10642984 DOI: 10.1152/ajpendo.00033.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
Nonobese diabetic (NOD) mice are the most commonly used rodent model to study mechanisms relevant to the autoimmunity and immunology of type 1 diabetes. Although many different strains of mice have been used as controls for studies comparing nondiabetic lines to the NOD strain, we hypothesized that the parental strain that gave rise to the NOD line might be one of the best options. Therefore, we compared female ICR and NOD mice, which are matched at key major histocompatibility complex (MHC) loci, to understand their metabolic and immunologic similarities and differences. Several novel observations emerged: 1) NOD mice have greater circulating proinsulin when compared with ICR mice. 2) NOD mice display CD3+ and IBA1+ cell infiltration into and near pancreatic islets before hyperglycemia. 3) NOD mice show increased expression of the Il1b and Cxcl11 genes in islets when compared with islets from age-matched ICR mice. 4) NOD mice have a greater abundance of STAT1 and ICAM-1 protein in islets when compared with ICR mice. These data show that ICR mice, which are genetically similar to NOD mice, do not retain the same immunologic outcomes. Thus, ICR mice are an excellent choice as a genetically similar and MHC-matched control for NOD mice in studies designed to understand mechanisms relevant to autoimmune-mediated diabetes onset as well as novel therapeutic interventions.NEW & NOTEWORTHY Nonobese diabetic (NOD) mice have more proinsulin in circulation and STAT1 protein in islets compared with the major histocompatibility complex (MHC)-matched ICR line. NOD mice also display greater expression of cytokines and chemokines in pancreatic islets consistent with immune cell infiltration before hyperglycemia when compared with age-matched ICR mice. Thus, ICR mice represent an excellent control for autoimmunity and inflammation studies using the NOD line of mice.
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Affiliation(s)
- Heidi M Batdorf
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - Luz de Luna Lawes
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - Jeremy T Richardson
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - David H Burk
- Cell Biology and Bioimaging Core Facility, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - Samuel D Dupuy
- Department of Surgery, Graduate School of Medicine, University of Tennessee Health Science Center, Knoxville, Tennessee, United States
| | - Michael D Karlstad
- Department of Surgery, Graduate School of Medicine, University of Tennessee Health Science Center, Knoxville, Tennessee, United States
| | - Robert C Noland
- Skeletal Muscle Metabolism Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - Susan J Burke
- Laboratory of Immunogenetics, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
| | - J Jason Collier
- Laboratory of Islet Biology and Inflammation, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States
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20
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Lee EY, Dai Z, Jaiswal A, Wang EHC, Anandasabapathy N, Christiano AM. Functional interrogation of lymphocyte subsets in alopecia areata using single-cell RNA sequencing. Proc Natl Acad Sci U S A 2023; 120:e2305764120. [PMID: 37428932 PMCID: PMC10629527 DOI: 10.1073/pnas.2305764120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/05/2023] [Indexed: 07/12/2023] Open
Abstract
Alopecia areata (AA) is among the most prevalent autoimmune diseases, but the development of innovative therapeutic strategies has lagged due to an incomplete understanding of the immunological underpinnings of disease. Here, we performed single-cell RNA sequencing (scRNAseq) of skin-infiltrating immune cells from the graft-induced C3H/HeJ mouse model of AA, coupled with antibody-based depletion to interrogate the functional role of specific cell types in AA in vivo. Since AA is predominantly T cell-mediated, we focused on dissecting lymphocyte function in AA. Both our scRNAseq and functional studies established CD8+ T cells as the primary disease-driving cell type in AA. Only the depletion of CD8+ T cells, but not CD4+ T cells, NK, B, or γδ T cells, was sufficient to prevent and reverse AA. Selective depletion of regulatory T cells (Treg) showed that Treg are protective against AA in C3H/HeJ mice, suggesting that failure of Treg-mediated immunosuppression is not a major disease mechanism in AA. Focused analyses of CD8+ T cells revealed five subsets, whose heterogeneity is defined by an "effectorness gradient" of interrelated transcriptional states that culminate in increased effector function and tissue residency. scRNAseq of human AA skin showed that CD8+ T cells in human AA follow a similar trajectory, underscoring that shared mechanisms drive disease in both murine and human AA. Our study represents a comprehensive, systematic interrogation of lymphocyte heterogeneity in AA and uncovers a novel framework for AA-associated CD8+ T cells with implications for the design of future therapeutics.
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Affiliation(s)
- Eunice Y. Lee
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY10032
- Medical Scientist Training Program, Columbia University, New York, NY10032
| | - Zhenpeng Dai
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY10032
| | - Abhinav Jaiswal
- Department of Dermatology, Weill Cornell Medicine, New York, NY10021
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY10065
| | - Eddy Hsi Chun Wang
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY10032
| | - Niroshana Anandasabapathy
- Department of Dermatology, Weill Cornell Medicine, New York, NY10021
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY10065
| | - Angela M. Christiano
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY10032
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY10032
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21
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Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023; 13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [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: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023] Open
Abstract
Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.
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Affiliation(s)
- Baocai Xie
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Biqiang Zhou
- Department of Geriatric & Spinal Pain Multi-Department Treatment, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Shi Chen
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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22
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Sun L, Su Y, Jiao A, Wang X, Zhang B. T cells in health and disease. Signal Transduct Target Ther 2023; 8:235. [PMID: 37332039 DOI: 10.1038/s41392-023-01471-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/20/2023] Open
Abstract
T cells are crucial for immune functions to maintain health and prevent disease. T cell development occurs in a stepwise process in the thymus and mainly generates CD4+ and CD8+ T cell subsets. Upon antigen stimulation, naïve T cells differentiate into CD4+ helper and CD8+ cytotoxic effector and memory cells, mediating direct killing, diverse immune regulatory function, and long-term protection. In response to acute and chronic infections and tumors, T cells adopt distinct differentiation trajectories and develop into a range of heterogeneous populations with various phenotype, differentiation potential, and functionality under precise and elaborate regulations of transcriptional and epigenetic programs. Abnormal T-cell immunity can initiate and promote the pathogenesis of autoimmune diseases. In this review, we summarize the current understanding of T cell development, CD4+ and CD8+ T cell classification, and differentiation in physiological settings. We further elaborate the heterogeneity, differentiation, functionality, and regulation network of CD4+ and CD8+ T cells in infectious disease, chronic infection and tumor, and autoimmune disease, highlighting the exhausted CD8+ T cell differentiation trajectory, CD4+ T cell helper function, T cell contributions to immunotherapy and autoimmune pathogenesis. We also discuss the development and function of γδ T cells in tissue surveillance, infection, and tumor immunity. Finally, we summarized current T-cell-based immunotherapies in both cancer and autoimmune diseases, with an emphasis on their clinical applications. A better understanding of T cell immunity provides insight into developing novel prophylactic and therapeutic strategies in human diseases.
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Affiliation(s)
- Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China.
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China.
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23
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Krishnamurthy B, Lacorcia M, Kay TWH, Thomas HE, Mannering SI. Monitoring immunomodulation strategies in type 1 diabetes. Front Immunol 2023; 14:1206874. [PMID: 37346035 PMCID: PMC10279879 DOI: 10.3389/fimmu.2023.1206874] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Type 1 diabetes (T1D) is a T-cell mediated autoimmune disease. Short-term treatment with agents targeting T cells, B cells and inflammatory cytokines to modify the disease course resulted in a short-term pause in disease activity. Lessons learnt from these trials will be discussed in this review. It is expected that effective disease-modifying agents will become available for use in earlier stages of T1D. Progress has been made to analyze antigen-specific T cells with standardization of T cell assay and discovery of antigen epitopes but there are many challenges. High-dimensional profiling of gene, protein and TCR expression at single cell level with innovative computational tools should lead to novel biomarker discovery. With this, assays to detect, quantify and characterize the phenotype and function of antigen-specific T cells will continuously evolve. An improved understanding of T cell responses will help researchers and clinicians to better predict disease onset, and progression, and the therapeutic efficacy of interventions to prevent or arrest T1D.
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Affiliation(s)
- Balasubramanian Krishnamurthy
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Matthew Lacorcia
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
| | - Thomas W. H. Kay
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Helen E. Thomas
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Stuart I. Mannering
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
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24
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De George DJ, Ge T, Krishnamurthy B, Kay TWH, Thomas HE. Inflammation versus regulation: how interferon-gamma contributes to type 1 diabetes pathogenesis. Front Cell Dev Biol 2023; 11:1205590. [PMID: 37293126 PMCID: PMC10244651 DOI: 10.3389/fcell.2023.1205590] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Type 1 diabetes is an autoimmune disease with onset from early childhood. The insulin-producing pancreatic beta cells are destroyed by CD8+ cytotoxic T cells. The disease is challenging to study mechanistically in humans because it is not possible to biopsy the pancreatic islets and the disease is most active prior to the time of clinical diagnosis. The NOD mouse model, with many similarities to, but also some significant differences from human diabetes, provides an opportunity, in a single in-bred genotype, to explore pathogenic mechanisms in molecular detail. The pleiotropic cytokine IFN-γ is believed to contribute to pathogenesis of type 1 diabetes. Evidence of IFN-γ signaling in the islets, including activation of the JAK-STAT pathway and upregulation of MHC class I, are hallmarks of the disease. IFN-γ has a proinflammatory role that is important for homing of autoreactive T cells into islets and direct recognition of beta cells by CD8+ T cells. We recently showed that IFN-γ also controls proliferation of autoreactive T cells. Therefore, inhibition of IFN-γ does not prevent type 1 diabetes and is unlikely to be a good therapeutic target. In this manuscript we review the contrasting roles of IFN-γ in driving inflammation and regulating the number of antigen specific CD8+ T cells in type 1 diabetes. We also discuss the potential to use JAK inhibitors as therapy for type 1 diabetes, to inhibit both cytokine-mediated inflammation and proliferation of T cells.
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Affiliation(s)
- David J. De George
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Tingting Ge
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Balasubramaniam Krishnamurthy
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Thomas W. H. Kay
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Helen E. Thomas
- Immunology and Diabetes Unit, St Vincent’s Institute, Fitzroy, VIC, Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC, Australia
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25
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Zhao X, Zhang H, Han Y, Fang C, Liu J. Navigating the immunometabolic heterogeneity of B cells in murine hepatocellular carcinoma at single cell resolution. Int Immunopharmacol 2023; 120:110257. [PMID: 37182447 DOI: 10.1016/j.intimp.2023.110257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
Induction of antitumor immunity is critical for the therapeutic efficacy of hepatocellular carcinoma (HCC) immunotherapy. The cellular metabolic state underpins the effector function of immune cells, yet our understanding of the phenotypic and metabolic heterogeneity of B cells within HCC microenvironment is poorly developed. Herein, we investigated the composition, distribution, phenotype, function and metabolic profiles of B-cell subsets in HCC and adjacent liver tissues from an orthotopic HCC mouse model using single-cell RNA sequencing (scRNA-seq). Our results identified six B-cell clusters, which can be classified into plasma cells and activated and exhausted B cells according to marker expression, functional and temporal distribution. Exhausted B cells exhibited low metabolic activities and impaired effector functions. Activated B and plasma cells showed higher metabolic activity than exhausted B cells, but there were clear differences in their metabolic profiles. In addition, we found that the effector function of exhausted B cells was further diminished in HCC tissues compared with adjacent liver tissues, but their metabolic activity was significantly enhanced. Collectively, we comprehensively characterized the metabolic profile and alterations in B-cell subsets in HCC, which contributes to the understanding of B-cell immunology in HCC and lays the foundation for exploring novel targets in HCC immunotherapy.
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Affiliation(s)
- Xindong Zhao
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Huanran Zhang
- Department of Emergency Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China; The Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases of Zhejiang Province, Hangzhou City, Zhejiang Province 310003, China
| | - Yiru Han
- Department of Health Care, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Chengyu Fang
- Department of Ultrasound Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China
| | - Jingqi Liu
- Department of Ultrasound Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province 310003, China.
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26
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Stadinski BD, Cleveland SB, Brehm MA, Greiner DL, Huseby PG, Huseby ES. I-A g7 β56/57 polymorphisms regulate non-cognate negative selection to CD4 + T cell orchestrators of type 1 diabetes. Nat Immunol 2023; 24:652-663. [PMID: 36807641 PMCID: PMC10623581 DOI: 10.1038/s41590-023-01441-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 01/20/2023] [Indexed: 02/22/2023]
Abstract
Genetic susceptibility to type 1 diabetes is associated with homozygous expression of major histocompatibility complex class II alleles that carry specific beta chain polymorphisms. Why heterozygous expression of these major histocompatibility complex class II alleles does not confer a similar predisposition is unresolved. Using a nonobese diabetic mouse model, here we show that heterozygous expression of the type 1 diabetes-protective allele I-Ag7 β56P/57D induces negative selection to the I-Ag7-restricted T cell repertoire, including beta-islet-specific CD4+ T cells. Surprisingly, negative selection occurs despite I-Ag7 β56P/57D having a reduced ability to present beta-islet antigens to CD4+ T cells. Peripheral manifestations of non-cognate negative selection include a near complete loss of beta-islet-specific CXCR6+ CD4+ T cells, an inability to cross-prime islet-specific glucose-6-phosphatase catalytic subunit-related protein and insulin-specific CD8+ T cells and disease arrest at the insulitis stage. These data reveal that negative selection on non-cognate self-antigens in the thymus can promote T cell tolerance and protection from autoimmunity.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sarah B Cleveland
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michael A Brehm
- Department of Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dale L Greiner
- Department of Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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27
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Fu Q, Jiang H, Qian Y, Lv H, Dai H, Zhou Y, Chen Y, He Y, Gao R, Zheng S, Liang Y, Li S, Xu X, Xu K, Yang T. Single-cell RNA sequencing combined with single-cell proteomics identifies the metabolic adaptation of islet cell subpopulations to high-fat diet in mice. Diabetologia 2023; 66:724-740. [PMID: 36538064 PMCID: PMC9765371 DOI: 10.1007/s00125-022-05849-5] [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: 06/05/2022] [Accepted: 10/13/2022] [Indexed: 12/24/2022]
Abstract
AIMS/HYPOTHESIS Islets have complex heterogeneity and subpopulations. Cell surface markers representing alpha, beta and delta cell subpopulations are urgently needed for investigations to explore the compositional changes of each subpopulation in obesity progress and diabetes onset, and the adaptation mechanism of islet metabolism induced by a high-fat diet (HFD). METHODS Single-cell RNA sequencing (scRNA-seq) was applied to identify alpha, beta and delta cell subpopulation markers in an HFD-induced mouse model of glucose intolerance. Flow cytometry and immunostaining were used to sort and assess the proportion of each subpopulation. Single-cell proteomics was performed on sorted cells, and the functional status of each alpha, beta and delta cell subpopulation in glucose intolerance was deeply elucidated based on protein expression. RESULTS A total of 33,999 cells were analysed by scRNA-seq and clustered into eight populations, including alpha, beta and delta cells. For alpha cells, scRNA-seq revealed that the Ace2low subpopulation had downregulated expression of genes related to alpha cell function and upregulated expression of genes associated with beta cell characteristics in comparison with the Ace2high subpopulation. The impaired function and increased fragility of ACE2low alpha cells exposure to HFD was further suggested by single-cell proteomics. As for beta cells, the CD81high subpopulation may indicate an immature signature of beta cells compared with the CD81low subpopulation, which had robust function. We also found differential expression of Slc2a2 in delta cells and a potentially stronger cellular function and metabolism in GLUT2low delta cells than GLUT2high delta cells. Moreover, an increased proportion of ACE2low alpha cells and CD81low beta cells, with a constant proportion of GLUT2low delta cells, were observed in HFD-induced glucose intolerance. CONCLUSIONS/INTERPRETATION We identified ACE2, CD81 and GLUT2 as surface markers to distinguish, respectively, alpha, beta and delta cell subpopulations with heterogeneous maturation and function. The changes in the proportion and functional status of islet endocrine subpopulations reflect the metabolic adaptation of islets to high-fat stress, which weakened the function of alpha cells and enhanced the function of beta and delta cells to bring about glycaemic homeostasis. Our findings provide a fundamental resource for exploring the mechanisms maintaining each islet endocrine subpopulation's fate and function in health and disease. DATA AVAILABILITY The scRNA-seq analysis datasets from the current study are available in the Gene Expression Omnibus (GEO) repository under the accession number GSE203376.
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Affiliation(s)
- Qi Fu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hemin Jiang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Qian
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Lv
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Dai
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuncai Zhou
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Chen
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yunqiang He
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Gao
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuai Zheng
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yucheng Liang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Siqi Li
- BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Xinyu Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuanfeng Xu
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Tao Yang
- Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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Boldison J, Hopkinson JR, Davies J, Pearson JA, Leete P, Richardson S, Morgan NG, Wong FS. Gene expression profiling in NOD mice reveals that B cells are highly educated by the pancreatic environment during autoimmune diabetes. Diabetologia 2023; 66:551-566. [PMID: 36508037 PMCID: PMC9892163 DOI: 10.1007/s00125-022-05839-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS B cells play an important role in driving the development of type 1 diabetes; however, it remains unclear how they contribute to local beta cell destruction during disease progression. Here, we use gene expression profiling of B cell subsets identified in inflamed pancreatic tissue to explore their primary functional role during the progression of autoimmune diabetes. METHODS Transcriptional profiling was performed on FACS-sorted B cell subsets isolated from pancreatic islets and the pancreatic lymph nodes of NOD mice. RESULTS B cells are highly modified by the inflamed pancreatic tissue and can be distinguished by their transcriptional profile from those in the lymph nodes. We identified both a discrete and a core shared gene expression profile in islet CD19+CD138- and CD19+CD138+ B cell subsets, the latter of which is known to have enriched autoreactivity during diabetes development. On localisation to pancreatic islets, compared with CD138- B cells, CD138+ B cells overexpress genes associated with adhesion molecules and growth factors. Their shared signature consists of gene expression changes related to the differentiation of antibody-secreting cells and gene regulatory networks associated with IFN signalling pathways, proinflammatory cytokines and Toll-like receptor (TLR) activation. Finally, abundant TLR7 expression was detected in islet B cells and was enhanced specifically in CD138+ B cells. CONCLUSIONS/INTERPRETATION Our study provides a detailed transcriptional analysis of islet B cells. Specific gene signatures and interaction networks have been identified that point towards a functional role for B cells in driving autoimmune diabetes.
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Affiliation(s)
- Joanne Boldison
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK.
| | - Jessica R Hopkinson
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Joanne Davies
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James A Pearson
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Pia Leete
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Sarah Richardson
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - Noel G Morgan
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
| | - F Susan Wong
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
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29
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Hodgson R, Crockford TL, Bhandari A, Kepple JD, Back J, Cawthorne E, Abeler-Dörner L, Laing AG, Clare S, Speak A, Adams DJ, Dougan G, Hayday AC, Deobagkar-Lele M, Cornall RJ, Bull KR. Prolidase Deficiency Causes Spontaneous T Cell Activation and Lupus-like Autoimmunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:547-557. [PMID: 36637239 PMCID: PMC9946897 DOI: 10.4049/jimmunol.2200212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/10/2022] [Indexed: 01/14/2023]
Abstract
Prolidase deficiency (PD) is a multisystem disorder caused by mutations in the PEPD gene, which encodes a ubiquitously expressed metallopeptidase essential for the hydrolysis of dipeptides containing C-terminal proline or hydroxyproline. PD typically presents in childhood with developmental delay, skin ulcers, recurrent infections, and, in some patients, autoimmune features that can mimic systemic lupus erythematosus. The basis for the autoimmune association is uncertain, but might be due to self-antigen exposure with tissue damage, or indirectly driven by chronic infection and microbial burden. In this study, we address the question of causation and show that Pepd-null mice have increased antinuclear autoantibodies and raised serum IgA, accompanied by kidney immune complex deposition, consistent with a systemic lupus erythematosus-like disease. These features are associated with an accumulation of CD4 and CD8 effector T cells in the spleen and liver. Pepd deficiency leads to spontaneous T cell activation and proliferation into the effector subset, which is cell intrinsic and independent of Ag receptor specificity or antigenic stimulation. However, an increase in KLRG1+ effector CD8 cells is not observed in mixed chimeras, in which the autoimmune phenotype is also absent. Our findings link autoimmune susceptibility in PD to spontaneous T cell dysfunction, likely to be acting in combination with immune activators that lie outside the hemopoietic system but result from the abnormal metabolism or loss of nonenzymatic prolidase function. This knowledge provides insight into the role of prolidase in the maintenance of self-tolerance and highlights the importance of treatment to control T cell activation.
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Affiliation(s)
- Rose Hodgson
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tanya L. Crockford
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Aneesha Bhandari
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jessica D. Kepple
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer Back
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eleanor Cawthorne
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Adam G. Laing
- Department of Immunobiology, King’s College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom; and
| | - Simon Clare
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | - Adrian C. Hayday
- Department of Immunobiology, King’s College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom; and
| | - Mukta Deobagkar-Lele
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard J. Cornall
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Katherine R. Bull
- MRC Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Jung S, Lee JS. Single-Cell Genomics for Investigating Pathogenesis of Inflammatory Diseases. Mol Cells 2023; 46:120-129. [PMID: 36859476 PMCID: PMC9982059 DOI: 10.14348/molcells.2023.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023] Open
Abstract
Recent technical advances have enabled unbiased transcriptomic and epigenetic analysis of each cell, known as "single-cell analysis". Single-cell analysis has a variety of technical approaches to investigate the state of each cell, including mRNA levels (transcriptome), the immune repertoire (immune repertoire analysis), cell surface proteins (surface proteome analysis), chromatin accessibility (epigenome), and accordance with genome variants (eQTLs; expression quantitative trait loci). As an effective tool for investigating robust immune responses in coronavirus disease 2019 (COVID-19), many researchers performed single-cell analysis to capture the diverse, unbiased immune cell activation and differentiation. Despite challenges elucidating the complicated immune microenvironments of chronic inflammatory diseases using existing experimental methods, it is now possible to capture the simultaneous immune features of different cell types across inflamed tissues using various single-cell tools. In this review, we introduce patient-based and experimental mouse model research utilizing single-cell analyses in the field of chronic inflammatory diseases, as well as multi-organ atlas targeting immune cells.
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Affiliation(s)
- Seyoung Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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31
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Zhang Y, Lu Y, Gao Y, Liang X, Zhang R, Wang X, Zou X, Yang W. Effects of Aire on perforin expression in BMDCs via TLR7/8 and its therapeutic effect on type 1 diabetes. Int Immunopharmacol 2023; 117:109890. [PMID: 36805202 DOI: 10.1016/j.intimp.2023.109890] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023]
Abstract
AIMS Type 1 diabetes, as a kind of autoimmune diseases, usually results from the broken-down of self-tolerance. Autoimmune regulator (Aire), as a transcription factor, induces peripheral tolerance by regulating Toll-like receptor (TLR) expression in dendritic cells (DCs). Several studies have recently identified a small population of perforin-expressing DCs, which is an important population of tolerogenic DCs (tolDCs) that restricts autoreactive T cells in vivo through a perforin-mediated mechanism. Thus, the present study explored the specific relationship among Aire, perforin-expressing DCs and immune tolerance, as well as their roles in type 1 diabetes. METHODS We conducted studies based on the Aire-overexpressing bone marrow-derived dendritic cell (BMDC) model. And through in vitro and in vivo experiments to observe that Aire-overexpressing BMDCs which express perforin induce immune tolerance and treat type 1 diabetes via TLR7/8. RESULTS Aire enhances the expression of perforin in BMDCs after treatment with the TLR7/8 ligand as well as promotes the expression of TLR7/8 and myeloid differentiation primary response gene 88 (MyD88)-dependent pathway molecules. Aire-overexpressing BMDCs mediate apoptosis of allogeneic CD8+ T cells via perforin in vitro. Moreover, Aire-overexpressing BMDCs enhance the therapeutic effect of type 1 diabetes in non-obese diabetic (NOD) mice via perforin and induce apoptosis of autoreactive CD8+ T cells in vivo. CONCLUSIONS These results provide an experimental basis for comprehensively elucidating the role and significance of Aire expression in peripheral DCs, thereby providing new ideas for the treatment of autoimmune diseases by using Aire as a target to induce the production of perforin-expressing DCs.
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Affiliation(s)
- Yi Zhang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yaoping Lu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Yan Gao
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiaojing Liang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Rongchao Zhang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiaoya Wang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xueyang Zou
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Wei Yang
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, China.
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32
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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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Burke KP, Patterson DG, Liang D, Sharpe AH. Immune checkpoint receptors in autoimmunity. Curr Opin Immunol 2023; 80:102283. [PMID: 36709596 PMCID: PMC10019320 DOI: 10.1016/j.coi.2023.102283] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/04/2023] [Indexed: 01/30/2023]
Abstract
Immune checkpoint receptors such as programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte associated protein 4 (CTLA-4), lymphocyte-activation gene 3 (LAG-3), and T cell immunoglobulin and ITIM domain (TIGIT) have distinct and overlapping inhibitory functions that regulate Tcell activation, differentiation, and function. These inhibitory receptors also mediate tolerance, and dysregulation of these receptors can result in a breach of tolerance and the development of autoimmune syndromes. Similarly, antibody blockade of immune checkpoint receptors or their ligands for cancer immunotherapy may trigger a spectrum of organ inflammation that resembles autoimmunity, termed immune-related adverse events (irAE). In this review, we discuss recent advances in the regulation of autoimmunity by immune checkpoint receptors. We highlight coordinated gene expression programs linking checkpoint receptors, heterogeneity within autoreactive T-cell populations, parallels between irAE and autoimmunity, and bidirectional functional interactions between immune checkpoint receptors and their ligands.
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Affiliation(s)
- Kelly P Burke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Dillon G Patterson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Dan Liang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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34
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Liu Q, Liang Y, Wang D, Li J. LFSC: A linear fast semi-supervised clustering algorithm that integrates reference-bulk and single-cell transcriptomes. Front Genet 2022; 13:1068075. [PMID: 36531230 PMCID: PMC9754124 DOI: 10.3389/fgene.2022.1068075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/09/2022] [Indexed: 08/29/2023] Open
Abstract
The identification of cell types in complex tissues is an important step in research into cellular heterogeneity in disease. We present a linear fast semi-supervised clustering (LFSC) algorithm that utilizes reference samples generated from bulk RNA sequencing data to identify cell types from single-cell transcriptomes. An anchor graph is constructed to depict the relationship between reference samples and cells. By applying a connectivity constraint to the learned graph, LFSC enables the preservation of the underlying cluster structure. Moreover, the overall complexity of LFSC is linear to the size of the data, which greatly improves effectiveness and efficiency. By applying LFSC to real single-cell RNA sequencing datasets, we discovered that it has superior performance over existing baseline methods in clustering accuracy and robustness. An application using infiltrating T cells in liver cancer demonstrates that LFSC can successfully find new cell types, discover differently expressed genes, and explore new cancer-associated biomarkers.
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Affiliation(s)
- Qiaoming Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yingjian Liang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Dong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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35
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Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen YG, Cui W. Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage. Life Sci Alliance 2022; 5:5/10/e202201503. [PMID: 35667687 PMCID: PMC9170949 DOI: 10.26508/lsa.202201503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Paired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype. Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell–mediated destruction of pancreatic β cells. We have previously shown that diabetogenic CD8 T cells in the islets of non-obese diabetic mice are phenotypically heterogeneous, but clonal heterogeneity remains relatively unexplored. Here, we use paired single-cell RNA and T-cell receptor sequencing (scRNA-seq and scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of non-obese diabetic mice. scTCR-seq demonstrates that CD8 T cells targeting the immunodominant β-cell epitope IGRP206-214 exhibit restricted TCR gene usage. scRNA-seq identifies six clusters of autoreactive CD8 T cells in the islets and six in the spleen, including memory and exhausted cells. Clonal overlap between IGRP206-214–reactive CD8 T cells in the islets and spleen suggests these cells may circulate between the islets and periphery. Finally, we identify correlations between TCR genes and T-cell clonal expansion and effector fate. Collectively, our work demonstrates that IGRP206-214–specific CD8 T cells are phenotypically heterogeneous but clonally restricted, raising the possibility of selectively targeting these TCR structures for therapeutic benefit.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Ashley E Ciecko
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jack Gorski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
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36
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Abstract
Islet dysfunction is central in type 2 diabetes and full-blown type 2 diabetes develops first when the beta cells lose their ability to secrete adequate amounts of insulin in response to raised plasma glucose. Several mechanisms behind beta cell dysfunction have been put forward but many important questions still remain. Furthermore, our understanding of the contribution of each islet cell type in type 2 diabetes pathophysiology has been limited by technical boundaries. Closing this knowledge gap will lead to a leap forward in our understanding of the islet as an organ and potentially lead to improved treatments. The development of single-cell RNA sequencing (scRNAseq) has led to a breakthrough for characterising the transcriptome of each islet cell type and several important observations on the regulation of cell-type-specific gene expression have been made. When it comes to identifying type 2 diabetes disease mechanisms, the outcome is still limited. Several studies have identified differentially expressed genes, although there is very limited consensus between the studies. As with all new techniques, scRNAseq has limitations; in addition to being extremely expensive, genes expressed at low levels may not be detected, noise may not be appropriately filtered and selection biases for certain cell types are at hand. Furthermore, recent advances suggest that commonly used computational tools may be suboptimal for analysis of scRNAseq data in small-scale studies. Fortunately, development of new computational tools holds promise for harnessing the full potential of scRNAseq data. Here we summarise how scRNAseq has contributed to increasing the understanding of various aspects of islet biology as well as type 2 diabetes disease mechanisms. We also focus on challenges that remain and propose steps to promote the utilisation of the full potential of scRNAseq in this area.
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Affiliation(s)
| | - Nils Wierup
- Lund University Diabetes Centre, Malmö, Sweden.
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37
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Li Y, Jiang W, Mellins ED. TCR-like antibodies targeting autoantigen-mhc complexes: a mini-review. Front Immunol 2022; 13:968432. [PMID: 35967436 PMCID: PMC9363607 DOI: 10.3389/fimmu.2022.968432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
T cell receptors (TCRs) recognize peptide antigens bound to major histocompatibility complex (MHC) molecules (p/MHC) that are expressed on cell surfaces; while B cell-derived antibodies (Abs) recognize soluble or cell surface native antigens of various types (proteins, carbohydrates, etc.). Immune surveillance by T and B cells thus inspects almost all formats of antigens to mount adaptive immune responses against cancer cells, infectious organisms and other foreign insults, while maintaining tolerance to self-tissues. With contributions from environmental triggers, the development of autoimmune disease is thought to be due to the expression of MHC risk alleles by antigen-presenting cells (APCs) presenting self-antigen (autoantigen), breaking through self-tolerance and activating autoreactive T cells, which orchestrate downstream pathologic events. Investigating and treating autoimmune diseases have been challenging, both because of the intrinsic complexity of these diseases and the need for tools targeting T cell epitopes (autoantigen-MHC). Naturally occurring TCRs with relatively low (micromolar) affinities to p/MHC are suboptimal for autoantigen-MHC targeting, whereas the use of engineered TCRs and their derivatives (e.g., TCR multimers and TCR-engineered T cells) are limited by unpredictable cross-reactivity. As Abs generally have nanomolar affinity, recent advances in engineering TCR-like (TCRL) Abs promise advantages over their TCR counterparts for autoantigen-MHC targeting. Here, we compare the p/MHC binding by TCRs and TCRL Abs, review the strategies for generation of TCRL Abs, highlight their application for identification of autoantigen-presenting APCs, and discuss future directions and limitations of TCRL Abs as immunotherapy for autoimmune diseases.
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Affiliation(s)
- Ying Li
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Wei Jiang
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
| | - Elizabeth D. Mellins
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
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Yip L, Alkhataybeh R, Taylor C, Fuhlbrigge R, Fathman CG. Identification of Novel Disease-Relevant Genes and Pathways in the Pathogenesis of Type 1 Diabetes: A Potential Defect in Pancreatic Iron Homeostasis. Diabetes 2022; 71:1490-1507. [PMID: 35499603 PMCID: PMC9233262 DOI: 10.2337/db21-0948] [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: 10/22/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022]
Abstract
Multiple pathways contribute to the pathophysiological development of type 1 diabetes (T1D); however, the exact mechanisms involved are unclear. We performed differential gene expression analysis in pancreatic islets of NOD mice versus age-matched congenic NOD.B10 controls to identify genes that may contribute to disease pathogenesis. Novel genes related to extracellular matrix development and glucagon and insulin signaling/secretion were changed in NOD mice during early inflammation. During "respective" insulitis, the expression of genes encoding multiple chemosensory olfactory receptors were upregulated, and during "destructive" insulitis, the expression of genes involved in antimicrobial defense and iron homeostasis were downregulated. Islet inflammation reduced the expression of Hamp that encodes hepcidin. Hepcidin is expressed in β-cells and serves as the key regulator of iron homeostasis. We showed that Hamp and hepcidin levels were lower, while iron levels were higher in the pancreas of 12-week-old NOD versus NOD.B10 mice, suggesting that a loss of iron homeostasis may occur in the islets during the onset of "destructive" insulitis. Interestingly, we showed that the severity of NOD disease correlates with dietary iron intake. NOD mice maintained on low-iron diets had a lower incidence of hyperglycemia, while those maintained on high-iron diets had an earlier onset and higher incidence of disease, suggesting that high iron exposure combined with a loss of pancreatic iron homeostasis may exacerbate NOD disease. This mechanism may explain the link seen between high iron exposure and the increased risk for T1D in humans.
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Chen P, Yao F, Lu Y, Peng Y, Zhu S, Deng J, Wu Z, Chen J, Deng K, Li Q, Pu Z, Mou L. Single-Cell Landscape of Mouse Islet Allograft and Syngeneic Graft. Front Immunol 2022; 13:853349. [PMID: 35757709 PMCID: PMC9226584 DOI: 10.3389/fimmu.2022.853349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Islet transplantation to treat the late stage of type 1 diabetic patient (T1DM) has recently made inspiring success in clinical trials. However, most patients experience a decline in islet graft function in one to three years due to immune rejection. Although the mechanisms of immune cells, including macrophages, dendritic cells (DCs), neutrophils, natural killer cells (NKs), B cells, and T cells, that mediate immune rejection have been investigated, the overall characteristics of immune infiltrates in islet allografts and syngeneic grafts remain unclear. Single-cell RNA sequencing (scRNA-seq) has provided us with new opportunities to study the complexity of the immune microenvironment in islet transplants. In the present study, we used scRNA-seq to comprehensively analyze the immune heterogeneity in the mouse model of islet transplantation. Our data revealed T lymphocytes and myeloid cells as the main immune components of grafts 7 days post-islet transplantation, especially in allografts. Moreover, our results indicated that allogeneic islet cells were transformed into antigen-presenting cell-like cells with highly expressed MHC class I molecules and genes involved in MHC class I-mediated antigen presentation. This transformation may dramatically facilitate the interaction with cytotoxic CD8+ T cells and promote the destruction of islet allografts. Our study provides insight into the transcriptomics and diverse microenvironment of islet grafts and their impacts on immune rejection.
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Affiliation(s)
- Pengfei Chen
- Department of traumatic orthopedics, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Fuwen Yao
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.,Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Ying Lu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yuanzheng Peng
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Shufang Zhu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jing Deng
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Zijing Wu
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.,Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jiao Chen
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Kai Deng
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Qi Li
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Zuhui Pu
- Imaging Department, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Lisha Mou
- Department of Hepatopancreatobiliary Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.,Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
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40
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Grebinoski S, Zhang Q, Cillo AR, Manne S, Xiao H, Brunazzi EA, Tabib T, Cardello C, Lian CG, Murphy GF, Lafyatis R, Wherry EJ, Das J, Workman CJ, Vignali DAA. Autoreactive CD8 + T cells are restrained by an exhaustion-like program that is maintained by LAG3. Nat Immunol 2022; 23:868-877. [PMID: 35618829 DOI: 10.1038/s41590-022-01210-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
Impaired chronic viral and tumor clearance has been attributed to CD8+ T cell exhaustion, a differentiation state in which T cells have reduced and altered effector function that can be partially reversed upon blockade of inhibitory receptors. The role of the exhaustion program and transcriptional networks that control CD8+ T cell function and fate in autoimmunity is not clear. Here we show that intra-islet CD8+ T cells phenotypically, transcriptionally, epigenetically and metabolically possess features of canonically exhausted T cells, yet maintain important differences. This 'restrained' phenotype can be perturbed and disease accelerated by CD8+ T cell-restricted deletion of the inhibitory receptor lymphocyte activating gene 3 (LAG3). Mechanistically, LAG3-deficient CD8+ T cells have enhanced effector-like functions, trafficking to the islets, and have a diminished exhausted phenotype, highlighting a physiological role for an exhaustion program in limiting autoimmunity and implicating LAG3 as a target for autoimmune therapy.
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Affiliation(s)
- Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Qianxia Zhang
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Sasikanth Manne
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,CMU-Pitt Joint Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin A Brunazzi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christine G Lian
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - George F Murphy
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy at University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 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.
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41
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Liu Q, Luo X, Li J, Wang G. scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells. Brief Bioinform 2022; 23:6580519. [PMID: 35512331 DOI: 10.1093/bib/bbac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/14/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
The ubiquitous dropout problem in single-cell RNA sequencing technology causes a large amount of data noise in the gene expression profile. For this reason, we propose an evolutionary sparse imputation (ESI) algorithm for single-cell transcriptomes, which constructs a sparse representation model based on gene regulation relationships between cells. To solve this model, we design an optimization framework based on nondominated sorting genetics. This framework takes into account the topological relationship between cells and the variety of gene expression to iteratively search the global optimal solution, thereby learning the Pareto optimal cell-cell affinity matrix. Finally, we use the learned sparse relationship model between cells to improve data quality and reduce data noise. In simulated datasets, scESI performed significantly better than benchmark methods with various metrics. By applying scESI to real scRNA-seq datasets, we discovered scESI can not only further classify the cell types and separate cells in visualization successfully but also improve the performance in reconstructing trajectories differentiation and identifying differentially expressed genes. In addition, scESI successfully recovered the expression trends of marker genes in stem cell differentiation and can discover new cell types and putative pathways regulating biological processes.
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Affiliation(s)
- Qiaoming Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Ximei Luo
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Guohua Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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42
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Zhao TV, Sato Y, Goronzy JJ, Weyand CM. T-Cell Aging-Associated Phenotypes in Autoimmune Disease. FRONTIERS IN AGING 2022; 3:867950. [PMID: 35821833 PMCID: PMC9261367 DOI: 10.3389/fragi.2022.867950] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/28/2022] [Indexed: 01/10/2023]
Abstract
The aging process causes profound restructuring of the host immune system, typically associated with declining host protection against cancer and infection. In the case of T cells, aging leads to the accumulation of a diverse set of T-cell aging-associated phenotypes (TASP), some of which have been implicated in driving tissue inflammation in autoimmune diseases. T cell aging as a risk determinant for autoimmunity is exemplified in two classical autoimmune conditions: rheumatoid arthritis (RA), a disease predominantly affecting postmenopausal women, and giant cell arteritis (GCA), an inflammatory vasculopathy exclusively occurring during the 6th-9th decade of life. Pathogenic T cells in RA emerge as a consequence of premature immune aging. They have shortening and fragility of telomeric DNA ends and instability of mitochondrial DNA. As a result, they produce a distinct profile of metabolites, disproportionally expand their endoplasmic reticulum (ER) membranes and release excess amounts of pro-inflammatory effector cytokines. Characteristically, they are tissue invasive, activate the inflammasome and die a pyroptotic death. Patients with GCA expand pathogenic CD4+ T cells due to aberrant expression of the co-stimulatory receptor NOTCH1 and the failure of the PD-1/PD-L1 immune checkpoint. In addition, GCA patients lose anti-inflammatory Treg cells, promoting tissue-destructive granulomatous vasculitis. In summary, emerging data identify T cell aging as a risk factor for autoimmune disease and directly link TASPs to the breakdown of T cell tolerance and T-cell-induced tissue inflammation.
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Affiliation(s)
- Tuantuan V. Zhao
- Mayo Clinic Alix School of Medicine, College of Medicine and Science, Rochester, MN, United States
| | - Yuki Sato
- Mayo Clinic Alix School of Medicine, College of Medicine and Science, Rochester, MN, United States
| | - Jorg J. Goronzy
- Mayo Clinic Alix School of Medicine, College of Medicine and Science, Rochester, MN, United States,School of Medicine, Stanford University, Stanford, CA, United States
| | - Cornelia M. Weyand
- Mayo Clinic Alix School of Medicine, College of Medicine and Science, Rochester, MN, United States,School of Medicine, Stanford University, Stanford, CA, United States,*Correspondence: Cornelia M. Weyand,
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43
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Ma Y, Chen J, Wang T, Zhang L, Xu X, Qiu Y, Xiang AP, Huang W. Accurate Machine Learning Model to Diagnose Chronic Autoimmune Diseases Utilizing Information From B Cells and Monocytes. Front Immunol 2022; 13:870531. [PMID: 35515003 PMCID: PMC9065417 DOI: 10.3389/fimmu.2022.870531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/22/2022] [Indexed: 12/17/2022] Open
Abstract
Heterogeneity and limited comprehension of chronic autoimmune disease pathophysiology cause accurate diagnosis a challenging process. With the increasing resources of single-cell sequencing data, a reasonable way could be found to address this issue. In our study, with the use of large-scale public single-cell RNA sequencing (scRNA-seq) data, analysis of dataset integration (3.1 × 105 PBMCs from fifteen SLE patients and eight healthy donors) and cellular cross talking (3.8 × 105 PBMCs from twenty-eight SLE patients and eight healthy donors) were performed to identify the most crucial information characterizing SLE. Our findings revealed that the interactions among the PBMC subpopulations of SLE patients may be weakened under the inflammatory microenvironment, which could result in abnormal emergences or variations in signaling patterns within PBMCs. In particular, the alterations of B cells and monocytes may be the most significant findings. Utilizing this powerful information, an efficient mathematical model of unbiased random forest machine learning was established to distinguish SLE patients from healthy donors via not only scRNA-seq data but also bulk RNA-seq data. Surprisingly, our mathematical model could also accurately identify patients with rheumatoid arthritis and multiple sclerosis, not just SLE, via bulk RNA-seq data (derived from 688 samples). Since the variations in PBMCs should predate the clinical manifestations of these diseases, our machine learning model may be feasible to develop into an efficient tool for accurate diagnosis of chronic autoimmune diseases.
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Affiliation(s)
- Yuanchen Ma
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Jieying Chen
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Tao Wang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Liting Zhang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xinhao Xu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuxuan Qiu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Weijun Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Weijun Huang,
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Jin K, Gao S, Yang P, Guo R, Li D, Zhang Y, Lu X, Fan G, Fan X. Single-Cell RNA Sequencing Reveals the Temporal Diversity and Dynamics of Cardiac Immunity after Myocardial Infarction. SMALL METHODS 2022; 6:e2100752. [PMID: 35023642 DOI: 10.1002/smtd.202100752] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Myocardial infarction (MI) is strongly associated with the temporal regulation of cardiac immunity. However, a variety of current clinical trials have failed because of the lack of post-MI immunomodulating/anti-inflammatory targets. Single-cell RNA sequencing analysis of the cardiac Cd45+ immune cell at 0, 3, 7, and 14 d after injury in a mouse left anterior descending coronary artery ligation model is performed. Major immune cell populations, distinct subsets, and dynamic changes are identified. Macrophages (Mø) are most abundant, peaking at 3 d after infarction. Mø-5 and Mø-6 are the predominant infiltrated subsets at this time point, with strong expression of inflammatory factors. Further analysis demonstrates that suppressing these sets attenuated pathological MI progression by preventing subsequent leukocyte extravasation and adverse remodeling. Abundant apoptotic neutrophils and a profibrotic macrophage subset on days 7 and 14, respectively, are also detected. These results provide a basis for developing cell type- and time-specific interventions in MI.
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Affiliation(s)
- Kaiyu Jin
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shan Gao
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Penghui Yang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rongfang Guo
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan Li
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
| | - Yunsha Zhang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guanwei Fan
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, 300193, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300193, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin, 301617, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin, 301617, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310058, China
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Sona C, Yeh YT, Patsalos A, Halasz L, Yan X, Kononenko NL, Nagy L, Poy MN. Evidence of islet CADM1-mediated immune cell interactions during human type 1 diabetes. JCI Insight 2022; 7:153136. [PMID: 35133983 PMCID: PMC8986082 DOI: 10.1172/jci.insight.153136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Pathophysiology of type 1 diabetes (T1D) is illustrated by pancreatic islet infiltration of inflammatory lymphocytes, including CD8+ T cells; however, the molecular factors mediating their recruitment remain unknown. We hypothesized that single-cell RNA-sequencing (scRNA-Seq) analysis of immune cell populations isolated from islets of NOD mice captured gene expression dynamics providing critical insight into autoimmune diabetes pathogenesis. METHODS Pancreatic sections from human donors were investigated, including individuals with T1D, autoantibody-positive (aAb+) individuals, and individuals without diabetes who served as controls. IHC was performed to assess islet hormones and both novel and canonical immune cell markers that were identified from unbiased, state-of-the-art workflows after reanalyzing murine scRNA-Seq data sets. RESULTS Computational workflows identified cell adhesion molecule 1–mediated (Cadm1-mediated) homotypic binding among the most important intercellular interactions among all cell clusters, as well as Cadm1 enrichment in macrophages and DCs from pancreata of NOD mice. Immunostaining of human pancreata revealed an increased number of CADM1+glucagon+ cells adjacent to CD8+ T cells in sections from T1D and aAb+ donors compared with individuals without diabetes. Numbers of CADM1+CD68+ peri-islet myeloid cells adjacent to CD8+ T cells were also increased in pancreatic sections from both T1D and aAb+ donors compared with individuals without diabetes. CONCLUSION Increased detection of CADM1+ cells adjacent to CD8+ T cells in pancreatic sections of individuals with T1D and those who were aAb+ validated workflows and indicated CADM1-mediated intercellular contact may facilitate islet infiltration of cytotoxic T lymphocytes and serve as a potential therapeutic target for preventing T1D pathogenesis. FUNDING The Johns Hopkins All Children’s Foundation Institutional Research Grant Program, the National Natural Science Foundation of China (grant 82071326), and the Deutsche Forschungsgemeinschaft (grants 431549029–SFB1451, EXC2030–390661388, and 411422114-GRK2550).
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Affiliation(s)
- Chandan Sona
- Department of Medicine, John Hopkins University, St. Petersburg, United States of America
| | - Yu-Te Yeh
- Department of Medicine, John Hopkins University, St. Petersburg, United States of America
| | - Andreas Patsalos
- Institute for Fundamental Biomedical Research, John Hopkins University, St. Petersburg, United States of America
| | - Laszlo Halasz
- Institute for Fundamental Biomedical Research, John Hopkins University, St. Petersburg, United States of America
| | - Xin Yan
- Stem Cell and Biotherapy Technology Research Center, Xinxiang Medical University, Xinxiang, China
| | - Natalia L Kononenko
- CECAD Excellence Center & Center for Physiology and Pathophysiology, University of Cologne, Cologne, Germany
| | - Laszlo Nagy
- Institute for Fundamental Biomedical Research, John Hopkins University, St. Petersburg, United States of America
| | - Matthew N Poy
- Department of Medicine, John Hopkins University, St. Petersburg, United States of America
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46
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An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature 2022; 602:156-161. [PMID: 34847567 PMCID: PMC9315050 DOI: 10.1038/s41586-021-04248-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/15/2021] [Indexed: 01/02/2023]
Abstract
CD8 T cell-mediated autoimmune diseases result from the breakdown of self-tolerance mechanisms in autoreactive CD8 T cells1. How autoimmune T cell populations arise and are sustained, and the molecular programmes defining the autoimmune T cell state, are unknown. In type 1 diabetes, β-cell-specific CD8 T cells destroy insulin-producing β-cells. Here we followed the fate of β-cell-specific CD8 T cells in non-obese diabetic mice throughout the course of type 1 diabetes. We identified a stem-like autoimmune progenitor population in the pancreatic draining lymph node (pLN), which self-renews and gives rise to pLN autoimmune mediators. pLN autoimmune mediators migrate to the pancreas, where they differentiate further and destroy β-cells. Whereas transplantation of as few as 20 autoimmune progenitors induced type 1 diabetes, as many as 100,000 pancreatic autoimmune mediators did not. Pancreatic autoimmune mediators are short-lived, and stem-like autoimmune progenitors must continuously seed the pancreas to sustain β-cell destruction. Single-cell RNA sequencing and clonal analysis revealed that autoimmune CD8 T cells represent unique T cell differentiation states and identified features driving the transition from autoimmune progenitor to autoimmune mediator. Strategies aimed at targeting the stem-like autoimmune progenitor pool could emerge as novel and powerful immunotherapeutic interventions for type 1 diabetes.
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Miao YR, Xia M, Luo M, Luo T, Yang M, Guo AY. ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction. Bioinformatics 2022; 38:785-791. [PMID: 34636837 DOI: 10.1093/bioinformatics/btab711] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/22/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Immune cells are important components of the immune system and are crucial for disease initiation, progression, prognosis and survival. Although several computational methods have been designed for predicting the abundance of immune cells, very few tools are applicable to mouse. Given that, mouse is the most widely used animal model in biomedical research, there is an urgent need to develop a precise algorithm for predicting mouse immune cells. RESULTS We developed a tool named Immune Cell Abundance Identifier for mouse (ImmuCellAI-mouse), for estimating the abundance of 36 immune cell (sub)types from gene expression data in a hierarchical strategy of three layers. Reference expression profiles and robust marker gene sets of immune cell types were curated. The abundance of cells in three layers was predicted separately by calculating the ssGSEA enrichment score of the expression deviation profile per cell type. Benchmark results showed high accuracy of ImmuCellAI-mouse in predicting most immune cell types, with correlation coefficients between predicted value and real cell proportion of most cell types being larger than 0.8. We applied ImmuCellAI-mouse to a mouse breast tumor dataset and revealed the dynamic change of immune cell infiltration during treatment, which is consistent with the findings of the original study but with more details. We also constructed an online server for ImmuCellAI-mouse, on which users can upload expression matrices for analysis. ImmuCellAI-mouse will be a useful tool for studying the immune microenvironment, cancer immunology and immunotherapy in mouse models, providing an indispensable supplement for human disease studies. AVAILABILITY AND IMPLEMENTATION Software is available at http://bioinfo.life.hust.edu.cn/ImmuCellAI-mouse/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ya-Ru Miao
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mengxuan Xia
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mei Luo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Tao Luo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mei Yang
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
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Kuchroo JR, Hafler DA, Sharpe AH, Lucca LE. The double-edged sword: Harnessing PD-1 blockade in tumor and autoimmunity. Sci Immunol 2021; 6:eabf4034. [PMID: 34739340 DOI: 10.1126/sciimmunol.abf4034] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Juhi R Kuchroo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliana E Lucca
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
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49
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Budd MA, Monajemi M, Colpitts SJ, Crome SQ, Verchere CB, Levings MK. Interactions between islets and regulatory immune cells in health and type 1 diabetes. Diabetologia 2021; 64:2378-2388. [PMID: 34550422 DOI: 10.1007/s00125-021-05565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
Type 1 diabetes results from defects in immune self-tolerance that lead to inflammatory infiltrate in pancreatic islets, beta cell dysfunction and T cell-mediated killing of beta cells. Although therapies that broadly inhibit immunity show promise to mitigate autoinflammatory damage caused by effector T cells, these are unlikely to permanently reset tolerance or promote regeneration of the already diminished pool of beta cells. An emerging concept is that certain populations of immune cells may have the capacity to both promote tolerance and support the restoration of beta cells by supporting proliferation, differentiation and/or regeneration. Here we will highlight three immune cell types-macrophages, regulatory T cells and innate lymphoid cells-for which there is evidence of dual roles of immune regulation and tissue regeneration. We explore how findings in this area from other fields might be extrapolated to type 1 diabetes and highlight recent discoveries in the context of type 1 diabetes. We also discuss technological advances that are supporting this area of research and contextualise new therapeutic avenues to consider for type 1 diabetes.
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Affiliation(s)
- Matthew A Budd
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Mahdis Monajemi
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah J Colpitts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Sarah Q Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - C Bruce Verchere
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada.
- BC Children's Hospital Research Institute, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
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50
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Ciecko AE, Schauder DM, Foda B, Petrova G, Kasmani MY, Burns R, Lin CW, Drobyski WR, Cui W, Chen YG. Self-Renewing Islet TCF1 + CD8 T Cells Undergo IL-27-Controlled Differentiation to Become TCF1 - Terminal Effectors during the Progression of Type 1 Diabetes. THE JOURNAL OF IMMUNOLOGY 2021; 207:1990-2004. [PMID: 34507949 DOI: 10.4049/jimmunol.2100362] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022]
Abstract
In type 1 diabetes (T1D) autoreactive CD8 T cells infiltrate pancreatic islets and destroy insulin-producing β cells. Progression to T1D onset is a chronic process, which suggests that the effector activity of β-cell autoreactive CD8 T cells needs to be maintained throughout the course of disease development. The mechanism that sustains diabetogenic CD8 T cell effectors during the course of T1D progression has not been completely defined. Here we used single-cell RNA sequencing to gain further insight into the phenotypic complexity of islet-infiltrating CD8 T cells in NOD mice. We identified two functionally distinct subsets of activated CD8 T cells, CD44highTCF1+CXCR6- and CD44highTCF1-CXCR6+, in islets of prediabetic NOD mice. Compared with CD44highTCF1+CXCR6- CD8 T cells, the CD44highTCF1-CXCR6+ subset expressed higher levels of inhibitory and cytotoxic molecules and was more prone to apoptosis. Adoptive cell transfer experiments revealed that CD44highTCF1+CXCR6- CD8 T cells, through continuous generation of the CD44highTCF1-CXCR6+ subset, were more capable than the latter population to promote insulitis and the development of T1D. We further showed that direct IL-27 signaling in CD8 T cells promoted the generation of terminal effectors from the CD44highTCF1+CXCR6- population. These results indicate that islet CD44highTCF1+CXCR6- CD8 T cells are a progenitor-like subset with self-renewing capacity, and, under an IL-27-controlled mechanism, they differentiate into the CD44highTCF1-CXCR6+ terminal effector population. Our study provides new insight into the sustainability of the CD8 T cell response in the pathogenesis of T1D.
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Affiliation(s)
- Ashley E Ciecko
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - David M Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Bardees Foda
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI.,Department of Molecular Genetics and Enzymology, National Research Center, Dokki, Egypt
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | | | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Society, Medical College of Wisconsin, Milwaukee, WI; and
| | - William R Drobyski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI.,Versiti Blood Research Institute, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI; .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
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