1
|
Mauvais FX, van Endert PM. Type 1 Diabetes: A Guide to Autoimmune Mechanisms for Clinicians. Diabetes Obes Metab 2025. [PMID: 40375390 DOI: 10.1111/dom.16460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/27/2025] [Accepted: 04/30/2025] [Indexed: 05/18/2025]
Abstract
Type 1 diabetes (T1D) results from the destruction of pancreatic beta cells by autoreactive T lymphocytes, leading to insulin deficiency and lifelong insulin dependence. It develops in genetically predisposed individuals, triggered by environmental or immunological factors. Although the exact causes of T1D remain unknown, the autoimmune pathogenesis of the disease is clearly indicated by the genetic risk conferred by allelic human leukocyte antigens (HLA), the almost obligatory presence of islet cell autoantibodies (AAbs) and immune cell infiltration of pancreatic islets from patients. At the same time, epidemiological data point to a role of environmental factors, notably enteroviral infections, in the disease, although precise causative links between specific pathogens and T1D have been difficult to establish. Studies of human pancreas organs from patients made available through repositories and the advent of high-dimensional high-throughput technologies for genomic and proteomic studies have significantly elucidated our understanding of the disease in recent years and provided mechanistic insights that can be exploited for innovative targeted therapeutic approaches. This short overview will summarise current salient knowledge on immune cell and beta cell dysfunction in T1D pathogenesis. PLAIN LANGUAGE SUMMARY: Type 1 diabetes (T1D) is a chronic disease where the body's own immune system attacks and destroys the insulin-producing beta cells in the pancreas. This leads to a lack of insulin, a hormone essential for regulating blood sugar, which means people with T1D need insulin for life. The disease can develop at any age but is most diagnosed in children and young adults. Despite advances in treatment, T1D still significantly reduces life expectancy, especially in countries with fewer healthcare resources. T1D develops in people with a genetic predisposition, often triggered by environmental factors such as viral infections or changes in the gut microbiome. The disease progresses silently through three stages: Stage 1: Autoantibodies to beta cell components appear, signalling the immune system is reacting against the pancreas, but there are no symptoms; Stage 2: Beta cell function starts to decline, but fasting blood sugar is still normal; Stage 3: Enough beta cells are destroyed that fasting blood sugar rises, and symptoms of diabetes appear. The risk of progressing from stage 1 to full-blown diabetes is about 35-50% within five years, and even higher from stage 2. Over 60 genes are linked to T1D risk, most of which affect how the immune system works. The strongest genetic risk comes from specific versions of histocompatibility genes, which help the immune system distinguish between the body's own cells and invaders. Some types of these genes make it easier for the immune system to mistakenly attack beta cells. However, 90% of people diagnosed with T1D have no family member with T1D, showing that genetics is only part of the story. Environmental factors also play a big role. For example, certain viral infections, especially with viruses infecting the intestine, are associated with a higher risk of developing T1D. The gut microbiome - the community of bacteria living in our intestines - also influences risk, with healthier, more diverse microbiomes appearing to offer some protection. In T1D, immune cells - especially so-called T lymphocytes - mistake beta cells in the pancreas for threats and destroy them. This process is called autoimmunity. The attack is often reflected by the presence of autoantibodies against proteins found in beta cells. Over time, as more beta cells are lost, the body can no longer produce enough insulin, leading to the symptoms of diabetes. Interestingly, not all people with T1D have the same pattern of disease. For example, children diagnosed before age 7 often have more aggressive disease, more autoantibodies, and stronger genetic risk factors than those diagnosed later. Much of our understanding of T1D has come from studying animal models, but new technologies now allow researchers to study human pancreas tissue and blood immune cells in greater detail. Scientists are also exploring how the gut microbiome, diet, and environmental exposures contribute to T1D risk and progression. Treatment currently focuses on replacing insulin, but researchers are working on therapies that target the immune system or aim to protect or replace beta cells. Strategies include immunotherapy, gene therapy, and even modifying the gut microbiome. The goal is to prevent or reverse the disease, not just manage its symptoms. In summary, T1D is a complex autoimmune disease influenced by both genes and the environment. It progresses silently before symptoms appear, and while insulin therapy is life-saving, new research is paving the way for treatments that could one day halt or even prevent the disease.
Collapse
Affiliation(s)
- François-Xavier Mauvais
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Paris, France
- Service de Physiologie - Explorations Fonctionnelles Pédiatriques, AP-HP, Hôpital Universitaire Robert Debré, Paris, France
| | - Peter M van Endert
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Paris, France
- Service Immunologie Biologique, AP-HP, Hôpital Universitaire Necker - Enfants Malades, Paris, France
| |
Collapse
|
2
|
Wang SH, Serr I, Digigow R, Metzler B, Surnov A, Gottwick C, Alsamman M, Krzikalla D, Heine M, Zahlten M, Widera A, Mungalpara D, Şeleci M, Fanzutti M, Marques Mesquita LM, Vocaturo AL, Herkel J, Carambia A, Schröter C, Sarko D, Pohlner J, Daniel C, de Min C, Fleischer S. Nanoparticle platform preferentially targeting liver sinusoidal endothelial cells induces tolerance in CD4+ T cell-mediated disease models. Front Immunol 2025; 16:1542380. [PMID: 40165970 PMCID: PMC11955608 DOI: 10.3389/fimmu.2025.1542380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Accepted: 02/25/2025] [Indexed: 04/02/2025] Open
Abstract
Introduction Treating autoimmune diseases without nonspecific immunosuppression remains challenging. To prevent or treat these conditions through targeted immunotherapy, we developed a clinical-stage nanoparticle platform that leverages the tolerogenic capacity of liver sinusoidal endothelial cells (LSECs) to restore antigen-specific immune tolerance. Methods In vivo efficacy was evaluated in various CD4+ T cell-mediated disease models, including preventive and therapeutic models of myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis (EAE), ovalbumin-sensitized delayed-type hypersensitivity (DTH), and the spontaneous type 1 diabetes model. Nanoparticle-induced antigen-specific immune responses were also analyzed through adoptive transfers of 2D2 transgenic T cells into wild-type mice, followed by nanoparticle administration. Results The peptide-conjugated nanoparticles displayed a uniform size distribution (25-30 nm). Their coupling efficiency for peptides with unfavorable physicochemical properties was significantly enhanced by a proprietary linker technology. Preferential LSEC targeting of nanoparticles coupled with fluorescently labeled peptides was confirmed via intravital microscopy and flow cytometry. Intravenous nanoparticle administration significantly reduced disease severity and demyelination in EAE, independent of prednisone at maintenance doses, and suppressed target tissue inflammation in the DTH model. Furthermore, prophylactic administration of a mixture of nanoparticles coupled with five autoantigenic peptides significantly lowered the hyperglycemia incidence of the non-obese diabetic mice. Mechanistically, the tolerizing effects were associated with the induction of antigen-specific regulatory T cells and T cell anergy, which counteract proinflammatory T cells in the target tissue. Conclusion Our findings demonstrate that peptide-loaded nanoparticles preferentially deliver disease-relevant peptides to LSECs, thereby inducing antigen-specific immune tolerance. This versatile clinical-stage nanoparticle platform holds promise for clinical application across multiple autoimmune diseases.
Collapse
MESH Headings
- Animals
- Immune Tolerance
- Mice
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/therapy
- Endothelial Cells/immunology
- Endothelial Cells/metabolism
- Nanoparticles/administration & dosage
- Nanoparticles/chemistry
- CD4-Positive T-Lymphocytes/immunology
- Liver/immunology
- Disease Models, Animal
- Mice, Inbred C57BL
- Female
- Ovalbumin/immunology
- Hypersensitivity, Delayed/immunology
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/therapy
- Peptides
- Mice, Transgenic
Collapse
Affiliation(s)
- Shu-Hung Wang
- Department of Clinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Isabelle Serr
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Reinaldo Digigow
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Barbara Metzler
- Department of Preclinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Alexey Surnov
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Cornelia Gottwick
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Muhammad Alsamman
- Department of Preclinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Daria Krzikalla
- Department of Preclinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology (N30), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Miriam Zahlten
- Department of Preclinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Agata Widera
- Department of Preclinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Disha Mungalpara
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Muharrem Şeleci
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Marco Fanzutti
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | | | - Anna-Lisa Vocaturo
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Johannes Herkel
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Centre for Translational Immunology (HCTI), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Antonella Carambia
- Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Schröter
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Dikran Sarko
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Johannes Pohlner
- Department of Chemistry, Manufacturing & Controls, Topas Therapeutics GmbH, Hamburg, Germany
| | - Carolin Daniel
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig Maximilian University of Munich, Munich, Germany
| | - Cristina de Min
- Department of Clinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| | - Sabine Fleischer
- Department of Clinical Development, Topas Therapeutics GmbH, Hamburg, Germany
| |
Collapse
|
3
|
Chitale GG, Kulkarni SR, Bapat SA. Chimerism: A whole new perspective in gene regulation. Biochim Biophys Acta Gen Subj 2025; 1869:130767. [PMID: 39855315 DOI: 10.1016/j.bbagen.2025.130767] [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: 11/04/2024] [Revised: 01/10/2025] [Accepted: 01/16/2025] [Indexed: 01/27/2025]
Abstract
The diversity of molecular entities emerging from a single gene are recognized. Several studies have thus established the cellular role(s) of transcript variants and protein isoforms. A step ahead in challenging the central dogma towards expanding molecular diversity is the identification of fusion genes, chimeric transcripts and chimeric proteins that harbor sequences from more than one gene. The mechanisms for generation of chimeras largely follow similar patterns across all levels of gene regulation but also have interdependence and mutual exclusivity. Whole genome and RNA-seq technologies supported by development of computational algorithms and programs for processing datasets have increasingly enabled the identification of fusion genes and chimeric transcripts, while the discovery of chimeric proteins is as yet more subtle. Earlier thought to be associated with cellular transformation, the contribution of chimeric molecules to normal physiology is also realized and found to influence the expression of their parental genes and regulate cellular pathways. This review offers a collective and comprehensive overview of cellular chimeric entities encompassing the mechanisms involved in their generation, insights on their evolution, functions in gene regulation and their current and novel clinical applications.
Collapse
Affiliation(s)
- Gayatri G Chitale
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Shweta R Kulkarni
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| |
Collapse
|
4
|
Kosheleva L, Koshelev D, Lagunas-Rangel FA, Levit S, Rabinovitch A, Schiöth HB. Disease-modifying pharmacological treatments of type 1 diabetes: Molecular mechanisms, target checkpoints, and possible combinatorial treatments. Pharmacol Rev 2025; 77:100044. [PMID: 40014914 PMCID: PMC11964952 DOI: 10.1016/j.pharmr.2025.100044] [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: 10/05/2024] [Accepted: 01/10/2025] [Indexed: 03/01/2025] Open
Abstract
After a century of extensive scientific investigations, there is still no curative or disease-modifying treatment available that can provide long-lasting remission for patients diagnosed with type 1 diabetes (T1D). Although T1D has historically been regarded as a classic autoimmune disorder targeting and destroying pancreatic islet β-cells, significant research has recently demonstrated that β-cells themselves also play a substantial role in the disease's progression, which could explain some of the unfavorable clinical outcomes. We offer a thorough review of scientific and clinical insights pertaining to molecular mechanisms behind pathogenesis and the different therapeutic interventions in T1D covering over 20 possible pharmaceutical intervention treatments. The interventions are categorized as immune therapies, treatments targeting islet endocrine dysfunctions, medications with dual modes of action in immune and islet endocrine cells, and combination treatments with a broader spectrum of activity. We suggest that these collective findings can provide a valuable platform to discover new combinatorial synergies in search of the curative disease-modifying intervention for T1D. SIGNIFICANCE STATEMENT: This research delves into the underlying causes of T1D and identifies critical mechanisms governing β-cell function in both healthy and diseased states. Thus, we identify specific pathways that could be manipulated by existing or new pharmacological interventions. These interventions fall into several categories: (1) immunomodifying therapies individually targeting immune cell processes, (2) interventions targeting β-cells, (3) compounds that act simultaneously on both immune cell and β-cell pathways, and (4) combinations of compounds simultaneously targeting immune and β-cell pathways.
Collapse
Affiliation(s)
- Liudmila Kosheleva
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Daniil Koshelev
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Francisco Alejandro Lagunas-Rangel
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden; Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Shmuel Levit
- Diabetes and Metabolism Institute, Assuta Medical Centers, Tel Aviv, Israel
| | | | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden; Laboratory of Pharmaceutical Pharmacology, Latvian Institute of Organic Synthesis, Riga, Latvia.
| |
Collapse
|
5
|
Zhang F, Liu M, Wang Y, Zhao X, Zhao C, Liu D, Li Y, Xu X, Li X, Yang H, Tian J. Bailixiang tea, an herbal medicine formula, co-suppresses TLR2/MAPK8 and TLR2/NF-κB signaling pathways to protect against LPS-triggered cytokine storm in mice. JOURNAL OF ETHNOPHARMACOLOGY 2025; 337:118791. [PMID: 39265795 DOI: 10.1016/j.jep.2024.118791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/14/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicine (TCM) has shown notable effectiveness and safety in managing illnesses linked to cytokine storm(CS). Bailixiang tea (BLX), an herbal medicine formula, which is a compound Chinese medicine composed of Thymus mongolicus (Ronniger) Ronniger (Bailixiang), Glycyrrhiza uralensis Fisch. (Gancao), Citrus reticulata Blanco (Chenpi), Cyperus rotundus L. (Xiangfu), and Perilla frutescens (L.) Britton (Zisu). The objective of this study was to explore the capacity of BLX in improving LPS-induced CS. AIM OF THE STUDY This study aimed to validate the mitigating effect of BLX on CS and to further investigate its mechanism. MATERIALS AND METHODS mice were orally administered BLX for 24 h after being treated with 5 mg/kg lipopolysaccharide (LPS). Histopathological observations further confirmed the significant protective effect of BLX treatment against LPS-induced lung and spleen damage. Additionally, we aimed to explore the molecular mechanism underlying its effects through blood proteomics and transcriptomics analyses. Real-Time Quantitative PCR (RT-qPCR) was utilized to detect the levels of Toll-like receptor 2 (TLR2), Matrix metalloproteinase 8 (MMP8), Matrix metalloproteinase 9 (MMP9), Integrin beta 2 (ITGB2), Mitogen-activated protein kinase 8 (MAPK8), Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon (NFKBIE), Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (NFKB2), and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)expressions in the lung tissue. RESULTS The results demonstrated that BLX effectively down-regulated the overproduction of interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α) in both the serum and lung and spleen tissues. Furthermore, BLX effectively mitigated the overproduction of monocyte chemoattractant protein-1 (MCP-1) in the serum. Through comprehensive multi-omics analysis, it was revealed that BLX specifically targeted and regulated TLR2/MAPK8 and TLR2/NF-κB signaling pathways, which play a crucial role in the production of key cytokines. CONCLUSIONS The findings of this study demonstrate that Bailixiang tea possesses the ability to alleviate lung tissue damage and inhibit the development of LPS-induced cytokine storm in mice. These effects are attributed to the tea's ability to suppress the TLR2/MAPK8 and TLR2/NF-κB pathways. Consequently, this research highlights the potential application of Bailixiang tea as a treatment option for cytokine storm.
Collapse
Affiliation(s)
- Fengrong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yun Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaoang Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chunhui Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Dewen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Youming Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, 330004, China
| | - Xingyue Xu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xianyu Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jixiang Tian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| |
Collapse
|
6
|
Moradi N, Sanfrancesco VC, Champsi S, Hood DA. Regulation of lysosomes in skeletal muscle during exercise, disuse and aging. Free Radic Biol Med 2024; 225:323-332. [PMID: 39332541 DOI: 10.1016/j.freeradbiomed.2024.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/29/2024] [Accepted: 09/16/2024] [Indexed: 09/29/2024]
Abstract
Lysosomes play a critical role as a terminal organelle in autophagy flux and in regulating protein degradation, but their function and adaptability in skeletal muscle is understudied. Lysosome functions include both housekeeping and signaling functions essential for cellular homeostasis. This review focuses on the regulation of lysosomes in skeletal muscle during exercise, disuse, and aging, with a consideration of sex differences as well as the role of lysosomes in mediating the degradation of mitochondria, termed mitophagy. Exercise enhances mitophagy during elevated mitochondrial stress and energy demand. A critical response to this deviation from homeostasis is the activation of transcription factors TFEB and TFE3, which drive the expression of lysosomal and autophagic genes. Conversely, during muscle disuse, the suppression of lysosomal activity contributes to the accumulation of defective mitochondria and other cellular debris, impairing muscle function. Aging further exacerbates these effects by diminishing lysosomal efficacy, leading to the accumulation of damaged cellular components. mTORC1, a key nutrient sensor, modulates lysosomal activity by inhibiting TFEB/TFE3 translocation to the nucleus under nutrient-rich conditions, thereby suppressing autophagy. During nutrient deprivation or exercise, AMPK activation inhibits mTORC1, facilitating TFEB/TFE3 nuclear translocation and promoting lysosomal biogenesis and autophagy. TRPML1 activation by mitochondrial ROS enhances lysosomal calcium release, which is essential for autophagy and maintaining mitochondrial quality. Overall, the intricate regulation of lysosomal functions and signaling pathways in skeletal muscle is crucial for adaptation to physiological demands, and disruptions in these processes during disuse and aging underscore the ubiquitous power of exercise-induced adaptations, and also highlight the potential for targeted therapeutic interventions to preserve muscle health.
Collapse
Affiliation(s)
- N Moradi
- Muscle Health Research Centre, Kinesiology and Health Science, York University, Toronto, ON, Canada
| | - V C Sanfrancesco
- Muscle Health Research Centre, Kinesiology and Health Science, York University, Toronto, ON, Canada
| | - S Champsi
- Muscle Health Research Centre, Kinesiology and Health Science, York University, Toronto, ON, Canada
| | - D A Hood
- Muscle Health Research Centre, Kinesiology and Health Science, York University, Toronto, ON, Canada.
| |
Collapse
|
7
|
Bhattacharjee P, Pakusch M, Lacorcia M, Tresoldi E, Rubin AF, Foster A, King L, Chiu CY, Kay TWH, Karas JA, Cameron FJ, Mannering SI. Proinsulin C-peptide is a major source of HLA-DQ8 restricted hybrid insulin peptides recognized by human islet-infiltrating CD4 + T cells. PNAS NEXUS 2024; 3:pgae491. [PMID: 39554513 PMCID: PMC11565411 DOI: 10.1093/pnasnexus/pgae491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 10/11/2024] [Indexed: 11/19/2024]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that develops when T cells destroy the insulin-producing beta cells that reside in the pancreatic islets. Immune cells, including T cells, infiltrate the islets and gradually destroy the beta cells. Human islet-infiltrating CD4+ T cells recognize peptide epitopes derived from proinsulin, particularly C-peptide. Hybrid insulin peptides (HIPs) are neoepitopes formed by the fusion of two peptides derived from beta cell granule proteins and are known to be the targets of pathogenic CD4+ T cells in the non-obese diabetic (NOD) mouse and human islet-infiltrating CD4+ T cells. Proinsulin is widely recognized as a central antigen in T1D, but its role in forming HIPs is unclear. We developed a method to functionally screen TCRs derived from human islet-infiltrating CD4+ T cells and applied this to the identification of new proinsulin-derived HIPs. We generated a library of 4,488 candidate HIPs formed by fusion of proinsulin fragments and predicted to bind to HLA-DQ8. This library was screened against 109 islet-infiltrating CD4+ T cell receptors (TCRs) isolated from four organ donors who had T1D. We identified 13 unique HIPs recognized by nine different TCRs from two organ donors. HIP-specific T cell avatars responded specifically to a peptide extract from human islets. These new HIPs predominantly stimulated CD4+ T cell proliferation in peripheral blood mononuclear cells from individuals with T1D in contrast to HLA-matched controls. This is the first unbiased functional, islet-infiltrating T cell based, screen to identify proinsulin-derived HIPs. It has revealed many new HIPs and a central role of proinsulin C-peptide in their formation.
Collapse
Affiliation(s)
- Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Miha Pakusch
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Matthew Lacorcia
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Eleonora Tresoldi
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Alan F Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Abby Foster
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Laura King
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Chris Y Chiu
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - Thomas W H Kay
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
| | - John A Karas
- School of Chemistry, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Fergus J Cameron
- Department of Endocrinology and Diabetes, Royal Children's Hospital, Parkville, Melbourne, VIC 3052, Australia
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC 3065, Australia
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
- Department of Medicine, University of Melbourne, St. Vincent's Hospital, Fitzroy, VIC 3065, Australia
| |
Collapse
|
8
|
Mitchell JS, Spanier JA, Dwyer AJ, Knutson TP, Alkhatib MH, Qian G, Weno ME, Chen Y, Shaheen ZR, Tucker CG, Kangas TO, Morales MS, Silva N, Kaisho T, Farrar MA, Fife BT. CD4 + T cells reactive to a hybrid peptide from insulin-chromogranin A adopt a distinct effector fate and are pathogenic in autoimmune diabetes. Immunity 2024; 57:2399-2415.e8. [PMID: 39214091 DOI: 10.1016/j.immuni.2024.07.024] [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: 11/02/2023] [Revised: 06/04/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
T cell-mediated islet destruction is a hallmark of autoimmune diabetes. Here, we examined the dynamics and pathogenicity of CD4+ T cell responses to four different insulin-derived epitopes during diabetes initiation in non-obese diabetic (NOD) mice. Single-cell RNA sequencing of tetramer-sorted CD4+ T cells from the pancreas revealed that islet-antigen-specific T cells adopted a wide variety of fates and required XCR1+ dendritic cells for their activation. Hybrid-insulin C-chromogranin A (InsC-ChgA)-specific CD4+ T cells skewed toward a distinct T helper type 1 (Th1) effector phenotype, whereas the majority of insulin B chain and hybrid-insulin C-islet amyloid polypeptide-specific CD4+ T cells exhibited a regulatory phenotype and early or weak Th1 phenotype, respectively. InsC-ChgA-specific CD4+ T cells were uniquely pathogenic upon transfer, and an anti-InsC-ChgA:IAg7 antibody prevented spontaneous diabetes. Our findings highlight the heterogeneity of T cell responses to insulin-derived epitopes in diabetes and argue for the feasibility of antigen-specific therapies that blunts the response of pathogenic CD4+ T cells causing autoimmunity.
Collapse
Affiliation(s)
- Jason S Mitchell
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Justin A Spanier
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA; Center for Autoimmune Disease Research, University of Minnesota, Minneapolis, MN, USA
| | - Alexander J Dwyer
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Todd P Knutson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Mohannad H Alkhatib
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Gina Qian
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Matthew E Weno
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Yixin Chen
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Zachary R Shaheen
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Pediatrics, Division of Pediatric Rheumatology, Allergy, & Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Christopher G Tucker
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Takashi O Kangas
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Milagros Silva Morales
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Nubia Silva
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Tsuneyasu Kaisho
- Department of Immunology Institute for Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Michael A Farrar
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Brian T Fife
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA; Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, USA; Center for Autoimmune Disease Research, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
9
|
Hao M, Sebag SC, Qian Q, Yang L. Lysosomal physiology and pancreatic lysosomal stress in diabetes mellitus. EGASTROENTEROLOGY 2024; 2:e100096. [PMID: 39512752 PMCID: PMC11542681 DOI: 10.1136/egastro-2024-100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
Endocrine and exocrine functions of the pancreas control nutritional absorption, utilisation and systemic metabolic homeostasis. Under basal conditions, the lysosome is pivotal in regulating intracellular organelles and metabolite turnover. In response to acute or chronic stress, the lysosome senses metabolic flux and inflammatory challenges, thereby initiating the adaptive programme to re-establish cellular homeostasis. A growing body of evidence has demonstrated the pathophysiological relevance of the lysosomal stress response in metabolic diseases in diverse sets of tissues/organs, such as the liver and the heart. In this review, we discuss the pathological relevance of pancreatic lysosome stress in diabetes mellitus. We begin by summarising lysosomal biology, followed by exploring the immune and metabolic functions of lysosomes and finally discussing the interplay between lysosomal stress and the pathogenesis of pancreatic diseases. Ultimately, our review aims to enhance our understanding of lysosomal stress in disease pathogenesis, which could potentially lead to the discovery of innovative treatment methods for these conditions.
Collapse
Affiliation(s)
- Meihua Hao
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Sara C Sebag
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Qingwen Qian
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ling Yang
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| |
Collapse
|
10
|
Mishto M, Takala I, Bonfanti P, Liepe J. Proteasome isoforms in human thymi and mouse models. Immunol Lett 2024; 269:106899. [PMID: 39019403 DOI: 10.1016/j.imlet.2024.106899] [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: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024]
Abstract
The thymus is the organ where functional and self-tolerant T cells are selected through processes of positive and negative selection before migrating to the periphery. The antigenic peptides presented on MHC class I molecules of thymic epithelial cells (TECs) in the cortex and medulla of the thymus are key players in these processes. It has been theorized that these cells express different proteasome isoforms, which generate MHC class I immunopeptidomes with features that differentiate cortex and medulla, and hence positive and negative CD8+ T cell selection. This theory is largely based on mouse models and does not consider the large variety of noncanonical antigenic peptides that could be produced by proteasomes and presented on MHC class I molecules. Here, we review the multi-omics, biochemical and cellular studies carried out on mouse models and human thymi to investigate their content of proteasome isoforms, briefly summarize the implication that noncanonical antigenic peptide presentation in the thymus could have on CD8+ T cell repertoire and put these aspects in the larger framework of anatomical and immunological differences between these two species.
Collapse
Affiliation(s)
- Michele Mishto
- Molecular Immunology laboratory, the Francis Crick Institute, NW1 1AT London, United Kingdom; Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, United Kingdom.
| | - Iina Takala
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, London NW3 2PP, United Kingdom
| | - Juliane Liepe
- Research group of Quantitative System Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| |
Collapse
|
11
|
Hu H, Vomund AN, Peterson OJ, Srivastava N, Li T, Kain L, Beatty WL, Zhang B, Hsieh CS, Teyton L, Lichti CF, Unanue ER, Wan X. Crinophagic granules in pancreatic β cells contribute to mouse autoimmune diabetes by diversifying pathogenic epitope repertoire. Nat Commun 2024; 15:8318. [PMID: 39333495 PMCID: PMC11437215 DOI: 10.1038/s41467-024-52619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 09/13/2024] [Indexed: 09/29/2024] Open
Abstract
Autoimmune attack toward pancreatic β cells causes permanent loss of glucose homeostasis in type 1 diabetes (T1D). Insulin secretory granules store and secrete insulin but are also thought to be tissue messengers for T1D. Here, we show that the crinophagic granules (crinosome), a minor set of vesicles formed by fusing lysosomes with the conventional insulin dense-core granules (DCG), are pathogenic in T1D development in mouse models. Pharmacological inhibition of crinosome formation in β cells delays T1D progression without affecting the dominant DCGs. Mechanistically, crinophagy inhibition diminishes the epitope repertoire in pancreatic islets, including cryptic, modified and disease-relevant epitopes derived from insulin. These unconventional insulin epitopes are largely undetectable in the MHC-II epitope repertoire of the thymus, where only canonical insulin epitopes are presented. CD4+ T cells targeting unconventional insulin epitopes display autoreactive phenotypes, unlike tolerized T cells recognizing epitopes presented in the thymus. Thus, the crinophagic pathway emerges as a tissue-intrinsic mechanism that transforms insulin from a signature thymic self-protein to a critical autoantigen by creating a peripheral-thymic mismatch in the epitope repertoire.
Collapse
Affiliation(s)
- Hao Hu
- Department of Pathology and Immunology, Division of Immunobiology, 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
| | - 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
| | - 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
| | - Tiandao Li
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lisa Kain
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA
| | - Wandy L Beatty
- Department of Molecular Microbiology, 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
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Luc Teyton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, 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
| | - 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.
| |
Collapse
|
12
|
Dwyer AJ, Shaheen ZR, Fife BT. Antigen-specific T cell responses in autoimmune diabetes. Front Immunol 2024; 15:1440045. [PMID: 39211046 PMCID: PMC11358097 DOI: 10.3389/fimmu.2024.1440045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Autoimmune diabetes is a disease characterized by the selective destruction of insulin-secreting β-cells of the endocrine pancreas by islet-reactive T cells. Autoimmune disease requires a complex interplay between host genetic factors and environmental triggers that promote the activation of such antigen-specific T lymphocyte responses. Given the critical involvement of self-reactive T lymphocyte in diabetes pathogenesis, understanding how these T lymphocyte populations contribute to disease is essential to develop targeted therapeutics. To this end, several key antigenic T lymphocyte epitopes have been identified and studied to understand their contributions to disease with the aim of developing effective treatment approaches for translation to the clinical setting. In this review, we discuss the role of pathogenic islet-specific T lymphocyte responses in autoimmune diabetes, the mechanisms and cell types governing autoantigen presentation, and therapeutic strategies targeting such T lymphocyte responses for the amelioration of disease.
Collapse
Affiliation(s)
- Alexander J. Dwyer
- Center for Immunology, Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Zachary R. Shaheen
- Center for Immunology, Department of Pediatrics, Pediatric Rheumatology, Allergy, & Immunology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Brian T. Fife
- Center for Immunology, Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis, MN, United States
| |
Collapse
|
13
|
van Midden KP, Mantz M, Fonovič M, Gazvoda M, Svete J, Huesgen PF, van der Hoorn RAL, Klemenčič M. Mechanistic insights into CrCEP1: A dual-function cysteine protease with endo- and transpeptidase activity. Int J Biol Macromol 2024; 271:132505. [PMID: 38768911 DOI: 10.1016/j.ijbiomac.2024.132505] [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: 12/12/2023] [Revised: 04/05/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Proteases, essential regulators of plant stress responses, remain enigmatic in their precise functional roles. By employing activity-based probes for real-time monitoring, this study aimed to delve into protease activities in Chlamydomonas reinhardtii exposed to oxidative stress induced by hydrogen peroxide. However, our work revealed that the activity-based probes strongly labelled three non-proteolytic proteins-PsbO, PsbP, and PsbQ-integral components of photosystem II's oxygen-evolving complex. Subsequent biochemical assays and mass spectrometry experiments revealed the involvement of CrCEP1, a previously uncharacterized papain-like cysteine protease, as the catalyst of this labelling reaction. Further experiments with recombinant CrCEP1 and PsbO proteins replicated the reaction in vitro. Our data unveiled that endopeptidase CrCEP1 also has transpeptidase activity, ligating probes and peptides to the N-termini of Psb proteins, thereby expanding the repertoire of its enzymatic activities. The hitherto unknown transpeptidase activity of CrCEP1, working in conjunction with its proteolytic activity, unveils putative complex and versatile roles for proteases in cellular processes during stress responses.
Collapse
Affiliation(s)
- Katarina P van Midden
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
| | - Marko Fonovič
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Svete
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; CIBSS- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | - Marina Klemenčič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
| |
Collapse
|
14
|
Gu QH, Xu H, Cao X, Cheng X, Jia JY, Yan TK. The protease inhibitor E64d might attenuate the development of experimental anti-glomerular basement membrane disease through regulating the activation of Th1 cells. Int Immunopharmacol 2024; 129:111594. [PMID: 38295547 DOI: 10.1016/j.intimp.2024.111594] [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: 12/19/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Cathepsins have been recently identified as a regulator in the activation of Th1 and Th17 cells, which play an important role in the pathogenesis of anti-glomerular basement membrane (GBM) disease. Whether cathepsins contribute to the development of anti-GBM disease through regulating the activation of CD4+ T cell is still unclear. METHODS Rats with experimental anti-GBM disease was established by immunization with the nephritogenic T cell epitope α3127-148. E64d, a cysteine cathepsin inhibitor, was administered in vitro and vivo to evaluate the effect of cathepsins on regulating the activation of antigen specific T cells and the development of anti-GBM disease. RESULTS In rats with experimental anti-GBM diseases, E64d treatment not only reduced the levels of proteinuria, serum creatinine and anti-GBM antibody, but also ameliorated the kidney injury with less glomerular IgG deposition, a lower percentage of crescents and less infiltration of CD4+ T cells, CD8+ T cells and macrophages, as well as a lower percentage of splenic Th1 cells. In vitro, E64d treatment could significantly reduce the production of IFN-γ in the supernatant which might be produced by the activation of Th1 cells after being recalled with the autoantigen α3127-148. We also found the CD4+ T cells of rats with anti-GBM disease had an increased expression of cathepsin L (Cts-L), and the percentage of CD4+ T cells with extracellular expression of Cts-L was obviously higher, indicating it as a potential key regulator. CONCLUSIONS E64d might attenuate the development of anti-GBM disease by participating in the activation of Th1 cells, indicating it as a potential drug for anti-GBM disease in the future.
Collapse
Affiliation(s)
- Qiu-Hua Gu
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Hao Xu
- Department of Urology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300192, China; National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin 300192, China
| | - Xin Cao
- Department of Nephrology, Tianjin Medical University General Hospital Airport Hospital, Tianjin 300308, China
| | - Xi Cheng
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jun-Ya Jia
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Tie-Kun Yan
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin 300052, China.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 2024; 15:1147. [PMID: 38326304 PMCID: PMC10850103 DOI: 10.1038/s41467-024-45339-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
If and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow-and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
Collapse
Affiliation(s)
- Wai Tuck Soh
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Hanna P Roetschke
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Bei Fang Teo
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Nyet Cheng Chiam
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Monika Raabe
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ralf Pflanz
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ashwin Chari
- Research Group of Structural Biochemistry and Mechanisms, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Juliane Liepe
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK.
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK.
| |
Collapse
|
17
|
Vived C, Lee-Papastavros A, Aparecida da Silva Pereira J, Yi P, MacDonald TL. β Cell Stress and Endocrine Function During T1D: What Is Next to Discover? Endocrinology 2023; 165:bqad162. [PMID: 37947352 DOI: 10.1210/endocr/bqad162] [Citation(s) in RCA: 2] [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: 07/26/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Canonically, type 1 diabetes (T1D) is a disease characterized by autoreactive T cells as perpetrators of endocrine dysfunction and β cell death in the spiral toward loss of β cell mass, hyperglycemia, and insulin dependence. β Cells have mostly been considered as bystanders in a flurry of autoimmune processes. More recently, our framework for understanding and investigating T1D has evolved. It appears increasingly likely that intracellular β cell stress is an important component of T1D etiology/pathology that perpetuates autoimmunity during the progression to T1D. Here we discuss the emerging and complex role of β cell stress in initiating, provoking, and catalyzing T1D. We outline the bridges between hyperglycemia, endoplasmic reticulum stress, oxidative stress, and autoimmunity from the viewpoint of intrinsic β cell (dys)function, and we extend this discussion to the potential role for a therapeutic β cell stress-metabolism axis in T1D. Lastly, we mention research angles that may be pursued to improve β cell endocrine function during T1D. Biology gleaned from studying T1D will certainly overlap to innovate therapeutic strategies for T2D, and also enhance the pursuit of creating optimized stem cell-derived β cells as endocrine therapy.
Collapse
Affiliation(s)
- Celia Vived
- Section for Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jéssica Aparecida da Silva Pereira
- Section for Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yi
- Section for Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Program, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Tara L MacDonald
- Section for Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
18
|
Wenzlau JM, Gu Y, Michels A, Rewers M, Haskins K, Yu L. Identification of Autoantibodies to a Hybrid Insulin Peptide in Type 1 Diabetes. Diagnostics (Basel) 2023; 13:2859. [PMID: 37685398 PMCID: PMC10487141 DOI: 10.3390/diagnostics13172859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/21/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease that attacks the insulin-producing b cells of the pancreatic islets. Autoantibodies to b cell proteins typically appear in the circulation years before disease onset, and serve as the most accurate biomarkers of T1D risk. Our laboratory has recently discovered novel b cell proteins comprising hybrid proinsulin:islet amyloid polypeptide peptides (IAPP). T cells from a diabetic mouse model and T1D patients are activated by these hybrid peptides. In this study, we asked whether these hybrid molecules could serve as antigens for autoantibodies in T1D and prediabetic patients. We analyzed sera from T1D patients, prediabetics and healthy age-matched donors. Using a highly sensitive electrochemiluminescence assay, sera were screened for binding to recombinant proinsulin:IAPP probes or truncated derivatives. Our results show that sera from T1D patients contain antibodies that bind larger hybrid proinsulin:IAPP probes, but not proinsulin or insulin, at significantly increased frequencies compared to normal donors. Examination of sera from prediabetic patients confirms titers of antibodies to these hybrid probes in more than 80% of individuals, often before seroconversion. These results suggest that hybrid insulin peptides are common autoantigens in T1D and prediabetic patients, and that antibodies to these peptides may serve as valuable early biomarkers of the disease.
Collapse
Affiliation(s)
- Janet M. Wenzlau
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19th Avenue, Mail Stop 8333, Aurora, CO 80045, USA; (J.M.W.); (K.H.)
| | - Yong Gu
- Barbara Davis Center for Childhood Diabetes, 1775 Aurora Court, Mail Stop B140, Aurora, CO 80045, USA; (Y.G.); (A.M.); (M.R.)
| | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, 1775 Aurora Court, Mail Stop B140, Aurora, CO 80045, USA; (Y.G.); (A.M.); (M.R.)
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, 1775 Aurora Court, Mail Stop B140, Aurora, CO 80045, USA; (Y.G.); (A.M.); (M.R.)
| | - Kathryn Haskins
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 East 19th Avenue, Mail Stop 8333, Aurora, CO 80045, USA; (J.M.W.); (K.H.)
| | - Liping Yu
- Barbara Davis Center for Childhood Diabetes, 1775 Aurora Court, Mail Stop B140, Aurora, CO 80045, USA; (Y.G.); (A.M.); (M.R.)
| |
Collapse
|
19
|
Moustakas AK, Nguyen H, James EA, Papadopoulos GK. Autoimmune susceptible HLA class II motifs facilitate the presentation of modified neoepitopes to potentially autoreactive T cells. Cell Immunol 2023; 390:104729. [PMID: 37301094 DOI: 10.1016/j.cellimm.2023.104729] [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: 01/30/2023] [Revised: 03/27/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
Rheumatoid arthritis (RA), multiple sclerosis (MS), type 1 diabetes (T1D), and celiac disease (CD), are strongly associated with susceptible HLA class II haplotypes. The peptide-binding pockets of these molecules are polymorphic, thus each HLA class II protein presents a distinct set of peptides to CD4+ T cells. Peptide diversity is increased through post-translational modifications, generating non-templated sequences that enhance HLA binding and/or T cell recognition. The high-risk HLA-DR alleles that confer susceptibility to RA are notable for their ability to accommodate citrulline, promoting responses to citrullinated self-antigens. Likewise, HLA-DQ alleles associated with T1D and CD favor the binding of deamidated peptides. In this review, we discuss structural features that promote modified self-epitope presentation, provide evidence supporting the relevance of T cell recognition of such antigens in disease processes, and make a case that interrupting the pathways that generate such epitopes and reprogramming neoepitope-specific T cells are key strategies for effective therapeutic intervention.
Collapse
Affiliation(s)
- Antonis K Moustakas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, GR26100 Argostoli, Cephalonia, Greece
| | - Hai Nguyen
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - George K Papadopoulos
- Laboratory of Biophysics, Biochemistry, Bioprocessing and Bioproducts, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, GR47100 Arta, Greece
| |
Collapse
|
20
|
Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
Collapse
Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
| |
Collapse
|
21
|
Mohammadi-Motlagh HR, Sadeghalvad M, Yavari N, Primavera R, Soltani S, Chetty S, Ganguly A, Regmi S, Fløyel T, Kaur S, Mirza AH, Thakor AS, Pociot F, Yarani R. β Cell and Autophagy: What Do We Know? Biomolecules 2023; 13:biom13040649. [PMID: 37189396 DOI: 10.3390/biom13040649] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Pancreatic β cells are central to glycemic regulation through insulin production. Studies show autophagy as an essential process in β cell function and fate. Autophagy is a catabolic cellular process that regulates cell homeostasis by recycling surplus or damaged cell components. Impaired autophagy results in β cell loss of function and apoptosis and, as a result, diabetes initiation and progress. It has been shown that in response to endoplasmic reticulum stress, inflammation, and high metabolic demands, autophagy affects β cell function, insulin synthesis, and secretion. This review highlights recent evidence regarding how autophagy can affect β cells' fate in the pathogenesis of diabetes. Furthermore, we discuss the role of important intrinsic and extrinsic autophagy modulators, which can lead to β cell failure.
Collapse
Affiliation(s)
- Hamid-Reza Mohammadi-Motlagh
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 67155-1616, Iran
| | - Mona Sadeghalvad
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran 1416634793, Iran
| | - Niloofar Yavari
- Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rosita Primavera
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Setareh Soltani
- Clinical Research Development Center, Taleghani and Imam Ali Hospital, Kermanshah University of Medical Sciences, Kermanshah 67145-1673, Iran
| | - Shashank Chetty
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Abantika Ganguly
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Shobha Regmi
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Tina Fløyel
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
| | - Simranjeet Kaur
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
| | - Aashiq H Mirza
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
- Department of Pharmacology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Avnesh S Thakor
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Flemming Pociot
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
- Institute for Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Reza Yarani
- Interventional Regenerative Innovation at Stanford (IRIS), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
| |
Collapse
|
22
|
Lichti CF, Wan X. Using mass spectrometry to identify neoantigens in autoimmune diseases: The type 1 diabetes example. Semin Immunol 2023; 66:101730. [PMID: 36827760 PMCID: PMC10324092 DOI: 10.1016/j.smim.2023.101730] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
In autoimmune diseases, recognition of self-antigens presented by major histocompatibility complex (MHC) molecules elicits unexpected attack of tissue by autoantibodies and/or autoreactive T cells. Post-translational modification (PTM) may alter the MHC-binding motif or TCR contact residues in a peptide antigen, transforming the tolerance to self to autoreactivity. Mass spectrometry-based immunopeptidomics provides a valuable mechanism for identifying MHC ligands that contain PTMs and can thus provide valuable insights into pathogenesis and therapeutics of autoimmune diseases. A plethora of PTMs have been implicated in this process, and this review highlights their formation and identification.
Collapse
Affiliation(s)
- Cheryl F Lichti
- Department of Pathology and Immunology, Division of Immunobiology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, St. Louis, MO 63110, USA.
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Division of Immunobiology, The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, 660 S. Euclid Ave, Campus Box 8118, St. Louis, MO 63110, USA.
| |
Collapse
|
23
|
Levy R, Alter Regev T, Paes W, Gumpert N, Cohen Shvefel S, Bartok O, Dayan-Rubinov M, Alon M, Shmueli M, Levin Y, Merbl Y, Ternette N, Samuels Y. Large-Scale Immuno-Peptidome Analysis Reveals Recurrent Post-Translational Splicing of Cancer and Immune-Associated Genes. Mol Cell Proteomics 2023; 22:100519. [PMID: 36828127 PMCID: PMC10119686 DOI: 10.1016/j.mcpro.2023.100519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Post-translational spliced peptides (PTSPs) are a unique class of peptides that have been found to be presented by HLA-class-I molecules in cancer (1). Thus far, no consensus has been reached on the proportion of PTSPs in the immunopeptidome, with estimates ranging from 2% to as high as 45% and stirring significant debate (2-8). Furthermore, the role of the HLA-class-II pathway in PTSP presentation has been studied only in diabetes (9). Here, we exploit our large-scale cancer peptidomics database and our newly devised pipeline for filtering spliced peptide predictions to identify recurring spliced peptides, both for HLA-class-I and -II complexes. Our results indicate that HLA-class-I spliced peptides account for a low percentage of the immunopeptidome (less than 3.1%), yet are larger in number relative to other types of identified aberrant peptides. Therefore, spliced peptides significantly contribute to the repertoire of presented peptides in cancer cells. In addition, we identified HLA-class-II-bound spliced peptides, but to a lower extent (less than 0.5%). The identified spliced peptides include cancer- and immune-associated genes, such as the MITF oncogene, DAPK1 tumor suppressor and HLA-E, which were validated using synthetic peptides. The potential immunogenicity of the DAPK1- and HLA-E-derived PTSPs was also confirmed. In addition, a reanalysis of our published mouse single-cell clone immunopeptidome dataset showed that most of the spliced peptides were found repeatedly in a large number of the single-cell clones. Establishing a novel search-scheme for the discovery and evaluation of recurring PTSPs among cancer patients may assist in identifying potential novel targets for immunotherapy.
Collapse
Affiliation(s)
- Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Alter Regev
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nofar Gumpert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sapir Cohen Shvefel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osnat Bartok
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maria Dayan-Rubinov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - MeravD Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
24
|
Roetschke HP, Rodriguez-Hernandez G, Cormican JA, Yang X, Lynham S, Mishto M, Liepe J. InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides. Sci Data 2023; 10:18. [PMID: 36627305 PMCID: PMC9832164 DOI: 10.1038/s41597-022-01890-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/01/2022] [Indexed: 01/12/2023] Open
Abstract
Noncanonical epitopes presented by Human Leucocyte Antigen class I (HLA-I) complexes to CD8+ T cells attracted the spotlight in the research of novel immunotherapies against cancer, infection and autoimmunity. Proteasomes, which are the main producers of HLA-I-bound antigenic peptides, can catalyze both peptide hydrolysis and peptide splicing. The prediction of proteasome-generated spliced peptides is an objective that still requires a reliable (and large) database of non-spliced and spliced peptides produced by these proteases. Here, we present an extended database of proteasome-generated spliced and non-spliced peptides, which was obtained by analyzing in vitro digestions of 80 unique synthetic polypeptide substrates, measured by different mass spectrometers. Peptides were identified through invitroSPI method, which was validated through in silico and in vitro strategies. The peptide product database contains 16,631 unique peptide products (5,493 non-spliced, 6,453 cis-spliced and 4,685 trans-spliced peptide products), and a substrate sequence variety that is a valuable source for predictors of proteasome-catalyzed peptide hydrolysis and splicing. Potential artefacts and skewed results due to different identification and analysis strategies are discussed.
Collapse
Affiliation(s)
- Hanna P Roetschke
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK
| | - Guillermo Rodriguez-Hernandez
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK
- Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany
| | - Xiaoping Yang
- Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 9NU, London, UK
| | - Steven Lynham
- Proteomics Core Facility, James Black Centre, King's College London (KCL), SE5 9NU, London, UK
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London (KCL), SE1 1UL, London, UK.
- Francis Crick Institute, NW1 1AT, London, UK.
| | - Juliane Liepe
- Max-Planck-Institute for Multidisciplinary Sciences (MPI-NAT), 37077, Göttingen, Germany.
| |
Collapse
|
25
|
Crawford SA, Wiles TA, Wenzlau JM, Powell RL, Barbour G, Dang M, Groegler J, Barra JM, Burnette KS, Hohenstein AC, Baker RL, Tse HM, Haskins K, Delong T. Cathepsin D Drives the Formation of Hybrid Insulin Peptides Relevant to the Pathogenesis of Type 1 Diabetes. Diabetes 2022; 71:2793-2803. [PMID: 36041196 PMCID: PMC9750942 DOI: 10.2337/db22-0303] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/24/2022] [Indexed: 01/11/2023]
Abstract
Hybrid insulin peptides (HIPs) form in pancreatic β-cells through the formation of peptide bonds between proinsulin fragments and other peptides. HIPs have been identified in pancreatic islets by mass spectrometry and are targeted by CD4 T cells in patients with type 1 diabetes (T1D) as well as by pathogenic CD4 T-cell clones in nonobese diabetic (NOD) mice. The mechanism of HIP formation is currently poorly understood; however, it is well established that proteases can drive the formation of new peptide bonds in a side reaction during peptide bond hydrolysis. Here, we used a proteomic strategy on enriched insulin granules and identified cathepsin D (CatD) as the primary protease driving the specific formation of HIPs targeted by disease-relevant CD4 T cells in T1D. We also established that NOD islets deficient in cathepsin L (CatL), another protease implicated in the formation of disease-relevant HIPs, contain elevated levels of HIPs, indicating a role for CatL in the proteolytic degradation of HIPs. In summary, our data suggest that CatD may be a therapeutic target in efforts to prevent or slow the autoimmune destruction of β-cells mediated by HIP-reactive CD4 T cells in T1D.
Collapse
Affiliation(s)
- Samantha A Crawford
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Timothy A Wiles
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Janet M Wenzlau
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Roger L Powell
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Gene Barbour
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Mylinh Dang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jason Groegler
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jessie M Barra
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - KaLia S Burnette
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Anita C Hohenstein
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Rocky L Baker
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Hubert M Tse
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Kathryn Haskins
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Thomas Delong
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO
| |
Collapse
|
26
|
Li W, Li R, Wang Y, Zhang Y, Tomar MS, Dai S. Calcitonin gene-related peptide is a potential autoantigen for CD4 T cells in type 1 diabetes. Front Immunol 2022; 13:951281. [PMID: 36189304 PMCID: PMC9523785 DOI: 10.3389/fimmu.2022.951281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/04/2022] [Indexed: 12/01/2022] Open
Abstract
The calcitonin gene-related peptide (CGRP) is a 37-amino acid neuropeptide with critical roles in the development of peripheral sensitization and pain. One of the CGRP family peptides, islet amyloid polypeptide (IAPP), is an important autoantigen in type 1 diabetes. Due to the high structural and chemical similarity between CGRP and IAPP, we expected that the CGRP peptide could be recognized by IAPP-specific CD4 T cells. However, there was no cross-reactivity between the CGRP peptide and the diabetogenic IAPP-reactive T cells. A set of CGRP-specific CD4 T cells was isolated from non-obese diabetic (NOD) mice. The T-cell receptor (TCR) variable regions of both α and β chains were highly skewed towards TRAV13 and TRBV13, respectively. The clonal expansion of T cells suggested that the presence of activated T cells responded to CGRP stimulation. None of the CGRP-specific CD4 T cells were able to be activated by the IAPP peptide. This established that CGRP-reactive CD4 T cells are a unique type of autoantigen-specific T cells in NOD mice. Using IAg7-CGRP tetramers, we found that CGRP-specific T cells were present in the pancreas of both prediabetic and diabetic NOD mice. The percentages of CGRP-reactive T cells in the pancreas of NOD mice were correlated to the diabetic progression. We showed that the human CGRP peptide presented by IAg7 elicited strong CGRP-specific T-cell responses. These findings suggested that CGRP is a potential autoantigen for CD4 T cells in NOD mice and probably in humans. The CGRP-specific CD4 T cells could be a unique marker for type 1 diabetes. Given the ubiquity of CGRP in nervous systems, it could potentially play an important role in diabetic neuropathy.
Collapse
Affiliation(s)
- Wei Li
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Ronghui Li
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yang Wang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Yan Zhang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Munendra S. Tomar
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| |
Collapse
|
27
|
Lin Y, Perovanovic J, Kong Y, Igyarto BZ, Zurawski S, Tantin D, Zurawski G, Bettini M, Bettini ML. Antibody-Mediated Targeting of a Hybrid Insulin Peptide Toward Neonatal Thymic Langerin-Positive Cells Enhances T-Cell Central Tolerance and Delays Autoimmune Diabetes. Diabetes 2022; 71:1735-1745. [PMID: 35622068 PMCID: PMC9490359 DOI: 10.2337/db21-1069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022]
Abstract
Thymic presentation of self-antigens is critical for establishing a functional yet self-tolerant T-cell population. Hybrid peptides formed through transpeptidation within pancreatic β-cell lysosomes have been proposed as a new class of autoantigens in type 1 diabetes (T1D). While the production of hybrid peptides in the thymus has not been explored, due to the nature of their generation, it is thought to be highly unlikely. Therefore, hybrid peptide-reactive thymocytes may preferentially escape thymic selection and contribute significantly to T1D progression. Using an antibody-peptide conjugation system, we targeted the hybrid insulin peptide (HIP) 2.5HIP toward thymic resident Langerin-positive dendritic cells to enhance thymic presentation during the early neonatal period. Our results indicated that anti-Langerin-2.5HIP delivery can enhance T-cell central tolerance toward cognate thymocytes in NOD.BDC2.5 mice. Strikingly, a single dose treatment with anti-Langerin-2.5HIP during the neonatal period delayed diabetes onset in NOD mice, indicating the potential of antibody-mediated delivery of autoimmune neoantigens during early stages of life as a therapeutic option in the prevention of autoimmune diseases.
Collapse
Affiliation(s)
- Yong Lin
- Baylor College of Medicine, Houston, TX
| | | | | | - Botond Z. Igyarto
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA
| | - Sandra Zurawski
- Baylor Institute for Immunology Research, Baylor Scott and White Research Institute, Dallas, TX
| | - Dean Tantin
- Department of Pathology, University of Utah, Salt Lake City, UT
| | - Gerard Zurawski
- Baylor Institute for Immunology Research, Baylor Scott and White Research Institute, Dallas, TX
| | - Maria Bettini
- Department of Pathology, University of Utah, Salt Lake City, UT
| | - Matthew L. Bettini
- Department of Pathology, University of Utah, Salt Lake City, UT
- Corresponding author: Matthew L. Bettini,
| |
Collapse
|
28
|
Mishto M, Horokhovskyi Y, Cormican JA, Yang X, Lynham S, Urlaub H, Liepe J. Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes. Proteomics 2022; 22:e2100226. [PMID: 35184383 PMCID: PMC9286349 DOI: 10.1002/pmic.202100226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/19/2022] [Accepted: 02/10/2022] [Indexed: 11/08/2022]
Abstract
Unconventional epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry (MS) required development of novel methods to cope with the large number of theoretical candidates. Methods to identify post-translationally spliced peptides led to a broad range of outcomes. We here investigated the impact of three common database search engines - that is, Mascot, Mascot+Percolator, and PEAKS DB - as final identification step, as well as the features of target database on the ability to correctly identify non-spliced and cis-spliced peptides. We used ground truth datasets measured by MS to benchmark methods' performance and extended the analysis to HLA class I immunopeptidomes. PEAKS DB showed better precision and recall of cis-spliced peptides and larger number of identified peptides in HLA class I immunopeptidomes than the other search engine strategies. The better performance of PEAKS DB appears to result from better discrimination between target and decoy hits and hence a more robust FDR estimation, and seems independent to peptide and spectrum features here investigated.
Collapse
Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of ImmunobiologyKing's College LondonLondonUK
- Francis Crick InstituteLondonUK
| | | | - John A. Cormican
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
| | - Xiaoping Yang
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Steven Lynham
- Proteomics Core Facility, James Black CentreKing's CollegeLondonUK
| | - Henning Urlaub
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
- Institute of Clinical ChemistryUniversity Medical Center GöttingenGöttingenGermany
| | - Juliane Liepe
- Max‐Planck‐Institute for Multidisciplinary SciencesGöttingenGermany
| |
Collapse
|
29
|
Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
Collapse
Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
30
|
Zajec A, Trebušak Podkrajšek K, Tesovnik T, Šket R, Čugalj Kern B, Jenko Bizjan B, Šmigoc Schweiger D, Battelino T, Kovač J. Pathogenesis of Type 1 Diabetes: Established Facts and New Insights. Genes (Basel) 2022; 13:genes13040706. [PMID: 35456512 PMCID: PMC9032728 DOI: 10.3390/genes13040706] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 01/08/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by the T-cell-mediated destruction of insulin-producing β-cells in pancreatic islets. It generally occurs in genetically susceptible individuals, and genetics plays a major role in the development of islet autoimmunity. Furthermore, these processes are heterogeneous among individuals; hence, different endotypes have been proposed. In this review, we highlight the interplay between genetic predisposition and other non-genetic factors, such as viral infections, diet, and gut biome, which all potentially contribute to the aetiology of T1D. We also discuss a possible active role for β-cells in initiating the pathological processes. Another component in T1D predisposition is epigenetic influences, which represent a link between genetic susceptibility and environmental factors and may account for some of the disease heterogeneity. Accordingly, a shift towards personalized therapies may improve the treatment results and, therefore, result in better outcomes for individuals in the long-run. There is also a clear need for a better understanding of the preclinical phases of T1D and finding new predictive biomarkers for earlier diagnosis and therapy, with the final goal of reverting or even preventing the development of the disease.
Collapse
Affiliation(s)
- Ana Zajec
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Robert Šket
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
| | - Barbara Čugalj Kern
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Darja Šmigoc Schweiger
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Battelino
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Kovač
- Division of Paediatrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (K.T.P.); (T.T.); (R.Š.); (B.Č.K.); (B.J.B.); (D.Š.S.); (T.B.)
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
| |
Collapse
|
31
|
Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
Collapse
Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| |
Collapse
|
32
|
Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen-binding groove of an MHC-encoded class I or class II molecule. Insight into the precise composition and biology of self and non-self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large-scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non-self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
Collapse
Affiliation(s)
- Sebastian Joyce
- Department of Veterans AffairsTennessee Valley Healthcare System and the Department of PathologyMicrobiology and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Nicola Ternette
- Centre for Cellular and Molecular PhysiologyNuffield Department of MedicineUniversity of OxfordOxfordUK
| |
Collapse
|
33
|
Cathepsin C Regulates Cytokine-Induced Apoptosis in β-Cell Model Systems. Genes (Basel) 2021; 12:genes12111694. [PMID: 34828301 PMCID: PMC8622156 DOI: 10.3390/genes12111694] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Emerging evidence suggests that several of the lysosomal cathepsin proteases are genetically associated with type 1 diabetes (T1D) and participate in immune-mediated destruction of the pancreatic β cells. We previously reported that the T1D candidate gene cathepsin H is downregulated by pro-inflammatory cytokines in human pancreatic islets and regulates β-cell function, apoptosis, and disease progression in children with new-onset T1D. In the present study, the objective was to investigate the expression patterns of all 15 known cathepsins in β-cell model systems and examine their role in the regulation of cytokine-induced apoptosis. Real-time qPCR screening of the cathepsins in human islets, 1.1B4 and INS-1E β-cell models identified several cathepsins that were expressed and regulated by pro-inflammatory cytokines. Using small interfering RNAs to knock down (KD) the cytokine-regulated cathepsins, we identified an anti-apoptotic function of cathepsin C as KD increased cytokine-induced apoptosis. KD of cathepsin C correlated with increased phosphorylation of JNK and p38 mitogen-activated protein kinases, and elevated chemokine CXCL10/IP-10 expression. This study suggests that cathepsin C is a modulator of β-cell survival, and that immune modulation of cathepsin expression in islets may contribute to immune-mediated β-cell destruction in T1D.
Collapse
|
34
|
Toren E, Burnette KS, Banerjee RR, Hunter CS, Tse HM. Partners in Crime: Beta-Cells and Autoimmune Responses Complicit in Type 1 Diabetes Pathogenesis. Front Immunol 2021; 12:756548. [PMID: 34691077 PMCID: PMC8529969 DOI: 10.3389/fimmu.2021.756548] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/13/2021] [Indexed: 12/11/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease characterized by autoreactive T cell-mediated destruction of insulin-producing pancreatic beta-cells. Loss of beta-cells leads to insulin insufficiency and hyperglycemia, with patients eventually requiring lifelong insulin therapy to maintain normal glycemic control. Since T1D has been historically defined as a disease of immune system dysregulation, there has been little focus on the state and response of beta-cells and how they may also contribute to their own demise. Major hurdles to identifying a cure for T1D include a limited understanding of disease etiology and how functional and transcriptional beta-cell heterogeneity may be involved in disease progression. Recent studies indicate that the beta-cell response is not simply a passive aspect of T1D pathogenesis, but rather an interplay between the beta-cell and the immune system actively contributing to disease. Here, we comprehensively review the current literature describing beta-cell vulnerability, heterogeneity, and contributions to pathophysiology of T1D, how these responses are influenced by autoimmunity, and describe pathways that can potentially be exploited to delay T1D.
Collapse
Affiliation(s)
- Eliana Toren
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, AL, United States
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - KaLia S. Burnette
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ronadip R. Banerjee
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Chad S. Hunter
- Department of Medicine, Division of Endocrinology Diabetes and Metabolism, University of Alabama at Birmingham, Birmingham, AL, United States
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hubert M. Tse
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
35
|
Mishto M. Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome? Mol Cell Proteomics 2021; 20:100158. [PMID: 34607014 PMCID: PMC8724881 DOI: 10.1016/j.mcpro.2021.100158] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022] Open
Abstract
Proteasome-generated spliced epitopes presented by HLA class I complexes are emerging targets for T cell targeted immunotherapies. Their identification by mass spectrometry triggered heated debates, which find a representative opinion in one of the two fronts in the recent perspective article by Arie Admon. Briefly, he suggests that proteasomes cannot efficiently catalyze such a reaction, and, thus, that all spliced peptides identified in HLA class I immunopeptidomes and other specimens are artifacts. This hypothesis is in contrast with in vitro, in cellula, and in vivo results published since the discovery of proteasome-catalyzed peptide splicing in 2004.
Collapse
Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom; Francis Crick Institute, London, United Kingdom.
| |
Collapse
|
36
|
Dall E, Stanojlovic V, Demir F, Briza P, Dahms SO, Huesgen PF, Cabrele C, Brandstetter H. The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities. ACS Catal 2021; 11:11885-11896. [PMID: 34621593 PMCID: PMC8491156 DOI: 10.1021/acscatal.1c02057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Protein modification by enzymatic breaking and forming of peptide bonds significantly expands the repertoire of genetically encoded protein sequences. The dual protease-ligase legumain exerts the two opposing activities within a single protein scaffold. Primarily localized to the endolysosomal system, legumain represents a key enzyme in the generation of antigenic peptides for subsequent presentation on the MHCII complex. Here we show that human legumain catalyzes the ligation and cyclization of linear peptides at near-neutral pH conditions, where legumain is intrinsically unstable. Conformational stabilization significantly enhanced legumain's ligase activity, which further benefited from engineering the prime substrate recognition sites for improved affinity. Additionally, we provide evidence that specific legumain activation states allow for differential regulation of its activities. Together these results set the basis for engineering legumain proteases and ligases with applications in biotechnology and drug development.
Collapse
Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Peter Briza
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Sven O. Dahms
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, 50674 Cologne, Germany
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| |
Collapse
|
37
|
Muralidharan C, Linnemann AK. β-Cell autophagy in the pathogenesis of type 1 diabetes. Am J Physiol Endocrinol Metab 2021; 321:E410-E416. [PMID: 34338043 PMCID: PMC8461796 DOI: 10.1152/ajpendo.00151.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022]
Abstract
Type 1 diabetes is an insulin-dependent, autoimmune disease where the pancreatic β cells are destroyed resulting in hyperglycemia. This multifactorial disease involves multiple environmental and genetic factors, and has no clear etiology. Accumulating evidence suggests that early signaling defects within the β cells may promote a change in the local immune milieu leading to autoimmunity. Therefore, many studies have been focused on intrinsic β-cell mechanisms that aid in the restoration of cellular homeostasis under environmental conditions that cause dysfunction. One of these intrinsic mechanisms to promote homeostasis is autophagy, defects which are clearly linked with β-cell dysfunction in the context of type 2 diabetes. Recent studies have now also pointed towards β-cell autophagy defects in the context of type 1 diabetes. In this perspectives review, we will discuss the evidence supporting a role for β-cell autophagy in the pathogenesis of type 1 diabetes, including a potential role for unconventional secretion of autophagosomes/lysosomes in the changing dialogue between the β cell and immune cells.
Collapse
Affiliation(s)
- Charanya Muralidharan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amelia K Linnemann
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana
| |
Collapse
|
38
|
Tran MT, Faridi P, Lim JJ, Ting YT, Onwukwe G, Bhattacharjee P, Jones CM, Tresoldi E, Cameron FJ, La Gruta NL, Purcell AW, Mannering SI, Rossjohn J, Reid HH. T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8. Nat Commun 2021; 12:5110. [PMID: 34433824 PMCID: PMC8387461 DOI: 10.1038/s41467-021-25404-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
HLA-DQ8, a genetic risk factor in type I diabetes (T1D), presents hybrid insulin peptides (HIPs) to autoreactive CD4+ T cells. The abundance of spliced peptides binding to HLA-DQ8 and how they are subsequently recognised by the autoreactive T cell repertoire is unknown. Here we report, the HIP (GQVELGGGNAVEVLK), derived from splicing of insulin and islet amyloid polypeptides, generates a preferred peptide-binding motif for HLA-DQ8. HLA-DQ8-HIP tetramer+ T cells from the peripheral blood of a T1D patient are characterised by repeated TRBV5 usage, which matches the TCR bias of CD4+ T cells reactive to the HIP peptide isolated from the pancreatic islets of a patient with T1D. The crystal structure of three TRBV5+ TCR-HLA-DQ8-HIP complexes shows that the TRBV5-encoded TCR β-chain forms a common landing pad on the HLA-DQ8 molecule. The N- and C-termini of the HIP is recognised predominantly by the TCR α-chain and TCR β-chain, respectively, in all three TCR ternary complexes. Accordingly, TRBV5 + TCR recognition of HIP peptides might occur via a 'polarised' mechanism, whereby each chain within the αβTCR heterodimer recognises distinct origins of the spliced peptide presented by HLA-DQ8.
Collapse
Affiliation(s)
- Mai T Tran
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jia Jia Lim
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yi Tian Ting
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Goodluck Onwukwe
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Claerwen M Jones
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Eleonora Tresoldi
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Fergus J Cameron
- Department of Endocrinology and Diabetes, Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole L La Gruta
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia. .,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
| | - Hugh H Reid
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
39
|
Amdare N, Purcell AW, DiLorenzo TP. Noncontiguous T cell epitopes in autoimmune diabetes: From mice to men and back again. J Biol Chem 2021; 297:100827. [PMID: 34044020 PMCID: PMC8233151 DOI: 10.1016/j.jbc.2021.100827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
Type 1 diabetes (T1D) is a T cell-mediated autoimmune disease that affects the insulin-producing beta cells of the pancreatic islets. The nonobese diabetic mouse is a widely studied spontaneous model of the disease that has contributed greatly to our understanding of T1D pathogenesis. This is especially true in the case of antigen discovery. Upon review of existing knowledge concerning the antigens and peptide epitopes that are recognized by T cells in this model, good concordance is observed between mouse and human antigens. A fascinating recent illustration of the contribution of the nonobese diabetic mouse in the area of epitope identification is the discovery of noncontiguous CD4+ T cell epitopes. This novel epitope class is characterized by the linkage of an insulin-derived peptide to, most commonly, a fragment of a natural cleavage product of another beta cell secretory granule constituent. These so-called hybrid insulin peptides are also recognized by T cells in patients with T1D, although the precise mechanism for their generation has yet to be defined and is the subject of active investigation. Although evidence from the tumor immunology arena documented the existence of noncontiguous CD8+ T cell epitopes, generated by proteasome-mediated peptide splicing involving transpeptidation, such CD8+ T cell epitopes were thought to be a rare immunological curiosity. However, recent advances in bioinformatics and mass spectrometry have challenged this view. These developments, coupled with the discovery of hybrid insulin peptides, have spurred a search for noncontiguous CD8+ T cell epitopes in T1D, an exciting frontier area still in its infancy.
Collapse
Affiliation(s)
- Nitin Amdare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA; Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA; The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, USA.
| |
Collapse
|
40
|
Admon A. Are There Indeed Spliced Peptides in the Immunopeptidome? Mol Cell Proteomics 2021; 20:100099. [PMID: 34022431 PMCID: PMC8724635 DOI: 10.1016/j.mcpro.2021.100099] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The claims that a large fraction of the immunopeptidome is composed of spliced major histocompatibility complex (MHC) peptides have stirred significant excitement and raised controversy. Here, I suggest that there are likely no spliced peptides in the immunopeptidome, and if they exist at all, they are extremely rare. I base this claim on both biochemical and bioinformatics considerations. First, as a reactant in normal proteolytic reactions, water will compete with transpeptidation, which has been suggested as the mechanism of peptide splicing. The high mobility and abundance of water in aqueous solutions renders transpeptidation very inefficient and therefore unlikely to occur. Second, new studies have refuted the bioinformatics assignments to spliced peptides of most of the immunopeptidome MS data, suggesting that the correct assignments are likely other canonical, noncanonical, and post-translationally modified peptides. Therefore, I call for rigorous experimental methodology using heavy stable isotope peptides spiking into the immunoaffinity-purified mixtures of natural MHC peptides and analysis by the highly reliable targeted MS, to claim that MHC peptides are indeed spliced. Peptide splicing was suggested to contribute to the immunopeptidome. I suggest that this idea should be reconsidered based on new evidences. Both biochemical and bioinformatics considerations argue against peptide splicing.
Collapse
Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
41
|
Mannering SI, Rubin AF, Wang R, Bhattacharjee P. Identifying New Hybrid Insulin Peptides (HIPs) in Type 1 Diabetes. Front Immunol 2021; 12:667870. [PMID: 33995402 PMCID: PMC8120023 DOI: 10.3389/fimmu.2021.667870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
In 2016 Delong et al. discovered a new type of neoepitope formed by the fusion of two unrelated peptide fragments. Remarkably these neoepitopes, called hybrid insulin peptides, or HIPs, are recognized by pathogenic CD4+ T cells in the NOD mouse and human pancreatic islet-infiltrating T cells in people with type 1 diabetes. Current data implicates CD4+ T-cell responses to HIPs in the immune pathogenesis of human T1D. Because of their role in the immune pathogenesis of human T1D it is important to identify new HIPs that are recognized by CD4+ T cells in people at risk of, or with, T1D. A detailed knowledge of T1D-associated HIPs will allow HIPs to be used in assays to monitor changes in T cell mediated beta-cell autoimmunity. They will also provide new targets for antigen-specific therapies for T1D. However, because HIPs are formed by the fusion of two unrelated peptides there are an enormous number of potential HIPs which makes it technically challenging to identify them. Here we review the discovery of HIPs, how they form and discuss approaches to identifying new HIPs relevant to the immune pathogenesis of human type 1 diabetes.
Collapse
Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Alan F Rubin
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ruike Wang
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| |
Collapse
|
42
|
Reed BK, Kappler JW. Hidden in Plain View: Discovery of Chimeric Diabetogenic CD4 T Cell Neo-Epitopes. Front Immunol 2021; 12:669986. [PMID: 33986758 PMCID: PMC8111216 DOI: 10.3389/fimmu.2021.669986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
The T cell antigens driving autoimmune Type 1 Diabetes (T1D) have been pursued for more than three decades. When diabetogenic CD4 T cell clones and their relevant MHCII antigen presenting alleles were first identified in rodents and humans, the path to discovering the peptide epitopes within pancreatic beta cell proteins seemed straightforward. However, as experimental results accumulated, definitive data were often absent or controversial. Work within the last decade has helped to clear up some of the controversy by demonstrating that a number of the important MHCII presented epitopes are not encoded in the natural beta cell proteins, but in fact are fusions between peptide fragments derived from the same or different proteins. Recently, the mechanism for generating these MHCII diabetogenic chimeric epitopes has been attributed to a form of reverse proteolysis, called transpeptidation, a process that has been well-documented in the production of MHCI presented epitopes. In this mini-review we summarize these data and their implications for T1D and other autoimmune responses.
Collapse
Affiliation(s)
- Brendan K Reed
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | - John W Kappler
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States.,Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, United States
| |
Collapse
|
43
|
Rodriguez-Calvo T, Johnson JD, Overbergh L, Dunne JL. Neoepitopes in Type 1 Diabetes: Etiological Insights, Biomarkers and Therapeutic Targets. Front Immunol 2021; 12:667989. [PMID: 33953728 PMCID: PMC8089389 DOI: 10.3389/fimmu.2021.667989] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The mechanisms underlying type 1 diabetes (T1D) pathogenesis remain largely unknown. While autoantibodies to pancreatic beta-cell antigens are often the first biological response and thereby a useful biomarker for identifying individuals in early stages of T1D, their role in T1D pathogenesis is not well understood. Recognition of these antigenic targets by autoreactive T-cells plays a pathological role in T1D development. Recently, several beta-cell neoantigens have been described, indicating that both neoantigens and known T1D antigens escape central or peripheral tolerance. Several questions regarding the mechanisms by which tolerance is broken in T1D remain unanswered. Further delineating the timing and nature of antigenic responses could allow their use as biomarkers to improve staging, as targets for therapeutic intervention, and lead to a better understanding of the mechanisms leading to loss of tolerance. Multiple factors that contribute to cellular stress may result in the generation of beta-cell derived neoepitopes and contribute to autoimmunity. Understanding the cellular mechanisms that induce beta-cells to produce neoantigens has direct implications on development of therapies to intercept T1D disease progression. In this perspective, we will discuss evidence for the role of neoantigens in the pathogenesis of T1D, including antigenic responses and cellular mechanisms. We will additionally discuss the pathways leading to neoepitope formation and the cross talk between the immune system and the beta-cells in this regard. Ultimately, delineating the timing of neoepitope generation in T1D pathogenesis will determine their role as biomarkers as well as therapeutic targets.
Collapse
Affiliation(s)
- Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Munich, Germany
| | - James D. Johnson
- Diabetes Research Group, Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Lut Overbergh
- Laboratory Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Jessica L. Dunne
- Janssen Research and Development, LLC, Raritan, NJ, United States
| |
Collapse
|
44
|
Mishto M, Mansurkhodzhaev A, Rodriguez-Calvo T, Liepe J. Potential Mimicry of Viral and Pancreatic β Cell Antigens Through Non-Spliced and cis-Spliced Zwitter Epitope Candidates in Type 1 Diabetes. Front Immunol 2021; 12:656451. [PMID: 33936085 PMCID: PMC8082463 DOI: 10.3389/fimmu.2021.656451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence suggests that post-translational peptide splicing can play a role in the immune response under pathological conditions. This seems to be particularly relevant in Type 1 Diabetes (T1D) since post-translationally spliced epitopes derived from T1D-associated antigens have been identified among those peptides bound to Human Leucocyte Antigen (HLA) class I and II complexes. Their immunogenicity has been confirmed through CD4+ and CD8+ T cell-mediated responses in T1D patients. Spliced peptides theoretically have a large sequence variability. This might increase the frequency of viral-human zwitter peptides, i.e. peptides that share a complete sequence homology irrespective of whether they originate from human or viral antigens, thereby impinging upon the discrimination between self and non-self antigens by T cells. This might increase the risk of autoimmune responses triggered by viral infections. Since enteroviruses and other viral infections have historically been associated with T1D, we investigated whether cis-spliced peptides derived from selected viruses might be able to trigger CD8+ T cell-mediated autoimmunity. We computed in silico viral-human non-spliced and cis-spliced zwitter epitope candidates, and prioritized peptide candidates based on: (i) their binding affinity to HLA class I complexes, (ii) human pancreatic β cell and medullary thymic epithelial cell (mTEC) antigens' mRNA expression, (iii) antigen association with T1D, and (iv) potential hotspot regions in those antigens. Neglecting potential T cell receptor (TCR) degeneracy, no viral-human zwitter non-spliced peptide was found to be an optimal candidate to trigger a virus-induced CD8+ T cell response against human pancreatic β cells. Conversely, we identified some zwitter peptide candidates, which may be produced by proteasome-catalyzed peptide splicing, and might increase the likelihood of pancreatic β cells recognition by virus-specific CD8+ T cell clones, therefore promoting β cell destruction in the context of viral infections.
Collapse
Affiliation(s)
- Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King’s College London, London, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | | | - Teresa Rodriguez-Calvo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Juliane Liepe
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
45
|
Kim YK, Sussel L, Davidson HW. Inherent Beta Cell Dysfunction Contributes to Autoimmune Susceptibility. Biomolecules 2021; 11:biom11040512. [PMID: 33808310 PMCID: PMC8065553 DOI: 10.3390/biom11040512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 01/10/2023] Open
Abstract
The pancreatic beta cell is a highly specialized cell type whose primary function is to secrete insulin in response to nutrients to maintain glucose homeostasis in the body. As such, the beta cell has developed unique metabolic characteristics to achieve functionality; in healthy beta cells, the majority of glucose-derived carbons are oxidized and enter the mitochondria in the form of pyruvate. The pyruvate is subsequently metabolized to induce mitochondrial ATP and trigger the downstream insulin secretion response. Thus, in beta cells, mitochondria play a pivotal role in regulating glucose stimulated insulin secretion (GSIS). In type 2 diabetes (T2D), mitochondrial impairment has been shown to play an important role in beta cell dysfunction and loss. In type 1 diabetes (T1D), autoimmunity is the primary trigger of beta cell loss; however, there is accumulating evidence that intrinsic mitochondrial defects could contribute to beta cell susceptibility during proinflammatory conditions. Furthermore, there is speculation that dysfunctional mitochondrial responses could contribute to the formation of autoantigens. In this review, we provide an overview of mitochondrial function in the beta cells, and discuss potential mechanisms by which mitochondrial dysfunction may contribute to T1D pathogenesis.
Collapse
Affiliation(s)
- Yong Kyung Kim
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA; (Y.K.K.); (L.S.)
| | - Lori Sussel
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA; (Y.K.K.); (L.S.)
| | - Howard W. Davidson
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA; (Y.K.K.); (L.S.)
- Department of Immunology & Microbiology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence: ; Tel.: +1-303-724-6852; Fax: +1-303-724-6830
| |
Collapse
|
46
|
Mannering SI, Bhattacharjee P. Insulin's other life: an autoantigen in type 1 diabetes. Immunol Cell Biol 2021; 99:448-460. [PMID: 33524197 DOI: 10.1111/imcb.12442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/21/2020] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
One hundred years ago, Frederick Banting, John Macleod, Charles Best and James Collip, and their collaborators, discovered insulin. This discovery paved the way to saving countless lives and ushered in the "Insulin Era." Since the discovery of insulin, we have made enormous strides in understanding its role in metabolism and diabetes. Insulin has played a dramatic role in the treatment of people with diabetes; particularly type 1 diabetes (T1D). Insulin replacement is a life-saving therapy for people with T1D and some with type 2 diabetes. T1D is an autoimmune disease caused by the T-cell-mediated destruction of the pancreatic insulin-producing beta cells that leads to a primary insulin deficiency. It has become increasingly clear that insulin, and its precursors preproinsulin (PPI) and proinsulin (PI), can play another role-not as a hormone but as an autoantigen in T1D. Here we review the role played by the products of the INS gene as autoantigens in people with T1D. From many elegant animal studies, it is clear that T-cell responses to insulin, PPI and PI are essential for T1D to develop. Here we review the evidence that autoimmune responses to insulin and PPI arise in people with T1D and discuss the recently described neoepitopes derived from the products of the insulin gene. Finally, we look forward to new approaches to deliver epitopes derived from PPI, PI and insulin that may allow immune tolerance to pancreatic beta cells to be restored in people with, or at risk of, T1D.
Collapse
Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.,Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, VIC, Australia
| | - Pushpak Bhattacharjee
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| |
Collapse
|