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Coomans de Brachène A, Alvelos MI, Szymczak F, Zimath PL, Castela A, Marmontel de Souza B, Roca Rivada A, Marín-Cañas S, Yi X, Op de Beeck A, Morgan NG, Sonntag S, Jawurek S, Title AC, Yesildag B, Pattou F, Kerr-Conte J, Montanya E, Nacher M, Marselli L, Marchetti P, Richardson SJ, Eizirik DL. Interferons are key cytokines acting on pancreatic islets in type 1 diabetes. Diabetologia 2024; 67:908-927. [PMID: 38409439 DOI: 10.1007/s00125-024-06106-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
AIMS/HYPOTHESIS The proinflammatory cytokines IFN-α, IFN-γ, IL-1β and TNF-α may contribute to innate and adaptive immune responses during insulitis in type 1 diabetes and therefore represent attractive therapeutic targets to protect beta cells. However, the specific role of each of these cytokines individually on pancreatic beta cells remains unknown. METHODS We used deep RNA-seq analysis, followed by extensive confirmation experiments based on reverse transcription-quantitative PCR (RT-qPCR), western blot, histology and use of siRNAs, to characterise the response of human pancreatic beta cells to each cytokine individually and compared the signatures obtained with those present in islets of individuals affected by type 1 diabetes. RESULTS IFN-α and IFN-γ had a greater impact on the beta cell transcriptome when compared with IL-1β and TNF-α. The IFN-induced gene signatures have a strong correlation with those observed in beta cells from individuals with type 1 diabetes, and the level of expression of specific IFN-stimulated genes is positively correlated with proteins present in islets of these individuals, regulating beta cell responses to 'danger signals' such as viral infections. Zinc finger NFX1-type containing 1 (ZNFX1), a double-stranded RNA sensor, was identified as highly induced by IFNs and shown to play a key role in the antiviral response in beta cells. CONCLUSIONS/INTERPRETATION These data suggest that IFN-α and IFN-γ are key cytokines at the islet level in human type 1 diabetes, contributing to the triggering and amplification of autoimmunity.
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Affiliation(s)
| | - Maria Ines Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Priscila L Zimath
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Angela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Arturo Roca Rivada
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandra Marín-Cañas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Op de Beeck
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Noel G Morgan
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Sebastian Sonntag
- InSphero AG, Schlieren, Switzerland
- University of Applied Sciences and Arts Northwestern Switzerland, Basel, Switzerland
| | | | | | | | - François Pattou
- European Genomic Institute for Diabetes, UMR 1190 Translational Research for Diabetes, Inserm, CHU Lille, University of Lille, Lille, France
| | - Julie Kerr-Conte
- European Genomic Institute for Diabetes, UMR 1190 Translational Research for Diabetes, Inserm, CHU Lille, University of Lille, Lille, France
| | - Eduard Montanya
- Hospital Universitari Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) and University of Barcelona, Barcelona, Spain
| | - Montserrat Nacher
- Hospital Universitari Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM) and University of Barcelona, Barcelona, Spain
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sarah J Richardson
- Islet Biology Exeter (IBEx), Exeter Centre of Excellence for Diabetes Research (EXCEED), Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium.
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Piron A, Szymczak F, Papadopoulou T, Alvelos MI, Defrance M, Lenaerts T, Eizirik DL, Cnop M. RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures. Life Sci Alliance 2024; 7:e202302203. [PMID: 38081640 PMCID: PMC10709657 DOI: 10.26508/lsa.202302203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
High-throughput omics technologies have generated a wealth of large protein, gene, and transcript datasets that have exacerbated the need for new methods to analyse and compare big datasets. Rank-rank hypergeometric overlap is an important threshold-free method to combine and visualize two ranked lists of P-values or fold-changes, usually from differential gene expression analyses. Here, we introduce a new rank-rank hypergeometric overlap-based method aimed at gene level and alternative splicing analyses at transcript or exon level, hitherto unreachable as transcript numbers are an order of magnitude larger than gene numbers. We tested the tool on synthetic and real datasets at gene and transcript levels to detect correlation and anticorrelation patterns and found it to be fast and accurate, even on very large datasets thanks to an evolutionary algorithm-based minimal P-value search. The tool comes with a ready-to-use permutation scheme allowing the computation of adjusted P-values at low time cost. The package compatibility mode is a drop-in replacement to previous packages. RedRibbon holds the promise to accurately extricate detailed information from large comparative analyses.
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Affiliation(s)
- Anthony Piron
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Szymczak
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
| | - Theodora Papadopoulou
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
| | - Maria Inês Alvelos
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Matthieu Defrance
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Brussels, Belgium
- https://ror.org/01r9htc13 Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Décio L Eizirik
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Miriam Cnop
- https://ror.org/01r9htc13 ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
- https://ror.org/01r9htc13 Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
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Eizirik DL, Szymczak F, Mallone R. Why does the immune system destroy pancreatic β-cells but not α-cells in type 1 diabetes? Nat Rev Endocrinol 2023; 19:425-434. [PMID: 37072614 DOI: 10.1038/s41574-023-00826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 04/20/2023]
Abstract
A perplexing feature of type 1 diabetes (T1D) is that the immune system destroys pancreatic β-cells but not neighbouring α-cells, even though both β-cells and α-cells are dysfunctional. Dysfunction, however, progresses to death only for β-cells. Recent findings indicate important differences between these two cell types. First, expression of BCL2L1, a key antiapoptotic gene, is higher in α-cells than in β-cells. Second, endoplasmic reticulum (ER) stress-related genes are differentially expressed, with higher expression levels of pro-apoptotic CHOP in β-cells than in α-cells and higher expression levels of HSPA5 (which encodes the protective chaperone BiP) in α-cells than in β-cells. Third, expression of viral recognition and innate immune response genes is higher in α-cells than in β-cells, contributing to the enhanced resistance of α-cells to coxsackievirus infection. Fourth, expression of the immune-inhibitory HLA-E molecule is higher in α-cells than in β-cells. Of note, α-cells are less immunogenic than β-cells, and the CD8+ T cells invading the islets in T1D are reactive to pre-proinsulin but not to glucagon. We suggest that this finding is a result of the enhanced capacity of the α-cell to endure viral infections and ER stress, which enables them to better survive early stressors that can cause cell death and consequently amplify antigen presentation to the immune system. Moreover, the processing of the pre-proglucagon precursor in enteroendocrine cells might favour immune tolerance towards this potential self-antigen compared to pre-proinsulin.
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Affiliation(s)
- Decio L Eizirik
- Université Libre de Bruxelles (ULB) Center for Diabetes Research and Welbio, Medical Faculty, Brussels, Belgium.
| | - Florian Szymczak
- Université Libre de Bruxelles (ULB) Center for Diabetes Research and Welbio, Medical Faculty, Brussels, Belgium
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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Castellá M, Blasco-Roset A, Peyrou M, Gavaldà-Navarro A, Villarroya J, Quesada-López T, Lorente-Poch L, Sancho J, Szymczak F, Piron A, Rodríguez-Fernández S, Carobbio S, Goday A, Domingo P, Vidal-Puig A, Giralt M, Eizirik DL, Villarroya F, Cereijo R. Adipose tissue plasticity in pheochromocytoma patients suggests a role of the splicing machinery in human adipose browning. iScience 2023; 26:106847. [PMID: 37250773 PMCID: PMC10209542 DOI: 10.1016/j.isci.2023.106847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/31/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Adipose tissue from pheochromocytoma patients acquires brown fat features, making it a valuable model for studying the mechanisms that control thermogenic adipose plasticity in humans. Transcriptomic analyses revealed a massive downregulation of splicing machinery components and splicing regulatory factors in browned adipose tissue from patients, with upregulation of a few genes encoding RNA-binding proteins potentially involved in splicing regulation. These changes were also observed in cell culture models of human brown adipocyte differentiation, confirming a potential involvement of splicing in the cell-autonomous control of adipose browning. The coordinated changes in splicing are associated with a profound modification in the expression levels of splicing-driven transcript isoforms for genes involved in the specialized metabolism of brown adipocytes and those encoding master transcriptional regulators of adipose browning. Splicing control appears to be a relevant component of the coordinated gene expression changes that allow human adipose tissue to acquire a brown phenotype.
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Affiliation(s)
- Moisés Castellá
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Albert Blasco-Roset
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Marion Peyrou
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Aleix Gavaldà-Navarro
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Joan Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Tania Quesada-López
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | | | - Juan Sancho
- Endocrine Surgery Unit, Hospital del Mar, 08003 Barcelona, Spain
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Anthony Piron
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sonia Rodríguez-Fernández
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Stefania Carobbio
- Bases Moleculares de Patologías Humanas, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain
| | - Albert Goday
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Endocrinology Service, Hospital del Mar, IMIM, 08003 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Pere Domingo
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Vidal-Puig
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge 289, UK
| | - Marta Giralt
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), 1070 Brussels, Belgium
| | - Francesc Villarroya
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
| | - Rubén Cereijo
- Departament de Bioquímica i Biomedicina Molecular, Universitat de Barcelona; Institut de Biomedicina de la Universitat de Barcelona (IBUB); and Institut de Recerca de Sant Joan de Déu, 08028 Barcelona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, 28029 Madrid, Spain
- Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, and Department of Infectious Diseases, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
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Yi X, Marmontel de Souza B, Sawatani T, Szymczak F, Marselli L, Marchetti P, Cnop M, Eizirik DL. Mining the transcriptome of target tissues of autoimmune and degenerative pancreatic β-cell and brain diseases to discover therapies. iScience 2022; 25:105376. [PMID: 36345338 PMCID: PMC9636054 DOI: 10.1016/j.isci.2022.105376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/26/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Target tissues of autoimmune and degenerative diseases show signals of inflammation. We used publicly available RNA-seq data to study whether pancreatic β-cells in type 1 and type 2 diabetes and neuronal tissue in multiple sclerosis and Alzheimer’s disease share inflammatory gene signatures. We observed concordantly upregulated genes in pairwise diseases, many of them related to signaling by interleukins and interferons. We next mined these signatures to identify therapies that could be re-purposed/shared among the diseases and identified the bromodomain inhibitors as potential perturbagens to revert the transcriptional signatures. We experimentally confirmed in human β-cells that bromodomain inhibitors I-BET151 and GSK046 prevent the deleterious effects of the pro-inflammatory cytokines interleukin-1β and interferon-γ and at least some of the effects of the metabolic stressor palmitate. These results demonstrate that key inflammation-induced molecular mechanisms are shared between β-cells and brain in autoimmune and degenerative diseases and that these signatures can be mined for drug discovery. Similar gene transcription signatures in diabetes, multiple sclerosis, and Alzheimer’s Inflammatory mechanisms are present in the target tissues of the four diseases Common gene expression signatures were mined for the identification of drug targets Bromodomain inhibitors decrease islet inflammation in models of types 1 and 2 diabetes
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Szymczak F, Alvelos MI, Marín-Cañas S, Castela Â, Demine S, Colli ML, Op de Beeck A, Thomaidou S, Marselli L, Zaldumbide A, Marchetti P, Eizirik DL. Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β cells. Sci Adv 2022; 8:eabn5732. [PMID: 36103539 PMCID: PMC9473574 DOI: 10.1126/sciadv.abn5732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
IFNα is a key regulator of the dialogue between pancreatic β cells and the immune system in early type 1 diabetes (T1D). IFNα up-regulates HLA class I expression in human β cells, fostering autoantigen presentation to the immune system. We observed by bulk and single-cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNα induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-βH1 and human islet cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I, antigen presentation-related genes, and chemokines. NLRC5 also mediates the effects of IFNα on alternative splicing, a generator of β cell neoantigens, suggesting that it is a central player of the effects of IFNα on β cells that contribute to trigger and amplify autoimmunity in T1D.
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Affiliation(s)
- Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Sandra Marín-Cañas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Stéphane Demine
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Anne Op de Beeck
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
| | - Sofia Thomaidou
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre De Bruxelles (ULB), Brussels, Belgium
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Szymczak F, Cohen-Fultheim R, Thomaidou S, de Brachène AC, Castela A, Colli M, Marchetti P, Levanon E, Eizirik D, Zaldumbide A. ADAR1-dependent editing regulates human β cell transcriptome diversity during inflammation. Front Endocrinol (Lausanne) 2022; 13:1058345. [PMID: 36518246 PMCID: PMC9742459 DOI: 10.3389/fendo.2022.1058345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Enterovirus infection has long been suspected as a possible trigger for type 1 diabetes. Upon infection, viral double-stranded RNA (dsRNA) is recognized by membrane and cytosolic sensors that orchestrate type I interferon signaling and the recruitment of innate immune cells to the pancreatic islets. In this context, adenosine deaminase acting on RNA 1 (ADAR1) editing plays an important role in dampening the immune response by inducing adenosine mispairing, destabilizing the RNA duplexes and thus preventing excessive immune activation. METHODS Using high-throughput RNA sequencing data from human islets and EndoC-βH1 cells exposed to IFNα or IFNγ/IL1β, we evaluated the role of ADAR1 in human pancreatic β cells and determined the impact of the type 1 diabetes pathophysiological environment on ADAR1-dependent RNA editing. RESULTS We show that both IFNα and IFNγ/IL1β stimulation promote ADAR1 expression and increase the A-to-I RNA editing of Alu-Containing mRNAs in EndoC-βH1 cells as well as in primary human islets. DISCUSSION We demonstrate that ADAR1 overexpression inhibits type I interferon response signaling, while ADAR1 silencing potentiates IFNα effects. In addition, ADAR1 overexpression triggers the generation of alternatively spliced mRNAs, highlighting a novel role for ADAR1 as a regulator of the β cell transcriptome under inflammatory conditions.
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Affiliation(s)
- Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Roni Cohen-Fultheim
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Sofia Thomaidou
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Angela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Maikel Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Erez Levanon
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Decio Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Arnaud Zaldumbide,
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Abstract
Completion of the Human Genome Project enabled a novel systems- and network-level understanding of biology, but this remains to be applied for understanding the pathogenesis of type 1 diabetes (T1D). We propose that defining the key gene regulatory networks that drive β-cell dysfunction and death in T1D might enable the design of therapies that target the core disease mechanism, namely, the progressive loss of pancreatic β-cells. Indeed, many successful drugs do not directly target individual disease genes but, rather, modulate the consequences of defective steps, targeting proteins located one or two steps downstream. If we transpose this to the T1D situation, it makes sense to target the pathways that modulate the β-cell responses to the immune assault-in relation to signals that may stimulate the immune response (e.g., HLA class I and chemokine overexpression and/or neoantigen expression) or inhibit the invading immune cells (e.g., PDL1 and HLA-E expression)-instead of targeting only the immune system, as it is usually proposed. Here we discuss the importance of a focus on β-cells in T1D, lessons learned from other autoimmune diseases, the "alternative splicing connection," data mining, and drug repurposing to protect β-cells in T1D and then some of the initial candidates under testing for β-cell protection.
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Affiliation(s)
- Decio L Eizirik
- Indiana Biosciences Research Institute, Indianapolis, IN
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Florian Szymczak
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Maria Inês Alvelos
- ULB Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
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Alvelos MI, Szymczak F, Castela Â, Marín-Cañas S, de Souza BM, Gkantounas I, Colli M, Fantuzzi F, Cosentino C, Igoillo-Esteve M, Marselli L, Marchetti P, Cnop M, Eizirik DL. A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis. Islets 2021; 13:51-65. [PMID: 34241569 PMCID: PMC8280887 DOI: 10.1080/19382014.2021.1948282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Exposure of human pancreatic beta cells to pro-inflammatory cytokines or metabolic stressors is used to model events related to type 1 and type 2 diabetes, respectively. Quantitative real-time PCR is commonly used to quantify changes in gene expression. The selection of the most adequate reference gene(s) for gene expression normalization is an important pre-requisite to obtain accurate and reliable results. There are no universally applicable reference genes, and the human beta cell expression of commonly used reference genes can be altered by different stressors. Here we aimed to identify the most stably expressed genes in human beta cells to normalize quantitative real-time PCR gene expression.We used comprehensive RNA-sequencing data from the human pancreatic beta cell line EndoC-βH1, human islets exposed to cytokines or the free fatty acid palmitate in order to identify the most stably expressed genes. Genes were filtered based on their level of significance (adjusted P-value >0.05), fold-change (|fold-change| <1.5) and a coefficient of variation <10%. Candidate reference genes were validated by quantitative real-time PCR in independent samples.We identified a total of 264 genes stably expressed in EndoC-βH1 cells and human islets following cytokines - or palmitate-induced stress, displaying a low coefficient of variation. Validation by quantitative real-time PCR of the top five genes ARF1, CWC15, RAB7A, SIAH1 and VAPA corroborated their expression stability under most of the tested conditions. Further validation in independent samples indicated that the geometric mean of ACTB and VAPA expression can be used as a reliable normalizing factor in human beta cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
- CONTACT Maria Inês Alvelos ULB Center for Diabetic Research, Medical Faculty, Université Libre De Bruxelles (ULB), Route De Lennik, 808 – CP618, B-1070 – Brussels – Belgium
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Sandra Marín-Cañas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Bianca Marmontel de Souza
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Ioannis Gkantounas
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Maikel Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Federica Fantuzzi
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Cristina Cosentino
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - Miriam Cnop
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
- Division of Endocrinology, Erasmus Hospital, Université Libre De Bruxelles, Brussels, Belgium
| | - Décio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
- Welbio, Medical Faculty, Université Libre De Bruxelles, Brussels (ULB)Belgium
- Diabetes Center, Indiana Biosciences Research Institute, Indianapolis, IN, USA
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Szymczak F, Colli ML, Mamula MJ, Evans-Molina C, Eizirik DL. Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. Sci Adv 2021; 7:7/2/eabd7600. [PMID: 33523973 PMCID: PMC7787485 DOI: 10.1126/sciadv.abd7600] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/16/2020] [Indexed: 05/05/2023]
Abstract
Autoimmune diseases are typically studied with a focus on the immune system, and less attention is paid to responses of target tissues exposed to the immune assault. We presently evaluated, based on available RNA sequencing data, whether inflammation induces similar molecular signatures at the target tissues in type 1 diabetes, systemic lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. We identified confluent signatures, many related to interferon signaling, indicating pathways that may be targeted for therapy, and observed a high (>80%) expression of candidate genes for the different diseases at the target tissue level. These observations suggest that future research on autoimmune diseases should focus on both the immune system and the target tissues, and on their dialog. Discovering similar disease-specific signatures may allow the identification of key pathways that could be targeted for therapy, including the repurposing of drugs already in clinical use for other diseases.
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Affiliation(s)
- F Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - M L Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - M J Mamula
- Section of Rheumatology, Yale University School of Medicine, New Haven, CT, USA
| | - C Evans-Molina
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - D L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium.
- Indiana Biosciences Research Institute (IBRI), Indianapolis, IN, USA
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Colli ML, Szymczak F, Eizirik DL. Molecular Footprints of the Immune Assault on Pancreatic Beta Cells in Type 1 Diabetes. Front Endocrinol (Lausanne) 2020; 11:568446. [PMID: 33042023 PMCID: PMC7522353 DOI: 10.3389/fendo.2020.568446] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/17/2020] [Indexed: 12/25/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic disease caused by the selective destruction of the insulin-producing pancreatic beta cells by infiltrating immune cells. We presently evaluated the transcriptomic signature observed in beta cells in early T1D and compared it with the signatures observed following in vitro exposure of human islets to inflammatory or metabolic stresses, with the aim of identifying "footprints" of the immune assault in the target beta cells. We detected similarities between the beta cell signatures induced by cytokines present at different moments of the disease, i.e., interferon-α (early disease) and interleukin-1β plus interferon-γ (later stages) and the beta cells from T1D patients, identifying biological process and signaling pathways activated during early and late stages of the disease. Among the first responses triggered on beta cells was an enrichment in antiviral responses, pattern recognition receptors activation, protein modification and MHC class I antigen presentation. During putative later stages of insulitis the processes were dominated by T-cell recruitment and activation and attempts of beta cells to defend themselves through the activation of anti-inflammatory pathways (i.e., IL10, IL4/13) and immune check-point proteins (i.e., PDL1 and HLA-E). Finally, we mined the beta cell signature in islets from T1D patients using the Connectivity Map, a large database of chemical compounds/drugs, and identified interesting candidates to potentially revert the effects of insulitis on beta cells.
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Affiliation(s)
- Maikel L. Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- *Correspondence: Maikel L. Colli
| | - Florian Szymczak
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, United States
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