1
|
Manduchi E, Descamps HC, Schug J, Da T, Lahori D, El-Mekkoussi H, Betts MR, Kaestner KH. No Evidence for Persistent Enteroviral B Infection of Pancreatic Islets in Patients With Type 1 Diabetes and Prediabetes From RNA Sequencing Data. Diabetes 2024; 73:1697-1704. [PMID: 39083653 PMCID: PMC11417435 DOI: 10.2337/db24-0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
Persistent enterovirus B infection has been proposed as an important contributor to the etiology of type 1 diabetes. We leveraged extensive bulk RNA-sequencing (RNA-seq) data from α-, β-, and exocrine cells, as well as islet single-cell RNA-seq data from the Human Pancreas Analysis Program (HPAP), to evaluate the presence of enterovirus B sequences in the pancreas of patients with type 1 diabetes and prediabetes (no diabetes but positive for autoantibodies). We examined all available HPAP data for either assay type, including donors without diabetes and with type 1 and type 2 diabetes. To assess the presence of viral reads, we analyzed all reads not mapping to the human genome with the taxonomic classification system Kraken2 and its full viral database augmented to encompass representatives for all 28 enterovirus B serotypes for which a complete genome is available. As a secondary approach, we input the same sequence reads into the STAR aligner using these 28 enterovirus B genomes as the reference. No enterovirus B sequences were detected by either approach in any of the 243 bulk RNA libraries or in any of the 79 single-cell RNA libraries. While we cannot rule out the possibility of a very-low-grade persistent enterovirus B infection in the donors analyzed, our data do not support the notion of chronic viral infection by these viruses as a major driver of type 1 diabetes. ARTICLE HIGHLIGHTS
Collapse
Affiliation(s)
- Elisabetta Manduchi
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hélène C. Descamps
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jonathan Schug
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Tong Da
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deeksha Lahori
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hilana El-Mekkoussi
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Klaus H. Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
2
|
Imai J. Possible etiological role of impaired endogenous double strand RNA editing in β-cells in type 1 diabetes. J Diabetes Investig 2024; 15:1171-1173. [PMID: 38661313 PMCID: PMC11363094 DOI: 10.1111/jdi.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024] Open
Abstract
Proposed mechanisms by which disruption of endogenous dsRNA editing in β-cells leads to type 1 diabetes-like phenotypes in βAdarKO mice. Disruption of endogenous dsRNA editing in β-cells initiates IFN responses, thereby inducing pancreatic islet inflammation and β-cell dysfunction. Hyperglycemia induced by β-cell dysfunction further promotes islet inflammation, likely via increased dsRNA resulting from increased β-cell workload, thereby producing a vicious cycle. The mechanism by which impairment of dsRNA editing is integrated with autoimmune-mediated pathogenesis of type 1 diabetes remains to be clarified.
Collapse
Affiliation(s)
- Junta Imai
- Department of Diabetes, Metabolism and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| |
Collapse
|
3
|
Staels W, Berthault C, Bourgeois S, Laville V, Lourenço C, De Leu N, Scharfmann R. Comprehensive alpha, beta, and delta cell transcriptomics reveal an association of cellular aging with MHC class I upregulation. Mol Metab 2024; 87:101990. [PMID: 39009220 PMCID: PMC11327396 DOI: 10.1016/j.molmet.2024.101990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
OBJECTIVES This study aimed to evaluate the efficacy of a purification method developed for isolating alpha, beta, and delta cells from pancreatic islets of adult mice, extending its application to islets from newborn and aged mice. Furthermore, it sought to examine transcriptome dynamics in mouse pancreatic endocrine islet cells throughout postnatal development and to validate age-related alterations within these cell populations. METHODS We leveraged the high surface expression of CD71 on beta cells and CD24 on delta cells to FACS-purify alpha, beta, and delta cells from newborn (1-week-old), adult (12-week-old), and old (18-month-old) mice. Bulk RNA sequencing was conducted on these purified cell populations, and subsequent bioinformatic analyses included differential gene expression, overrepresentation, and intersection analysis. RESULTS Alpha, beta, and delta cells from newborn and aged mice were successfully FACS-purified using the same method employed for adult mice. Our analysis of the age-related transcriptional changes in alpha, beta, and delta cell populations revealed a decrease in cell cycling and an increase in neuron-like features processes during the transition from newborn to adult mice. Progressing from adult to old mice, we identified an inflammatory gene signature related to aging (inflammaging) encompassing an increase in β-2 microglobulin and major histocompatibility complex (MHC) Class I expression. CONCLUSIONS Our study demonstrates the effectiveness of our cell sorting technique in purifying endocrine subsets from mouse islets at different ages. We provide a valuable resource for better understanding endocrine pancreas aging and identified an inflammaging gene signature with increased β-2 microglobulin and MHC Class I expression as a common hallmark of old alpha, beta, and delta cells, with potential implications for immune response regulation and age-related diabetes.
Collapse
Affiliation(s)
- W Staels
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France; Genetics, Reproduction and Development (GRAD), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Division of Pediatric Endocrinology, Department of Pediatrics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium.
| | - C Berthault
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - S Bourgeois
- Genetics, Reproduction and Development (GRAD), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - V Laville
- Stem Cells and Development Unit, Institut Pasteur, Paris, France; UMR CNRS 3738, Institut Pasteur, Paris, France; Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - C Lourenço
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - N De Leu
- Genetics, Reproduction and Development (GRAD), Vrije Universiteit Brussel (VUB), Brussels, Belgium; Endocrinology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium; Endocrinology, ASZ Aalst, 9300 Aalst, Belgium
| | - R Scharfmann
- Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| |
Collapse
|
4
|
Robertson CC, Elgamal RM, Henry-Kanarek BA, Arvan P, Chen S, Dhawan S, Eizirik DL, Kaddis JS, Vahedi G, Parker SCJ, Gaulton KJ, Soleimanpour SA. Untangling the genetics of beta cell dysfunction and death in type 1 diabetes. Mol Metab 2024; 86:101973. [PMID: 38914291 PMCID: PMC11283044 DOI: 10.1016/j.molmet.2024.101973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex multi-system disease which arises from both environmental and genetic factors, resulting in the destruction of insulin-producing pancreatic beta cells. Over the past two decades, human genetic studies have provided new insight into the etiology of T1D, including an appreciation for the role of beta cells in their own demise. SCOPE OF REVIEW Here, we outline models supported by human genetic data for the role of beta cell dysfunction and death in T1D. We highlight the importance of strong evidence linking T1D genetic associations to bona fide candidate genes for mechanistic and therapeutic consideration. To guide rigorous interpretation of genetic associations, we describe molecular profiling approaches, genomic resources, and disease models that may be used to construct variant-to-gene links and to investigate candidate genes and their role in T1D. MAJOR CONCLUSIONS We profile advances in understanding the genetic causes of beta cell dysfunction and death at individual T1D risk loci. We discuss how genetic risk prediction models can be used to address disease heterogeneity. Further, we present areas where investment will be critical for the future use of genetics to address open questions in the development of new treatment and prevention strategies for T1D.
Collapse
Affiliation(s)
- Catherine C Robertson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ruth M Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Belle A Henry-Kanarek
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Peter Arvan
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA; Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Scott A Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
5
|
Maestas MM, Ishahak M, Augsornworawat P, Veronese-Paniagua DA, Maxwell KG, Velazco-Cruz L, Marquez E, Sun J, Shunkarova M, Gale SE, Urano F, Millman JR. Identification of unique cell type responses in pancreatic islets to stress. Nat Commun 2024; 15:5567. [PMID: 38956087 PMCID: PMC11220140 DOI: 10.1038/s41467-024-49724-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
Diabetes involves the death or dysfunction of pancreatic β-cells. Analysis of bulk sequencing from human samples and studies using in vitro and in vivo models suggest that endoplasmic reticulum and inflammatory signaling play an important role in diabetes progression. To better characterize cell type-specific stress response, we perform multiplexed single-cell RNA sequencing to define the transcriptional signature of primary human islet cells exposed to endoplasmic reticulum and inflammatory stress. Through comprehensive pair-wise analysis of stress responses across pancreatic endocrine and exocrine cell types, we define changes in gene expression for each cell type under different diabetes-associated stressors. We find that β-, α-, and ductal cells have the greatest transcriptional response. We utilize stem cell-derived islets to study islet health through the candidate gene CIB1, which was upregulated under stress in primary human islets. Our findings provide insights into cell type-specific responses to diabetes-associated stress and establish a resource to identify targets for diabetes therapeutics.
Collapse
Affiliation(s)
- Marlie M Maestas
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Punn Augsornworawat
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Daniel A Veronese-Paniagua
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Kristina G Maxwell
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Leonardo Velazco-Cruz
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Erica Marquez
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Jiameng Sun
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Mira Shunkarova
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Sarah E Gale
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
| | - Fumihiko Urano
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA
| | - Jeffrey R Millman
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
- Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, St. Louis, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA.
| |
Collapse
|
6
|
Webster KL, Mirmira RG. Beta cell dedifferentiation in type 1 diabetes: sacrificing function for survival? Front Endocrinol (Lausanne) 2024; 15:1427723. [PMID: 38904049 PMCID: PMC11187278 DOI: 10.3389/fendo.2024.1427723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
The pathogeneses of type 1 and type 2 diabetes involve the progressive loss of functional beta cell mass, primarily attributed to cellular demise and/or dedifferentiation. While the scientific community has devoted significant attention to unraveling beta cell dedifferentiation in type 2 diabetes, its significance in type 1 diabetes remains relatively unexplored. This perspective article critically analyzes the existing evidence for beta cell dedifferentiation in type 1 diabetes, emphasizing its potential to reduce beta cell autoimmunity. Drawing from recent advancements in both human studies and animal models, we present beta cell identity as a promising target for managing type 1 diabetes. We posit that a better understanding of the mechanisms of beta cell dedifferentiation in type 1 diabetes is key to pioneering interventions that balance beta cell function and immunogenicity.
Collapse
Affiliation(s)
| | - Raghavendra G. Mirmira
- Kovler Diabetes Center and the Department of Medicine, The University of Chicago, Chicago, IL, United States
| |
Collapse
|
7
|
Buschard K, Haupt-Jorgensen M. Autoimmune vulnerability of beta versus alpha cells might be due to increased 2',5' synthetase. APMIS 2024; 132:371-372. [PMID: 38344946 DOI: 10.1111/apm.13384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 04/16/2024]
Affiliation(s)
- Karsten Buschard
- Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen, Denmark
| | | |
Collapse
|
8
|
Jarmoskaite I, Li JB. Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity. RNA (NEW YORK, N.Y.) 2024; 30:500-511. [PMID: 38531645 PMCID: PMC11019752 DOI: 10.1261/rna.079953.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Innate immunity must be tightly regulated to enable sensitive pathogen detection while averting autoimmunity triggered by pathogen-like host molecules. A hallmark of viral infection, double-stranded RNAs (dsRNAs) are also abundantly encoded in mammalian genomes, necessitating surveillance mechanisms to distinguish "self" from "nonself." ADAR1, an RNA editing enzyme, has emerged as an essential safeguard against dsRNA-induced autoimmunity. By converting adenosines to inosines (A-to-I) in long dsRNAs, ADAR1 covalently marks endogenous dsRNAs, thereby blocking the activation of the cytoplasmic dsRNA sensor MDA5. Moreover, beyond its editing function, ADAR1 binding to dsRNA impedes the activation of innate immune sensors PKR and ZBP1. Recent landmark studies underscore the utility of silencing ADAR1 for cancer immunotherapy, by exploiting the ADAR1-dependence developed by certain tumors to unleash an antitumor immune response. In this perspective, we summarize the genetic and mechanistic evidence for ADAR1's multipronged role in suppressing dsRNA-mediated autoimmunity and explore the evolving roles of ADAR1 as an immuno-oncology target.
Collapse
Affiliation(s)
- Inga Jarmoskaite
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- AIRNA Corporation, Cambridge, Massachusetts 02142, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
9
|
Levanon EY, Cohen-Fultheim R, Eisenberg E. In search of critical dsRNA targets of ADAR1. Trends Genet 2024; 40:250-259. [PMID: 38160061 DOI: 10.1016/j.tig.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Recent studies have underscored the pivotal role of adenosine-to-inosine RNA editing, catalyzed by ADAR1, in suppressing innate immune interferon responses triggered by cellular double-stranded RNA (dsRNA). However, the specific ADAR1 editing targets crucial for this regulatory function remain elusive. We review analyses of transcriptome-wide ADAR1 editing patterns and their evolutionary dynamics, which offer valuable insights into this unresolved query. The growing appreciation of the significance of immunogenic dsRNAs and their editing in inflammatory and autoimmune diseases and cancer calls for a more comprehensive understanding of dsRNA immunogenicity, which may promote our understanding of these diseases and open doors to therapeutic avenues.
Collapse
Affiliation(s)
- Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - Roni Cohen-Fultheim
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv, University, Tel Aviv 6997801, Israel.
| |
Collapse
|