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Wang B, Zhang B, Wu M, Xu T. Unlocking therapeutic potential: Targeting lymphocyte activation Gene-3 (LAG-3) with fibrinogen-like protein 1 (FGL1) in systemic lupus erythematosus. J Transl Autoimmun 2024; 9:100249. [PMID: 39228513 PMCID: PMC11369448 DOI: 10.1016/j.jtauto.2024.100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 09/05/2024] Open
Abstract
Systemic lupus erythematosus (SLE) represents an autoimmune disorder that affects multiple systems. In the treatment of this condition, the focus primarily revolves around inflammation suppression and immunosuppression. Consequently, targeted therapy has emerged as a prevailing approach. Currently, the quest for highly sensitive and specifically effective targets has gained significant momentum in the context of SLE treatment. Lymphocyte activation gene-3 (LAG-3) stands out as a crucial inhibitory receptor that binds to pMHC-II, thereby effectively dampening autoimmune responses. Fibrinogen-like protein 1 (FGL1) serves as the principal immunosuppressive ligand for LAG-3, and their combined action demonstrates a potent immunosuppressive effect. This intricate mechanism paves the way for potential SLE treatment by targeting LAG-3 with FGL1. This work provides a comprehensive summary of LAG-3's role in the pathogenesis of SLE and elucidates the feasibility of leveraging FGL1 as a therapeutic approach for SLE management. It introduces a novel therapeutic target and opens up new avenues of therapeutic consideration in the clinical context of SLE treatment.
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Affiliation(s)
- Bing Wang
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Biqing Zhang
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Min Wu
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Ting Xu
- Department of Rheumatology and Immunology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
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2
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Garcia JPT, Tayo LL. Theoretical Studies of DNA Microarray Present Potential Molecular and Cellular Interconnectivity of Signaling Pathways in Immune System Dysregulation. Genes (Basel) 2024; 15:393. [PMID: 38674328 PMCID: PMC11049615 DOI: 10.3390/genes15040393] [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: 02/16/2024] [Revised: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Autoimmunity is defined as the inability to regulate immunological activities in the body, especially in response to external triggers, leading to the attack of the tissues and organs of the host. Outcomes include the onset of autoimmune diseases whose effects are primarily due to dysregulated immune responses. In past years, there have been cases that show an increased susceptibility to other autoimmune disorders in patients who are already experiencing the same type of disease. Research in this field has started analyzing the potential molecular and cellular causes of this interconnectedness, bearing in mind the possibility of advancing drugs and therapies for the treatment of autoimmunity. With that, this study aimed to determine the correlation of four autoimmune diseases, which are type 1 diabetes (T1D), psoriasis (PSR), systemic sclerosis (SSc), and systemic lupus erythematosus (SLE), by identifying highly preserved co-expressed genes among datasets using WGCNA. Functional annotation was then employed to characterize these sets of genes based on their systemic relationship as a whole to elucidate the biological processes, cellular components, and molecular functions of the pathways they are involved in. Lastly, drug repurposing analysis was performed to screen candidate drugs for repositioning that could regulate the abnormal expression of genes among the diseases. A total of thirteen modules were obtained from the analysis, the majority of which were associated with transcriptional, post-transcriptional, and post-translational modification processes. Also, the evaluation based on KEGG suggested the possible role of TH17 differentiation in the simultaneous onset of the four diseases. Furthermore, clomiphene was the top drug candidate for regulating overexpressed hub genes; meanwhile, prilocaine was the top drug for regulating under-expressed hub genes. This study was geared towards utilizing transcriptomics approaches for the assessment of microarray data, which is different from the use of traditional genomic analyses. Such a research design for investigating correlations among autoimmune diseases may be the first of its kind.
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Affiliation(s)
- Jon Patrick T. Garcia
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines;
- Department of Biology, School of Medicine and Health Sciences, Mapúa University, Makati 1200, Philippines
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3
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Roberts BK, Collado G, Barnes BJ. Role of interferon regulatory factor 5 (IRF5) in tumor progression: Prognostic and therapeutic potential. Biochim Biophys Acta Rev Cancer 2024; 1879:189061. [PMID: 38141865 DOI: 10.1016/j.bbcan.2023.189061] [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: 11/09/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Canonically, the transcription factor interferon regulatory factor 5 (IRF5) is a key mediator of innate and adaptive immunity downstream of pathogen recognition receptors such as Toll-like receptors (TLRs). Hence, dysregulation of IRF5 function has been widely implicated in inflammatory and autoimmune diseases. Over the last few decades, dysregulation of IRF5 expression has been also reported in hematologic malignancies and solid cancers that support a role for IRF5 in malignant transformation, tumor immune regulation, clinical prognosis, and treatment response. This review will provide an in-depth overview of the current literature regarding the mechanisms by which IRF5 functions as either a tumor suppressor or oncogene, its role in metastasis, regulation of the tumor-immune microenvironment, utility as a prognostic indicator of disease, and new developments in IRF5 therapeutics that may be used to remodel tumor immunity.
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Affiliation(s)
- Bailey K Roberts
- Center for Autoimmune Musculoskeletal and Hematopoietic Disease, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, United States of America; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, NY 11030, United States of America
| | - Gilbert Collado
- Center for Autoimmune Musculoskeletal and Hematopoietic Disease, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, United States of America
| | - Betsy J Barnes
- Center for Autoimmune Musculoskeletal and Hematopoietic Disease, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, United States of America; Departments of Pediatrics and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States of America.
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4
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Ren P, Lu L, Cai S, Chen J, Lin W, Han F. Alternative Splicing: A New Cause and Potential Therapeutic Target in Autoimmune Disease. Front Immunol 2021; 12:713540. [PMID: 34484216 PMCID: PMC8416054 DOI: 10.3389/fimmu.2021.713540] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is a complex coordinated transcriptional regulatory mechanism. It affects nearly 95% of all protein-coding genes and occurs in nearly all human organs. Aberrant alternative splicing can lead to various neurological diseases and cancers and is responsible for aging, infection, inflammation, immune and metabolic disorders, and so on. Though aberrant alternative splicing events and their regulatory mechanisms are widely recognized, the association between autoimmune disease and alternative splicing has not been extensively examined. Autoimmune diseases are characterized by the loss of tolerance of the immune system towards self-antigens and organ-specific or systemic inflammation and subsequent tissue damage. In the present review, we summarized the most recent reports on splicing events that occur in the immunopathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) and attempted to clarify the role that splicing events play in regulating autoimmune disease progression. We also identified the changes that occur in splicing factor expression. The foregoing information might improve our understanding of autoimmune diseases and help develop new diagnostic and therapeutic tools for them.
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Affiliation(s)
- Pingping Ren
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Luying Lu
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Shasha Cai
- Department of Nephrology, The First People's Hospital of Wenling, Taizhou, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Weiqiang Lin
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University of Medicine, Hangzhou, China
| | - Fei Han
- Kidney Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Nephropathy, Zhejiang Province, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
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5
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Hurley HJ, Dewald H, Rothkopf ZS, Singh S, Jenkins F, Deb P, De S, Barnes BJ, Fitzgerald-Bocarsly P. Frontline Science: AMPK regulates metabolic reprogramming necessary for interferon production in human plasmacytoid dendritic cells. J Leukoc Biol 2020; 109:299-308. [PMID: 32640499 DOI: 10.1002/jlb.3hi0220-130] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 01/09/2023] Open
Abstract
Plasmacytoid dendritic cells (pDCs) play a crucial role in innate viral immunity as the most potent producers of type I interferons (IFN) in the human body. However, the metabolic regulation of IFN production in such vast quantity remains poorly understood. In this study, AMP-activated protein kinase (AMPK) is strongly implicated as a driver of metabolic reprogramming that the authors and others have observed in pDCs after activation via TLR7/9. Oxygen consumption and mitochondrial membrane potential (MMP) were elevated following stimulation of pDCs with influenza or herpes simplex virus. Blocking these changes using mitochondrial inhibitors abrogated IFN-α production. While it appears that multiple carbon sources can be used by pDCs, blocking pyruvate metabolism had the strongest effect on IFN-α production. Furthermore, we saw no evidence of aerobic glycolysis (AG) during pDC activation and blocking lactate dehydrogenase activity did not inhibit IFN-α. TLR7/9 ligation induces a posttranslational modification in Raptor that is catalyzed by AMPK, and blocking TLR7/9 before virus introduction prevents this change. Finally, it is demonstrated that Dorsomorphin, an AMPK inhibitor, inhibited both IFN-α production and MMP in a dose-dependent manner. Taken together, these data reveal a potential cellular mechanism for the metabolic reprogramming in TLR 7/9-activated pDCs that supports activation and IFN-α production.
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Affiliation(s)
- Harry J Hurley
- Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA.,School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Hannah Dewald
- School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Zachary S Rothkopf
- School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Sukhwinder Singh
- Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Frank Jenkins
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Pratik Deb
- School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Saurav De
- School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA.,Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Betsy J Barnes
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Patricia Fitzgerald-Bocarsly
- Department of Pathology, Immunology, and Laboratory Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA.,School of Graduate Studies, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
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6
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Banga J, Srinivasan D, Sun CC, Thompson CD, Milletti F, Huang KS, Hamilton S, Song S, Hoffman AF, Qin YG, Matta B, LaPan M, Guo Q, Lu G, Li D, Qian H, Bolin DR, Liang L, Wartchow C, Qiu J, Downing M, Narula S, Fotouhi N, DeMartino JA, Tan SL, Chen G, Barnes BJ. Inhibition of IRF5 cellular activity with cell-penetrating peptides that target homodimerization. SCIENCE ADVANCES 2020; 6:eaay1057. [PMID: 32440537 PMCID: PMC7228753 DOI: 10.1126/sciadv.aay1057] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 03/05/2020] [Indexed: 05/07/2023]
Abstract
The transcription factor interferon regulatory factor 5 (IRF5) plays essential roles in pathogen-induced immunity downstream of Toll-, nucleotide-binding oligomerization domain-, and retinoic acid-inducible gene I-like receptors and is an autoimmune susceptibility gene. Normally, inactive in the cytoplasm, upon stimulation, IRF5 undergoes posttranslational modification(s), homodimerization, and nuclear translocation, where dimers mediate proinflammatory gene transcription. Here, we report the rational design of cell-penetrating peptides (CPPs) that disrupt IRF5 homodimerization. Biochemical and imaging analysis shows that IRF5-CPPs are cell permeable, noncytotoxic, and directly bind to endogenous IRF5. IRF5-CPPs were selective and afforded cell type- and species-specific inhibition. In plasmacytoid dendritic cells, inhibition of IRF5-mediated interferon-α production corresponded to a dose-dependent reduction in nuclear phosphorylated IRF5 [p(Ser462)IRF5], with no effect on pIRF5 levels. These data support that IRF5-CPPs function downstream of phosphorylation. Together, data support the utility of IRF5-CPPs as novel tools to probe IRF5 activation and function in disease.
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Affiliation(s)
- Jaspreet Banga
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | | | - Chia-Chi Sun
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
| | - Cherrie D. Thompson
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Francesca Milletti
- Roche Innovation Center New York, 430 East 29th Street, New York, NY 10016, USA
| | - Kuo-Sen Huang
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Shannon Hamilton
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Su Song
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Ann F. Hoffman
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Yajuan Gu Qin
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Bharati Matta
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Margaret LaPan
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Qin Guo
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Gang Lu
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Dan Li
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
| | - Hong Qian
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - David R. Bolin
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Lena Liang
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Charles Wartchow
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Jin Qiu
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
| | - Michelle Downing
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
| | - Satwant Narula
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Nader Fotouhi
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Julie A. DeMartino
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
| | - Seng-Lai Tan
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Gang Chen
- Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, MA 01821, USA
- Corresponding author. (B.J.B.); (G.C.)
| | - Betsy J. Barnes
- The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, 350 Community Dr., Manhasset, NY 11030, USA
- Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Corresponding author. (B.J.B.); (G.C.)
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7
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Li D, Matta B, Song S, Nelson V, Diggins K, Simpfendorfer KR, Gregersen PK, Linsley P, Barnes BJ. IRF5 genetic risk variants drive myeloid-specific IRF5 hyperactivation and presymptomatic SLE. JCI Insight 2020; 5:124020. [PMID: 31877114 DOI: 10.1172/jci.insight.124020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic variants within or near the interferon regulatory factor 5 (IRF5) locus associate with systemic lupus erythematosus (SLE) across ancestral groups. The major IRF5-SLE risk haplotype is common across populations, yet immune functions for the risk haplotype are undefined. We characterized the global immune phenotype of healthy donors homozygous for the major risk and nonrisk haplotypes and identified cell lineage-specific alterations that mimic presymptomatic SLE. Contrary to previous studies in B lymphoblastoid cell lines and SLE immune cells, IRF5 genetic variants had little effect on IRF5 protein levels in healthy donors. Instead, we detected basal IRF5 hyperactivation in the myeloid compartment of risk donors that drives the SLE immune phenotype. Risk donors were anti-nuclear antibody positive with anti-Ro and -MPO specificity, had increased circulating plasma cells and plasmacytoid dendritic cells, and had enhanced spontaneous NETosis. The IRF5-SLE immune phenotype was conserved over time and probed mechanistically by ex vivo coculture, indicating that risk neutrophils are drivers of the global immune phenotype. RNA-Seq of risk neutrophils revealed increased IRF5 transcript expression, IFN pathway enrichment, and decreased expression of ROS pathway genes. Altogether, the data support that individuals carrying the IRF5-SLE risk haplotype are more susceptible to environmental/stochastic influences that trigger chronic immune activation, predisposing to the development of clinical SLE.
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Affiliation(s)
- Dan Li
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Bharati Matta
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Su Song
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Victoria Nelson
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Kirsten Diggins
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Kim R Simpfendorfer
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Peter Linsley
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Betsy J Barnes
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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8
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Ban T, Sato GR, Tamura T. Regulation and role of the transcription factor IRF5 in innate immune responses and systemic lupus erythematosus. Int Immunol 2019; 30:529-536. [PMID: 29860420 DOI: 10.1093/intimm/dxy032] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/29/2018] [Indexed: 02/07/2023] Open
Abstract
The transcription factor interferon regulatory factor-5 (IRF5) plays an important role in innate immune responses via the TLR-MyD88 (Toll-like receptor - myeloid differentiation primary response 88) pathway. IRF5 is also involved in the pathogenesis of the autoimmune disease systemic lupus erythematosus (SLE). Recent studies have identified new regulators, both positive and negative, which act on IRF5 activation events in the TLR-MyD88 pathway such as post-translational modifications, dimerization and nuclear translocation. A model of the causal relationship between IRF5 activation and SLE pathogenesis proposes that a loss of the negative regulation of IRF5 causes its hyperactivation, resulting in hyperproduction of type I interferons and other cytokines, and ultimately in the development of SLE. Importantly, to our knowledge, all murine models of SLE studied thus far have shown that IRF5 is required for the pathogenesis of SLE-like diseases. During the development of SLE-like diseases, IRF5 plays key roles in various cell types, including dendritic cells and B cells. It is noteworthy that the onset of SLE-like diseases can be inhibited by reducing the activity or amount of IRF5 by half. Therefore, IRF5 is an important therapeutic target of SLE, and selective suppression of its activity and expression may potentially lead to the development of new therapies.
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Affiliation(s)
- Tatsuma Ban
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Go R Sato
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan
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9
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Zhang Q, Liang Y, Yuan H, Li S, Wang JB, Li XM, Tao JH, Pan HF, Ye DQ. Integrated analysis of lncRNA, miRNA and mRNA expression profiling in patients with systemic lupus erythematosus. Arch Med Sci 2019; 15:872-879. [PMID: 31360182 PMCID: PMC6657242 DOI: 10.5114/aoms.2018.79145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/11/2018] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION A great deal of research has reported dysregulated expression of genes in systemic lupus erythematosus (SLE). This study aimed to analyze the lncRNA, miRNA and mRNA expression profile in SLE. MATERIAL AND METHODS RNA sequencing (RNA-seq) was used to detect the dysregulated RNAs in SLE. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were used to explore the function of these differentially expressed RNAs. RESULTS 2,353 lncRNAs, 827 mRNAs and 24 miRNAs were shown to be differentially expressed. GO analyses demonstrated that differentially expressed RNAs were enriched in a variety of molecular functions and biological processes including ribonucleotide, protein serine/threonine kinase activity function, regulation of B cell differentiation and others. KEGG pathway analyses revealed that differentially expressed mRNAs and lncRNAs were both enriched in FcγR-mediated phagocytosis, glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate and glyoxylate and dicarboxylate metabolism pathways. The up-regulated miRNAs target genes were mainly enriched in the nuclear factor-κB (NF-κB) signaling pathway. The down-regulated miRNAs target genes were significantly enriched in metabolism of xenobiotics by cytochrome P450, bile secretion and terpenoid backbone biosynthesis pathways. CONCLUSIONS The current study reveals a comprehensive expression profile of lncRNAs, miRNAs and mRNAs and implies potential regulatory functions of these RNAs which are involved in the pathogenesis of SLE.
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Affiliation(s)
- Qin Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Yan Liang
- Department of Nephrology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Yuan
- Department of Preventive Medicine, Wannan Medical College, Wuhu, Anhui, China
| | - Si Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Jie-Bing Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Xiao-Mei Li
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Hefei, Anhui, China
| | - Jin-Hui Tao
- Department of Rheumatology and Immunology, Anhui Provincial Hospital, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
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10
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Matta B, Barnes BJ. Coordination between innate immune cells, type I IFNs and IRF5 drives SLE pathogenesis. Cytokine 2019; 132:154731. [PMID: 31130331 DOI: 10.1016/j.cyto.2019.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 05/16/2019] [Accepted: 05/19/2019] [Indexed: 12/18/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease which affects multiple organs. The type I interferon (IFN) gene signature and circulating autoantibodies are hallmarks of SLE. Plasmacytoid dendritic cells (pDCs) are considered the main producers of type I IFN and production is modulated by multiple other immune cell types. In SLE, essentially every immune cell type is dysregulated and aberrant deregulation is thought to be due, in part, to direct or indirect exposure to IFN. Genetic variants within or around the transcription factor interferon regulatory factor 5 (IRF5) associate with SLE risk. Elevated IFNα activity was detected in the sera of SLE patients carrying IRF5 risk polymorphisms who were positive for either anti-RNA binding protein (anti-RBP) or anti-double-stranded DNA (anti-dsDNA) autoantibodies. Neutrophils are also an important source of type I IFNs and are found in abundance in human blood. Neutrophil extracellular traps (NETs) are considered a potential source of antigenic trigger in SLE that can lead to type I IFN gene induction, as well as increased autoantibody production. In this review, we will focus on immune cell types that produce type I IFNs and/or are affected by type I IFN in SLE. In addition, we will discuss potential inducers of endogenous type I IFN production in SLE. Last, we will postulate how the different immune cell populations may be affected by an IRF5-SLE risk haplotype.
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Affiliation(s)
- Bharati Matta
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Betsy J Barnes
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA; Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA.
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11
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Ocampo-Candiani J, Salinas-Santander M, Trevino V, Ortiz-López R, Ocampo-Garza J, Sanchez-Dominguez CN. Evaluation of skin expression profiles of patients with vitiligo treated with narrow-band UVB therapy by targeted RNA-seq. An Bras Dermatol 2019; 93:843-851. [PMID: 30484529 PMCID: PMC6256230 DOI: 10.1590/abd1806-4841.20187589] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 10/20/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Vitiligo is characterized by a lack of pigmentation in the skin. To date, there are no studies that analyze the changes in gene expression in the skin of vitiligo patients in response to narrow-band ultraviolet B (nb-UVB) phototherapy treatment. OBJECTIVE Explore the usefulness of new generation RNA sequencing in the identification of gene expression changes in the skin of vitiligo patients treated with nb-UVB phototherapy. METHODS Four skin biopsies (4mm in diameter) were collected from 45 Mexican vitiligo vulgaris patients, 2 specimens before and 2 after treatment with nb-UVB phototherapy, obtained from pigmented and non-pigmented tissue. RNA extracted from the biopsies was analyzed using the Illumina TruSeq Targeted RNA Expression protocol to study the expression of genes that participate in pathways of skin homeostasis. The 2 groups were compared using Student's t-test and the Mann-Whitney U-test. RESULTS The expression analysis identified differences in 12 genes included in this study after comparing the samples obtained before and after treatment: 5 genes involved in skin pigmentation, 2 genes involved in apoptosis, 2 genes involved in cell survival, 2 genes involved in oxidative stress responses and 1 gene involved in signal transduction mechanisms (p<0.05). STUDY LIMITATIONS The small size of skin biopsies limits the amount of RNA obtained, the number of genes to be analyzed and the use of conventional techniques such as RT-qPCR. CONCLUSION We demonstrated usefulness of new generation RNA sequencing in the identification of gene expression changes, in addition to identifying new targets in the study of vitiligo.
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Affiliation(s)
- Jorge Ocampo-Candiani
- Dermatology Service, Hospital Universitario Dr. José
Eleuterio González, Facultad de Medicina, Universidad Autónoma de
Nuevo León, Nuevo León, México
| | - Mauricio Salinas-Santander
- Department of Investigation, Facultad de Medicina Unidad Saltillo,
Universidad Autónoma de Coahuila, Saltillo, México
| | - Victor Trevino
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de
Monterrey, Tecnológico de Monterrey, México
| | - Rocio Ortiz-López
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de
Monterrey, Tecnológico de Monterrey, México
| | - Jorge Ocampo-Garza
- Dermatology Service, Hospital Universitario Dr. José
Eleuterio González, Facultad de Medicina, Universidad Autónoma de
Nuevo León, Nuevo León, México
| | - Celia Nohemi Sanchez-Dominguez
- Department of Biochemistry and Molecular Medicine, Facultad de
Medicina, Universidad Autónoma de Nuevo León, Nuevo León,
México
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12
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Li X, Islam S, Xiong M, Nsumu NN, Lee MW, Zhang LQ, Ueki Y, Heruth DP, Lei G, Ye SQ. Epigenetic regulation of NfatC1 transcription and osteoclastogenesis by nicotinamide phosphoribosyl transferase in the pathogenesis of arthritis. Cell Death Discov 2019; 5:62. [PMID: 30774990 PMCID: PMC6365567 DOI: 10.1038/s41420-018-0134-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/15/2018] [Accepted: 11/29/2018] [Indexed: 01/17/2023] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) functions in NAD synthesis, apoptosis, and inflammation. Dysregulation of NAMPT has been associated with several inflammatory diseases, including rheumatoid arthritis (RA). The purpose of this study was to investigate NAMPT’s role in arthritis using mouse and cellular models. Collagen-induced arthritis (CIA) in DBA/1J Nampt+/− mice was evaluated by ELISA, micro-CT, and RNA-sequencing (RNA-seq). In vitro Nampt loss-of-function and gain-of-function studies on osteoclastogenesis were examined by TRAP staining, nascent RNA capture, luciferase reporter assays, and ChIP-PCR. Nampt-deficient mice presented with suppressed inflammatory bone destruction and disease progression in a CIA mouse model. Nampt expression was required for the epigenetic regulation of the Nfatc1 promoter and osteoclastogenesis. Finally, RNA-seq identified 690 differentially expressed genes in whole ankle joints which associated (P < 0.05) with Nampt expression and CIA. Selected target was validated by RT-PCR or functional characterization. We have provided evidence that NAMPT functions as a genetic risk factor and a potential therapeutic target to RA.
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Affiliation(s)
- Xuanan Li
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA.,2Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO 64108 USA.,3Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410005 China
| | - Shamima Islam
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA
| | - Min Xiong
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA
| | - Ndona N Nsumu
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA
| | - Mark W Lee
- 4Department of Chemistry, University of Missouri, Columbia, MO 65211 USA
| | - Li Qin Zhang
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA.,2Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO 64108 USA
| | - Yasuyoshi Ueki
- 5Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri-Kansas City, Kansas City, MO 64108 USA
| | - Daniel P Heruth
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA
| | - Guanghua Lei
- 3Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, 410005 China
| | - Shui Qing Ye
- 1Division of Experimental and Translational Genetics, Children's Mercy, Kansas City, MO 64108 USA.,2Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO 64108 USA
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13
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Genetic Versus Non-genetic Drivers of SLE: Implications of IRF5 Dysregulation in Both Roads Leading to SLE. Curr Rheumatol Rep 2019; 21:2. [PMID: 30645688 DOI: 10.1007/s11926-019-0803-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
PURPOSE OF REVIEW Systemic lupus erythematosus (SLE) is characterized by a breakdown of immune tolerance, resulting in inflammation and tissue destruction. While the primary causes of SLE are still obscure, the disorder is highly heritable. Genetic risk variants, on their own, are rarely causal or fully explain disease pathogenesis. We discuss the possibility that IRF5, a SLE susceptibility gene, has both genetic and non-genetic contributions to disease pathogenesis. RECENT FINDINGS Genetic variants within and around IRF5 robustly associate with SLE risk. In SLE blood cells, IRF5 risk variants associate with elevated IRF5 expression and IFN production. Whether the observed increase in expression is due to risk variants or other disease-associated factors is not clear. Data from Irf5-/- mice backcrossed to multiple models of murine lupus support that IRF5's role in disease pathogenesis is non-genetic. Studies of IRF5 expression and function in genotyped healthy donors will address the question of whether IRF5 dysregulation in SLE is driven by genetic or non-genetic factors.
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14
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Thompson CD, Matta B, Barnes BJ. Therapeutic Targeting of IRFs: Pathway-Dependence or Structure-Based? Front Immunol 2018; 9:2622. [PMID: 30515152 PMCID: PMC6255967 DOI: 10.3389/fimmu.2018.02622] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/25/2018] [Indexed: 12/12/2022] Open
Abstract
The interferon regulatory factors (IRFs) are a family of master transcription factors that regulate pathogen-induced innate and acquired immune responses. Aberration(s) in IRF signaling pathways due to infection, genetic predisposition and/or mutation, which can lead to increased expression of type I interferon (IFN) genes, IFN-stimulated genes (ISGs), and other pro-inflammatory cytokines/chemokines, has been linked to the development of numerous diseases, including (but not limited to) autoimmune and cancer. What is currently lacking in the field is an understanding of how best to therapeutically target these transcription factors. Many IRFs are regulated by post-translational modifications downstream of pattern recognition receptors (PRRs) and some of these modifications lead to activation or inhibition. We and others have been able to utilize structural features of the IRFs in order to generate dominant negative mutants that inhibit function. Here, we will review potential therapeutic strategies for targeting all IRFs by using IRF5 as a candidate targeting molecule.
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Affiliation(s)
- Cherrie D Thompson
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Bharati Matta
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Betsy J Barnes
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institute for Medical Research, Manhasset, NY, United States
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15
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Almuttaqi H, Udalova IA. Advances and challenges in targeting IRF5, a key regulator of inflammation. FEBS J 2018; 286:1624-1637. [PMID: 30199605 PMCID: PMC6563445 DOI: 10.1111/febs.14654] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/26/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
Abstract
Interferon regulatory factor 5 (IRF5) belongs to a family of transcription factors, originally implicated in antiviral responses and interferon production. However, studies conducted in different laboratories over the last decade have placed IRF5 as a central regulator of the inflammatory response. It has become clear that IRF5 contributes to the pathogenesis of many inflammatory and autoimmune diseases, such as rheumatoid arthritis, inflammatory bowel disease and systemic lupus erythematosus. Given the role of IRF5 in physiology and disease, IRF5 represents a potential therapeutic target. However, despite a significant interest from the pharmaceutical industry, inhibitors that interfere with the IRF5 pathway remain elusive. Here, we review the advances made by various studies in targeting multiple steps of signalling leading to IRF5 activation with their therapeutic potential, and the possible complications of such strategies are discussed.
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16
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Kaur A, Lee LH, Chow SC, Fang CM. IRF5-mediated immune responses and its implications in immunological disorders. Int Rev Immunol 2018; 37:229-248. [PMID: 29985675 DOI: 10.1080/08830185.2018.1469629] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transcription factors are gene regulators that activate or repress target genes. One family of the transcription factors that have been extensively studied for their crucial role in regulating gene network in the immune system is the interferon regulatory factors (IRFs). IRFs possess a novel turn-helix turn motif that recognizes a specific DNA consensus found in the promoters of many genes that are involved in immune responses. IRF5, a member of IRFs has recently gained much attention for its role in regulating inflammatory responses and autoimmune diseases. Here, we discuss the role of IRF5 in regulating immune cells functions and how the dysregulation of IRF5 contributes to the pathogenesis of immune disorders. We also review the latest findings of potential IRF5 inhibitors that modulate IRF5 activity in the effort of developing therapeutic approaches for treating inflammatory disorders.
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Affiliation(s)
- Ashwinder Kaur
- a School of Pharmacy, Faculty of Science , The University of Nottingham Malaysia Campus , Selangor Darul , Ehsan , Malaysia
| | - Learn-Han Lee
- c School of Pharmacy , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia.,e Jeffrey Cheah School of Medicine and Health Sciences , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia
| | - Sek-Chuen Chow
- d School of Science , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia
| | - Chee-Mun Fang
- b Department of Biomedical Sciences, Faculty of Science , The University of Nottingham Malaysia Campus , Selangor Darul , Ehsan , Malaysia
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17
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Laufer VA, Chen JY, Langefeld CD, Bridges SL. Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases. Rheum Dis Clin North Am 2018; 43:449-466. [PMID: 28711145 DOI: 10.1016/j.rdc.2017.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses. We illustrate how analyses of large datasets provide hope for improved approaches to the diagnosis, treatment, and prevention of rheumatic diseases.
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Affiliation(s)
- Vincent A Laufer
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, SHEL 236, Birmingham, AL 35294-2182, USA
| | - Jake Y Chen
- The Informatics Institute, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, THT 137, Birmingham, AL 35294-0006, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA; Public Health Genomics, Division of Public Health Sciences, Department of Biostatistical Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, School of Medicine, University of Alabama at Birmingham, 1720 2nd Avenue South, SHEL 178, Birmingham, AL 35294-2182, USA.
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18
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Salinas-Santander M, Trevino V, De la Rosa-Moreno E, Verduzco-Garza B, Sánchez-Domínguez CN, Cantú-Salinas C, Ocampo-Garza J, Lagos-Rodríguez A, Ocampo-Candiani J, Ortiz-López R. CAPN3, DCT, MLANA and TYRP1 are overexpressed in skin of vitiligo vulgaris Mexican patients. Exp Ther Med 2018; 15:2804-2811. [PMID: 29456684 PMCID: PMC5795480 DOI: 10.3892/etm.2018.5764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/05/2018] [Indexed: 12/18/2022] Open
Abstract
Vitiligo is a disorder causing skin depigmentation, in which several factors have been proposed for its pathogenesis: Environmental, genetic and biological aspects of melanocytes, even those of the surrounding keratinocytes. However, the lack of understanding of the mechanisms has complicated the task of predicting the development and progression. The present study used microarray analysis to characterize the transcriptional profile of skin from Vitiligo Vulgaris (VV) patients and the identified transcripts were validated using targeted high-throughput RNA sequencing in a broader set of patients. For microarrays, mRNA was taken from 20 skin biopsies of 10 patients with VV (pigmented and depigmented skin biopsy of each), and 5 biopsies of healthy subjects matched for age and sex were used as a control. A signature was identified that contains the expression pattern of 722 genes between depigmented vitiligo skin vs. healthy control, 1,108 between the pigmented skin of vitiligo vs. healthy controls and 1,927 between pigmented skin, depigmented vitiligo and healthy controls (P<0.05; false discovery rate, <0.1). When comparing the pigmented and depigmented skin of patients with vitiligo, which reflects the real difference between both skin types, 5 differentially expressed genes were identified and further validated in 45 additional VV patients by RNA sequencing. This analysis showed significantly higher RNA levels of calpain-3, dopachrome tautomerase, melan-A and tyrosinase-related protein-1 genes. The data revealed that the pigmented skin of vitiligo is already affected at the level of gene expression and that the main differences between pigmented and non-pigmented skin are explained by the expression of genes associated with pigment metabolism.
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Affiliation(s)
- Mauricio Salinas-Santander
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México.,Departamento de Investigación, Facultad de Medicina Unidad Saltillo, Universidad Autónoma de Coahuila, Saltillo, Coahuila 25000, México
| | - Víctor Trevino
- Grupo de Investigación en Bioinformática, Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
| | - Eduardo De la Rosa-Moreno
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Bárbara Verduzco-Garza
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México
| | - Celia N Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Universidad Autónoma de Nuevo León, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Cristina Cantú-Salinas
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Garza
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Armando Lagos-Rodríguez
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Jorge Ocampo-Candiani
- Servicio de Dermatología, Universidad Autónoma de Nuevo León, Hospital Universitario Dr. José Eleuterio González, Facultad de Medicina, Monterrey, Nuevo León 64460, México
| | - Rocio Ortiz-López
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León 64460, México.,Escuela de Medicina, Tecnológico de Monterrey, Monterrey, Nuevo León 64849, México
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19
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Corrected and Republished from: The COP9 Signalosome Interacts with and Regulates Interferon Regulatory Factor 5 Protein Stability. Mol Cell Biol 2018; 38:38/3/e00493-17. [PMID: 29339435 DOI: 10.1128/mcb.00493-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/17/2017] [Indexed: 11/20/2022] Open
Abstract
The transcription factor interferon regulatory factor 5 (IRF5) exerts crucial functions in the regulation of host immunity against extracellular pathogens, DNA damage-induced apoptosis, death receptor signaling, and macrophage polarization. Tight regulation of IRF5 is thus warranted for an efficient response to extracellular stressors and for limiting autoimmune and inflammatory responses. Here we report that the COP9 signalosome (CSN), a general modulator of diverse cellular and developmental processes, associates constitutively with IRF5 and promotes its protein stability. The constitutive CSN/IRF5 interaction was identified using proteomics and confirmed by endogenous immunoprecipitations. The CSN/IRF5 interaction occurred on the carboxyl and amino termini of IRF5; a single internal deletion (Δ455-466) was found to significantly reduce IRF5 protein stability. CSN3 was identified as a direct interacting partner of IRF5, and knockdown of this subunit with small interfering RNAs (siRNAs) resulted in enhanced degradation. Degradation was further augmented by knockdown of CSN1 and CSN3 together. The ubiquitin E1 inhibitor UBEI-41 or the proteasome inhibitor MG132 prevented IRF5 degradation, supporting that its stability is regulated by the ubiquitin-proteasome system. Importantly, activation of IRF5 by the death receptor ligand tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) resulted in enhanced degradation via loss of the CSN/IRF5 interaction. This study defines the CSN as a new interacting partner of IRF5 that controls its stability.
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20
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Banchereau R, Cepika AM, Banchereau J, Pascual V. Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics. Annu Rev Immunol 2017; 35:337-370. [PMID: 28142321 PMCID: PMC5937945 DOI: 10.1146/annurev-immunol-051116-052225] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.
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Affiliation(s)
| | | | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030;
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Dallas, Texas 75204; , ,
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21
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Microarray to deep sequencing: transcriptome and miRNA profiling to elucidate molecular pathways in systemic lupus erythematosus. Immunol Res 2016; 64:14-24. [PMID: 26188428 DOI: 10.1007/s12026-015-8672-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with diverse clinical manifestations and autoantibody repertoires. The etiology of SLE is multifactorial involving genetic, epigenetic and environmental factors. This complexity leads to poor prognosis, which poses major challenges in the treatment of SLE. Understanding the complex genetic pathways and regulatory mechanisms operative in SLE was feasible by utilizing several highly efficient molecular biological tools during the past few years. In this perspective, DNA microarray technology offered a high-throughput platform in unraveling SLE-associated genes. Additionally, extensive microarray analysis had demonstrated aberrant DNA methylation pattern and differential microRNAs, thus contributing to the knowledge of epigenetic modulators and posttranscriptional regulatory machinery in SLE. It was through the aid of these technologies that interferon signature was identified as an important contributor in SLE pathogenesis along with dysregulation of cytokine-, chemokine- and apoptosis-related genes. The emergence of next-generation sequencing technologies such as RNA sequencing has added new dimensions in understanding the dynamics of the disease processes. Compared with microarrays, deep sequencing has provided higher resolution in gene expression measurement along with identification of different splicing events, noncoding RNAs and novel loci in SLE. The focus, therefore, has now been shifted toward the identification of novel gene loci and their isoforms, and their implication in disease pathogenesis. This advancement in the technology from microarray to deep sequencing has helped in deciphering the molecular pathways involved in pathogenesis of SLE and opens new avenues to develop novel treatment strategies for SLE.
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22
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Specific detection of interferon regulatory factor 5 (IRF5): A case of antibody inequality. Sci Rep 2016; 6:31002. [PMID: 27481535 PMCID: PMC4969615 DOI: 10.1038/srep31002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Interferon regulatory factor 5 (IRF5) is a member of the IRF family of transcription factors. IRF5 was first identified and characterized as a transcriptional regulator of type I interferon expression after virus infection. In addition to its critical role(s) in the regulation and development of host immunity, subsequent studies revealed important roles for IRF5 in autoimmunity, cancer, obesity, pain, cardiovascular disease, and metabolism. Based on these important disease-related findings, a large number of commercial antibodies have become available to study the expression and function of IRF5. Here we validate a number of these antibodies for the detection of IRF5 by immunoblot, flow cytometry, and immunofluorescence or immunohistochemistry using well-established positive and negative controls. Somewhat surprising, the majority of commercial antibodies tested were unable to specifically recognize human or mouse IRF5. We present data on antibodies that do specifically recognize human or mouse IRF5 in a particular application. These findings reiterate the importance of proper controls and molecular weight standards for the analysis of protein expression. Given that dysregulated IRF5 expression has been implicated in the pathogenesis of numerous diseases, including autoimmune and cancer, results indicate that caution should be used in the evaluation and interpretation of IRF5 expression analysis.
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Abstract
Interferon regulatory factor 5 (IRF5) has been demonstrated as a key transcription factor of the immune system, playing important roles in modulating inflammatory immune responses in numerous cell types including dendritic cells, macrophages, and B cells. As well as driving the expression of type I interferon in antiviral responses, IRF5 is also crucial for driving macrophages toward a proinflammatory phenotype by regulating cytokine and chemokine expression and modulating B-cell maturity and antibody production. This review highlights the functional importance of IRF5 in a disease setting, by discussing polymorphic mutations at the human Irf5 locus that lead to susceptibility to systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease. In concordance with this, we also discuss lessons in IRF5 functionality learned from murine in vivo models of autoimmune disease and inflammation and hypothesize that modulation of IRF5 activity and expression could provide potential therapeutic benefits in the clinic.
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Affiliation(s)
- Hayley L Eames
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.
| | - Alastair L Corbin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.
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Wiley GB, Kelly JA, Gaffney PM. Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease. Arthritis Res Ther 2015; 16:490. [PMID: 25789374 PMCID: PMC4396863 DOI: 10.1186/s13075-014-0490-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Next-generation DNA sequencing has revolutionized the field of genetics and genomics, providing researchers with the tools to efficiently identify novel rare and low frequency risk variants, which was not practical with previously available methodologies. These methods allow for the sequence capture of a specific locus or small genetic region all the way up to the entire six billion base pairs of the diploid human genome. Rheumatic diseases are a huge burden on the US population, affecting more than 46 million Americans. Those afflicted suffer from one or more of the more than 100 diseases characterized by inflammation and loss of function, mainly of the joints, tendons, ligaments, bones, and muscles. While genetics studies of many of these diseases (for example, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease) have had major successes in defining their genetic architecture, causal alleles and rare variants have still been elusive. This review describes the current high-throughput DNA sequencing methodologies commercially available and their application to rheumatic diseases in both case–control as well as family-based studies.
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25
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Ma Y, Shi N, Li M, Chen F, Niu H. Applications of Next-generation Sequencing in Systemic Autoimmune Diseases. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:242-9. [PMID: 26432094 PMCID: PMC4610970 DOI: 10.1016/j.gpb.2015.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/04/2015] [Accepted: 09/14/2015] [Indexed: 12/14/2022]
Abstract
Systemic autoimmune diseases are a group of heterogeneous disorders caused by both genetic and environmental factors. Although numerous causal genes have been identified by genome-wide association studies (GWAS), these susceptibility genes are correlated to a relatively low disease risk, indicating that environmental factors also play an important role in the pathogenesis of disease. The intestinal microbiome, as the main symbiotic ecosystem between the host and host-associated microorganisms, has been demonstrated to regulate the development of the body’s immune system and is likely related to genetic mutations in systemic autoimmune diseases. Next-generation sequencing (NGS) technology, with high-throughput capacity and accuracy, provides a powerful tool to discover genomic mutations, abnormal transcription and intestinal microbiome identification for autoimmune diseases. In this review, we briefly outlined the applications of NGS in systemic autoimmune diseases. This review may provide a reference for future studies in the pathogenesis of systemic autoimmune diseases.
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Affiliation(s)
- Yiyangzi Ma
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China
| | - Na Shi
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Beijing 100730, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Niu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China.
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26
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Giannopoulou EG, Elemento O, Ivashkiv LB. Use of RNA sequencing to evaluate rheumatic disease patients. Arthritis Res Ther 2015; 17:167. [PMID: 26126608 PMCID: PMC4488125 DOI: 10.1186/s13075-015-0677-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the detection of non-coding transcripts and alternative splicing events. In this review, we describe how RNA sequencing enables unbiased interrogation of the abundance and complexity of the transcriptome, and present a typical experimental workflow and bioinformatics tools that are often used for RNA sequencing analysis. We also discuss different uses of this next-generation sequencing technology to evaluate rheumatic disease patients and investigate the pathogenesis of rheumatic diseases such as rheumatoid arthritis, systemic lupus erythematosus, juvenile idiopathic arthritis and Sjögren’s syndrome.
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Affiliation(s)
- Eugenia G Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, 11201, USA. .,Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10021, USA.
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program and the David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, 10021, USA.
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27
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Development of a T7 Phage Display Library to Detect Sarcoidosis and Tuberculosis by a Panel of Novel Antigens. EBioMedicine 2015; 2:341-350. [PMID: 26086036 PMCID: PMC4465182 DOI: 10.1016/j.ebiom.2015.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sarcoidosis is a granulomatous inflammatory disease, diagnosed through tissue biopsy of involved organs in the absence of other causes such as tuberculosis (TB). No specific serologic test is available to diagnose and differentiate sarcoidosis from TB. Using a high throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This complex cDNA library was biopanned to obtain 1152 potential sarcoidosis antigens and a microarray was constructed to immunoscreen two different sets of sera from healthy controls and sarcoidosis. Meta-analysis identified 259 discriminating sarcoidosis antigens, and multivariate analysis identified 32 antigens with a sensitivity of 89% and a specificity of 83% to classify sarcoidosis from healthy controls. Additionally, interrogating the same microarray platform with sera from subjects with TB, we identified 50 clones that distinguish between TB, sarcoidosis and healthy controls. The top 10 sarcoidosis and TB specific clones were sequenced and homologies were searched in the public database revealing unique epitopes and mimotopes in each group. Here, we show for the first time that immunoscreenings of a library derived from sarcoidosis tissue differentiates between sarcoidosis and tuberculosis antigens. These novel biomarkers can improve diagnosis of sarcoidosis and TB, and may aid to develop or evaluate a TB vaccine. Immunity plays a major role in a vast array of human diseases. Sarcoidosis shares similarities with non-infectious and infectious granulomatous diseases, including tuberculosis. A highly sensitive and specific T7 phage library discriminates the immune signature between sarcoidosis patients and TB.
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28
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Berggren O, Alexsson A, Morris DL, Tandre K, Weber G, Vyse TJ, Syvanen AC, Ronnblom L, Eloranta ML. IFN- production by plasmacytoid dendritic cell associations with polymorphisms in gene loci related to autoimmune and inflammatory diseases. Hum Mol Genet 2015; 24:3571-81. [DOI: 10.1093/hmg/ddv095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/12/2015] [Indexed: 12/12/2022] Open
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29
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Pawar RD, Goilav B, Xia Y, Zhuang H, Herlitz L, Reeves WH, Putterman C. Serum autoantibodies in pristane induced lupus are regulated by neutrophil gelatinase associated lipocalin. Clin Immunol 2014; 154:49-65. [PMID: 24971701 PMCID: PMC4119527 DOI: 10.1016/j.clim.2014.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 11/28/2022]
Abstract
The onset of autoantibodies in systemic autoimmunity can be the result of a breakdown in tolerance at multiple checkpoints. Genetic, hormonal, and immunological factors can combine with environmental influences to accelerate the onset of disease and aggravate disease outcome. Here, we describe a novel mechanism relating to the regulatory role of Neutrophil Gelatinase Associated Lipocalin (NGAL) in modulating the levels of autoantibodies in pristane induced lupus. Following a single injection of pristane intraperitoneally, NGAL expression was induced in both the serum and spleen. Furthermore, NGAL deficient mice were more susceptible to the induction of pristane stimulated autoimmunity, and displayed higher numbers of autoantibody secreting cells and increased expression of activation induced cytidine deaminase (AID) and other inflammatory mediators in the spleen. In contrast, kidney damage was milder in NGAL deficient mice, indicating that NGAL was detrimental in autoantibody mediated kidney disease. These studies indicate that NGAL plays differential roles in different tissues in the context of lupus, and suggest a previously unrecognized role for NGAL in adaptive immunity.
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Affiliation(s)
- Rahul D Pawar
- The Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Beatrice Goilav
- The Division of Pediatric Nephrology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yumin Xia
- The Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Haoyang Zhuang
- The Division of Rheumatology & Clinical Immunology, University of Florida, Gainesville, FL 32611, USA
| | - Leal Herlitz
- The Department of Pathology, Columbia University Medical Center, NY 10032, USA
| | - Westley H Reeves
- The Division of Rheumatology & Clinical Immunology, University of Florida, Gainesville, FL 32611, USA
| | - Chaim Putterman
- The Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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30
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TRIpartite motif 21 (TRIM21) differentially regulates the stability of interferon regulatory factor 5 (IRF5) isoforms. PLoS One 2014; 9:e103609. [PMID: 25084355 PMCID: PMC4118895 DOI: 10.1371/journal.pone.0103609] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
IRF5 is a member of the Interferon Regulatory Factor (IRF) family of transcription factors activated downstream of the Toll-Like receptors (TLRs). Polymorphisms in IRF5 have been shown to be associated with the autoimmune disease Systemic Lupus Erythematosus (SLE) and other autoimmune conditions, suggesting a central role for IRF5 in the regulation of the immune response. Four different IRF5 isoforms originate due to alternative splicing and to the presence or absence of a 30 nucleotide insertion in IRF5 exon 6. Since the polymorphic region disturbs a PEST domain, a region associated with protein degradation, we hypothesized that the isoforms bearing the insertion might have increased stability, thus explaining the association of individual IRF5 isoforms with SLE. As the E3 ubiquitin ligase TRIpartite Motif 21 (TRIM21) has been shown to regulate the stability and hence activity of members of the IRF family, we investigated whether IRF5 is subjected to regulation by TRIM21 and whether dysregulation of this mechanism could explain the association of IRF5 with SLE. Our results show that IRF5 is degraded following TLR7 activation and that TRIM21 is involved in this process. Comparison of the individual IRF5 variants demonstrates that isoforms generated by alternative splicing are resistant to TRIM21-mediated degradation following TLR7 stimulation, thus providing a functional link between isoforms expression and stability/activity which contributes to explain the association of IRF5 with SLE.
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31
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McInnis EA, Badhwar AK, Muthigi A, Lardinois OM, Allred SC, Yang J, Free ME, Jennette JC, Preston GA, Falk RJ, Ciavatta DJ. Dysregulation of autoantigen genes in ANCA-associated vasculitis involves alternative transcripts and new protein synthesis. J Am Soc Nephrol 2014; 26:390-9. [PMID: 25060059 DOI: 10.1681/asn.2013101092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Proteinase 3 (PR3) and myeloperoxidase (MPO) are two major autoantigens in patients with vasculitis with ANCA. The genes encoding these autoantigens are abnormally expressed in peripheral granulocytes of patients with active ANCA-associated vasculitis. This study provides evidence that this transcriptional dysregulation results in a variety of mRNA processing events from the PRTN3 gene locus. In addition to elevated levels of PR3 message, leukocyte RNA from patients contained PR3 transcripts with an alternative 3' untranslated region. Furthermore, we detected usage of an alternative transcription start site within intron 1 of the PRTN3 gene locus that coincided with active disease (odds ratio, 3.3; 95% confidence interval, 1.3 to 8.4; P=0.01). This promoter may be developmentally regulated, because it was active in normal human bone marrow, multiple leukemia cell lines, MCF-7 cells, and subjects after GM-CSF treatment but not subjects with a neutrophil left shift. This transcript, which lacks exon 1 of PRTN3, encodes a 24-kD protein (p24(PR3/MBN)) with a sequence similar to that previously described for myeloblastin. Notably, PR3, p24(PR3/MBN), and MPO were synthesized in cultured neutrophils from patients with active ANCA-associated vasculitis, indicating that increased transcription results in newly synthesized autoantigens in peripheral neutrophils of patients. The synthesis of p24(PR3/MBN) seems to expand the autoantigen repertoire, because immunoblots showed that sera from patients recognized p24(PR3/MBN). These findings emphasize the importance of transcriptional dysregulation of the autoantigen in autoimmune disease.
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Affiliation(s)
- Elizabeth A McInnis
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Anshul K Badhwar
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Akhil Muthigi
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Olivier M Lardinois
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - S Colby Allred
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Jiajin Yang
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Meghan E Free
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - J Charles Jennette
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and Departments of Pathology and Laboratory Medicine and
| | - Gloria A Preston
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Ronald J Falk
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and
| | - Dominic J Ciavatta
- University of North Carolina Kidney Center, Division of Nephrology and Hypertension, Department of Medicine and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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32
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Sorrentino R. Reprint of "genetics of autoimmunity: an update". Immunol Lett 2014; 161:196-9. [PMID: 25023136 DOI: 10.1016/j.imlet.2014.07.001] [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: 10/22/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 11/27/2022]
Abstract
The advent of genome-wide association studies (GWAS) has produced tremendous insights into the genetics of immune-mediated diseases allowing to identify hundreds of associated variants, some of which disease-specific and some others shared by groups of diseases. However, each variant usually accounts for a small genetic risk and all together they explain a relatively small portion of heritability for each disease. In addition, many of the associated variants map in regions of still undisclosed functions. This opens up to a new era of studies in search of the "missing heritability" which might partially be explained by gene-gene interactions and/or additive effects impacting on biochemical pathways relevant for the disease pathogenesis. The introduction of the immunochip analysis that allows to analyze thousands of patients for variations more strictly correlated with the immune/inflammatory functions is now allowing to single out relevant pathways shared by different diseases. Finally, great expectations are brought about from the studies on the effects that epigenetic modifications can have on the tuning of the expression of single allele/s in myeloid cells as well as in target tissues. Some of these topics have been discussed at the 15th International Congress of Immunology.
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Affiliation(s)
- Rosa Sorrentino
- Department of Biology and Biotechnology "Charles Darwin" and Istituto Pasteur-Cenci Bolognetti, Sapienza University, Rome, Italy.
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33
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Lazzari E, Jefferies CA. IRF5-mediated signaling and implications for SLE. Clin Immunol 2014; 153:343-52. [PMID: 24928322 DOI: 10.1016/j.clim.2014.06.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/12/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
Transcription of the type I IFN genes is regulated by members of the Interferon Regulatory Factor (IRF) family of transcription factors, composed in humans of 9 distinct proteins. In addition to IRF3 and IRF7, the transcription factor IRF5 has been shown to be involved in type I IFN production and interestingly, polymorphisms of the IRF5 gene in humans can result in risk or protective haplotypes with regard to SLE susceptibility. In addition to regulation of type I IFN expression, IRF5 is involved in other signaling pathways, including IgG switching in B cells, macrophage polarization and apoptosis, and its role in SLE pathogenesis may therefore not be limited to dysregulated control of IFN expression. In this review we will comprehensively discuss the role of IRF5 in immune-mediated responses and its potential multifaceted role in conferring SLE susceptibility.
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Affiliation(s)
- Elisa Lazzari
- Molecular and Cellular Therapeutics, Research Institute, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland.
| | - Caroline A Jefferies
- Molecular and Cellular Therapeutics, Research Institute, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, Ireland.
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34
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B cell transcription factors: Potential new therapeutic targets for SLE. Clin Immunol 2014; 152:140-51. [DOI: 10.1016/j.clim.2014.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 02/06/2023]
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35
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J DAS, C A, P SG, S C. Systemic Lupus Erythematosus: Old and New Susceptibility Genes versus Clinical Manifestations. Curr Genomics 2014; 15:52-65. [PMID: 24653663 PMCID: PMC3958959 DOI: 10.2174/138920291501140306113715] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is one of the most relevant world-wide autoimmune disorders. The formation of autoantibodies and the deposition of antibody-containing immune complexes in blood vessels throughout the body is the main pathogenic mechanism of SLE leading to heterogeneous clinical manifestations and target tissue damage. The complexity of etiology and pathogenesis in SLE, enclosing genetic and environmental factors, apparently is one of the greatest challenges for both researchers and clinicians. Strong indications for a genetic background in SLE come from studies in families as well as in monozygotic and dizygotic twins, discovering several SLE-associated loci and genes (e.g. IRF5, PTPN22, CTLA4, STAT4 and BANK1). As SLE has a complex genetic background, none of these genes is likely to be entirely responsible for triggering autoimmune response in SLE even if they disclosure a potentially novel molecular mechanisms in the pathogenesis' disease. The clinical manifestations and disease severity varies greatly among patients, thus several studies try to associate clinical heterogeneity and prognosis with specific genetic polymorphisms in SLE associated genes. The continue effort to describe new predisposing or modulating genes in SLE is justified by the limited knowledge about the pathogenesis, assorted clinical manifestation and the possible prevention strategies. In this review we describe newly discovered, as well as the most studied genes associated to SLE susceptibility, and relate them to clinical manifestations of the disease.
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Affiliation(s)
- De Azevêdo Silva J
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Addobbati C
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco, Recife, Pernambuco, Brazil ; Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Sandrin-Garcia P
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco, Recife, Pernambuco, Brazil ; Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Crovella S
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco, Recife, Pernambuco, Brazil ; Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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36
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Genetics of autoimmunity: an update. Immunol Lett 2013; 158:116-9. [PMID: 24370643 DOI: 10.1016/j.imlet.2013.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 01/12/2023]
Abstract
The advent of genome-wide association studies (GWAS) has produced tremendous insights into the genetics of immune-mediated diseases allowing to identify hundreds of associated variants, some of which disease-specific and some others shared by groups of diseases. However, each variant usually accounts for a small genetic risk and all together they explain a relatively small portion of heritability for each disease. In addition, many of the associated variants map in regions of still undisclosed functions. This opens up to a new era of studies in search of the "missing heritability" which might partially be explained by gene-gene interactions and/or additive effects impacting on biochemical pathways relevant for the disease pathogenesis. The introduction of the immunochip analysis that allows to analyze thousands of patients for variations more strictly correlated with the immune/inflammatory functions is now allowing to single out relevant pathways shared by different diseases. Finally, great expectations are brought about from the studies on the effects that epigenetic modifications can have on the tuning of the expression of single allele/s in myeloid cells as well as in target tissues. Some of these topics have been discussed at the 15th International Congress of Immunology.
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37
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Frangou EA, Bertsias GK, Boumpas DT. Gene expression and regulation in systemic lupus erythematosus. Eur J Clin Invest 2013; 43:1084-96. [PMID: 23902282 DOI: 10.1111/eci.12130] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/21/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease. Genome-wide (GW) association studies have identified more than 40 disease-associated loci, together accounting for only 10-20% of disease heritability. Gene expression represents the intermediate phenotype between DNA and disease phenotypic variation, and provides insights regarding genetic and epigenetic effects. We review data on gene expression and regulation in SLE by our group and other investigators. MATERIALS AND METHODS Systematic PubMed search for GW expression studies in SLE published since the year 2000. RESULTS Deregulation of genes involved in type I interferon signaling is a consistent finding in the peripheral blood of active and severe SLE patients. Upregulation of granulocyte-specific transcripts especially in bone marrow mononuclear cells (BMMCs), and of myeloid lineage transcripts in lupus nephritis, provide evidence for pathogenic role of these cells. Gene network analysis in BMMCs identified central gene regulators which could represent therapeutic targets and a high similarity between SLE and non-Hodgkin lymphoma providing a molecular basis for the reported association of the two diseases. Gene expression abnormalities driven by deregulated expression of certain microRNAs in SLE contribute to interferon production, T- and B-cell hyperactivity, DNA hypomethylation, and defective tissue response to injury. Methylation arrays have revealed alterations in white blood cell DNA methylation in SLE suggesting an important role of epigenetics and the environment. CONCLUSIONS Gene expression studies have contributed to the characterization of pathogenic processes in SLE. Integrated approaches utilizing genetic variation, transcriptome and epigenome profiling will facilitate efforts towards a molecular-based disease taxonomy.
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Affiliation(s)
- Eleni A Frangou
- Biomedical Research Foundation of the Academy of Athens, Medical School of National and Kapodistrian University of Athens, Athens, Greece
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38
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Banchereau R, Cepika AM, Pascual V. Systems approaches to human autoimmune diseases. Curr Opin Immunol 2013; 25:598-605. [PMID: 24055331 DOI: 10.1016/j.coi.2013.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/22/2013] [Indexed: 02/06/2023]
Abstract
Systemic autoimmune diseases result from interactions between genes and environmental triggers that lead to dysregulation of both innate and adaptive immunity. Systems biology approaches enable the global characterization of complex systems at the DNA, RNA and protein levels. Recent technological breakthroughs such as deep sequencing or high-throughput proteomics are revealing novel inflammatory pathways involved in autoimmunity. Herein, we review recent developments, challenges and promising avenues in the use of systems approaches to understand human systemic autoimmune and autoinflammatory diseases.
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Affiliation(s)
- Romain Banchereau
- Baylor Institute for Immunology Research, 3434 Live Oak, Dallas, TX 75204, USA
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39
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The COP9 signalosome interacts with and regulates interferon regulatory factor 5 protein stability. Mol Cell Biol 2012; 33:1124-38. [PMID: 23275442 DOI: 10.1128/mcb.00802-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The transcription factor interferon regulatory factor 5 (IRF5) exerts crucial functions in the regulation of host immunity against extracellular pathogens, DNA damage-induced apoptosis, death receptor signaling, and macrophage polarization. Tight regulation of IRF5 is thus warranted for an efficient response toward extracellular stressors and for limiting autoimmune and inflammatory responses. Here we report that the COP9 signalosome (CSN), a general modulator of diverse cellular and developmental processes, associates constitutively with IRF5 and promotes its protein stability. The constitutive CSN/IRF5 interaction was identified using proteomics and confirmed by endogenous immunoprecipitations. The CSN/IRF5 interaction occurred on the carboxyl and amino termini of IRF5; a single internal deletion from amino acids 455 to 466 (Δ455-466) was found to significantly reduce IRF5 protein stability. CSN subunit 3 (CSN3) was identified as a direct interacting partner of IRF5, and knockdown of this subunit with small interfering RNAs resulted in enhanced degradation. Degradation was further augmented by knockdown of CSN1 and CSN3 together. The ubiquitin E1 inhibitor UBEI-41 or the proteasome inhibitor MG132 prevented IRF5 degradation, supporting the idea that its stability is regulated by the ubiquitin-proteasome system. Importantly, activation of IRF5 by the death receptor ligand tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) resulted in enhanced degradation via loss of the CSN/IRF5 interaction. This study defines CSN to be a new interacting partner of IRF5 that controls its stability.
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