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Asgari N, Ghaemi EA, Naeimi MH, Tahamtan A, Sechi LA, Zamani S. Cross-reactivity between Mycobacterium avium subspecies paratuberculosis 4027 peptide and Human IRF5 may contribute to Multiple Sclerosis in Iranian patients. Heliyon 2023; 9:e22137. [PMID: 38034802 PMCID: PMC10686849 DOI: 10.1016/j.heliyon.2023.e22137] [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: 05/18/2023] [Revised: 10/21/2023] [Accepted: 11/05/2023] [Indexed: 12/02/2023] Open
Abstract
Background The etiology of Multiple sclerosis (MS) is complicated and can be affected by several environmental factors, such as Mycobacterium avium subspecies paratuberculosis (MAP) infection in genetically predisposed individuals. The link between MAP and MS depends on host genetic and epigenetic aspects and population-based features that require further investigation. We aimed to study the possible role of MAP in triggering MS using molecular and serological methods. Materials and methods This case-control study examined 200 blood samples (100 MS patients and 100 HCs) to search for the MAP-specific IS900 gene. In addition, ELISA was conducted to determine the humoral response against MAP_402718-32 and its human IRF5424-434 peptide homolog. Results The frequency of MAP detection based on the molecular method in MS patients and HCs was 48 % and 13 %, respectively (p < 0.0001). The presence of antibodies against MAP_402718-32 and IRF5424-434 was 55 % and 65 % in MS patients versus 9 % and 7 % in HCs, respectively (p < 0.0001). A good correlation was observed between MAP_4027 and IRF5 antibodies (r = 0.5782, p < 0.0001), indicating that the same antibodies recognized common peptide epitopes. Conclusion Our research revealed a significant association between MAP and MS, highlighting the possible role of MAP as an important infection trigger factor of MS. It is hypothesized that cross-reactivity between MAP4027 and IRF5 may dysregulate immune homeostasis.
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Affiliation(s)
- Negar Asgari
- Neuroscience Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ezzat Allah Ghaemi
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Hasan Naeimi
- Department of Neurology, Sayyad Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alireza Tahamtan
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Leonardo Antonio Sechi
- Azienda Ospedaliera Universitaria, Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100, Sassari, Italy
| | - Samin Zamani
- Neuroscience Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
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2
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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3
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Gokhale NS, Smith JR, Van Gelder RD, Savan R. RNA regulatory mechanisms that control antiviral innate immunity. Immunol Rev 2021; 304:77-96. [PMID: 34405416 DOI: 10.1111/imr.13019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022]
Abstract
From the initial sensing of viral nucleotides by pattern recognition receptors, through the induction of type I and III interferons (IFN), upregulation of antiviral effector proteins, and resolution of the inflammatory response, each step of innate immune signaling is under tight control. Though innate immunity is often associated with broad regulation at the level of gene transcription, RNA-centric post-transcriptional processes have emerged as critical mechanisms for ensuring a proper antiviral response. Here, we explore the diverse RNA regulatory mechanisms that modulate the innate antiviral immune response, with a focus on RNA sensing by RIG-I-like receptors (RLR), interferon (IFN) and IFN signaling pathways, viral pathogenesis, and host genetic variation that contributes to these processes. We address the post-transcriptional interactions with RNA-binding proteins, non-coding RNAs, transcript elements, and modifications that control mRNA stability, as well as alternative splicing events that modulate the innate immune antiviral response.
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Affiliation(s)
- Nandan S Gokhale
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Julian R Smith
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Rachel D Van Gelder
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
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4
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Dukhinova M, Kokinos E, Kuchur P, Komissarov A, Shtro A. Macrophage-derived cytokines in pneumonia: Linking cellular immunology and genetics. Cytokine Growth Factor Rev 2020; 59:46-61. [PMID: 33342718 PMCID: PMC8035975 DOI: 10.1016/j.cytogfr.2020.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Macrophages represent the first line of anti-pathogen defense - they encounter invading pathogens to perform the phagocytic activity, to deliver the plethora of pro- and anti-inflammatory cytokines, and to shape the tissue microenvironment. Throughout pneumonia course, alveolar macrophages and infiltrated blood monocytes produce increasing cytokine amounts, which activates the antiviral/antibacterial immunity but can also provoke the risk of the so-called cytokine “storm” and normal tissue damage. Subsequently, the question of how the cytokine spectrum is shaped and balanced in the pneumonia context remains a hot topic in medical immunology, particularly in the COVID19 pandemic era. The diversity in cytokine profiles, involved in pneumonia pathogenesis, is determined by the variations in cytokine-receptor interactions, which may lead to severe cytokine storm and functional decline of particular tissues and organs, for example, cardiovascular and respiratory systems. Cytokines and their receptors form unique profiles in individual patients, depending on the (a) microenvironmental context (comorbidities and associated treatment), (b) lung monocyte heterogeneity, and (c) genetic variations. These multidisciplinary strategies can be proactively considered beforehand and during the pneumonia course and potentially allow the new age of personalized immunotherapy.
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Affiliation(s)
- Marina Dukhinova
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia.
| | - Elena Kokinos
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Polina Kuchur
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Alexey Komissarov
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia
| | - Anna Shtro
- International Institute "Solution Chemistry of Advanced Materials and Technology", ITMO University, St. Petersburg, Russia; Department of Chemotherapy, Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
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5
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Correlations of Expression Levels of a Panel of Genes ( IRF5, STAT4, TNFSF4, MECP2, and TLR7) and Cytokine Levels (IL-2, IL-6, IL-10, IL-12, IFN- γ, and TNF- α) with Systemic Lupus Erythematosus Outcomes in Jordanian Patients. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1703842. [PMID: 31871930 PMCID: PMC6907047 DOI: 10.1155/2019/1703842] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022]
Abstract
Systemic lupus erythematosus (SLE) is characterized by systemic end-organ damage. We investigated the involvement of IRF5, TLR-7, MECP2, STAT4, and TNFSF4 genes and TNF-α, IFN-γ, IL-2, IL-12, IL-6, and IL-10 cytokines in SLE pathogenesis and in organ damage in Jordanian patients. Blood was collected from 51 patients and 50 controls. Expression levels of SLE genes in PBMCs and cytokine levels were determined using RT-PCR and ELISA, respectively. Expression levels of all genes and levels of TNF-α, IL-12, IL-6, and IL-10 were higher in SLE patients than those in controls (p < 0.05), whereas IL-2 level was lower. High STAT4 (α), TNFSF4, and IL-10 levels correlated with cardiovascular damage, and high MECP2 (α) and TNF-α correlated with renal damage. Pulmonary and musculoskeletal damages correlated with high levels of TNFSF4. We concluded that STAT4 and TNFSF4 genes with TNF-α and IL-10 cytokines could be used as biomarkers to assess SLE activity and manage treatment.
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Arvaniti P, Le Dantec C, Charras A, Arleevskaya MA, Hedrich CM, Zachou K, Dalekos GN, Renaudineau Y. Linking genetic variation with epigenetic profiles in Sjögren's syndrome. Clin Immunol 2019; 210:108314. [PMID: 31765834 DOI: 10.1016/j.clim.2019.108314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation represents an important regulatory event governing gene expression that is dysregulated in Sjögren's syndrome (SjS) and a number of autoimmune/inflammatory diseases. As disease-associated single-nucleotide polymorphisms (SNPs) have relevance in controlling DNA methylation, 94 non-HLA SjS-SNPs were investigated, among them 57 (60.6%) with widespread effects on 197 individual DNA methylation quantitative trait loci (meQTL) were selected. Typically, these SNPs are intronic, possess an active promoter histone mark, and control cis-meQTLs located around transcription start sites. Interplay is independent of the physical distance between SNPs and meQTLs. Using epigenome-wide association study datasets, SjS-meQTLs were characterized (41 genes and 13 DNA methylation CpG motifs) and for the most part map to a pro-inflammatory cytokine pathway, which is important for the control of DNA methylation in autoimmune diseases. In conclusion, exploring meQTLs represents a valuable tool to predict and investigate downstream effects of genetic factors in complex diseases such as SjS.
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Affiliation(s)
- Pinelopi Arvaniti
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France; Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - Christelle Le Dantec
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France.
| | - Amandine Charras
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France; Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, UK & Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
| | | | - Christian M Hedrich
- Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, UK & Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
| | - Kalliopi Zachou
- Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - Yves Renaudineau
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France; UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France.
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7
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Wang J, Huang A, Yuan Z, Su L, Xu W. Association of IRF5 rs2004640 polymorphism and systemic lupus erythematosus: A meta‐analysis. Int J Rheum Dis 2019; 22:1598-1606. [PMID: 31347288 DOI: 10.1111/1756-185x.13654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/29/2019] [Accepted: 06/18/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Jia‐Min Wang
- Department of Evidence‐Based Medicine, School of Public Health Southwest Medical University Luzhou Sichuan China
| | - An‐Fang Huang
- Department of Rheumatology and Immunology Affiliated Hospital of Southwest Medical University Luzhou Sichuan China
| | - Zhi‐Chao Yuan
- Department of Evidence‐Based Medicine, School of Public Health Southwest Medical University Luzhou Sichuan China
| | - Lin‐Chong Su
- Department of Rheumatology and Immunology Minda Hospital of Hubei Minzu University Enshi Hubei China
| | - Wang‐Dong Xu
- Department of Evidence‐Based Medicine, School of Public Health Southwest Medical University Luzhou Sichuan China
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8
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A promising role of interferon regulatory factor 5 as an early warning biomarker for the development of human non-small cell lung cancer. Lung Cancer 2019; 135:47-55. [PMID: 31447002 DOI: 10.1016/j.lungcan.2019.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 06/09/2019] [Accepted: 07/08/2019] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Non-small cell lung cancer (NSCLC) accounts for 85%-90% of lung cancer cases and is a covert disease lacking early symptoms. Since cancer is recognised as an inflammation-associated condition, we analysed the relationship between the expression of interferon regulatory factor 5 (IRF5), a key transcription factor controlling inflammatory responses, and NSCLC development with the aim of identifying a warning biomarker for early diagnosis of the disease. MATERIALS AND METHODS The expression of IRF5 and its associated inflammatory factors IL-6, IL-10, IP-10, and TNF-α in the peripheral blood of NSCLC patients (n = 66) and healthy controls (n = 42) was analysed by quantitative RT-PCR, flow cytometry, and a cytometric bead array. IRF5 protein expression in NSCLC tissues (n = 102) was detected by Western blotting. The diagnostic value of IRF5 expression was determined by a receiver-operating characteristic (ROC) curve analysis. RESULTS The protein levels of IRF5, IL-6, and IP-10 were significantly higher in the peripheral blood of NSCLC patients than in that of healthy controls. IP-10 levels in plasma and IL-10 mRNA expression in white blood cells (WBCs) were significantly upregulated in early-stage NSCLC, whereas plasma IL-6 and IL-10 were elevated in the progressive stage. IRF5 protein levels in WBCs were positively correlated with plasma IP-10 but negatively correlated with plasma IL-10. Furthermore, the mRNA and protein levels of IRF5 in WBCs were significantly elevated in patients with early stage NSCLC compared to those in the progressive stage. Additionally, IRF5 protein levels were significantly lower in NSCLC tumour tissues than those in normal lung tissues. CONCLUSIONS IRF5 levels in WBCs can be significantly upregulated in early stage NSCLC and were shown to have diagnostic value as an early warning biomarker of NSCLC development.
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9
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Antonczyk A, Krist B, Sajek M, Michalska A, Piaszyk-Borychowska A, Plens-Galaska M, Wesoly J, Bluyssen HAR. Direct Inhibition of IRF-Dependent Transcriptional Regulatory Mechanisms Associated With Disease. Front Immunol 2019; 10:1176. [PMID: 31178872 PMCID: PMC6543449 DOI: 10.3389/fimmu.2019.01176] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Interferon regulatory factors (IRFs) are a family of homologous proteins that regulate the transcription of interferons (IFNs) and IFN-induced gene expression. As such they are important modulating proteins in the Toll-like receptor (TLR) and IFN signaling pathways, which are vital elements of the innate immune system. IRFs have a multi-domain structure, with the N-terminal part acting as a DNA binding domain (DBD) that recognizes a DNA-binding motif similar to the IFN-stimulated response element (ISRE). The C-terminal part contains the IRF-association domain (IAD), with which they can self-associate, bind to IRF family members or interact with other transcription factors. This complex formation is crucial for DNA binding and the commencing of target-gene expression. IRFs bind DNA and exert their activating potential as homo or heterodimers with other IRFs. Moreover, they can form complexes (e.g., with Signal transducers and activators of transcription, STATs) and collaborate with other co-acting transcription factors such as Nuclear factor-κB (NF-κB) and PU.1. In time, more of these IRF co-activating mechanisms have been discovered, which may play a key role in the pathogenesis of many diseases, such as acute and chronic inflammation, autoimmune diseases, and cancer. Detailed knowledge of IRFs structure and activating mechanisms predisposes IRFs as potential targets for inhibition in therapeutic strategies connected to numerous immune system-originated diseases. Until now only indirect IRF modulation has been studied in terms of antiviral response regulation and cancer treatment, using mainly antisense oligonucleotides and siRNA knockdown strategies. However, none of these approaches so far entered clinical trials. Moreover, no direct IRF-inhibitory strategies have been reported. In this review, we summarize current knowledge of the different IRF-mediated transcriptional regulatory mechanisms and how they reflect the diverse functions of IRFs in homeostasis and in TLR and IFN signaling. Moreover, we present IRFs as promising inhibitory targets and propose a novel direct IRF-modulating strategy employing a pipeline approach that combines comparative in silico docking to the IRF-DBD with in vitro validation of IRF inhibition. We hypothesize that our methodology will enable the efficient identification of IRF-specific and pan-IRF inhibitors that can be used for the treatment of IRF-dependent disorders and malignancies.
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Affiliation(s)
- Aleksandra Antonczyk
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Bart Krist
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Malgorzata Sajek
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Agata Michalska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Piaszyk-Borychowska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Martyna Plens-Galaska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
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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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11
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Calise J, Marquez Renteria S, Gregersen PK, Diamond B. Lineage-Specific Functionality of an Interferon Regulatory Factor 5 Lupus Risk Haplotype: Lack of B Cell Intrinsic Effects. Front Immunol 2018; 9:996. [PMID: 29867973 PMCID: PMC5949527 DOI: 10.3389/fimmu.2018.00996] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022] Open
Abstract
Interferon regulatory factor 5 (IRF5) is widely recognized as a risk locus for systemic lupus erythematosus (SLE). Risk gene and IRF5 activation is triggered through toll-like receptor signaling. In myeloid cells, this leads to production of type I interferon and inflammatory cytokines, with enhanced production in cells of individuals harboring IRF5 risk alleles. Mouse models have also demonstrated the importance of IRF5 in B cell function, particularly plasma cell differentiation and isotype switching. Here, we evaluated the major SLE risk haplotype of IRF5 on the functional attributes of freshly isolated B cells from human subjects who do not have evidence of SLE or other forms of autoimmunity. We took this approach to avoid the complications of studying genotype-phenotype relationships in B cells that have been chronically exposed to an inflammatory disease environment before isolation. We focused on B cell endophenotypes that included gene expression, antibody secretion, class switching, and apoptotic susceptibility. We performed IRF5 overexpression studies, genetic reporter assays and electro-mobility shift assays on B and myeloid cell lines. Somewhat surprisingly, the results of our analyses indicate that IRF5 risk genotypes do not have a B cell intrinsic effect on these B cell functions. By contrast, we confirmed that the IRF5 risk and non-risk haplotypes exert differential effects in myeloid cells, including an increased susceptibility to apoptosis conferred by the risk haplotype. We also demonstrated an increased binding of the transcription factor specificity protein 1 to an insertion/deletion present in the risk haplotype. Our findings raise the specter that genetic risk alleles can have complex and unexpected lineage-specific effects, and these must be carefully considered when guiding or developing therapies based on understanding disease risk haplotypes.
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Affiliation(s)
- Justine Calise
- PhD Program in Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra-Northwell, Hempstead, NY, United States.,Laboratory of Autoimmune & Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases, Northwell Health, Manhasset, NY, United States
| | - Susana Marquez Renteria
- Laboratory of Genomics & Human Genetics, The Feinstein Institute for Medical Research, Center for Genomics and Human Genetics, Northwell Health, Manhasset, NY, United States
| | - Peter K Gregersen
- Laboratory of Genomics & Human Genetics, The Feinstein Institute for Medical Research, Center for Genomics and Human Genetics, Northwell Health, Manhasset, NY, United States
| | - Betty Diamond
- Laboratory of Autoimmune & Musculoskeletal Diseases, The Feinstein Institute for Medical Research, Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases, Northwell Health, Manhasset, NY, United States
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12
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Babaian A, Mager DL. Endogenous retroviral promoter exaptation in human cancer. Mob DNA 2016; 7:24. [PMID: 27980689 PMCID: PMC5134097 DOI: 10.1186/s13100-016-0080-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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13
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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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14
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Shu J, Wang XH, Zhou LB, Jiang CM, Yang WX, Jin R, Wang LL, Zhou GP. Expression of interferon regulatory factor 5 is regulated by the Sp1 transcription factor. Mol Med Rep 2016; 14:2815-22. [PMID: 27484157 DOI: 10.3892/mmr.2016.5565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 07/20/2016] [Indexed: 11/05/2022] Open
Abstract
The transcription factor, interferon regulatory factor 5 (IRF5), is important in the induction of type I interferon, proinflammatory cytokines and chemokines, and is involved in autoimmune diseases and tumourigenesis. However, the mechanisms underlying the transcriptional regulation of wild‑type IRF5 remain to be fully elucidated. The present study was primarily designed to clarify whether specificity protein 1 (Sp1) was involved in the regulation of IRF5. Initially, the IRF5 promoter region was cloned and its promoter activity was examined using Hela and HEK 293 cells. Deletion analyses revealed that the region spanning ‑179 to +62 was the minimal promoter of IRF5. Bioinformatics analyses showed that this region contained three putative Sp1 binding sites, and mutational analyses revealed that all the Sp1 sites contributed to transcriptional activity. Secondly, the overexpression of Sp1 was found to increase the activity of the IRF5 promoter and the mRNA level of IRF5, determined using reporter gene assays and polymerase chain reaction analysis, respectively. By contrast, treatment with mithramycin and Sp1 small interfering RNA significantly reduced the activity of the IRF5 promoter and the mRNA level of IRF5. Finally, the results of an electrophoretic mobility shift assay and a chromatin immunoprecipitation assay demonstrated that Sp1 bound to the promoter region of IRF5 in vitro and in vivo. These results suggested that the Sp1 transcription factor is the primary determinant for activating the basal transcription of the IRF5.
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Affiliation(s)
- Jin Shu
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xiao-Hua Wang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Lan-Bo Zhou
- 2013 Clinical Class 7, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Chun-Ming Jiang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wei-Xia Yang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Rui Jin
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Lu-Lu Wang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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15
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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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16
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Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 2015; 43:10612-22. [PMID: 26578562 PMCID: PMC4678817 DOI: 10.1093/nar/gkv1099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/09/2015] [Indexed: 01/27/2023] Open
Abstract
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to the reference genome. We developed and evaluated an approach to identify ‘hidden’ splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Computational analysis and experimental validation indicate that this approach identifies personal specific splice junctions at a low false positive rate. Applying this approach to an RNA-seq data set of 75 individuals, we identified 506 personal specific splice junctions, among which 437 were novel splice junctions not documented in current human transcript annotations. 94 splice junctions had splice site SNPs associated with GWAS signals of human traits and diseases. These involve genes whose splicing variations have been implicated in diseases (such as OAS1), as well as novel associations between alternative splicing and diseases (such as ICA1). Collectively, our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
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Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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17
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Griesbeck M, Ziegler S, Laffont S, Smith N, Chauveau L, Tomezsko P, Sharei A, Kourjian G, Porichis F, Hart M, Palmer CD, Sirignano M, Beisel C, Hildebrandt H, Cénac C, Villani AC, Diefenbach TJ, Le Gall S, Schwartz O, Herbeuval JP, Autran B, Guéry JC, Chang JJ, Altfeld M. Sex Differences in Plasmacytoid Dendritic Cell Levels of IRF5 Drive Higher IFN-α Production in Women. THE JOURNAL OF IMMUNOLOGY 2015; 195:5327-36. [PMID: 26519527 DOI: 10.4049/jimmunol.1501684] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/30/2015] [Indexed: 01/17/2023]
Abstract
Increased IFN-α production contributes to the pathogenesis of infectious and autoimmune diseases. Plasmacytoid dendritic cells (pDCs) from females produce more IFN-α upon TLR7 stimulation than pDCs from males, yet the mechanisms underlying this difference remain unclear. In this article, we show that basal levels of IFN regulatory factor (IRF) 5 in pDCs were significantly higher in females compared with males and positively correlated with the percentage of IFN-α-secreting pDCs. Delivery of recombinant IRF5 protein into human primary pDCs increased TLR7-mediated IFN-α secretion. In mice, genetic ablation of the estrogen receptor 1 (Esr1) gene in the hematopoietic compartment or DC lineage reduced Irf5 mRNA expression in pDCs and IFN-α production. IRF5 mRNA levels furthermore correlated with ESR1 mRNA levels in human pDCs, consistent with IRF5 regulation at the transcriptional level by ESR1. Taken together, these data demonstrate a critical mechanism by which sex differences in basal pDC IRF5 expression lead to higher IFN-α production upon TLR7 stimulation in females and provide novel targets for the modulation of immune responses and inflammation.
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Affiliation(s)
- Morgane Griesbeck
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139; Centre d'Immunonologie et des Maladies Infectieuses-Paris, Université Pierre et Marie Curie/INSERM U1135, Hôpital Pitié Salpêtrière, Paris 75013, France
| | - Susanne Ziegler
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg 20246, Germany
| | - Sophie Laffont
- INSERM U1043, Toulouse F-31300, France; CNRS, U5282, Toulouse F-31300, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31300, France
| | - Nikaïa Smith
- Chemistry and Biology, Nucleotides and Immunology for Therapy, CNRS UMR-8601, Université Paris Descartes, Paris 75270, France
| | - Lise Chauveau
- Institut Pasteur, Unité de recherche associée CNRS 3015, Unite Virus et Immunité, Paris 75015, France
| | | | - Armon Sharei
- The David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139
| | | | | | - Meghan Hart
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | | | | | - Claudia Beisel
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg 20246, Germany; Medical Department, University Hospital Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Heike Hildebrandt
- Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg 20246, Germany
| | - Claire Cénac
- INSERM U1043, Toulouse F-31300, France; CNRS, U5282, Toulouse F-31300, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31300, France
| | | | | | - Sylvie Le Gall
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Olivier Schwartz
- Institut Pasteur, Unité de recherche associée CNRS 3015, Unite Virus et Immunité, Paris 75015, France
| | - Jean-Philippe Herbeuval
- Chemistry and Biology, Nucleotides and Immunology for Therapy, CNRS UMR-8601, Université Paris Descartes, Paris 75270, France
| | - Brigitte Autran
- Centre d'Immunonologie et des Maladies Infectieuses-Paris, Université Pierre et Marie Curie/INSERM U1135, Hôpital Pitié Salpêtrière, Paris 75013, France
| | - Jean-Charles Guéry
- INSERM U1043, Toulouse F-31300, France; CNRS, U5282, Toulouse F-31300, France; Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31300, France
| | - J Judy Chang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139; Department of Infectious Diseases, Monash University, Melbourne, Victoria 3800, Australia
| | - Marcus Altfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139; Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg 20246, Germany;
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18
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Cossu D, Mameli G, Galleri G, Cocco E, Masala S, Frau J, Marrosu MG, Manetti R, Sechi LA. Human interferon regulatory factor 5 homologous epitopes of Epstein-Barr virus and Mycobacterium avium subsp. paratuberculosis induce a specific humoral and cellular immune response in multiple sclerosis patients. Mult Scler 2014; 21:984-95. [PMID: 25392335 DOI: 10.1177/1352458514557304] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/07/2014] [Indexed: 12/26/2022]
Abstract
BACKGROUND A large number of reports indicate the association of Epstein-Barr virus (EBV), and Mycobacterium avium subsp. paratuberculosis (MAP) with multiple sclerosis (MS). OBJECTIVE To gain a better understanding of the role of these two pathogens, we investigated the host response induced by selected antigenic peptides. METHODS We examined both humoral and cell-mediated responses against peptides deriving from EBV tegument protein BOLF1, the MAP_4027 and the human interferon regulatory factor 5 (IRF5424-434) homolog in several MS patients and healthy controls (HCs). RESULTS Antibodies against these peptides were highly prevalent in MS patients compared to HCs. Concerning MS patients, BOLF1305-320, MAP_402718-32 and IRF5424-434 peptides were able to induce mainly Th1-related cytokines secretion, whereas Th2-related cytokines were down-regulated. Flow cytometry analyses performed on a subset of MS patients highlighted that these peptides were capable of inducing the release of pro-inflammatory cytokines: IFN-γ and TNF-α by CD4(+) and CD8(+) T lymphocytes, and IL-6 and TNF-α by CD14(+) monocyte cells. CONCLUSION Our data demonstrated that both EBV and MAP epitopes elicit a consistent humoral response in MS patients compared to HCs, and that the aforementioned peptides are able to induce a T-cell-mediated response that is MS correlated.
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Affiliation(s)
- Davide Cossu
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università di Sassari, Italy
| | - Giuseppe Mameli
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università di Sassari, Italy
| | - Grazia Galleri
- Dipartimento di Medicina Clinica e Sperimentale, Università di Sassari, Italy
| | - Eleonora Cocco
- Centro Sclerosi Multipla, Dipartimento di Sanità Pubblica Medicina Clinica e Molecolare, Università di Cagliari, Italy
| | - Speranza Masala
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università di Sassari, Italy
| | - Jessica Frau
- Centro Sclerosi Multipla, Dipartimento di Sanità Pubblica Medicina Clinica e Molecolare, Università di Cagliari, Italy
| | - Maria Giovanna Marrosu
- Centro Sclerosi Multipla, Dipartimento di Sanità Pubblica Medicina Clinica e Molecolare, Università di Cagliari, Italy
| | - Roberto Manetti
- Dipartimento di Medicina Clinica e Sperimentale, Università di Sassari, Italy
| | - Leonardo Antonio Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia e Virologia, Università di Sassari, Italy
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19
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Niewold TB. Type I interferon in human autoimmunity. Front Immunol 2014; 5:306. [PMID: 25071767 PMCID: PMC4074699 DOI: 10.3389/fimmu.2014.00306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 12/17/2022] Open
Affiliation(s)
- Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic , Rochester, MN , USA
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20
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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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