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Mascia E, Nale V, Ferrè L, Sorosina M, Clarelli F, Chiodi A, Santoro S, Giordano A, Misra K, Cannizzaro M, Moiola L, Martinelli V, Milanesi L, Filippi M, Mosca E, Esposito F. Genetic Contribution to Medium-Term Disease Activity in Multiple Sclerosis. Mol Neurobiol 2024:10.1007/s12035-024-04264-8. [PMID: 38850349 DOI: 10.1007/s12035-024-04264-8] [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: 03/12/2024] [Accepted: 05/25/2024] [Indexed: 06/10/2024]
Abstract
Multiple sclerosis (MS) is a complex disorder characterized by high heterogeneity in terms of phenotypic expression, prognosis and treatment response. In the present study, we aimed to explore the genetic contribution to MS disease activity at different levels: genes, pathways and tissue-specific networks. Two cohorts of relapsing-remitting MS patients who started a first-line treatment (n = 1294) were enrolled to evaluate the genetic association with disease activity after 4 years of follow-up. The analyses were performed at whole-genome SNP and gene level, followed by the construction of gene-gene interaction networks specific for brain and lymphocytes. The resulting gene modules were evaluated to highlight key players from a topological and functional perspective. We identified 23 variants and 223 genes with suggestive association to 4-years disease activity, highlighting genes like PON2 involved in oxidative stress and in mitochondria functions and other genes, like ILRUN, involved in the modulation of the immune system. Network analyses led to the identification of a brain module composed of 228 genes and a lymphocytes module composed of 287 genes. The network analysis allowed us to prioritize genes relevant for their topological properties; among them, there are MPHOSPH9 (connector hub in both brain and lymphocyte module) and OPA1 (in brain module), two genes already implicated in MS. Modules showed the enrichment of both shared and tissue-specific pathways, mainly implicated in inflammation. In conclusion, our results suggest that the processes underlying disease activity act on shared mechanisms across brain and lymphocyte tissues.
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Affiliation(s)
- Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Laura Ferrè
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonino Giordano
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Kaalindi Misra
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miryam Cannizzaro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Moiola
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vittorio Martinelli
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Massimo Filippi
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Neurophysiology Service, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Segrate, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Neurology and Neurorehabilitation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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2
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Tribolet L, Brice AM, Fulford TS, Layton DS, Godfrey DI, Bean AGD, Stewart CR. Identification of a novel role for the immunomodulator ILRUN in the development of several T cell subsets in mice. Immunobiology 2023; 228:152380. [PMID: 37031606 DOI: 10.1016/j.imbio.2023.152380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Inflammation and lipid regulator with UBA-like and NBR1-like domains (ILRUN) is a protein-encoding gene associated with innate immune signaling, lipid metabolism and cancer. In the context of innate immunity, ILRUN inhibits IRF3-mediated transcription of antimicrobial and proinflammatory cytokines by inducing degradation of the transcriptional coactivators CBP and p300. There remains a paucity of information, however, regarding the innate immune roles of ILRUN beyond in vitro analyses. To address this, we utilize a knockout mouse model to investigate the effect of ILRUN on cytokine expression in splenocytes and on the development of immune cell populations in the spleen and thymus. We show elevated production of tumor necrosis factor and interleukin-6 cytokines in ILRUN-deficient splenocytes following stimulation with the innate immune ligands polyinosinic:polycytidylic acid or lipopolysaccharide. Differences were also observed in the populations of several T cell subsets, including regulatory, mucosal-associated invariant and natural killer. These data identify novel functions for ILRUN in the development of certain immune cell populations and support previous in vitro findings that ILRUN negatively regulates the synthesis of pathogen-stimulated cytokines. This establishes the ILRUN knockout mouse model as a valuable resource for further study of the functions of ILRUN in health and disease.
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Affiliation(s)
- Leon Tribolet
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Aaron M Brice
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Thomas S Fulford
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Daniel S Layton
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Victoria, Australia
| | - Andrew G D Bean
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia
| | - Cameron R Stewart
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong 3220, Victoria, Australia.
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3
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Bi X, Stankov S, Lee PC, Wang Z, Wu X, Li L, Ko YA, Cheng L, Zhang H, Hand NJ, Rader DJ. ILRUN Promotes Atherosclerosis Through Lipid-Dependent and Lipid-Independent Factors. Arterioscler Thromb Vasc Biol 2022; 42:1139-1151. [PMID: 35861973 PMCID: PMC9420832 DOI: 10.1161/atvbaha.121.317156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Common genetic variation in close proximity to the ILRUN gene are significantly associated with coronary artery disease as well as with plasma lipid traits. We recently demonstrated that hepatic inflammation and lipid regulator with ubiquitin-associated domain-like and NBR1-like domains (ILRUN) regulates lipoprotein metabolism in vivo in mice. However, whether ILRUN, which is expressed in vascular cells, directly impacts atherogenesis remains unclear. We sought to determine the role of ILRUN in atherosclerosis development in mice. METHODS For our study, we generated global Ilrun-deficient (IlrunKO) male and female mice on 2 hyperlipidemic backgrounds: low density lipoprotein receptor knockout (LdlrKO) and apolipoprotein E knockout (ApoeKO; double knockout [DKO]). RESULTS Compared with littermate control mice (single LdlrKO or ApoeKO), deletion of Ilrun in DKO mice resulted in significantly attenuated both early and advanced atherosclerotic lesion development, as well as reduced necrotic area. DKO mice also had significantly decreased plasma cholesterol levels, primarily attributable to non-HDL (high-density lipoprotein) cholesterol. Hepatic-specific reconstitution of ILRUN in DKO mice on the ApoeKO background normalized plasma lipids, but atherosclerotic lesion area and necrotic area remained reduced in DKO mice. Further analysis showed that loss of Ilrun increased efferocytosis receptor MerTK expression in macrophages, enhanced in vitro efferocytosis, and significantly improved in situ efferocytosis in advanced lesions. CONCLUSIONS Our results support ILRUN as an important novel regulator of atherogenesis that promotes lesion progression and necrosis. It influences atherosclerosis through both plasma lipid-dependent and lipid-independent mechanisms. These findings support ILRUN as the likely causal gene responsible for genetic association of variants with coronary artery disease at this locus and suggest that suppression of ILRUN activity might be expected to reduce atherosclerosis.
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Affiliation(s)
- Xin Bi
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul C. Lee
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ziyi Wang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Li Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-An Ko
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lan Cheng
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas J. Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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4
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Getz GS, Reardon CA. ILRUNing to Atherosclerosis. Arterioscler Thromb Vasc Biol 2022; 42:1152-1153. [PMID: 35924556 DOI: 10.1161/atvbaha.122.318107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Godfrey S Getz
- Department of Pathology, University of Chicago, IL (G.S.G.)
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5
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Zhang J, Wang YY, Pan ZQ, Li Y, Sui J, Du LL, Ye K. Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1. Nat Commun 2022; 13:3650. [PMID: 35752625 PMCID: PMC9233695 DOI: 10.1038/s41467-022-31439-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/16/2022] [Indexed: 12/21/2022] Open
Abstract
Neighbor of BRCA1 (Nbr1) is a conserved autophagy receptor that provides cargo selectivity to autophagy. The four-tryptophan (FW) domain is a signature domain of Nbr1, but its exact function remains unclear. Here, we show that Nbr1 from the filamentous fungus Chaetomium thermophilum uses its FW domain to bind the α-mannosidase Ams1, a cargo of selective autophagy in both budding yeast and fission yeast, and delivers Ams1 to the vacuole by conventional autophagy in heterologous fission yeast. The structure of the Ams1-FW complex was determined at 2.2 Å resolution by cryo-electron microscopy. The FW domain adopts an immunoglobulin-like β-sandwich structure and recognizes the quaternary structure of the Ams1 tetramer. Notably, the N-terminal di-glycine of Ams1 is specifically recognized by a conserved pocket of the FW domain. The FW domain becomes degenerated in fission yeast Nbr1, which binds Ams1 with a ZZ domain instead. Our findings illustrate the protein binding mode of the FW domain and reveal the versatility of Nbr1-mediated cargo recognition. Nbr1 recognizes cargos in selective autophagy. Here, authors show filamentous yeast Nbr1 binds Ams1 via an FW domain, and the cryo-EM structure reveals that Nbr1 recognizes the N-terminal di-glycine and tetrameric assembly of Ams1.
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Affiliation(s)
- Jianxiu Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Ying Wang
- College of Life Sciences, Beijing Normal University, 100875, Beijing, China.,National Institute of Biological Sciences, 102206, Beijing, China.,School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Zhao-Qian Pan
- National Institute of Biological Sciences, 102206, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences, 102206, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, 102206, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, 102206, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China.
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Henriques-Pons A, Beghini DG, Silva VDS, Iwao Horita S, da Silva FAB. Pulmonary Mesenchymal Stem Cells in Mild Cases of COVID-19 Are Dedicated to Proliferation; In Severe Cases, They Control Inflammation, Make Cell Dispersion, and Tissue Regeneration. Front Immunol 2022; 12:780900. [PMID: 35095855 PMCID: PMC8793136 DOI: 10.3389/fimmu.2021.780900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are multipotent adult stem cells present in virtually all tissues; they have potent self-renewal capacity and differentiate into multiple cell types. For many reasons, these cells are a promising therapeutic alternative to treat patients with severe COVID-19 and pulmonary post-COVID sequelae. These cells are not only essential for tissue regeneration; they can also alter the pulmonary environment through the paracrine secretion of several mediators. They can control or promote inflammation, induce other stem cells differentiation, restrain the virus load, and much more. In this work, we performed single-cell RNA-seq data analysis of MSCs in bronchoalveolar lavage samples from control individuals and COVID-19 patients with mild and severe clinical conditions. When we compared samples from mild cases with control individuals, most genes transcriptionally upregulated in COVID-19 were involved in cell proliferation. However, a new set of genes with distinct biological functions was upregulated when we compared severely affected with mild COVID-19 patients. In this analysis, the cells upregulated genes related to cell dispersion/migration and induced the γ-activated sequence (GAS) genes, probably triggered by IFNGR1 and IFNGR2. Then, IRF-1 was upregulated, one of the GAS target genes, leading to the interferon-stimulated response (ISR) and the overexpression of many signature target genes. The MSCs also upregulated genes involved in the mesenchymal-epithelial transition, virus control, cell chemotaxis, and used the cytoplasmic RNA danger sensors RIG-1, MDA5, and PKR. In a non-comparative analysis, we observed that MSCs from severe cases do not express many NF-κB upstream receptors, such as Toll-like (TLRs) TLR-3, -7, and -8; tumor necrosis factor (TNFR1 or TNFR2), RANK, CD40, and IL-1R1. Indeed, many NF-κB inhibitors were upregulated, including PPP2CB, OPTN, NFKBIA, and FHL2, suggesting that MSCs do not play a role in the "cytokine storm" observed. Therefore, lung MSCs in COVID-19 sense immune danger and act protectively in concert with the pulmonary environment, confirming their therapeutic potential in cell-based therapy for COVID-19. The transcription of MSCs senescence markers is discussed.
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Affiliation(s)
- Andrea Henriques-Pons
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
| | - Daniela Gois Beghini
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
| | | | - Samuel Iwao Horita
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Inovações em Terapias, Ensino e Bioprodutos, Rio de Janeiro, Brazil
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7
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ILRUN Downregulates ACE2 Expression and Blocks Infection of Human Cells by SARS-CoV-2. J Virol 2021; 95:e0032721. [PMID: 33963054 DOI: 10.1128/jvi.00327-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human protein-coding gene ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains; previously C6orf106) was identified as a proviral factor for Hendra virus infection and was recently characterized to function as an inhibitor of type I interferon expression. Here, we have utilized transcriptome sequencing (RNA-seq) to define cellular pathways regulated by ILRUN in the context of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of Caco-2 cells. We find that inhibition of ILRUN expression by RNA interference alters transcription profiles of numerous cellular pathways, including upregulation of the SARS-CoV-2 entry receptor ACE2 and several other members of the renin-angiotensin aldosterone system. In addition, transcripts of the SARS-CoV-2 coreceptors TMPRSS2 and CTSL were also upregulated. Inhibition of ILRUN also resulted in increased SARS-CoV-2 replication, while overexpression of ILRUN had the opposite effect, identifying ILRUN as a novel antiviral factor for SARS-CoV-2 replication. This represents, to our knowledge, the first report of ILRUN as a regulator of the renin-angiotensin-aldosterone system (RAAS). IMPORTANCE There is no doubt that the current rapid global spread of COVID-19 has had significant and far-reaching impacts on our health and economy and will continue to do so. Research in emerging infectious diseases, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is growing rapidly, with new breakthroughs in the understanding of host-virus interactions to assist with the development of innovative and exciting therapeutic strategies. Here, we present the first evidence that modulation of the human protein-coding gene ILRUN functions as an antiviral factor for SARS-CoV-2 infection, likely through its newly identified role in regulating the expression of SARS-CoV-2 entry receptors ACE2, TMPRSS2, and CTSL. These data improve our understanding of biological pathways that regulate host factors critical to SARS-CoV-2 infection, contributing to the development of antiviral strategies to deal with the current SARS-CoV-2 pandemic.
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8
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Ding X, Cai M, Wang S, Yang Q, Zheng X, Zuo X, Liu S. Gene-based association analysis identified a novel gene associated with systemic lupus erythematosus. Ann Hum Genet 2021; 85:213-220. [PMID: 34145571 DOI: 10.1111/ahg.12439] [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: 12/05/2020] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disease with strong genetic predisposition. Genome-wide association studies (GWAS) of SLE have identified more than 50 robust susceptibility loci. However, traditional individual SNP-based GWAS have made it difficult to identify variants with small effects. Moreover, variants revealed by GWAS only explain a limited disease heritability, suggesting that many susceptibility genes remain uncovered. METHODS We first curated the published SLE GWAS data from 1047 SLE patients and 1205 healthy controls of Chinese ancestry and performed a gene-based association study. Then quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was conducted to verify novel genes identified above. RESULTS Gene-based association study identified 10 SLE-associated genes, nine of which were reported by previous GWAS, the other one, ILRUN, is a newly identified gene and was further validated by qRT-PCR. Gene expression analysis of Gene Expression Omnibus (GEO) datasets also showed that the expression of ILRUN in patients with SLE was lower than that in normal subjects. CONCLUSION In this study, gene-based association study and qRT-PCR identified that ILRUN is a novel susceptibility gene of SLE. ILRUN may regulate inflammation and antiviral response through its effect on the transcription of type I interferons )I-IFN, and participate in the pathogenesis of SLE.
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Affiliation(s)
- Xian Ding
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Minglong Cai
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Sun Wang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qingqing Yang
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xiaodong Zheng
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xianbo Zuo
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Shengxiu Liu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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9
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Petro TM. IFN Regulatory Factor 3 in Health and Disease. THE JOURNAL OF IMMUNOLOGY 2021; 205:1981-1989. [PMID: 33020188 DOI: 10.4049/jimmunol.2000462] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Immunity to viruses requires an array of critical cellular proteins that include IFN regulatory factor 3 (IRF3). Consequently, most viruses that infect vertebrates encode proteins that interfere with IRF3 activation. This review describes the cellular pathways linked to IRF3 activation and where those pathways are targeted by human viral pathogens. Moreover, key regulatory pathways that control IRF3 are discussed. Besides viral infections, IRF3 is also involved in resistance to some bacterial infections, in anticancer immunity, and in anticancer therapies involving DNA damage agents. A recent finding shows that IRF3 is needed for T cell effector functions that are involved in anticancer immunity and also in T cell autoimmune diseases. In contrast, unregulated IRF3 activity is clearly not beneficial, considering it is implicated in certain interferonopathies, in which heightened IRF3 activity leads to IFN-β-induced disease. Therefore, IRF3 is involved largely in maintaining health but sometimes contributing to disease.
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Affiliation(s)
- Thomas M Petro
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583; and Nebraska Center for Virology, University of Nebraska Medical Center, Lincoln, NE 68583
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10
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Hu S, Uniken Venema WT, Westra HJ, Vich Vila A, Barbieri R, Voskuil MD, Blokzijl T, Jansen BH, Li Y, Daly MJ, Xavier RJ, Dijkstra G, Festen EA, Weersma RK. Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease. Nat Commun 2021; 12:1122. [PMID: 33602935 PMCID: PMC7892863 DOI: 10.1038/s41467-021-21458-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
More than 240 genetic risk loci have been associated with inflammatory bowel disease (IBD), but little is known about how they contribute to disease development in involved tissue. Here, we hypothesized that host genetic variation affects gene expression in an inflammation-dependent way, and investigated 299 snap-frozen intestinal biopsies from inflamed and non-inflamed mucosa from 171 IBD patients. RNA-sequencing was performed, and genotypes were determined using whole exome sequencing and genome wide genotyping. In total, 28,746 genes and 6,894,979 SNPs were included. Linear mixed models identified 8,881 independent intestinal cis-expression quantitative trait loci (cis-eQTLs) (FDR < 0.05) and interaction analysis revealed 190 inflammation-dependent intestinal cis-eQTLs (FDR < 0.05), including known IBD-risk genes and genes encoding immune-cell receptors and antibodies. The inflammation-dependent cis-eQTL SNPs (eSNPs) mainly interact with prevalence of immune cell types. Inflammation-dependent intestinal cis-eQTLs reveal genetic susceptibility under inflammatory conditions that can help identify the cell types involved in and the pathways underlying inflammation, knowledge that may guide future drug development and profile patients for precision medicine in IBD. Inflammatory bowel diseases are heterogeneous, and little is known about how underlying genetic variation can affect their development. Here, the authors report that intestinal inflammation modulates the effect of host genetics on the gut mucosal expression of 190 genes in the context of inflammatory bowel diseases.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Werna T Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ruggero Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Yanni Li
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Daly
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ramnik J Xavier
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutic, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
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11
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Bi X, Kuwano T, Lee PC, Millar JS, Li L, Shen Y, Soccio RE, Hand NJ, Rader DJ. ILRUN, a Human Plasma Lipid GWAS Locus, Regulates Lipoprotein Metabolism in Mice. Circ Res 2020; 127:1347-1361. [PMID: 32912065 PMCID: PMC7644615 DOI: 10.1161/circresaha.120.317175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RATIONALE Single-nucleotide polymorphisms near the ILRUN (inflammation and lipid regulator with ubiquitin-associated-like and NBR1 [next to BRCA1 gene 1 protein]-like domains) gene are genome-wide significantly associated with plasma lipid traits and coronary artery disease (CAD), but the biological basis of this association is unknown. OBJECTIVE To investigate the role of ILRUN in plasma lipid and lipoprotein metabolism. METHODS AND RESULTS ILRUN encodes a protein that contains a ubiquitin-associated-like domain, suggesting that it may interact with ubiquitinylated proteins. We generated mice globally deficient for Ilrun and found they had significantly lower plasma cholesterol levels resulting from reduced liver lipoprotein production. Liver transcriptome analysis uncovered altered transcription of genes downstream of lipid-related transcription factors, particularly PPARα (peroxisome proliferator-activated receptor alpha), and livers from Ilrun-deficient mice had increased PPARα protein. Human ILRUN was shown to bind to ubiquitinylated proteins including PPARα, and the ubiquitin-associated-like domain of ILRUN was found to be required for its interaction with PPARα. CONCLUSIONS These findings establish ILRUN as a novel regulator of lipid metabolism that promotes hepatic lipoprotein production. Our results also provide functional evidence that ILRUN may be the casual gene underlying the observed genetic associations with plasma lipids at 6p21 in human.
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Affiliation(s)
- Xin Bi
- Division of Translational Medicine and Human Genetics, Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Takashi Kuwano
- Division of Translational Medicine and Human Genetics, Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul C. Lee
- Division of Translational Medicine and Human Genetics, Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John S. Millar
- Division of Translational Medicine and Human Genetics, Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Li
- Penn Cardiovascular Institute; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yachen Shen
- Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond E. Soccio
- Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas J. Hand
- Department of Genetics; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine; University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics; University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Affiliation(s)
- Michael J Thomas
- Department of Pharmacology & Toxicology (M.J.T., M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary G Sorci-Thomas
- Department of Pharmacology & Toxicology (M.J.T., M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Medicine (M.G.S.-T.), Section on Endocrinology, Medical College of Wisconsin, Milwaukee, Wisconsin
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13
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Ambrose RL, Brice AM, Caputo AT, Alexander MR, Tribolet L, Liu YC, Adams TE, Bean AG, Stewart CR. Molecular characterisation of ILRUN, a novel inhibitor of proinflammatory and antimicrobial cytokines. Heliyon 2020; 6:e04115. [PMID: 32518853 PMCID: PMC7270589 DOI: 10.1016/j.heliyon.2020.e04115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
Regulation of type-I interferon (IFN) production is essential to the balance between antimicrobial defence and autoimmune disorders. The human protein-coding gene ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains, previously C6orf106) was recently characterised as an inhibitor of antiviral and proinflammatory cytokine (interferon-alpha/beta and tumor necrosis factor alpha) transcription. Currently there is a paucity of information about the molecular characteristics of ILRUN, despite it being associated with several diseases including virus infection, coronary artery disease, obesity and cancer. Here, we characterise ILRUN as a highly phylogenetically conserved protein containing UBA-like and a NBR1-like domains that are both essential for inhibition of type-I interferon and tumor necrosis factor alpha) transcription in human cells. We also solved the crystal structure of the NBR1-like domain, providing insights into its potential role in ILRUN function. This study provides critical information for future investigations into the role of ILRUN in health and disease.
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Affiliation(s)
- Rebecca L. Ambrose
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Aaron M. Brice
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | | | - Marina R. Alexander
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Leon Tribolet
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Yu Chih Liu
- CSIRO Manufacturing, Parkville, Victoria, 3010, Australia
| | | | - Andrew G.D. Bean
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Cameron R. Stewart
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
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