1
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Moran EA, Salas-Briceno K, Zhao W, Enya T, Aguilera AN, Acosta I, Alonzo F, Kiani D, Behnsen J, Alvarez C, Keane TM, Adams DJ, Lilue J, Ross SR. IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway. mBio 2024; 15:e0120924. [PMID: 38860764 PMCID: PMC11253629 DOI: 10.1128/mbio.01209-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 06/12/2024] Open
Abstract
Mammalian AIM-2-like receptor (ALR) proteins bind nucleic acids and initiate production of type I interferons or inflammasome assembly, thereby contributing to host innate immunity. In mice, the Alr locus is highly polymorphic at the sequence and copy number level, and we show here that it is one of the most dynamic regions of the genome. One rapidly evolving gene within this region, Ifi207, was introduced to the Mus genome by gene conversion or an unequal recombination event a few million years ago. Ifi207 has a large, distinctive repeat region that differs in sequence and length among Mus species and even closely related inbred Mus musculus strains. We show that IFI207 controls murine leukemia virus (MLV) infection in vivo and that it plays a role in the STING-mediated response to cGAMP, dsDNA, DMXXA, and MLV. IFI207 binds to STING, and inclusion of its repeat region appears to stabilize STING protein. The Alr locus and Ifi207 provide a clear example of the evolutionary innovation of gene function, possibly as a result of host-pathogen co-evolution.IMPORTANCEThe Red Queen hypothesis predicts that the arms race between pathogens and the host may accelerate evolution of both sides, and therefore causes higher diversity in virulence factors and immune-related proteins, respectively . The Alr gene family in mice has undergone rapid evolution in the last few million years and includes the creation of two novel members, MndaL and Ifi207. Ifi207, in particular, became highly divergent, with significant genetic changes between highly related inbred mice. IFI207 protein acts in the STING pathway and contributes to anti-retroviral resistance via a novel mechanism. The data show that under the pressure of host-pathogen coevolution in a dynamic locus, gene conversion and recombination between gene family members creates new genes with novel and essential functions that play diverse roles in biological processes.
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Affiliation(s)
- Eileen A. Moran
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Karen Salas-Briceno
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Wenming Zhao
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Takuji Enya
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Alexya N. Aguilera
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Ivan Acosta
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Dara Kiani
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | | | | | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jingtao Lilue
- Gulbenkian Institute of Science, Oeiras, Portugal
- Oujiang Laboratory, Wenzhou, Zhejiang, China
| | - Susan R. Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
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2
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Wang H, Canasto-Chibuque C, Kim JH, Hohl M, Leslie C, Reis-Filho JS, Petrini JH. Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562529. [PMID: 37905095 PMCID: PMC10614814 DOI: 10.1101/2023.10.16.562529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The Mre11 complex (comprising Mre11, Rad50, Nbs1) is integral to the maintenance of genome stability. We previously showed that a hypomorphic Mre11 mutant mouse strain ( Mre11 ATLD1/ATLD1 ) was highly susceptible to oncogene induced breast cancer. Here we used a mammary organoid system to examine which Mre11 dependent responses are tumor suppressive. We found that Mre11 ATLD1/ATLD1 organoids exhibited an elevated interferon stimulated gene (ISG) signature and sustained changes in chromatin accessibility. This Mre11 ATLD1/ATLD1 phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation of Ifi205 in Mre11 ATLD1/ATLD1 organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed in WT . Implantation of Mre11 ATLD1/ATLD1 organoids and activation of oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implanted Ifi205 -/- Mre11 ATLD1/ATLD1 organoids. These data reveal a connection between innate immune signaling and tumor suppression in mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to tonic innate immune transcriptional programs.
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3
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Baran M, Feriotti C, McGinley A, Carlile SR, Jiang Z, Calderon-Gonzalez R, Dumigan A, Sá-Pessoa J, Sutton CE, Kearney J, McLoughlin RM, Mills KHG, Fitzgerald KA, Bengeochea JA, Bowie AG. PYHIN protein IFI207 regulates cytokine transcription and IRF7 and contributes to the establishment of K. pneumoniae infection. Cell Rep 2023; 42:112341. [PMID: 37018072 DOI: 10.1016/j.celrep.2023.112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 02/02/2023] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
PYHIN proteins AIM2 and IFI204 sense pathogen DNA, while other PYHINs have been shown to regulate host gene expression through as-yet unclear mechanisms. We characterize mouse PYHIN IFI207, which we find is not involved in DNA sensing but rather is required for cytokine promoter induction in macrophages. IFI207 co-localizes with both active RNA polymerase II (RNA Pol II) and IRF7 in the nucleus and enhances IRF7-dependent gene promoter induction. Generation of Ifi207-/- mice shows no role for IFI207 in autoimmunity. Rather, IFI207 is required for the establishment of a Klebsiella pneumoniae lung infection and for Klebsiella macrophage phagocytosis. These insights into IFI207 function illustrate that PYHINs can have distinct roles in innate immunity independent of DNA sensing and highlight the need to better characterize the whole mouse locus, one gene at a time.
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Affiliation(s)
- Marcin Baran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Claudia Feriotti
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Aoife McGinley
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Simon R Carlile
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Zhaozhao Jiang
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ricardo Calderon-Gonzalez
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Caroline E Sutton
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Jay Kearney
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Rachel M McLoughlin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Kingston H G Mills
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Katherine A Fitzgerald
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jose A Bengeochea
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland.
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4
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Gu L, Casserly D, Brady G, Carpenter S, Bracken AP, Fitzgerald KA, Unterholzner L, Bowie AG. Myeloid cell nuclear differentiation antigen controls the pathogen-stimulated type I interferon cascade in human monocytes by transcriptional regulation of IRF7. Nat Commun 2022; 13:14. [PMID: 35013241 PMCID: PMC8748983 DOI: 10.1038/s41467-021-27701-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
Type I interferons (IFNs) are critical for anti-viral responses, and also drive autoimmunity when dysregulated. Upon viral sensing, monocytes elicit a sequential cascade of IFNβ and IFNα production involving feedback amplification, but how exactly this cascade is regulated in human cells is incompletely understood. Here we show that the PYHIN protein myeloid cell nuclear differentiation antigen (MNDA) is required for IFNα induction in monocytes. Unlike other PYHINs, this is not due to a pathogen sensing role, but rather MNDA regulated expression of IRF7, a transcription factor essential for IFNα induction. Mechanistically, MNDA is required for recruitment of STAT2 and RNA polymerase II to the IRF7 gene promoter, and in fact MNDA is itself recruited to the IRF7 promoter after type I IFN stimulation. These data implicate MNDA as a critical regulator of the type I IFN cascade in human myeloid cells and reveal a new role for human PYHINs in innate immune gene induction. The interferon response is a critical component of the innate immune response. Here the authors implicate MNDA in the regulation of type I interferon responses to pathogen infection.
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Affiliation(s)
- Lili Gu
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - David Casserly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Gareth Brady
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Susan Carpenter
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Katherine A Fitzgerald
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Leonie Unterholzner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.,Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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5
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Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P, Unterholzner L, Xiao TS, Jin T. Structural mechanism of DNA recognition by the p204 HIN domain. Nucleic Acids Res 2021; 49:2959-2972. [PMID: 33619523 PMCID: PMC7969034 DOI: 10.1093/nar/gkab076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/22/2021] [Accepted: 02/14/2021] [Indexed: 12/25/2022] Open
Abstract
The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins. Moreover, we obtained the crystal structure of p204 HINab domain in complex with dsDNA and provided insights into the dsDNA binding mode. p204 HINab binds dsDNA mainly through α2 helix of HINa and HINb, and the linker between them, revealing a similar HIN:DNA binding mode. Both HINa and HINb are vital for HINab recognition of dsDNA, as confirmed by fluorescence polarization assays. Furthermore, a HINa dimerization interface was observed in structures of p204 HINa and HINab:dsDNA complex, which is involved in binding dsDNA. The linker between HINa and HINb reveals dynamic flexibility in solution and changes its direction at ∼90° angle in comparison with crystal structure of HINab:dsDNA complex. These structural information provide insights into the mechanism of DNA recognition by different HIN domains, and shed light on the unique roles of two HIN domains in activating the IFI16/p204 signaling pathway.
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Affiliation(s)
- Xiaojiao Fan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, P.R. China
| | - Jiansheng Jiang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan Zhao
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027 China
| | - Feng Chen
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027 China
| | - Huan Ma
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027 China
| | - Patrick Smith
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leonie Unterholzner
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YQ, UK
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, P.R. China
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027 China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
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6
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Dong X, Hu X, Bao Y, Li G, Yang XD, Slauch JM, Chen LF. Brd4 regulates NLRC4 inflammasome activation by facilitating IRF8-mediated transcription of Naips. J Cell Biol 2021; 220:e202005148. [PMID: 33535228 PMCID: PMC7863722 DOI: 10.1083/jcb.202005148] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/13/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
NLRC4 inflammasome activation and the subsequent maturation of IL-1β and IL-18 are critical for protection against infection by bacterial pathogens. The epigenetic regulator Brd4 has emerged as a key player in inflammation by regulating the expression of inflammatory cytokines. However, whether Brd4 has any role in inflammasome activation remains undetermined. Here, we demonstrated that Brd4 is an important regulator of NLRC4 inflammasome activation in response to Salmonella typhimurium infection. Brd4-deficient bone marrow-derived macrophages (BMDMs) displayed impaired caspase-1 activation, ASC oligomerization, IL-1β maturation, gasdermin-D cleavage, and pyroptosis in response to S.typhimurium infection. RNA sequencing and RT-PCR results revealed that the transcription of Naips was decreased in Brd4-deficient BMDMs. Brd4 formed a complex with IRF8/PU.1 and bound to the IRF8 and PU.1 binding motifs on the promoters of Naips to maintain the expression of Naips. Furthermore, myeloid lineage-specific Brd4 conditional knockout mice were more susceptible to S.typhimurium infection with increased mortality, bacterial loads, and tissue damage; impaired inflammasome-dependent cytokine production; and pyroptosis. Our studies identify a novel function of Brd4 in innate immunity by controlling inflammasome-mediated cytokine release and pyroptosis to effectively battle S.typhimurium infection.
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Affiliation(s)
- Xingchen Dong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Xiangming Hu
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yan Bao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Guo Li
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xiao-dong Yang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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7
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Transcriptional Regulation of Inflammasomes. Int J Mol Sci 2020; 21:ijms21218087. [PMID: 33138274 PMCID: PMC7663688 DOI: 10.3390/ijms21218087] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Inflammasomes are multimolecular complexes with potent inflammatory activity. As such, their activity is tightly regulated at the transcriptional and post-transcriptional levels. In this review, we present the transcriptional regulation of inflammasome genes from sensors (e.g., NLRP3) to substrates (e.g., IL-1β). Lineage-determining transcription factors shape inflammasome responses in different cell types with profound consequences on the responsiveness to inflammasome-activating stimuli. Pro-inflammatory signals (sterile or microbial) have a key transcriptional impact on inflammasome genes, which is largely mediated by NF-κB and that translates into higher antimicrobial immune responses. Furthermore, diverse intrinsic (e.g., circadian clock, metabolites) or extrinsic (e.g., xenobiotics) signals are integrated by signal-dependent transcription factors and chromatin structure changes to modulate transcriptionally inflammasome responses. Finally, anti-inflammatory signals (e.g., IL-10) counterbalance inflammasome genes induction to limit deleterious inflammation. Transcriptional regulations thus appear as the first line of inflammasome regulation to raise the defense level in front of stress and infections but also to limit excessive or chronic inflammation.
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8
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Insights into Sensing of Murine Retroviruses. Viruses 2020; 12:v12080836. [PMID: 32751803 PMCID: PMC7472155 DOI: 10.3390/v12080836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Retroviruses are major causes of disease in animals and human. Better understanding of the initial host immune response to these viruses could provide insight into how to limit infection. Mouse retroviruses that are endemic in their hosts provide an important genetic tool to dissect the different arms of the innate immune system that recognize retroviruses as foreign. Here, we review what is known about the major branches of the innate immune system that respond to mouse retrovirus infection, Toll-like receptors and nucleic acid sensors, and discuss the importance of these responses in activating adaptive immunity and controlling infection.
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9
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Cartland SP, Lin RCY, Genner S, Patil MS, Martínez GJ, Barraclough JY, Gloss B, Misra A, Patel S, Kavurma MM. Vascular transcriptome landscape of Trail -/- mice: Implications and therapeutic strategies for diabetic vascular disease. FASEB J 2020; 34:9547-9562. [PMID: 32501591 DOI: 10.1096/fj.201902785r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/30/2020] [Accepted: 05/08/2020] [Indexed: 12/20/2022]
Abstract
Circulating plasma TRAIL levels are suppressed in patients with cardiovascular and diabetic diseases. To identify novel targets in vascular metabolic diseases, genome-wide transcriptome of aortic tissue from Trail-/- versus Trail+/+ mice were interrogated. We found 861 genes differentially expressed with TRAIL deletion. Gene enrichment analyses showed many of these genes were related to inflammation, cell-to-cell cytoskeletal interactions, and transcriptional modulation. We identified vascular protective and pathological gene clusters, with Ifi205 as the most significantly reduced vascular protective gene, whereas Glut1, the most significantly increased pathological gene with TRAIL deletion. We hypothesized that therapeutic targets could be devised from such integrated analysis and validated our findings from vascular tissues of diabetic mice. From the differentially expressed gene targets, enriched transcription factor (TF) and microRNA binding motifs were identified. The top two TFs were Elk1 and Sp1, with enrichment to eight gene targets common to both. miR-520d-3p and miR-377-3p were the top enriched microRNAs with TRAIL deletion; with four overlapping genes enriched for both microRNAs. Our findings offer an alternate in silico approach for therapeutic target identification and present a deeper understanding of gene signatures and pathways altered with TRAIL suppression in the vasculature.
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Affiliation(s)
- Siân P Cartland
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ruby C Y Lin
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Scott Genner
- Heart Research Institute, Sydney, NSW, Australia
| | - Manisha S Patil
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gonzalo J Martínez
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, Sydney, NSW, Australia.,División de Enfermedades Cardiovasculares, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Nucleus for Cardiovascular Magnetic Resonance, Santiago, Chile
| | - Jennifer Y Barraclough
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Brian Gloss
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Ashish Misra
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sanjay Patel
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Mary M Kavurma
- Heart Research Institute, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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10
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Massa D, Baran M, Bengoechea JA, Bowie AG. PYHIN1 regulates pro-inflammatory cytokine induction rather than innate immune DNA sensing in airway epithelial cells. J Biol Chem 2020; 295:4438-4450. [PMID: 32102850 PMCID: PMC7135979 DOI: 10.1074/jbc.ra119.011400] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/23/2020] [Indexed: 12/16/2022] Open
Abstract
Animal cells use pattern-recognition receptors (PRRs) to detect specific pathogens. Pathogen detection mounts an appropriate immune response, including interferon and cytokine induction. The intracellular PRR-signaling pathways that detect DNA viruses have been characterized, particularly in myeloid cells. In these pathways, cGMP-AMP synthase (cGAS) and the pyrin and HIN domain family member (PYHIN) protein interferon-γ–inducible protein 16 (IFI16) detect DNA and signal via stimulator of interferon genes protein (STING). However, although airway epithelial cells are frontline sentinels in detecting pathogens, information on how they respond to DNA viruses is limited, and the roles of PYHIN proteins in these cells are unknown. Here, we examined expression and activities of cGAS, STING, and PYHINs in human lung epithelial cells. A549 epithelial cells, commonly used for RNA-sensing studies, failed to respond to DNA because they lacked STING expression, and ectopic STING expression restored a cGAS-dependent DNA response in these cells. In contrast, NuLi-1 immortalized human bronchial epithelial cells did express STING, which was activated after DNA stimulation and mediated DNA-dependent gene induction. PYHIN1, which like IFI16 has been proposed to be a viral DNA sensor, was the only PYHIN protein expressed in both airway epithelial cell types. However, rather than having a role in DNA sensing, PYHIN1 induced proinflammatory cytokines in response to interleukin-1 (IL-1) or tumor necrosis factor α (TNFα) stimulation. Of note, PYHIN1, via its HIN domain, directly induced IL-6 and TNFα transcription, revealing that PYHIN proteins play a role in proinflammatory gene induction in airway epithelial cells.
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Affiliation(s)
- Davide Massa
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Marcin Baran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Jose A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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11
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Roy A, Ghosh A, Kumar B, Chandran B. IFI16, a nuclear innate immune DNA sensor, mediates epigenetic silencing of herpesvirus genomes by its association with H3K9 methyltransferases SUV39H1 and GLP. eLife 2019; 8:49500. [PMID: 31682228 PMCID: PMC6855800 DOI: 10.7554/elife.49500] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/01/2019] [Indexed: 12/25/2022] Open
Abstract
IFI16, an innate immune DNA sensor, recognizes the nuclear episomal herpes viral genomes and induces the inflammasome and interferon-β responses. IFI16 also regulates cellular transcription and act as a DNA virus restriction factor. IFI16 knockdown disrupted the latency of Kaposi’s sarcoma associated herpesvirus (KSHV) and induced lytic transcripts. However, the mechanism of IFI16’s transcription regulation is unknown. Here, we show that IFI16 is in complex with the H3K9 methyltransferase SUV39H1 and GLP and recruits them to the KSHV genome during de novo infection and latency. The resulting depositions of H3K9me2/me3 serve as a docking site for the heterochromatin-inducing HP1α protein leading into the IFI16-dependent epigenetic modifications and silencing of KSHV lytic genes. These studies suggest that IFI16’s interaction with H3K9MTases is one of the potential mechanisms by which IFI16 regulates transcription and establish an important paradigm of an innate immune sensor’s involvement in epigenetic silencing of foreign DNA.
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Affiliation(s)
- Arunava Roy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Anandita Ghosh
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
| | - Binod Kumar
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, United States
| | - Bala Chandran
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, United States
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12
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Mancini M, Vidal SM. Insights into the pathogenesis of herpes simplex encephalitis from mouse models. Mamm Genome 2018; 29:425-445. [PMID: 30167845 PMCID: PMC6132704 DOI: 10.1007/s00335-018-9772-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/09/2018] [Indexed: 01/05/2023]
Abstract
A majority of the world population is infected with herpes simplex viruses (HSV; human herpesvirus types 1 and 2). These viruses, perhaps best known for their manifestation in the genital or oral mucosa, can also cause herpes simplex encephalitis, a severe and often fatal disease of the central nervous system. Antiviral therapies for HSV are only partially effective since the virus can establish latent infections in neurons, and severe pathological sequelae in the brain are common. A better understanding of disease pathogenesis is required to develop new strategies against herpes simplex encephalitis, including the precise viral and host genetic determinants that promote virus invasion into the central nervous system and its associated immunopathology. Here we review the current understanding of herpes simplex encephalitis from the host genome perspective, which has been illuminated by groundbreaking work on rare herpes simplex encephalitis patients together with mechanistic insight from single-gene mouse models of disease. A complex picture has emerged, whereby innate type I interferon-mediated antiviral signaling is a central pathway to control viral replication, and the regulation of immunopathology and the balance between apoptosis and autophagy are critical to disease severity in the central nervous system. The lessons learned from mouse studies inform us on fundamental defense mechanisms at the interface of host–pathogen interactions within the central nervous system, as well as possible rationales for intervention against infections from severe neuropathogenic viruses.
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Affiliation(s)
- Mathieu Mancini
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill Research Centre on Complex Traits, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill Research Centre on Complex Traits, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada.
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13
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Wang PH, Ye ZW, Deng JJ, Siu KL, Gao WW, Chaudhary V, Cheng Y, Fung SY, Yuen KS, Ho TH, Chan CP, Zhang Y, Kok KH, Yang W, Chan CP, Jin DY. Inhibition of AIM2 inflammasome activation by a novel transcript isoform of IFI16. EMBO Rep 2018; 19:embr.201845737. [PMID: 30104205 DOI: 10.15252/embr.201845737] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
Mouse p202 is a disease locus for lupus and a dominant-negative inhibitor of AIM2 inflammasome activation. A human homolog of p202 has not been identified so far. Here, we report a novel transcript isoform of human IFI16-designated IFI16-β, which has a domain architecture similar to that of mouse p202. Like p202, IFI16-β contains two HIN domains, but lacks the pyrin domain. IFI16-β is ubiquitously expressed in various human tissues and cells. Its mRNA levels are also elevated in leukocytes of patients with lupus, virus-infected cells, and cells treated with interferon-β or phorbol ester. IFI16-β co-localizes with AIM2 in the cytoplasm, whereas IFI16-α is predominantly found in the nucleus. IFI16-β interacts with AIM2 to impede the formation of a functional AIM2-ASC complex. In addition, IFI16-β sequesters cytoplasmic dsDNA and renders it unavailable for AIM2 sensing. Enforced expression of IFI16-β inhibits the activation of AIM2 inflammasome, whereas knockdown of IFI16-β augments interleukin-1β secretion triggered by dsDNA but not dsRNA Thus, cytoplasm-localized IFI16-β is functionally equivalent to mouse p202 that exerts an inhibitory effect on AIM2 inflammasome.
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Affiliation(s)
- Pei-Hui Wang
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zi-Wei Ye
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jian-Jun Deng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wei-Wei Gao
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Vidyanath Chaudhary
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yun Cheng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kit-San Yuen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ting-Hin Ho
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ching-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yan Zhang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kin-Hang Kok
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wanling Yang
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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