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Graves D, Akkerman N, Fulham L, Helwer R, Pelka P. Molecular insights into type I interferon suppression and enhanced pathogenicity by species B human adenoviruses B7 and B14. mBio 2024:e0103824. [PMID: 38940561 DOI: 10.1128/mbio.01038-24] [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: 04/05/2024] [Accepted: 05/22/2024] [Indexed: 06/29/2024] Open
Abstract
Human adenoviruses (HAdVs) are small DNA viruses that generally cause mild disease. Certain strains, particularly those belonging to species B HAdVs, can cause severe pneumonia and have a relatively high mortality rate. Little is known about the molecular aspects of how these highly pathogenic species affect the infected cell and how they suppress innate immunity. The present study provides molecular insights into how species B adenoviruses suppress the interferon signaling pathway. Our study shows that these viruses, unlike HAdV-C2, are resistant to type I interferon. This resistance likely arises due to the highly efficient suppression of interferon-stimulated gene expression. Unlike in HAdV-C2, HAdV-B7 and B14 sequester STAT2 and RNA polymerase II from interferon-stimulated gene promoters in infected cells. This results in suppressed interferon- stimulated gene activation. In addition, we show that RuvBL1 and RuvBL2, cofactors important for RNA polymerase II recruitment to promoters and interferon-stimulated gene activation, are redirected to the cytoplasm forming high molecular weight complexes that, likely, are unable to associate with chromatin. Proteomic analysis also identified key differences in the way these viruses affect the host cell, providing insights into species B-associated high pathogenicity. Curiously, we observed that at the level of protein expression changes to the infected cell, HAdV-C2 and B7 were more similar than those of the same species, B7 and B14. Collectively, our study represents the first such study of innate immune suppression by the highly pathogenic HAdV-B7 and B14, laying an important foundation for future investigations.IMPORTANCEHuman adenoviruses form a large family of double-stranded DNA viruses known for a variety of usually mild diseases. Certain strains of human adenovirus cause severe pneumonia leading to much higher mortality and morbidity than most other strains. The reasons for this enhanced pathogenicity are unknown. Our study provides a molecular investigation of how these highly pathogenic strains might inactivate the interferon signaling pathway, highlighting the lack of sensitivity of these viruses to type I interferon in general while providing a global picture of how viral changes in cellular proteins drive worse disease outcomes.
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Affiliation(s)
- Drayson Graves
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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Ravi Sundar Jose Geetha A, Fischer K, Babadei O, Smesnik G, Vogt A, Platanitis E, Müller M, Farlik M, Decker T. Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling. EMBO J 2024; 43:2233-2263. [PMID: 38658796 PMCID: PMC11148166 DOI: 10.1038/s44318-024-00092-7] [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: 06/20/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Type I interferons (IFN-I, including IFNβ) and IFNγ produce overlapping, yet clearly distinct immunological activities. Recent data show that the distinctness of global transcriptional responses to the two IFN types is not apparent when comparing their immediate effects. By analyzing nascent transcripts induced by IFN-I or IFNγ over a period of 48 h, we now show that the distinctiveness of the transcriptomes emerges over time and is based on differential employment of the ISGF3 complex as well as of the second-tier transcription factor IRF1. The distinct transcriptional properties of ISGF3 and IRF1 correspond with a largely diverse nuclear protein interactome. Mechanistically, we describe the specific input of ISGF3 and IRF1 into enhancer activation and the regulation of chromatin accessibility at interferon-stimulated genes (ISG). We further report differences between the IFN types in altering RNA polymerase II pausing at ISG 5' ends. Our data provide insight how transcriptional regulators create immunological identities of IFN-I and IFNγ.
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Affiliation(s)
- Aarathy Ravi Sundar Jose Geetha
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Katrin Fischer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Olga Babadei
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Georg Smesnik
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | | | - Ekaterini Platanitis
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, 1090, Austria
| | - Thomas Decker
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, 1030, Austria.
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna, 1030, Austria.
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3
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Ji Y, Chen W, Wang X. Bromodomain and Extraterminal Domain Protein 2 in Multiple Human Diseases. J Pharmacol Exp Ther 2024; 389:277-288. [PMID: 38565308 DOI: 10.1124/jpet.123.002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Bromodomain and extraterminal domain protein 2 (BRD2), a member of the bromodomain and extraterminal domain (BET) protein family, is a crucial epigenetic regulator with significant function in various diseases and cellular processes. The central function of BRD2 is modulating gene transcription by binding to acetylated lysine residues on histones and transcription factors. This review highlights key findings on BRD2 in recent years, emphasizing its roles in maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. BRD2's diverse functions are underscored by its involvement in diseases such as malignant tumors, neurologic disorders, inflammatory conditions, metabolic diseases, and virus infection. Notably, the potential role of BRD2 as a diagnostic marker and therapeutic target is discussed in the context of various diseases. Although pan inhibitors targeting the BET family have shown promise in preclinical studies, a critical need exists for the development of highly selective BRD2 inhibitors. In conclusion, this review offers insights into the multifaceted nature of BRD2 and calls for continued research to unravel its intricate mechanisms and harness its therapeutic potential. SIGNIFICANCE STATEMENT: BRD2 is involved in the occurrence and development of diseases through maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. Targeting BRD2 through protein degradation-targeting complexes technology is emerging as a promising therapeutic approach for malignant cancer and inflammatory diseases.
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Affiliation(s)
- Yikang Ji
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Wantao Chen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Xu Wang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
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4
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Cao LB, Ruan ZL, Yang YL, Zhang NC, Gao C, Cai C, Zhang J, Hu MM, Shu HB. Estrogen receptor α-mediated signaling inhibits type I interferon response to promote breast carcinogenesis. J Mol Cell Biol 2024; 15:mjad047. [PMID: 37442610 PMCID: PMC11066933 DOI: 10.1093/jmcb/mjad047] [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: 10/20/2022] [Revised: 02/22/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Estrogen receptor α (ERα) is an important driver and therapeutic target in ∼70% of breast cancers. How ERα drives breast carcinogenesis is not fully understood. In this study, we show that ERα is a negative regulator of type I interferon (IFN) response. Activation of ERα by its natural ligand estradiol inhibits IFN-β-induced transcription of downstream IFN-stimulated genes (ISGs), whereas ERα deficiency or the stimulation with its antagonist fulvestrant has opposite effects. Mechanistically, ERα induces the expression of the histone 2A variant H2A.Z to restrict the engagement of the IFN-stimulated gene factor 3 (ISGF3) complex to the promoters of ISGs and also interacts with STAT2 to disrupt the assembly of the ISGF3 complex. These two events mutually lead to the inhibition of ISG transcription induced by type I IFNs. In a xenograft mouse model, fulvestrant enhances the ability of IFN-β to suppress ERα+ breast tumor growth. Consistently, clinical data analysis reveals that ERα+ breast cancer patients with higher levels of ISGs exhibit higher long-term survival rates. Taken together, our findings suggest that ERα inhibits type I IFN response via two distinct mechanisms to promote breast carcinogenesis.
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Affiliation(s)
- Li-Bo Cao
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Zi-Lun Ruan
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Yu-Lin Yang
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Nian-Chao Zhang
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Chuan Gao
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Cheguo Cai
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Jing Zhang
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Ming-Ming Hu
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
| | - Hong-Bing Shu
- Department of Infectious Diseases, Medical Research Institute, Zhongnan Hospital of Wuhan University, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
- Research Unit of Innate Immune and Inflammatory Diseases, Chinese Academy of Medical Sciences, Wuhan 430072, China
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5
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Galieva A, Egorov A, Malogolovkin A, Brovin A, Karabelsky A. RNA-Seq Analysis of Trans-Differentiated ARPE-19 Cells Transduced by AAV9-AIPL1 Vectors. Int J Mol Sci 2023; 25:197. [PMID: 38203368 PMCID: PMC10778816 DOI: 10.3390/ijms25010197] [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: 11/18/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Inherited retinal disorders (IRD) have become a primary focus of gene therapy research since the success of adeno-associated virus-based therapeutics (voretigene neparvovec-rzyl) for Leber congenital amaurosis type 2 (LCA2). Dozens of monogenic IRDs could be potentially treated with a similar approach using an adeno-associated virus (AAV) to transfer a functional gene into the retina. Here, we present the results of the design, production, and in vitro testing of the AAV serotype 9 (AAV9) vector carrying the codon-optimized (co) copy of aryl hydrocarbon receptor-interacting protein like-1 (AIPL1) as a possible treatment for LCA4. The pAAV-AIPL1co was able to successfully transduce retinal pigment epithelium cells (ARPE-19) and initiate the expression of human AIPL1. Intriguingly, cells transduced with AAV9-AIPL1co showed much less antiviral response than AAV9-AIPL1wt (wild-type AIPL1) transduced. RNA-sequencing (RNA-seq) analysis of trans-differentiated ARPE-19 cells transduced with AAV9-AIPL1co demonstrated significant differences in the expression of genes involved in the innate immune response. In contrast, AAV9-AIPL1wt induced the prominent activation of multiple interferon-stimulated genes. The key part of the possible regulatory molecular mechanism is the activation of dsRNA-responsive antiviral oligoadenylate synthetases, and a significant increase in the level of histone coding genes' transcripts overrepresented in RNA-seq data (i.e., H1, H2A, H2B, H3, and H4). The RNA-seq data suggests that AAV9-AIPL1co exhibiting less immunogenicity than AAV9-AIPL1wt can be used for potency testing, using relevant animal models to develop future therapeutics for LCA4.
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Affiliation(s)
- Alima Galieva
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.G.); (A.M.); (A.B.)
| | - Alexander Egorov
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.G.); (A.M.); (A.B.)
| | - Alexander Malogolovkin
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.G.); (A.M.); (A.B.)
- Molecular Virology Laboratory, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Andrew Brovin
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.G.); (A.M.); (A.B.)
| | - Alexander Karabelsky
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sirius, Russia; (A.G.); (A.M.); (A.B.)
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6
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Jiang Z, Lozano-Durán R. Do plant histone variants stand idly by while DNA viruses invade the nucleus? STRESS BIOLOGY 2023; 3:46. [PMID: 37955829 PMCID: PMC10643808 DOI: 10.1007/s44154-023-00129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023]
Affiliation(s)
- Zhihao Jiang
- Department of Plant Biochemistry, Center for Molecular Plant Biology (ZMBP), Eberhard-Karls University of Tübingen, Tübingen, Germany.
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Center for Molecular Plant Biology (ZMBP), Eberhard-Karls University of Tübingen, Tübingen, Germany
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7
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Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development 2023; 150:dev202338. [PMID: 37938830 PMCID: PMC10651094 DOI: 10.1242/dev.202338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, long interspersed nuclear elements and long terminal repeats, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the levels of the repressive histone modification H3K9me3 and a moderate increase in chromatin accessibility. Notably, however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein via transgenic overexpression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes.
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Affiliation(s)
- Fanju W. Meng
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | - Benjamin Delatte
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA 92008, USA
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Yang C, He Y, Wang Y, McKinnon PJ, Shahani V, Miller DD, Pfeffer LM. Next-generation bromodomain inhibitors of the SWI/SNF complex enhance DNA damage and cell death in glioblastoma. J Cell Mol Med 2023; 27:2770-2781. [PMID: 37593885 PMCID: PMC10494295 DOI: 10.1111/jcmm.17907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive brain cancer with a poor prognosis. While surgical resection is the primary treatment, adjuvant temozolomide (TMZ) chemotherapy and radiotherapy only provide slight improvement in disease course and outcome. Unfortunately, most treated patients experience recurrence of highly aggressive, therapy-resistant tumours and eventually succumb to the disease. To increase chemosensitivity and overcome therapy resistance, we have modified the chemical structure of the PFI-3 bromodomain inhibitor of the BRG1 and BRM catalytic subunits of the SWI/SNF chromatin remodelling complex. Our modifications resulted in compounds that sensitized GBM to the DNA alkylating agent TMZ and the radiomimetic bleomycin. We screened these chemical analogues using a cell death ELISA with GBM cell lines and a cellular thermal shift assay using epitope tagged BRG1 or BRM bromodomains expressed in GBM cells. An active analogue, IV-129, was then identified and further modified, resulting in new generation of bromodomain inhibitors with distinct properties. IV-255 and IV-275 had higher bioactivity than IV-129, with IV-255 selectively binding to the bromodomain of BRG1 and not BRM, while IV-275 bound well to both BRG1 and BRM bromodomains. In contrast, IV-191 did not bind to either bromodomain or alter GBM chemosensitivity. Importantly, both IV-255 and IV-275 markedly increased the extent of DNA damage induced by TMZ and bleomycin as determined by nuclear γH2AX staining. Our results demonstrate that these next-generation inhibitors selectively bind to the bromodomains of catalytic subunits of the SWI/SNF complex and sensitize GBM to the anticancer effects of TMZ and bleomycin. This approach holds promise for improving the treatment of GBM.
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Affiliation(s)
- Chuanhe Yang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yali He
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yinan Wang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - Vijay Shahani
- Recursion Pharmaceuticals IncTorontoOntarioM5V 2A2Canada
| | - Duane D. Miller
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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9
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Duan Z, Shi H, Xing J, Zhang Q, Liu M. Mutation of Basic Residues R283, R286, and K288 in the Matrix Protein of Newcastle Disease Virus Attenuates Viral Replication and Pathogenicity. Int J Mol Sci 2023; 24:ijms24020980. [PMID: 36674496 PMCID: PMC9864103 DOI: 10.3390/ijms24020980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
The matrix (M) protein of Newcastle disease virus (NDV) contains large numbers of unevenly distributed basic residues, but the precise function of most basic residues in the M protein remains enigmatic. We previously demonstrated that the C-terminus (aa 264-313) of M protein interacted with the extra-terminal (ET) domain of chicken bromodomain-containing protein 2 (chBRD2), which promoted NDV replication by downregulating chBRD2 expression and facilitating viral RNA synthesis and transcription. However, the key amino acid sites determining M's interaction with chBRD2/ET and their roles in the replication and pathogenicity of NDV are not known. In this study, three basic residues-R283, R286, and K288-in the NDV M protein were verified to be responsible for its interaction with chBRD2/ET. In addition, mutation of these basic residues (R283A/R286A/K288A) in the M protein changed its electrostatic pattern and abrogated the decreased expression of endogenic chBRD2. Moreover, a recombinant virus harboring these mutations resulted in a pathotype change of NDV and attenuated viral replication and pathogenicity in chickens due to the decreased viral RNA synthesis and transcription. Our findings therefore provide a better understanding of the crucial biological functions of M's basic residues and also aid in understanding the poorly understood pathogenesis of NDV.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence: ; Tel.: +86-(851)-8829-8005
| | - Haiying Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jingru Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qianyong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Menglan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
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Boccuni L, Podgorschek E, Schmiedeberg M, Platanitis E, Traxler P, Fischer P, Schirripa A, Novoszel P, Nebreda AR, Arthur JSC, Fortelny N, Farlik M, Sexl V, Bock C, Sibilia M, Kovarik P, Müller M, Decker T. Stress signaling boosts interferon-induced gene transcription in macrophages. Sci Signal 2022; 15:eabq5389. [PMID: 36512641 DOI: 10.1126/scisignal.abq5389] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Promoters of antimicrobial genes function as logic boards, integrating signals of innate immune responses. One such set of genes is stimulated by interferon (IFN) signaling, and the expression of these genes [IFN-stimulated genes (ISGs)] can be further modulated by cell stress-induced pathways. Here, we investigated the global effect of stress-induced p38 mitogen-activated protein kinase (MAPK) signaling on the response of macrophages to IFN. In response to cell stress that coincided with IFN exposure, the p38 MAPK-activated transcription factors CREB and c-Jun, in addition to the IFN-activated STAT family of transcription factors, bound to ISGs. In addition, p38 MAPK signaling induced activating histone modifications at the loci of ISGs and stimulated nuclear translocation of the CREB coactivator CRTC3. These actions synergistically enhanced ISG expression. Disrupting this synergy with p38 MAPK inhibitors improved the viability of macrophages infected with Listeria monocytogenes. Our findings uncover a mechanism of transcriptional synergism and highlight the biological consequences of coincident stress-induced p38 MAPK and IFN-stimulated signal transduction.
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Affiliation(s)
- Laura Boccuni
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Elke Podgorschek
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Moritz Schmiedeberg
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Ekaterini Platanitis
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Peter Traxler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
| | - Philipp Fischer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Alessia Schirripa
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna 1210, Austria
| | - Philipp Novoszel
- Center for Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - J Simon C Arthur
- Division of Cell Signaling and Immunology and University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Medical Research Council Protein Phosphorylation Unit, School of Life Sciences, Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Nikolaus Fortelny
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Computational Systems Biology Group, Department of Biosciences and Medical Biology, Paris Lodron University of Salzburg, Salzburg 5020, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna 1210, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Institute of Artificial Intelligence, Medical University of Vienna, Vienna 1090, Austria
| | - Maria Sibilia
- Center for Cancer Research, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Pavel Kovarik
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Decker
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna 1030, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, Vienna 1030, Austria
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11
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Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
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Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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12
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Platanitis E, Gruener S, Ravi Sundar Jose Geetha A, Boccuni L, Vogt A, Novatchkova M, Sommer A, Barozzi I, Müller M, Decker T. Interferons reshape the 3D conformation and accessibility of macrophage chromatin. iScience 2022; 25:103840. [PMID: 35243225 PMCID: PMC8857492 DOI: 10.1016/j.isci.2022.103840] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022] Open
Abstract
Engagement of macrophages in innate immune responses is directed by type I and type II interferons (IFN-I and IFN-γ, respectively). IFN triggers drastic changes in cellular transcriptomes, executed by JAK-STAT signal transduction and the transcriptional control of interferon-stimulated genes (ISG) by STAT transcription factors. Here, we study the immediate-early nuclear response to IFN-I and IFN-γ in murine macrophages. We show that the mechanism of gene control by both cytokines includes a rapid increase of DNA accessibility and rearrangement of the 3D chromatin contacts particularly between open chromatin of ISG loci. IFN-stimulated gene factor 3 (ISGF3), the major transcriptional regulator of ISG, controlled homeostatic and, most notably, induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.
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Affiliation(s)
| | - Stephan Gruener
- Max Perutz Labs, University of Vienna, Vienna, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | | | - Laura Boccuni
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Alexander Vogt
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Andreas Sommer
- Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Iros Barozzi
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Decker
- Max Perutz Labs, University of Vienna, Vienna, Austria
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13
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Detilleux D, Raynaud P, Pradet-Balade B, Helmlinger D. The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells. eLife 2022; 11:69705. [PMID: 35244540 PMCID: PMC8926402 DOI: 10.7554/elife.69705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Transcription is essential for cells to respond to signaling cues and involves factors with multiple distinct activities. One such factor, TRRAP, functions as part of two large complexes, SAGA and TIP60, which have crucial roles during transcription activation. Structurally, TRRAP belongs to the phosphoinositide 3 kinase-related kinases (PIKK) family but is the only member classified as a pseudokinase. Recent studies established that a dedicated HSP90 co-chaperone, the triple T (TTT) complex, is essential for PIKK stabilization and activity. Here, using endogenous auxin-inducible degron alleles, we show that the TTT subunit TELO2 promotes TRRAP assembly into SAGA and TIP60 in human colorectal cancer cells (CRCs). Transcriptomic analysis revealed that TELO2 contributes to TRRAP regulatory roles in CRC cells, most notably of MYC target genes. Surprisingly, TELO2 and TRRAP depletion also induced the expression of type I interferon genes. Using a combination of nascent RNA, antibody-targeted chromatin profiling (CUT&RUN), ChIP, and kinetic analyses, we propose a model by which TRRAP directly represses the transcription of IRF9, which encodes a master regulator of interferon-stimulated genes. We have therefore uncovered an unexpected transcriptional repressor role for TRRAP, which we propose contributes to its tumorigenic activity.
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Affiliation(s)
| | - Peggy Raynaud
- CRBM, University of Montpellier, CNRS, Montpellier, France
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14
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Dowling JW, Forero A. Beyond Good and Evil: Molecular Mechanisms of Type I and III IFN Functions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:247-256. [PMID: 35017214 DOI: 10.4049/jimmunol.2100707] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022]
Abstract
IFNs are comprised of three families of cytokines that confer protection against pathogen infection and uncontrolled cellular proliferation. The broad role IFNs play in innate and adaptive immune regulation has placed them under heavy scrutiny to position them as "friend" or "foe" across pathologies. Genetic lesions in genes involving IFN synthesis and signaling underscore the disparate outcomes of aberrant IFN signaling. Abrogation of the response leads to susceptibility to microbial infections whereas unabated IFN induction underlies a variety of inflammatory diseases and tumor immune evasion. Type I and III IFNs have overlapping roles in antiviral protection, yet the mechanisms by which they are induced and promote the expression of IFN-stimulated genes and inflammation can distinguish their biological functions. In this review, we examine the molecular factors that shape the shared and distinct roles of type I and III IFNs in immunity.
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Affiliation(s)
- Jack W Dowling
- Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, OH 43210; and.,Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
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15
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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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16
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Samelson AJ, Tran QD, Robinot R, Carrau L, Rezelj VV, Kain AM, Chen M, Ramadoss GN, Guo X, Lim SA, Lui I, Nuñez JK, Rockwood SJ, Wang J, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin BR, TenOever BR, Chakrabarti LA, Vignuzzi M, Tian R, Kampmann M. BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. Nat Cell Biol 2022; 24:24-34. [PMID: 35027731 PMCID: PMC8820466 DOI: 10.1038/s41556-021-00821-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 11/24/2021] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. Here we show that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a therapeutic target for COVID-19.
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Affiliation(s)
- Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Rémy Robinot
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Lucia Carrau
- Microbiology Department, NYU-Langone, New York, NY, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Merissa Chen
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Gokul N Ramadoss
- Gladstone Institutes, San Francisco, CA, USA
- Biomedical Sciences PhD Program, University of California San Francisco, San Francisco, CA, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Antibody Engineering, Genentech Inc., San Francisco, CA, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | | | - Jianhui Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Na Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | | | | | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | - James A Wells
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Lisa A Chakrabarti
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, Université de Paris, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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17
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Lu J, He X, Zhang L, Zhang R, Li W. Acetylation in Tumor Immune Evasion Regulation. Front Pharmacol 2021; 12:771588. [PMID: 34880761 PMCID: PMC8645962 DOI: 10.3389/fphar.2021.771588] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022] Open
Abstract
Acetylation is considered as one of the most common types of epigenetic modifications, and aberrant histone acetylation modifications are associated with the pathological process of cancer through the regulation of oncogenes and tumor suppressors. Recent studies have shown that immune system function and tumor immunity can also be affected by acetylation modifications. A comprehensive understanding of the role of acetylation function in cancer is essential, which may help to develop new therapies to improve the prognosis of cancer patients. In this review, we mainly discussed the functions of acetylase and deacetylase in tumor, immune system and tumor immunity, and listed the information of drugs targeting these enzymes in tumor immunotherapy.
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Affiliation(s)
- Jun Lu
- Hunan Normal University School of Medicine, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Xiang He
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China.,Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China
| | - Lijuan Zhang
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Ran Zhang
- Hunan Normal University School of Medicine, Changsha, China
| | - Wenzheng Li
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
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18
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Wu XM, Fang H, Zhang J, Bi YH, Chang MX. Histone H2A Nuclear/Cytoplasmic Trafficking Is Essential for Negative Regulation of Antiviral Immune Response and Lysosomal Degradation of TBK1 and IRF3. Front Immunol 2021; 12:771277. [PMID: 34868031 PMCID: PMC8636446 DOI: 10.3389/fimmu.2021.771277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 11/20/2022] Open
Abstract
Histone H2A is a nuclear molecule tightly associated in the form of the nucleosome. Our previous studies have demonstrated the antibacterial property of piscine H2A variants against gram-negative bacteria Edwardsiella piscicida and Gram-positive bacteria Streptococcus agalactiae. In this study, we show the function and mechanism of piscine H2A in the negative regulation of RLR signaling pathway and host innate immune response against spring viremia of carp virus (SVCV) infection. SVCV infection significantly inhibits the expression of histone H2A during an early stage of infection, but induces the expression of histone H2A during the late stage of infection such as at 48 and 72 hpi. Under normal physiological conditions, histone H2A is nuclear-localized. However, SVCV infection promotes the migration of histone H2A from the nucleus to the cytoplasm. The in vivo studies revealed that histone H2A overexpression led to the increased expression of SVCV gene and decreased survival rate. The overexpression of histone H2A also significantly impaired the expression levels of those genes involved in RLR antiviral signaling pathway. Furthermore, histone H2A targeted TBK1 and IRF3 to promote their protein degradation via the lysosomal pathway and impair the formation of TBK1-IRF3 functional complex. Importantly, histone H2A completely abolished TBK1-mediated antiviral activity and enormously impaired the protein expression of IRF3, especially nuclear IRF3. Further analysis demonstrated that the inhibition of histone H2A nuclear/cytoplasmic trafficking could relieve the protein degradation of TBK1 and IRF3, and blocked the negative regulation of histone H2A on the SVCV infection. Collectively, our results suggest that histone H2A nuclear/cytoplasmic trafficking is essential for negative regulation of RLR signaling pathway and antiviral immune response in response to SVCV infection.
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Affiliation(s)
- Xiao Man Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yong Hong Bi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
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19
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Samelson AJ, Tran QD, Robinot R, Carrau L, Rezelj VV, Mac Kain A, Chen M, Ramadoss GN, Guo X, Lim SA, Lui I, Nunez J, Rockwood SJ, Wang J, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin BR, TenOever BR, Chakrabarti LA, Vignuzzi M, Tian R, Kampmann M. BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.19.427194. [PMID: 33501440 PMCID: PMC7836110 DOI: 10.1101/2021.01.19.427194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. We found that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a novel therapeutic target for COVID-19.
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Affiliation(s)
- Avi J Samelson
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Quang Dinh Tran
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, 75006 Paris, France
| | - Rémy Robinot
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, CNRS UMR 3569, 75015 Paris, France
| | - Lucia Carrau
- Department of Microbiology, Icahn School of Medicine, New York, NY 10029
| | - Veronica V Rezelj
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France
- École Doctorale BioSPC, Université de Paris, Sorbonne Paris Cité, 75006 Paris, France
| | - Merissa Chen
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Gokul N Ramadoss
- Gladstone Institutes, San Francisco, 94158, CA, USA
- Biomedical Sciences PhD Program, University of California, San Francisco, CA, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Shion A Lim
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Present address: Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
| | - James Nunez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
| | | | - Jianhui Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China 518055
| | - Na Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, China 518055
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA 94063, USA, Department of Biology, Massachusetts Institute of Technology, Cambridge, 02142, USA
| | - Jennifer Oki
- Synthego Corporation, Redwood City, CA 94063, USA, Department of Biology, Massachusetts Institute of Technology, Cambridge, 02142, USA
| | - Travis Maures
- Synthego Corporation, Redwood City, CA 94063, USA, Department of Biology, Massachusetts Institute of Technology, Cambridge, 02142, USA
| | - Kevin Holden
- Synthego Corporation, Redwood City, CA 94063, USA, Department of Biology, Massachusetts Institute of Technology, Cambridge, 02142, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94158, USA
- Whitehead Institute for Biomedical Research, Cambridge, 02142, USA, Innovative Genomics Institute, Berkeley, 94720, CA, USA
| | - James A Wells
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA. 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | - Lisa A Chakrabarti
- Institut Pasteur, CIVIC Group, Virus and Immunity Unit, CNRS UMR 3569, 75015 Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- School of Medicine, Southern University of Science and Technology, Shenzhen, China 518055
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
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20
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Cheung KL, Kim C, Zhou MM. The Functions of BET Proteins in Gene Transcription of Biology and Diseases. Front Mol Biosci 2021; 8:728777. [PMID: 34540900 PMCID: PMC8446420 DOI: 10.3389/fmolb.2021.728777] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/31/2021] [Indexed: 12/25/2022] Open
Abstract
The BET (bromodomain and extra-terminal domain) family proteins, consisting of BRD2, BRD3, BRD4, and testis-specific BRDT, are widely acknowledged as major transcriptional regulators in biology. They are characterized by two tandem bromodomains (BDs) that bind to lysine-acetylated histones and transcription factors, recruit transcription factors and coactivators to target gene sites, and activate RNA polymerase II machinery for transcriptional elongation. Pharmacological inhibition of BET proteins with BD inhibitors has been shown as a promising therapeutic strategy for the treatment of many human diseases including cancer and inflammatory disorders. The recent advances in bromodomain protein biology have further uncovered the complex and versatile functions of BET proteins in the regulation of gene expression in chromatin. In this review article, we highlight our current understanding of BET proteins' functions in mediating protein-protein interactions required for chromatin-templated gene transcription and splicing, chromatin remodeling, DNA replication, and DNA damage repair. We further discuss context-dependent activator vs. repressor functions of individual BET proteins, isoforms, and bromodomains that may be harnessed for future development of BET bromodomain inhibitors as emerging epigenetic therapies for cancer and inflammatory disorders.
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21
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Leviyang S. Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state. Cytokine X 2021; 3:100056. [PMID: 34409284 PMCID: PMC8361084 DOI: 10.1016/j.cytox.2021.100056] [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] [Indexed: 11/28/2022] Open
Abstract
IFN stimulated binding of ISRE by ISGF3 is cell specific, particularly for ISRE in enhancer regions. IFN stimulated binding of ISRE in enhancer regions associates with differential expression. The homeostatic, chromatin state of an ISRE is predictive of IFN stimulated binding.
The type I interferon (IFN) signaling pathway involves binding of the transcription factor ISGF3 to IFN-stimulated response elements, ISREs. Gene expression under IFN stimulation is known to vary across cell types, but variation in ISGF3 binding to ISRE across cell types has not been characterized. We examined ISRE binding patterns under IFN stimulation across six cell types using existing ChIPseq datasets. We find that ISRE binding is largely cell specific for ISREs distal to transcription start sites (TSS) and largely conserved across cell types for ISREs proximal to TSS. We show that bound ISRE distal to TSS associate with differential expression of ISGs, although at weaker levels than bound ISRE proximal to TSS. Using existing ATACseq and ChIPseq datasets, we show that the chromatin state of ISRE at homeostasis is cell type specific and is predictive of cell specific, ISRE binding under IFN stimulation. Our results support a model in which the chromatin state of ISRE in enhancer elements is modulated in a cell type specific manner at homeostasis, leading to cell type specific differences in ISRE binding patterns under IFN stimulation.
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22
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Börold J, Eletto D, Busnadiego I, Mair NK, Moritz E, Schiefer S, Schmidt N, Petric PP, Wong WWL, Schwemmle M, Hale BG. BRD9 is a druggable component of interferon-stimulated gene expression and antiviral activity. EMBO Rep 2021; 22:e52823. [PMID: 34397140 PMCID: PMC8490982 DOI: 10.15252/embr.202152823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Interferon (IFN) induction of IFN-stimulated genes (ISGs) creates a formidable protective antiviral state. However, loss of appropriate control mechanisms can result in constitutive pathogenic ISG upregulation. Here, we used genome-scale loss-of-function screening to establish genes critical for IFN-induced transcription, identifying all expected members of the JAK-STAT signaling pathway and a previously unappreciated epigenetic reader, bromodomain-containing protein 9 (BRD9), the defining subunit of non-canonical BAF (ncBAF) chromatin-remodeling complexes. Genetic knockout or small-molecule-mediated degradation of BRD9 limits IFN-induced expression of a subset of ISGs in multiple cell types and prevents IFN from exerting full antiviral activity against several RNA and DNA viruses, including influenza virus, human immunodeficiency virus (HIV1), and herpes simplex virus (HSV1). Mechanistically, BRD9 acts at the level of transcription, and its IFN-triggered proximal association with the ISG transcriptional activator, STAT2, suggests a functional localization at selected ISG promoters. Furthermore, BRD9 relies on its intact acetyl-binding bromodomain and unique ncBAF scaffolding interaction with GLTSCR1/1L to promote IFN action. Given its druggability, BRD9 is an attractive target for dampening ISG expression under certain autoinflammatory conditions.
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Affiliation(s)
- Jacob Börold
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Davide Eletto
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nina K Mair
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Eva Moritz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samira Schiefer
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Nora Schmidt
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Philipp P Petric
- Faculty of Medicine, Institute of Virology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - W Wei-Lynn Wong
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Martin Schwemmle
- Faculty of Medicine, Institute of Virology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Benjamin G Hale
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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23
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Duan Z, Han Y, Zhou L, Yuan C, Wang Y, Zhao C, Tang H, Chen J. Chicken bromodomain-containing protein 2 interacts with the Newcastle disease virus matrix protein and promotes viral replication. Vet Res 2020; 51:120. [PMID: 32962745 PMCID: PMC7509934 DOI: 10.1186/s13567-020-00846-1] [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: 04/15/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Bromodomain-containing protein 2 (BRD2) is a nucleus-localized serine-threonine kinase that plays pivotal roles in the transcriptional control of diverse genes. In our previous study, the chicken BRD2 (chBRD2) protein was found to interact with the Newcastle disease virus (NDV) matrix (M) protein using a yeast two-hybrid screening system, but the role of the chBRD2 protein in the replication of NDV remains unclear. In this study, we first confirmed the interaction between the M protein and chBRD2 protein using fluorescence co-localization, co-immunoprecipitation and pull-down assays. Intracellular binding studies indicated that the C-terminus (aa 264-313) of the M protein and the extra-terminal (ET) domain (aa 619-683) of the chBRD2 protein were responsible for interactions with each other. Interestingly, although two amino acids (T621 and S649) found in the chBRD2/ET domain were different from those in the human BRD2/ET domain and in that of other mammals, they did not disrupt the BRD2-M interaction or the chBRD2-M interaction. In addition, we found that the transcription of the chBRD2 gene was obviously decreased in both NDV-infected cells and pEGFP-M-transfected cells in a dose-dependent manner. Moreover, small interfering RNA-mediated knockdown of chBRD2 or overexpression of chBRD2 remarkably enhanced or reduced NDV replication by upregulating or downregulating viral RNA synthesis and transcription, respectively. Overall, we demonstrate for the first time that the interaction of the M protein with the chBRD2 protein in the nucleus promotes NDV replication by downregulating chBRD2 expression and facilitating viral RNA synthesis and transcription. These results will provide further insight into the biological functions of the M protein in the replication of NDV.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China. .,College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China.
| | - Yifan Han
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Lei Zhou
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Chao Yuan
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Yanbi Wang
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Caiqin Zhao
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Hong Tang
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
| | - Jiaqi Chen
- College of Animal Science, Guizhou University, Jiaxiu South Road, Huaxi District, Guiyang, 550025, Guizhou, China
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24
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Lin D, Lin B, Bhanot H, Riou R, Abt NB, Rajagopal J, Saladi SV. RUVBL1 is an amplified epigenetic factor promoting proliferation and inhibiting differentiation program in head and neck squamous cancers. Oral Oncol 2020; 111:104930. [PMID: 32745900 DOI: 10.1016/j.oraloncology.2020.104930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/24/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Mutations in histone modifying enzymes and histone variants were identified in multiple cancers in The Cancer Genome Atlas (TCGA) studies. However, very little progress and understanding has been made in identifying the contribution of epigenetic factors in head and neck squamous cell carcinoma (HNSCC). Here, we report the identification of RUVBL1 (TIP49a), a component of the TIP60 histone modifying complex as being amplified and overexpressed in HNSCC. RUVBL1 plays a key role in incorporating histone variant H2AZ in chromatin thereby regulating transcription of key genes involved in differentiation, cancer cell proliferation and invasion. H2AZ is also overexpressed in HNSCC tumors thereby regulating RUVBL1/H2AZ dependent transcriptional programs. Patient data analysis of multiple cohorts including TCGA and single cell HNSCC data indicated RUVBL1 overexpression as a poor prognostic marker and predicts poor survival. In vitro experiments indicate a pro-proliferative role for RUVBL1/H2AZ in HNSCC cells. RUVBL1 inversely correlates with differentiation program and positively correlates with oncogenic programs, making it a key contributor to tumorigenesis and a vulnerable therapeutic target in HNSCC patients.
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Affiliation(s)
- Derrick Lin
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, United States; Massachusetts General Hospital Cancer Center, United States
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, United States
| | - Haymanti Bhanot
- Dana Farber Cancer Institute, Harvard Medical School, United States
| | - Rozenn Riou
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, United States
| | - Nicholas B Abt
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, United States; Massachusetts General Hospital Cancer Center, United States
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, United States; Broad Institute of MIT and Harvard, United States
| | - Srinivas Vinod Saladi
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, United States; Massachusetts General Hospital Cancer Center, United States; Broad Institute of MIT and Harvard, United States.
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25
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Ranjan A, Nguyen VQ, Liu S, Wisniewski J, Kim JM, Tang X, Mizuguchi G, Elalaoui E, Nickels TJ, Jou V, English BP, Zheng Q, Luk E, Lavis LD, Lionnet T, Wu C. Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction. eLife 2020; 9:e55667. [PMID: 32338606 PMCID: PMC7259955 DOI: 10.7554/elife.55667] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.
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Affiliation(s)
- Anand Ranjan
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Vu Q Nguyen
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Gaku Mizuguchi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Ejlal Elalaoui
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Timothy J Nickels
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook UniversityStony BrookUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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26
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Csumita M, Csermely A, Horvath A, Nagy G, Monori F, Göczi L, Orbea HA, Reith W, Széles L. Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5' and 3' flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion. Nucleic Acids Res 2020; 48:589-604. [PMID: 31799619 PMCID: PMC6954429 DOI: 10.1093/nar/gkz1112] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 12/28/2022] Open
Abstract
IRF3, IRF5 and IRF9 are transcription factors, which play distinct roles in the regulation of antiviral and inflammatory responses. The determinants that mediate IRF-specific enhancer selection are not fully understood. To uncover regions occupied predominantly by IRF3, IRF5 or IRF9, we performed ChIP-seq experiments in activated murine dendritic cells. The identified regions were analysed with respect to the enrichment of DNA motifs, the interferon-stimulated response element (ISRE) and ISRE half-site variants, and chromatin accessibility. Using a machine learning method, we investigated the predictability of IRF-dominance. We found that IRF5-dominant regions differed fundamentally from the IRF3- and IRF9-dominant regions: ISREs were rare, while the NFKB motif and special ISRE half-sites, such as 5'-GAGA-3' and 5'-GACA-3', were enriched. IRF3- and IRF9-dominant regions were characterized by the enriched ISRE motif and lower frequency of accessible chromatin. Enrichment analysis and the machine learning method uncovered the features that favour IRF3 or IRF9 dominancy (e.g. a tripartite form of ISRE and motifs for NF-κB for IRF3, and the GAS motif and certain ISRE variants for IRF9). This study contributes to our understanding of how IRF members, which bind overlapping sets of DNA sequences, can initiate signal-dependent responses without activating superfluous or harmful programmes.
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Affiliation(s)
- Mária Csumita
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Attila Csermely
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Fanny Monori
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Loránd Göczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Hans-Acha Orbea
- Department of Biochemistry, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Walter Reith
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Centre Médical Universitaire (CMU), CH-1211 Geneva, Switzerland
| | - Lajos Széles
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
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27
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Semer M, Bidon B, Larnicol A, Caliskan G, Catez P, Egly JM, Coin F, Le May N. DNA repair complex licenses acetylation of H2A.Z.1 by KAT2A during transcription. Nat Chem Biol 2019; 15:992-1000. [PMID: 31527837 DOI: 10.1038/s41589-019-0354-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/24/2019] [Indexed: 12/11/2022]
Abstract
Post-translational modifications of histone variant H2A.Z accompany gene transactivation, but its modifying enzymes still remain elusive. Here, we reveal a hitherto unknown function of human KAT2A (GCN5) as a histone acetyltransferase (HAT) of H2A.Z at the promoters of a set of transactivated genes. Expression of these genes also depends on the DNA repair complex XPC-RAD23-CEN2. We established that XPC-RAD23-CEN2 interacts both with H2A.Z and KAT2A to drive the recruitment of the HAT at promoters and license H2A.Z acetylation. KAT2A selectively acetylates H2A.Z.1 versus H2A.Z.2 in vitro on several well-defined lysines and we unveiled that alanine-14 in H2A.Z.2 is responsible for inhibiting the activity of KAT2A. Notably, the use of a nonacetylable H2A.Z.1 mutant shows that H2A.Z.1ac recruits the epigenetic reader BRD2 to promote RNA polymerase II recruitment. Our studies identify KAT2A as an H2A.Z.1 HAT in mammals and implicate XPC-RAD23-CEN2 as a transcriptional co-activator licensing the reshaping of the promoter epigenetic landscape.
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Affiliation(s)
- M Semer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - B Bidon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - A Larnicol
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - G Caliskan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Department of Pharmaceutical Biotechnology, Faculty of pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - P Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - J M Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - F Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
| | - N Le May
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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28
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Platanitis E, Demiroz D, Schneller A, Fischer K, Capelle C, Hartl M, Gossenreiter T, Müller M, Novatchkova M, Decker T. A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription. Nat Commun 2019; 10:2921. [PMID: 31266943 PMCID: PMC6606597 DOI: 10.1038/s41467-019-10970-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 06/11/2019] [Indexed: 01/12/2023] Open
Abstract
Cells maintain the balance between homeostasis and inflammation by adapting and integrating the activity of intracellular signaling cascades, including the JAK-STAT pathway. Our understanding of how a tailored switch from homeostasis to a strong receptor-dependent response is coordinated remains limited. Here, we use an integrated transcriptomic and proteomic approach to analyze transcription-factor binding, gene expression and in vivo proximity-dependent labelling of proteins in living cells under homeostatic and interferon (IFN)-induced conditions. We show that interferons (IFN) switch murine macrophages from resting-state to induced gene expression by alternating subunits of transcription factor ISGF3. Whereas preformed STAT2-IRF9 complexes control basal expression of IFN-induced genes (ISG), both type I IFN and IFN-γ cause promoter binding of a complete ISGF3 complex containing STAT1, STAT2 and IRF9. In contrast to the dogmatic view of ISGF3 formation in the cytoplasm, our results suggest a model wherein the assembly of the ISGF3 complex occurs on DNA.
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Affiliation(s)
| | - Duygu Demiroz
- Max Perutz Labs (MPL), University of Vienna, Vienna, 1030, Austria
| | - Anja Schneller
- Max Perutz Labs (MPL), University of Vienna, Vienna, 1030, Austria
| | - Katrin Fischer
- Max Perutz Labs (MPL), University of Vienna, Vienna, 1030, Austria
| | | | - Markus Hartl
- Max Perutz Labs (MPL), University of Vienna, Vienna, 1030, Austria
| | | | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, 1030, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, 1030, Austria
| | - Thomas Decker
- Max Perutz Labs (MPL), University of Vienna, Vienna, 1030, Austria.
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29
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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30
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Lu Y, Stuart JH, Talbot-Cooper C, Agrawal-Singh S, Huntly B, Smid AI, Snowden JS, Dupont L, Smith GL. Histone deacetylase 4 promotes type I interferon signaling, restricts DNA viruses, and is degraded via vaccinia virus protein C6. Proc Natl Acad Sci U S A 2019; 116:11997-12006. [PMID: 31127039 PMCID: PMC6575207 DOI: 10.1073/pnas.1816399116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interferons (IFNs) represent an important host defense against viruses. Type I IFNs induce JAK-STAT signaling and expression of IFN-stimulated genes (ISGs), which mediate antiviral activity. Histone deacetylases (HDACs) perform multiple functions in regulating gene expression and some class I HDACs and the class IV HDAC, HDAC11, influence type I IFN signaling. Here, HDAC4, a class II HDAC, is shown to promote type I IFN signaling and coprecipitate with STAT2. Pharmacological inhibition of class II HDAC activity, or knockout of HDAC4 from HEK-293T and HeLa cells, caused a defective response to IFN-α. This defect in HDAC4-/- cells was rescued by reintroduction of HDAC4 or catalytically inactive HDAC4, but not HDAC1 or HDAC5. ChIP analysis showed HDAC4 was recruited to ISG promoters following IFN stimulation and was needed for binding of STAT2 to these promoters. The biological importance of HDAC4 as a virus restriction factor was illustrated by the observations that (i) the replication and spread of vaccinia virus (VACV) and herpes simplex virus type 1 (HSV-1) were enhanced in HDAC4-/- cells and inhibited by overexpression of HDAC4; and (ii) HDAC4 is targeted for proteasomal degradation during VACV infection by VACV protein C6, a multifunctional IFN antagonist that coprecipitates with HDAC4 and is necessary and sufficient for HDAC4 degradation.
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Affiliation(s)
- Yongxu Lu
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Jennifer H Stuart
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Callum Talbot-Cooper
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Shuchi Agrawal-Singh
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, United Kingdom
| | - Brian Huntly
- Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, United Kingdom
| | - Andrei I Smid
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Joseph S Snowden
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Liane Dupont
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, United Kingdom;
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31
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Platanitis E, Decker T. Regulatory Networks Involving STATs, IRFs, and NFκB in Inflammation. Front Immunol 2018; 9:2542. [PMID: 30483250 PMCID: PMC6242948 DOI: 10.3389/fimmu.2018.02542] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/16/2018] [Indexed: 01/10/2023] Open
Abstract
Cells engaging in inflammation undergo drastic changes of their transcriptomes. In order to tailor these alterations in gene expression to the requirements of the inflammatory process, tight and coordinate regulation of gene expression by environmental cues, microbial or danger-associated molecules or cytokines, are mandatory. The transcriptional response is set off by signal-regulated transcription factors (SRTFs) at the receiving end of pathways originating at pattern recognition- and cytokine receptors. These interact with a genome that has been set for an appropriate response by prior activity of pioneer or lineage determining transcription factors (LDTFs). The same types of transcription factors are also critical determinants of the changes in chromatin landscapes and transcriptomes that specify potential consequences of inflammation: tissue repair, training, and tolerance. Here we focus on the role of three families of SRTFs in inflammation and its sequels: signal transducers and activators of transcription (STATs), interferon regulatory factors (IRFs), and nuclear factor κB (NFκB). We describe recent findings about their interactions and about their networking with LDTFs. Our aim is to provide a snapshot of a highly dynamic research area.
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Affiliation(s)
- Ekaterini Platanitis
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Thomas Decker
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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Au-Yeung N, Horvath CM. Transcriptional and chromatin regulation in interferon and innate antiviral gene expression. Cytokine Growth Factor Rev 2018; 44:11-17. [PMID: 30509403 DOI: 10.1016/j.cytogfr.2018.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022]
Abstract
In response to virus infections, a cell-autonomous, transcription-based antiviral program is engaged to create resistance, impair pathogen replication, and alert professional cells in innate and adaptive immunity. This dual phase antiviral program consists of type I interferon (IFN) production followed by the response to IFN signaling. Pathogen recognition leads to activation of IRF and NFκB factors that function independently and together to recruit cellular coactivators that remodel chromatin, modify histones and activate RNA polymerase II (Pol II) at target gene loci, including the well-characterized IFNβ enhanceosome. In the subsequent response to IFN, a receptor-mediated JAK-STAT signaling cascade directs the assembly of the IRF9-STAT1-STAT2 transcription factor complex called ISGF3, which recruits its own cohort of remodelers, coactivators, and Pol II machinery to activate transcription of a wide range of IFN-stimulated genes. Regulation of the IFN and antiviral gene regulatory networks is not only important for driving innate immune responses to infections, but also may inform treatment of a growing list of chronic diseases that are characterized by hyperactive and constitutive IFN and IFN-stimulated gene (ISG) expression. Here, gene-specific and genome-wide investigations of the chromatin landscape at IFN and ISGs is discussed in parallel with IRF- and STAT- dependent regulation of Pol II transcription.
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Affiliation(s)
- Nancy Au-Yeung
- Department of Molecular Biosciences, Northwestern University, 2200 Campus Drive, Evanston, IL 60208, USA
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, 2200 Campus Drive, Evanston, IL 60208, USA.
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