1
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He M, Jiang H, Li S, Xue M, Wang H, Zheng C, Tong J. The crosstalk between DNA-damage responses and innate immunity. Int Immunopharmacol 2024; 140:112768. [PMID: 39088918 DOI: 10.1016/j.intimp.2024.112768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
DNA damage is typically caused during cell growth by DNA replication stress or exposure to endogenous or external toxins. The accumulation of damaged DNA causes genomic instability, which is the root cause of many serious disorders. Multiple cellular organisms utilize sophisticated signaling pathways against DNA damage, collectively known as DNA damage response (DDR) networks. Innate immune responses are activated following cellular abnormalities, including DNA damage. Interestingly, recent studies have indicated that there is an intimate relationship between the DDR network and innate immune responses. Diverse kinds of cytosolic DNA sensors, such as cGAS and STING, recognize damaged DNA and induce signals related to innate immune responses, which link defective DDR to innate immunity. Moreover, DDR components operate in immune signaling pathways to induce IFNs and/or a cascade of inflammatory cytokines via direct interactions with innate immune modulators. Consistently, defective DDR factors exacerbate the innate immune imbalance, resulting in severe diseases, including autoimmune disorders and tumorigenesis. Here, the latest progress in understanding crosstalk between the DDR network and innate immune responses is reviewed. Notably, the dual function of innate immune modulators in the DDR network may provide novel insights into understanding and developing targeted immunotherapies for DNA damage-related diseases, even carcinomas.
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Affiliation(s)
- Mei He
- College of Life Sciences, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hua Jiang
- Department of Hematology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200000, China
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610041, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China.
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Jie Tong
- College of Life Sciences, Hebei University, Baoding 071002, China.
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2
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Ohnezeit D, Huang J, Westerkamp U, Brinschwitz V, Schmidt C, Günther T, Czech-Sioli M, Weißelberg S, Schlemeyer T, Nakel J, Mai J, Schreiner S, Schneider C, Friedel CC, Schwanke H, Brinkmann MM, Grundhoff A, Fischer N. Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling. PLoS Pathog 2024; 20:e1012426. [PMID: 39110744 PMCID: PMC11333005 DOI: 10.1371/journal.ppat.1012426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/19/2024] [Accepted: 07/15/2024] [Indexed: 08/21/2024] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the causative agent of the majority of Merkel cell carcinomas (MCC). The virus has limited coding capacity, with its early viral proteins, large T (LT) and small T (sT), being multifunctional and contributing to infection and transformation. A fundamental difference in early viral gene expression between infection and MCPyV-driven tumorigenesis is the expression of a truncated LT (LTtr) in the tumor. In contrast, sT is expressed in both conditions and contributes significantly to oncogenesis. Here, we identified novel functions of early viral proteins by performing genome-wide transcriptome and chromatin studies in primary human fibroblasts. Due to current limitations in infection and tumorigenesis models, we mimic these conditions by ectopically expressing sT, LT or LTtr, individually or in combination, at different time points. In addition to its known function in cell cycle and inflammation modulation, we reveal a fundamentally new function of sT. We show that sT regulates the type I interferon (IFN) response downstream of the type I interferon receptor (IFNAR) by interfering with the interferon-stimulated gene factor 3 (ISGF3)-induced interferon-stimulated gene (ISG) response. Expression of sT leads to a reduction in the expression of interferon regulatory factor 9 (IRF9) which is a central component of the ISGF3 complex. We further show that this function of sT is conserved in BKPyV. We provide a first mechanistic understanding of which early viral proteins trigger and control the type I IFN response, which may influence MCPyV infection, persistence and, during MCC progression, regulation of the tumor microenvironment.
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Affiliation(s)
- Denise Ohnezeit
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ute Westerkamp
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Veronika Brinschwitz
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Schmidt
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samira Weißelberg
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tabea Schlemeyer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Freiburg, Germany
| | - Sabrina Schreiner
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, Freiburg, Germany
| | | | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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3
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Djerir B, Marois I, Dubois JC, Findlay S, Morin T, Senoussi I, Cappadocia L, Orthwein A, Maréchal A. An E3 ubiquitin ligase localization screen uncovers DTX2 as a novel ADP-ribosylation-dependent regulator of DNA double-strand break repair. J Biol Chem 2024; 300:107545. [PMID: 38992439 PMCID: PMC11345397 DOI: 10.1016/j.jbc.2024.107545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
DNA double-strand breaks (DSBs) elicit an elaborate response to signal damage and trigger repair via two major pathways: nonhomologous end-joining (NHEJ), which functions throughout the interphase, and homologous recombination (HR), restricted to S/G2 phases. The DNA damage response relies, on post-translational modifications of nuclear factors to coordinate the mending of breaks. Ubiquitylation of histones and chromatin-associated factors regulates DSB repair and numerous E3 ubiquitin ligases are involved in this process. Despite significant progress, our understanding of ubiquitin-mediated DNA damage response regulation remains incomplete. Here, we have performed a localization screen to identify RING/U-box E3 ligases involved in genome maintenance. Our approach uncovered 7 novel E3 ligases that are recruited to microirradiation stripes, suggesting potential roles in DNA damage signaling and repair. Among these factors, the DELTEX family E3 ligase DTX2 is rapidly mobilized to lesions in a poly ADP-ribosylation-dependent manner. DTX2 is recruited and retained at DSBs via its WWE and DELTEX conserved C-terminal domains. In cells, both domains are required for optimal binding to mono and poly ADP-ribosylated proteins with WWEs playing a prominent role in this process. Supporting its involvement in DSB repair, DTX2 depletion decreases HR efficiency and moderately enhances NHEJ. Furthermore, DTX2 depletion impeded BRCA1 foci formation and increased 53BP1 accumulation at DSBs, suggesting a fine-tuning role for this E3 ligase in repair pathway choice. Finally, DTX2 depletion sensitized cancer cells to X-rays and PARP inhibition and these susceptibilities could be rescued by DTX2 reexpression. Altogether, our work identifies DTX2 as a novel ADP-ribosylation-dependent regulator of HR-mediated DSB repair.
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Affiliation(s)
- Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jean-Christophe Dubois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montréal, Quebec, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Issam Senoussi
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Quebec, Canada
| | - Alexandre Orthwein
- Lady Davis Institute for Medical Research, Segal Cancer Centre, Jewish General Hospital, Montréal, Quebec, Canada; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada; Cancer Research Institute of the Université de Sherbrooke, Sherbrooke, Quebec, Canada.
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4
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Feijs-Žaja KLH, Ikenga NJ, Žaja R. Pathological and physiological roles of ADP-ribosylation: established functions and new insights. Biol Chem 2024:hsz-2024-0057. [PMID: 39066732 DOI: 10.1515/hsz-2024-0057] [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: 04/12/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
The posttranslational modification of proteins with poly(ADP-ribose) was discovered in the sixties. Since then, we have learned that the enzymes involved, the so-called poly(ADP-ribosyl)polymerases (PARPs), are transferases which use cofactor NAD+ to transfer ADP-ribose to their targets. Few PARPs are able to create poly(ADP-ribose), whereas the majority transfers a single ADP-ribose. In the last decade, hydrolases were discovered which reverse mono(ADP-ribosyl)ation, detection methods were developed and new substrates were defined, including nucleic acids. Despite the continued effort, relatively little is still known about the biological function of most PARPs. In this review, we summarise key functions of ADP-ribosylation and introduce emerging insights.
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Affiliation(s)
- Karla L H Feijs-Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Nonso J Ikenga
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Roko Žaja
- 9165 Institute of Biochemistry and Molecular Biology, RWTH Aachen University , Pauwelsstrasse 30, D-52074 Aachen, Germany
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5
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Kar P, Chatrin C, Đukić N, Suyari O, Schuller M, Zhu K, Prokhorova E, Bigot N, Ahel J, Elsborg JD, Nielsen ML, Clausen T, Huet S, Niepel M, Sanyal S, Ahel D, Smith R, Ahel I. PARP14 and PARP9/DTX3L regulate interferon-induced ADP-ribosylation. EMBO J 2024; 43:2929-2953. [PMID: 38834853 PMCID: PMC11251020 DOI: 10.1038/s44318-024-00126-0] [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: 10/07/2023] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
PARP-catalysed ADP-ribosylation (ADPr) is important in regulating various cellular pathways. Until recently, PARP-dependent mono-ADP-ribosylation has been poorly understood due to the lack of sensitive detection methods. Here, we utilised an improved antibody to detect mono-ADP-ribosylation. We visualised endogenous interferon (IFN)-induced ADP-ribosylation and show that PARP14 is a major enzyme responsible for this modification. Fittingly, this signalling is reversed by the macrodomain from SARS-CoV-2 (Mac1), providing a possible mechanism by which Mac1 counteracts the activity of antiviral PARPs. Our data also elucidate a major role of PARP9 and its binding partner, the E3 ubiquitin ligase DTX3L, in regulating PARP14 activity through protein-protein interactions and by the hydrolytic activity of PARP9 macrodomain 1. Finally, we also present the first visualisation of ADPr-dependent ubiquitylation in the IFN response. These approaches should further advance our understanding of IFN-induced ADPr and ubiquitin signalling processes and could shed light on how different pathogens avoid such defence pathways.
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Affiliation(s)
- Pulak Kar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Department of Biological Sciences, SRM University-AP, Amaravati, 522502, India
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Nina Đukić
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Nicolas Bigot
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, F-35000, Rennes, France
| | - Juraj Ahel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
| | - Jonas Damgaard Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT - UMS3480, F-35000, Rennes, France
| | | | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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6
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Ribeiro VC, Russo LC, Hoch NC. PARP14 is regulated by the PARP9/DTX3L complex and promotes interferon γ-induced ADP-ribosylation. EMBO J 2024; 43:2908-2928. [PMID: 38834852 PMCID: PMC11251048 DOI: 10.1038/s44318-024-00125-1] [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: 10/07/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Protein ADP-ribosylation plays important but ill-defined roles in antiviral signalling cascades such as the interferon response. Several viruses of clinical interest, including coronaviruses, express hydrolases that reverse ADP-ribosylation catalysed by host enzymes, suggesting an important role for this modification in host-pathogen interactions. However, which ADP-ribosyltransferases mediate host ADP-ribosylation, what proteins and pathways they target and how these modifications affect viral infection and pathogenesis is currently unclear. Here we show that host ADP-ribosyltransferase activity induced by IFNγ signalling depends on PARP14 catalytic activity and that the PARP9/DTX3L complex is required to uphold PARP14 protein levels via post-translational mechanisms. Both the PARP9/DTX3L complex and PARP14 localise to IFNγ-induced cytoplasmic inclusions containing ADP-ribosylated proteins, and both PARP14 itself and DTX3L are likely targets of PARP14 ADP-ribosylation. We provide evidence that these modifications are hydrolysed by the SARS-CoV-2 Nsp3 macrodomain, shedding light on the intricate cross-regulation between IFN-induced ADP-ribosyltransferases and the potential roles of the coronavirus macrodomain in counteracting their activity.
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Affiliation(s)
| | | | - Nícolas Carlos Hoch
- Department of Biochemistry, University of São Paulo, São Paulo, 05508-000, Brazil.
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7
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Davila KMS, Nelli RK, Mora-Díaz JC, Sang Y, Miller LC, Giménez-Lirola LG. Transcriptome Analysis in Air-Liquid Interface Porcine Respiratory Epithelial Cell Cultures Reveals That the Betacoronavirus Porcine Encephalomyelitis Hemagglutinating Virus Induces a Robust Interferon Response to Infection. Viruses 2024; 16:939. [PMID: 38932231 PMCID: PMC11209522 DOI: 10.3390/v16060939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV) replicates in the upper respiratory tract and tonsils of pigs. Using an air-liquid interface porcine respiratory epithelial cells (ALI-PRECs) culture system, we demonstrated that PHEV disrupts respiratory epithelia homeostasis by impairing ciliary function and inducing antiviral, pro-inflammatory cytokine, and chemokine responses. This study explores the mechanisms driving early innate immune responses during PHEV infection through host transcriptome analysis. Total RNA was collected from ALI-PRECs at 24, 36, and 48 h post inoculation (hpi). RNA-seq analysis was performed using an Illumina Hiseq 600 to generate 100 bp paired-end reads. Differential gene expression was analyzed using DeSeq2. PHEV replicated actively in ALI-PRECs, causing cytopathic changes and progressive mucociliary disruption. Transcriptome analysis revealed downregulation of cilia-associated genes such as CILK1, DNAH11, LRRC-23, -49, and -51, and acidic sialomucin CD164L2. PHEV also activated antiviral signaling pathways, significantly increasing the expression of interferon-stimulated genes (RSAD2, MX1, IFIT, and ISG15) and chemokine genes (CCL5 and CXCL10), highlighting inflammatory regulation. This study contributes to elucidating the molecular mechanisms of the innate immune response to PHEV infection of the airway epithelium, emphasizing the critical roles of the mucociliary, interferon, and chemokine responses.
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Affiliation(s)
- Kaitlyn M. Sarlo Davila
- Infectious Bacterial Disease Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA 50010, USA;
| | - Rahul K. Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
| | - Juan C. Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA;
| | - Laura C. Miller
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA 50010, USA
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (R.K.N.); (J.C.M.-D.)
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8
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Saleh M, Hummel K, Schlosser S, Razzazi-Fazeli E, Bartholomew JL, Holzer A, Secombes CJ, El-Matbouli M. The myxozoans Myxobolus cerebralis and Tetracapsuloides bryosalmonae modulate rainbow trout immune responses: quantitative shotgun proteomics at the portals of entry after single and co-infections. Front Cell Infect Microbiol 2024; 14:1369615. [PMID: 38803570 PMCID: PMC11129561 DOI: 10.3389/fcimb.2024.1369615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Little is known about the proteomic changes at the portals of entry in rainbow trout after infection with the myxozoan parasites, Myxobolus cerebralis, and Tetracapsuloides bryosalmonae. Whirling disease (WD) is a severe disease of salmonids, caused by the myxosporean M. cerebralis, while, proliferative kidney disease (PKD) is caused by T. bryosalmonae, which instead belongs to the class Malacosporea. Climate change is providing more suitable conditions for myxozoan parasites lifecycle, posing a high risk to salmonid aquaculture and contributing to the decline of wild trout populations in North America and Europe. Therefore, the aim of this study was to provide the first proteomic profiles of the host in the search for evasion strategies during single and coinfection with M. cerebralis and T. bryosalmonae. Methods One group of fish was initially infected with M. cerebralis and another group with T. bryosalmonae. After 30 days, half of the fish in each group were co-infected with the other parasite. Using a quantitative proteomic approach, we investigated proteomic changes in the caudal fins and gills of rainbow trout before and after co-infection. Results In the caudal fins, 16 proteins were differentially regulated post exposure to M. cerebralis, whereas 27 proteins were differentially modulated in the gills of the infected rainbow trout post exposure to T. bryosalmonae. After co-infection, 4 proteins involved in parasite recognition and the regulation of host immune responses were differentially modulated between the groups in the caudal fin. In the gills, 11 proteins involved in parasite recognition and host immunity, including 4 myxozoan proteins predicted to be virulence factors, were differentially modulated. Discussion The results of this study increase our knowledge on rainbow trout co-infections by myxozoan parasites and rainbow trout immune responses against myxozoans at the portals of entry, supporting a better understanding of these host-parasite interactions.
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Affiliation(s)
- Mona Saleh
- Division of Fish Health, University of Veterinary Medicine, Vienna, Austria
| | - Karin Hummel
- VetCore, University of Veterinary Medicine, Vienna, Austria
| | | | | | - Jerri L. Bartholomew
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Astrid Holzer
- Division of Fish Health, University of Veterinary Medicine, Vienna, Austria
| | - Christopher J. Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Scotland, United Kingdom
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9
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Everson RG, Hugo W, Sun L, Antonios J, Lee A, Ding L, Bu M, Khattab S, Chavez C, Billingslea-Yoon E, Salazar A, Ellingson BM, Cloughesy TF, Liau LM, Prins RM. TLR agonists polarize interferon responses in conjunction with dendritic cell vaccination in malignant glioma: a randomized phase II Trial. Nat Commun 2024; 15:3882. [PMID: 38719809 PMCID: PMC11078958 DOI: 10.1038/s41467-024-48073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
In this randomized phase II clinical trial, we evaluated the effectiveness of adding the TLR agonists, poly-ICLC or resiquimod, to autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination in patients with newly-diagnosed or recurrent WHO Grade III-IV malignant gliomas. The primary endpoints were to assess the most effective combination of vaccine and adjuvant in order to enhance the immune potency, along with safety. The combination of ATL-DC vaccination and TLR agonist was safe and found to enhance systemic immune responses, as indicated by increased interferon gene expression and changes in immune cell activation. Specifically, PD-1 expression increases on CD4+ T-cells, while CD38 and CD39 expression are reduced on CD8+ T cells, alongside an increase in monocytes. Poly-ICLC treatment amplifies the induction of interferon-induced genes in monocytes and T lymphocytes. Patients that exhibit higher interferon response gene expression demonstrate prolonged survival and delayed disease progression. These findings suggest that combining ATL-DC with poly-ICLC can induce a polarized interferon response in circulating monocytes and CD8+ T cells, which may represent an important blood biomarker for immunotherapy in this patient population.Trial Registration: ClinicalTrials.gov Identifier: NCT01204684.
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Affiliation(s)
- Richard G Everson
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Willy Hugo
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Lu Sun
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Joseph Antonios
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Alexander Lee
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Lizhong Ding
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Melissa Bu
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sara Khattab
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Carolina Chavez
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Emma Billingslea-Yoon
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Benjamin M Ellingson
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Timothy F Cloughesy
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Neurology/Neuro-Oncology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Robert M Prins
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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10
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Parthasarathy S, Saenjamsai P, Hao H, Ferkul A, Pfannenstiel JJ, Suder EL, Bejan DS, Chen Y, Schwarting N, Aikawa M, Muhlberger E, Orozco RC, Sullivan CS, Cohen MS, Davido DJ, Hume AJ, Fehr AR. PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591186. [PMID: 38712082 PMCID: PMC11071520 DOI: 10.1101/2024.04.26.591186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
PARP14 is a 203 kDa multi-domain protein that is primarily known as an ADP-ribosyltransferase, and is involved in a variety of cellular functions including DNA damage, microglial activation, inflammation, and cancer progression. In addition, PARP14 is upregulated by interferon (IFN), indicating a role in the antiviral response. Furthermore, PARP14 has evolved under positive selection, again indicating that it is involved in host-pathogen conflict. We found that PARP14 is required for increased IFN-I production in response to coronavirus infection lacking ADP-ribosylhydrolase (ARH) activity and poly(I:C), however, whether it has direct antiviral function remains unclear. Here we demonstrate that the catalytic activity of PARP14 enhances IFN-I and IFN-III responses and restricts ARH-deficient murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. To determine if PARP14's antiviral functions extended beyond CoVs, we tested the ability of herpes simplex virus 1 (HSV-1) and several negative-sense RNA viruses, including vesicular stomatitis virus (VSV), Ebola virus (EBOV), and Nipah virus (NiV), to infect A549 PARP14 knockout (KO) cells. HSV-1 had increased replication in PARP14 KO cells, indicating that PARP14 restricts HSV-1 replication. In contrast, PARP14 was critical for the efficient infection of VSV, EBOV, and NiV, with EBOV infectivity at less than 1% of WT cells. A PARP14 active site inhibitor had no impact on HSV-1 or EBOV infection, indicating that its effect on these viruses was independent of its catalytic activity. These data demonstrate that PARP14 promotes IFN production and has both pro- and anti-viral functions targeting multiple viruses.
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Affiliation(s)
| | - Pradtahna Saenjamsai
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Hongping Hao
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anna Ferkul
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Daniel S. Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Masanori Aikawa
- Center for Excellence in Vascular Biology (P.K.J., M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Interdisciplinary Cardiovascular Sciences (M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Channing Division of Network Medicine (M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elke Muhlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Michael S. Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - David J. Davido
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Adam J. Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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11
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Tong J, Song J, Zhang W, Zhai J, Guan Q, Wang H, Liu G, Zheng C. When DNA-damage responses meet innate and adaptive immunity. Cell Mol Life Sci 2024; 81:185. [PMID: 38630271 PMCID: PMC11023972 DOI: 10.1007/s00018-024-05214-2] [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: 11/04/2023] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024]
Abstract
When cells proliferate, stress on DNA replication or exposure to endogenous or external insults frequently results in DNA damage. DNA-Damage Response (DDR) networks are complex signaling pathways used by multicellular organisms to prevent DNA damage. Depending on the type of broken DNA, the various pathways, Base-Excision Repair (BER), Nucleotide Excision Repair (NER), Mismatch Repair (MMR), Homologous Recombination (HR), Non-Homologous End-Joining (NHEJ), Interstrand Crosslink (ICL) repair, and other direct repair pathways, can be activated separately or in combination to repair DNA damage. To preserve homeostasis, innate and adaptive immune responses are effective defenses against endogenous mutation or invasion by external pathogens. It is interesting to note that new research keeps showing how closely DDR components and the immune system are related. DDR and immunological response are linked by immune effectors such as the cyclic GMP-AMP synthase (cGAS)-Stimulator of Interferon Genes (STING) pathway. These effectors act as sensors of DNA damage-caused immune response. Furthermore, DDR components themselves function in immune responses to trigger the generation of inflammatory cytokines in a cascade or even trigger programmed cell death. Defective DDR components are known to disrupt genomic stability and compromise immunological responses, aggravating immune imbalance and leading to serious diseases such as cancer and autoimmune disorders. This study examines the most recent developments in the interaction between DDR elements and immunological responses. The DDR network's immune modulators' dual roles may offer new perspectives on treating infectious disorders linked to DNA damage, including cancer, and on the development of target immunotherapy.
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Affiliation(s)
- Jie Tong
- College of Life Science, Hebei University, Baoding, 071002, China
- Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jiangwei Song
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100089, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071000, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Qingli Guan
- The Affiliated Hospital of Chinese PLA 80th Group Army, Weifang, 261000, China
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Gentao Liu
- Department of Oncology, Tenth People's Hospital Affiliated to Tongji University & Cancer Center, Tongji University School of Medicine, Shanghai, 20000, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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12
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Zhu Y, He J, Wei R, Liu J. Construction and experimental validation of a novel ferroptosis-related gene signature for myelodysplastic syndromes. Immun Inflamm Dis 2024; 12:e1221. [PMID: 38578040 PMCID: PMC10996383 DOI: 10.1002/iid3.1221] [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: 11/12/2023] [Revised: 01/26/2024] [Accepted: 03/03/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders characterized by morphological abnormalities and peripheral blood cytopenias, carrying a risk of progression to acute myeloid leukemia. Although ferroptosis is a promising target for MDS treatment, the specific roles of ferroptosis-related genes (FRGs) in MDS diagnosis have not been elucidated. METHODS MDS-related microarray data were obtained from the Gene Expression Omnibus database. A comprehensive analysis of FRG expression levels in patients with MDS and controls was conducted, followed by the use of multiple machine learning methods to establish prediction models. The predictive ability of the optimal model was evaluated using nomogram analysis and an external data set. Functional analysis was applied to explore the underlying mechanisms. The mRNA levels of the model genes were verified in MDS clinical samples by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The extreme gradient boosting model demonstrated the best performance, leading to the identification of a panel of six signature genes: SREBF1, PTPN6, PARP9, MAP3K11, MDM4, and EZH2. Receiver operating characteristic curves indicated that the model exhibited high accuracy in predicting MDS diagnosis, with area under the curve values of 0.989 and 0.962 for the training and validation cohorts, respectively. Functional analysis revealed significant associations between these genes and the infiltrating immune cells. The expression levels of these genes were successfully verified in MDS clinical samples. CONCLUSION Our study is the first to identify a novel model using FRGs to predict the risk of developing MDS. FRGs may be implicated in MDS pathogenesis through immune-related pathways. These findings highlight the intricate correlation between ferroptosis and MDS, offering insights that may aid in identifying potential therapeutic targets for this debilitating disorder.
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Affiliation(s)
- Yidong Zhu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Jun He
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Rong Wei
- Department of Hematology, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
| | - Jun Liu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's HospitalTongji University School of MedicineShanghaiChina
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13
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Zhu Z, Weng S, Zheng F, Zhao Q, Xu Y, Wu J. Identification of Poly(ADP-ribose) Polymerase 9 (PARP9) as a Potent Suppressor for Mycobacterium tuberculosis Infection. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:158-170. [PMID: 38884060 PMCID: PMC11169154 DOI: 10.1007/s43657-023-00112-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/18/2024]
Abstract
ADP-ribosylation is a reversible and dynamic post-translational modification mediated by ADP-ribosyltransferases (ARTs). Poly(ADP-ribose) polymerases (PARPs) are an important family of human ARTs. ADP-ribosylation and PARPs have crucial functions in host-pathogen interaction, especially in viral infections. However, the functions and potential molecular mechanisms of ADP-ribosylation and PARPs in Mycobacterium infection remain unknown. In this study, bioinformatics analysis revealed significantly changed expression levels of several PARPs in tuberculosis patients compared to healthy individuals. Moreover, the expression levels of these PARPs returned to normal following tuberculosis treatment. Then, the changes in the expression levels of PARPs during Mycobacterium infection were validated in Tohoku Hospital Pediatrics-1 (THP1)-induced differentiated macrophages infected with Mycobacterium model strains bacillus Calmette-Guérin (BCG) and in human lung adenocarcinoma A549 cells infected with Mycobacterium smegmatis (Ms), respectively. The mRNA levels of PARP9, PARP10, PARP12, and PARP14 were most significantly increased during infection, with corresponding increases in protein levels, indicating the possible biological functions of these PARPs during Mycobacterium infection. In addition, the biological function of host PARP9 in Mycobacterium infection was further studied. PARP9 deficiency significantly increased the infection efficiency and intracellular proliferation ability of Ms, which was reversed by the reconstruction of PARP9. Collectively, this study updates the understanding of changes in PARP expression during Mycobacterium infection and provides evidence supporting PARP9 as a potent suppressor for Mycobacterium infection. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00112-2.
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Affiliation(s)
- Zhenyu Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Shufeng Weng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Fen Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Qi Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Ying Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
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14
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Pang Q, Chen L, An C, Zhou J, Xiao H. Single-cell and bulk RNA sequencing highlights the role of M1-like infiltrating macrophages in antibody-mediated rejection after kidney transplantation. Heliyon 2024; 10:e27865. [PMID: 38524599 PMCID: PMC10958716 DOI: 10.1016/j.heliyon.2024.e27865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024] Open
Abstract
Background Antibody-mediated rejection (ABMR) significantly affects transplanted kidney survival, yet the macrophage phenotype, ontogeny, and mechanisms in ABMR remain unclear. Method We analyzed post-transplant sequencing and clinical data from GEO and ArrayExpress. Using dimensionality reduction and clustering on scRNA-seq data, we identified macrophage subpopulations and compared their infiltration in ABMR and non-rejection cases. Cibersort quantified these subpopulations in bulk samples. Cellchat, SCENIC, monocle2, and monocle3 helped explore intercellular interactions, predict transcription factors, and simulate differentiation of cell subsets. The Scissor method linked macrophage subgroups with transplant prognosis. Furthermore, hdWGCNA, nichnet, and lasso regression identified key genes associated with core transcription factors in selected macrophages, validated by external datasets. Results Six macrophage subgroups were identified in five post-transplant kidney biopsies. M1-like infiltrating macrophages, prevalent in ABMR, correlated with pathological injury severity. MIF acted as a primary intercellular signal in these macrophages. STAT1 regulated monocyte-to-M1-like phenotype transformation, impacting transplant prognosis via the IFNγ pathway. The prognostic models built on the upstream and downstream genes of STAT1 effectively predicted transplant survival. The TLR4-STAT1-PARP9 axis may regulate the pro-inflammatory phenotype of M1-like infiltrating macrophages, identifying PARP9 as a potential target for mitigating ABMR inflammation. Conclusion Our study delineates the macrophage landscape in ABMR post-kidney transplantation, underscoring the detrimental impact of M1-like infiltrating macrophages on ABMR pathology and prognosis.
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Affiliation(s)
- Qidan Pang
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, 402760, China
| | - Liang Chen
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, 402760, China
| | - Changyong An
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, 402760, China
| | - Juan Zhou
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, 402760, China
| | - Hanyu Xiao
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, 402760, China
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15
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Pandi K, Angabo S, Makkawi H, Benyamini H, Elgavish S, Nussbaum G. P. gingivalis-Induced TLR2 Interactome Analysis Reveals Association with PARP9. J Dent Res 2024; 103:329-338. [PMID: 38344758 DOI: 10.1177/00220345231222181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobic bacterium strongly associated with periodontal disease. Toll-like receptor 2 (TLR2) is indispensable for the host response to P. gingivalis, but P. gingivalis escapes from immune clearance via TLR2-dependent activation of phosphoinositide-3-kinase (PI3K). To probe the TLR2-dependent escape pathway of P. gingivalis, we analyzed the TLR2 interactome induced following P. gingivalis infection or activation by a synthetic lipopeptide TLR2/1 agonist on human macrophages overexpressing TLR2. Interacting proteins were stabilized by cross-linking and then immunoprecipitated and analyzed by mass spectrometry. In total, 792 proteins were recovered and network analysis enabled mapping of the TLR2 interactome at baseline and in response to infection. The P. gingivalis infection-induced TLR2 interactome included the poly (ADP-ribose) polymerase family member mono-ADP-ribosyltransferase protein 9 (PARP9) and additional members of the PARP9 complex (DTX3L and NMI). PARP9 and its complex members are highly upregulated in macrophages exposed to P. gingivalis or to the synthetic TLR2/1 ligand Pam3Cys-Ser-(Lys)4 (PAM). Consistent with its known role in virally induced interferon production, PARP9 knockdown blocked type I interferon (IFN-I) production in response to P. gingivalis and reduced inflammatory cytokine production. We found that P. gingivalis drives signal transducer and activation of transcription (STAT) 1 (S727) phosphorylation through TLR2-PARP9, explaining PARP9's role in the induction of IFN-I downstream of TLR2. Furthermore, PARP9 knockdown reduced PI3K activation by P. gingivalis, leading to improved macrophage bactericidal activity. In summary, PARP9 is a novel TLR2 interacting partner that enables IFN-I induction and P. gingivalis immune escape in macrophages downstream of TLR2 sensing.
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Affiliation(s)
- K Pandi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - S Angabo
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - H Makkawi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
| | - H Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - S Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - G Nussbaum
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah Faculty of Dental Medicine, Jerusalem, Israel
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16
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Tao T, Tang A, Lv L, Yuan J, Wu L, Zhao L, Chen J. Investigating the causal relationship and potential shared diagnostic genes between primary biliary cholangitis and systemic lupus erythematosus using bidirectional Mendelian randomization and transcriptomic analyses. Front Immunol 2024; 15:1270401. [PMID: 38464525 PMCID: PMC10921416 DOI: 10.3389/fimmu.2024.1270401] [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: 07/31/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Background The co-occurrence of primary biliary cholangitis (PBC) and systemic lupus erythematosus (SLE) has been consistently reported in observational studies. Nevertheless, the underlying causal correlation between these two conditions still needs to be established. Methods We performed a bidirectional two-sample Mendelian randomization (MR) study to assess their causal association. Five MR analysis methods were utilized for causal inference, with inverse-variance weighted (IVW) selected as the primary method. The Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) and the IVW Radial method were applied to exclude outlying SNPs. To assess the robustness of the MR results, five sensitivity analyses were carried out. Multivariable MR (MVMR) analysis was also employed to evaluate the effect of possible confounders. In addition, we integrated transcriptomic data from PBC and SLE, employing Weighted Gene Co-expression Network Analysis (WGCNA) to explore shared genes between the two diseases. Then, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment methods to perform on the shared genes. The Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm was utilized to identify potential shared diagnostic genes. Finally, we verified the potential shared diagnostic genes in peripheral blood mononuclear cells (PBMCs)-specific cell populations of SLE patients by single-cell analysis. Results Our MR study provided evidence that PBC had a causal relationship with SLE (IVW, OR: 1.347, 95% CI: 1.276 - 1.422, P < 0.001) after removing outliers (MR-PRESSO, rs35464393, rs3771317; IVW Radial, rs11065987, rs12924729, rs3745516). Conversely, SLE also had a causal association with PBC (IVW, OR: 1.225, 95% CI: 1.141 - 1.315, P < 0.001) after outlier correction (MR-PRESSO, rs11065987, rs3763295, rs7774434; IVW Radial, rs2297067). Sensitivity analyses confirmed the robustness of the MR findings. MVMR analysis indicated that body mass index (BMI), smoking and drinking were not confounding factors. Moreover, bioinformatic analysis identified PARP9, ABCA1, CEACAM1, and DDX60L as promising diagnostic biomarkers for PBC and SLE. These four genes are highly expressed in CD14+ monocytes in PBMCs of SLE patients and potentially associated with innate immune responses and immune activation. Conclusion Our study confirmed the bidirectional causal relationship between PBC and SLE and identified PARP9, ABCA1, CEACAM1, and DDX60L genes as the most potentially shared diagnostic genes between the two diseases, providing insights for the exploration of the underlying mechanisms of these disorders.
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Affiliation(s)
- Tian Tao
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Anqi Tang
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lizeyu Lv
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jianhua Yuan
- Department of Cardiovascular Medicine, Chengdu Second People’s Hospital, Chengdu, Chengdu, China
| | - Ling Wu
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liangbin Zhao
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jun Chen
- Department of Intensive Care Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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17
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Saleh H, Liloglou T, Rigden DJ, Parsons JL, Grundy GJ. KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival. J Mol Biol 2024; 436:168434. [PMID: 38182103 PMCID: PMC11080071 DOI: 10.1016/j.jmb.2023.168434] [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: 09/18/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Certain members of the ADP-ribosyltransferase superfamily (ARTD or PARP enzymes) catalyse ADP-ribosylation in response to cellular stress, DNA damage and viral infection and are upregulated in various tumours. PARP9, its binding partner DTX3L and PARP14 protein levels are significantly correlated in head and neck squamous cell carcinoma (HNSCC) and other tumour types though a mechanism where PARP9/DTX3L regulates PARP14 post-transcriptionally. Depleting PARP9, DTX3L or PARP14 expression in HNSCC or HeLa cell lines decreases cell survival through a reduction of proliferation and an increase in apoptosis. A partial rescue of survival was achieved by expressing a PARP14 truncation containing a predicted eukaryotic type I KH domain. KH-like domains were also found in PARP9 and in DTX3L and contributed to protein-protein interactions between PARP9-DTX3L and PARP14-DTX3L. Homodimerization of DTX3L was also coordinated by a KH-like domain and was disrupted by site-specific mutation. Although, cell survival promoted by PARP14 did not require ADP-ribosyltransferase activity, interaction of DTX3L in vitro suppressed PARP14 auto-ADP-ribosylation and promoted trans-ADP-ribosylation of PARP9 and DTX3L. In summary, we characterised PARP9-DTX3L-PARP14 interactions important to pro-survival signalling in HNSCC cells, albeit in PARP14 catalytically independent fashion.
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Affiliation(s)
- Hadil Saleh
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK
| | - Triantafillos Liloglou
- Edge Hill University, Faculty of Health, Social Care & Medicine, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
| | - Daniel J Rigden
- University of Liverpool, Department of Biochemistry, Cell and Systems Biology, Liverpool L69 7ZB, UK
| | - Jason L Parsons
- University of Birmingham, Institute of Cancer and Genomic Sciences, IBR West, Birmingham B15 2TT, UK
| | - Gabrielle J Grundy
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK.
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18
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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19
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Zhu K, Suskiewicz MJ, Chatrin C, Strømland Ø, Dorsey B, Aucagne V, Ahel D, Ahel I. DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on nucleic acids. Nucleic Acids Res 2024; 52:801-815. [PMID: 38000390 PMCID: PMC10810221 DOI: 10.1093/nar/gkad1119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although ubiquitylation had traditionally been considered limited to proteins, the discovery of non-proteinaceous substrates (e.g. lipopolysaccharides and adenosine diphosphate ribose (ADPr)) challenged this perspective. Our recent study showed that DTX2 E3 ligase efficiently ubiquitylates ADPr. Here, we show that the ADPr ubiquitylation activity is also present in another DELTEX family member, DTX3L, analysed both as an isolated catalytic fragment and the full-length PARP9:DTX3L complex, suggesting that it is a general feature of the DELTEX family. Since structural predictions show that DTX3L possesses single-stranded nucleic acids binding ability and given the fact that nucleic acids have recently emerged as substrates for ADP-ribosylation, we asked whether DELTEX E3s might catalyse ubiquitylation of an ADPr moiety linked to nucleic acids. Indeed, we show that DTX3L and DTX2 are capable of ubiquitylating ADP-ribosylated DNA and RNA synthesized by PARPs, including PARP14. Furthermore, we demonstrate that the Ub-ADPr-nucleic acids conjugate can be reversed by two groups of hydrolases, which remove either the whole adduct (e.g. SARS-CoV-2 Mac1 or PARP14 macrodomain 1) or just the Ub (e.g. SARS-CoV-2 PLpro). Overall, this study reveals ADPr ubiquitylation as a general function of the DELTEX family E3s and presents the evidence of reversible ubiquitylation of ADP-ribosylated nucleic acids.
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Affiliation(s)
- Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Bryan W Dorsey
- Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge MA 02140, USA
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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20
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Vela-Rodríguez C, Scarpulla I, Ashok Y, Lehtiö L. Discovery of DTX3L inhibitors through a homogeneous FRET-based assay that monitors formation and removal of poly-ubiquitin chains. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:365-375. [PMID: 37579950 DOI: 10.1016/j.slasd.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Ubiquitination is a reversible protein post-translational modification in which consequent enzymatic activity results in the covalent linking of ubiquitin to a target protein. Once ubiquitinated, a protein can undergo multiple rounds of ubiquitination on multiple sites or form poly-ubiquitin chains. Ubiquitination regulates various cellular processes, and dysregulation of ubiquitination has been associated with more than one type of cancer. Therefore, efforts have been carried out to identify modulators of the ubiquitination cascade. Herein, we present the development of a FRET-based assay that allows us to monitor ubiquitination activity of DTX3L, a RING-type E3 ubiquitin ligase. Our method shows a good signal window with a robust average Z' factor of 0.76 on 384-well microplates, indicating a good assay for screening inhibitors in a high-throughput setting. From a validatory screening experiment, we have identified the first molecules that inhibit DTX3L with potencies in the low micromolar range. We also demonstrate that the method can be expanded to study deubiquitinases, such as USP28, that reduce FRET due to hydrolysis of fluorescent poly-ubiquitin chains.
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Affiliation(s)
- Carlos Vela-Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Ilaria Scarpulla
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Yashwanth Ashok
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.
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21
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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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22
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Suskiewicz MJ, Prokhorova E, Rack JGM, Ahel I. ADP-ribosylation from molecular mechanisms to therapeutic implications. Cell 2023; 186:4475-4495. [PMID: 37832523 PMCID: PMC10789625 DOI: 10.1016/j.cell.2023.08.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023]
Abstract
ADP-ribosylation is a ubiquitous modification of biomolecules, including proteins and nucleic acids, that regulates various cellular functions in all kingdoms of life. The recent emergence of new technologies to study ADP-ribosylation has reshaped our understanding of the molecular mechanisms that govern the establishment, removal, and recognition of this modification, as well as its impact on cellular and organismal function. These advances have also revealed the intricate involvement of ADP-ribosylation in human physiology and pathology and the enormous potential that their manipulation holds for therapy. In this review, we present the state-of-the-art findings covering the work in structural biology, biochemistry, cell biology, and clinical aspects of ADP-ribosylation.
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Affiliation(s)
| | | | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; MRC Centre of Medical Mycology, University of Exeter, Exeter, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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23
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Chai X, Tao Q, Li L. The role of RING finger proteins in chromatin remodeling and biological functions. Epigenomics 2023; 15:1053-1068. [PMID: 37964749 DOI: 10.2217/epi-2023-0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Mammalian DNA duplexes are highly condensed with different components, including histones, enabling chromatin formation. Chromatin remodeling is involved in multiple biological processes, including gene transcription regulation and DNA damage repair. Recent research has highlighted the significant involvement of really interesting new gene (RING) finger proteins in chromatin remodeling, primarily attributed to their E3 ubiquitin ligase activities. In this review, we highlight the pivotal role of RING finger proteins in chromatin remodeling and provide an overview of their capacity to ubiquitinate specific histones, modulate ATP-dependent chromatin remodeling complexes and interact with various histone post-translational modifications. We also discuss the diverse biological effects of RING finger protein-mediated chromatin remodeling and explore potential therapeutic strategies for targeting these proteins.
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Affiliation(s)
- Xiaoxue Chai
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer, The Chinese University of Hong Kong, Hong Kong
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24
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Wong CW, Evangelou C, Sefton KN, Leshem R, Zhang W, Gopalan V, Chattrakarn S, Fernandez Carro ML, Uzuner E, Mole H, Wilcock DJ, Smith MP, Sergiou K, Telfer BA, Isaac DT, Liu C, Perl NR, Marie K, Lorigan P, Williams KJ, Rao PE, Nagaraju RT, Niepel M, Hurlstone AFL. PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models. Nat Commun 2023; 14:5983. [PMID: 37752135 PMCID: PMC10522711 DOI: 10.1038/s41467-023-41737-1] [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: 11/25/2022] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
Resistance mechanisms to immune checkpoint blockade therapy (ICBT) limit its response duration and magnitude. Paradoxically, Interferon γ (IFNγ), a key cytokine for cellular immunity, can promote ICBT resistance. Using syngeneic mouse tumour models, we confirm that chronic IFNγ exposure confers resistance to immunotherapy targeting PD-1 (α-PD-1) in immunocompetent female mice. We observe upregulation of poly-ADP ribosyl polymerase 14 (PARP14) in chronic IFNγ-treated cancer cell models, in patient melanoma with elevated IFNG expression, and in melanoma cell cultures from ICBT-progressing lesions characterised by elevated IFNγ signalling. Effector T cell infiltration is enhanced in tumours derived from cells pre-treated with IFNγ in immunocompetent female mice when PARP14 is pharmacologically inhibited or knocked down, while the presence of regulatory T cells is decreased, leading to restoration of α-PD-1 sensitivity. Finally, we determine that tumours which spontaneously relapse in immunocompetent female mice following α-PD-1 therapy upregulate IFNγ signalling and can also be re-sensitised upon receiving PARP14 inhibitor treatment, establishing PARP14 as an actionable target to reverse IFNγ-driven ICBT resistance.
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Affiliation(s)
- Chun Wai Wong
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Christos Evangelou
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Kieran N Sefton
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Rotem Leshem
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Wei Zhang
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Vishaka Gopalan
- Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, 20814, USA
| | - Sorayut Chattrakarn
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Macarena Lucia Fernandez Carro
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Erez Uzuner
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK
| | - Holly Mole
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Daniel J Wilcock
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Michael P Smith
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Kleita Sergiou
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Brian A Telfer
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Dervla T Isaac
- Ribon Therapeutics Inc., 35 Cambridge Park Drive, Suite 300, Cambridge, MA, 02140, USA
| | - Chang Liu
- Ribon Therapeutics Inc., 35 Cambridge Park Drive, Suite 300, Cambridge, MA, 02140, USA
| | - Nicholas R Perl
- Ribon Therapeutics Inc., 35 Cambridge Park Drive, Suite 300, Cambridge, MA, 02140, USA
| | - Kerrie Marie
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Paul Lorigan
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Withington, Manchester, M20 4BX, UK
| | - Kaye J Williams
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | | | - Raghavendar T Nagaraju
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Wilmslow Road, Withington, Manchester, UK
| | - Mario Niepel
- Ribon Therapeutics Inc., 35 Cambridge Park Drive, Suite 300, Cambridge, MA, 02140, USA
| | - Adam F L Hurlstone
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
- Lydia Becker Institute of Immunology, The University of Manchester, Manchester, M13 9PT, UK.
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25
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Đukić N, Strømland Ø, Elsborg JD, Munnur D, Zhu K, Schuller M, Chatrin C, Kar P, Duma L, Suyari O, Rack JGM, Baretić D, Crudgington DRK, Groslambert J, Fowler G, Wijngaarden S, Prokhorova E, Rehwinkel J, Schüler H, Filippov DV, Sanyal S, Ahel D, Nielsen ML, Smith R, Ahel I. PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities. SCIENCE ADVANCES 2023; 9:eadi2687. [PMID: 37703374 PMCID: PMC10499325 DOI: 10.1126/sciadv.adi2687] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
PARP14 is a mono-ADP-ribosyl transferase involved in the control of immunity, transcription, and DNA replication stress management. However, little is known about the ADP-ribosylation activity of PARP14, including its substrate specificity or how PARP14-dependent ADP-ribosylation is reversed. We show that PARP14 is a dual-function enzyme with both ADP-ribosyl transferase and hydrolase activity acting on both protein and nucleic acid substrates. In particular, we show that the PARP14 macrodomain 1 is an active ADP-ribosyl hydrolase. We also demonstrate hydrolytic activity for the first macrodomain of PARP9. We reveal that expression of a PARP14 mutant with the inactivated macrodomain 1 results in a marked increase in mono(ADP-ribosyl)ation of proteins in human cells, including PARP14 itself and antiviral PARP13, and displays specific cellular phenotypes. Moreover, we demonstrate that the closely related hydrolytically active macrodomain of SARS2 Nsp3, Mac1, efficiently reverses PARP14 ADP-ribosylation in vitro and in cells, supporting the evolution of viral macrodomains to counteract PARP14-mediated antiviral response.
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Affiliation(s)
- Nina Đukić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Jonas Damgaard Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Pulak Kar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Gerissa Fowler
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sven Wijngaarden
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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26
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Everson RG, Hugo W, Sun L, Antonios J, Lee A, Ding L, Bu M, Khattab S, Chavez C, Billingslea-Yoon E, Salazar A, Ellingson BM, Cloughesy TF, Liau LM, Prins RM. Dendritic Cell Vaccination in Conjunction with a TLR Agonist Polarizes Interferon Immune Responses in Malignant Glioma Patients. RESEARCH SQUARE 2023:rs.3.rs-3287211. [PMID: 37790490 PMCID: PMC10543402 DOI: 10.21203/rs.3.rs-3287211/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination is a promising immunotherapy for patients with high grade gliomas, but responses have not been demonstrated in all patients. To determine the most effective combination of autologous tumor lysate-pulsed DC vaccination, with or without the adjuvant toll-like receptor (TLR) agonists poly-ICLC or resiquimod, we conducted a Phase 2 clinical trial in 23 patients with newly diagnosed or recurrent WHO Grade III-IV malignant gliomas. We then performed deep, high-dimensional immune profiling of these patients to better understand how TLR agonists may influence the systemic immune responses induced by ATL-DC vaccination. Bulk RNAseq data demonstrated highly significant upregulation of type 1 and type 2 interferon gene expression selectively in patients who received adjuvant a TLR agonist together with ATL-DC. CyTOF analysis of patient peripheral blood mononuclear cells (PBMCs) showed increased expression of PD-1 on CD4+ T-cells, decreases in CD38 and CD39 on CD8+ T cells and elevated proportion of monocytes after ATL-DC + TLR agonist administration. In addition, scRNA-seq demonstrated a higher expression fold change of IFN-induced genes with poly-ICLC treatment in both peripheral blood monocytes and T lymphocytes. Patients who had higher expression of interferon response genes lived significantly longer and had longer time to progression compared to those with lower expression. The results suggest that ATL-DC in conjunction with adjuvant poly-ICLC induces a polarized interferon response in circulating monocytes and specific activation of a CD8+ T cell population, which may represent an important blood biomarker for immunotherapy in this patient population. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT01204684.
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Affiliation(s)
- Richard G. Everson
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Richard Everson and Willy Hugo contributed equally to this work as first authors
| | - Willy Hugo
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Richard Everson and Willy Hugo contributed equally to this work as first authors
| | - Lu Sun
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Joseph Antonios
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Alexander Lee
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Department of Molecular and Medical Pharmacology , David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Lizhong Ding
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Melissa Bu
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Sarah Khattab
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Carolina Chavez
- Department of Molecular and Medical Pharmacology , David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Emma Billingslea-Yoon
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | | | - Benjamin M. Ellingson
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Timothy F. Cloughesy
- Department of Molecular and Medical Pharmacology , David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Department of Neurology/Neuro-Oncology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Linda M. Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
| | - Robert M. Prins
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
- Department of Molecular and Medical Pharmacology , David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, 90095, U.S.A
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Tang X, Zhan Y, Yang B, Du B, Huang J. Exploring the mechanism of Semen Strychni in treating amyotrophic lateral sclerosis based on network pharmacology. Medicine (Baltimore) 2023; 102:e35101. [PMID: 37682161 PMCID: PMC10489316 DOI: 10.1097/md.0000000000035101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Semen Strychni (SS), known as an agonist of central nervous system, is a traditional herb widely used in treating amyotrophic lateral sclerosis (ALS) in small doses to relieve muscle weakness and improve muscle strength. However, the potential mechanisms and the main components of SS in treating ALS remain unclear. To explore the underlying mechanism of SS in treating ALS based on network pharmacology and molecular docking. The active components of SS were obtained using TCMSP, Herb, ETCM, and BATMAN-TCM. The targets of SS were gained from PharmMapper. The targets of ALS were searched on Genecards, Drugbank, DisGeNET, OMIM, TTD and GEO database. After obtaining the coincidence targets, we submitted them to the STRING database to build a protein-protein interaction network. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed subsequently. The active components and targets were further investigated using molecular docking technology. 395 targets of SS and 1925 targets of ALS were obtained with 125 common targets. The protein-protein interaction analysis indicated that SRC, AKT1, MAPK1, EGFR, and HSP90AA1 received the higher degree value and were considered the central genes. The Ras, PI3K-Akt, and MAPK signaling pathway could be involved in the treatment of ALS. Brucine-N-oxide obtained the lowest binding energy in molecular docking. This study explored the mechanism of SS in the treatment of ALS and provides a new perspective for future study. However, further experimental studies are needed to validate the therapeutic effect.
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Affiliation(s)
- Xiaohui Tang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yingshi Zhan
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Biying Yang
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Baoxin Du
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Jingyan Huang
- Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biol Evol 2023; 15:evad148. [PMID: 37728212 PMCID: PMC10510315 DOI: 10.1093/gbe/evad148] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023] Open
Abstract
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Oppenheim
- American Museum of Natural History, Institute for Comparative Genomics, New York, New York, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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29
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Cai T, Xu J, Fang Y, Wu Y, Qin Q, Zhang JA. Shared biomarkers of multi-tissue origin for primary Sjogren's syndrome and their importance in immune microenvironment alterations. Immunobiology 2023; 228:152726. [PMID: 37591179 DOI: 10.1016/j.imbio.2023.152726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
With the recent advancement in omics and molecular techniques, a wealth of new molecular biomarkers have become available for the diagnosis and classification of primary Sjögren's syndrome (pSS) patients. However, whether these biomarkers are universal is of great interest to us. In this study, we used various methods to obtain shared biomarkers derived from multiple tissue in pSS patients and to explore their relationship with immune microenvironment alterations. First we identified differentially expressed genes (DEGs) between pSS and healthy controls utilizing nine mRNA microarray datasets obtained from the Gene Expression Omnibus (GEO). Then, shared biomarkers were filtered out using robust rank aggregation (RRA), data integration analysis, weighted gene co-expression network analysis (WGCNA), and least absolute selection and shrinkage operator (LASSO) regression; their roles in pSS and association with changes in the immune microenvironment were also analyzed. In addition, these biomarkers were further confirmed with both the testing set and immunohistochemistry (IHC). As a result, ten biomarkers, i.e., EPSTI1, IFI44, IFIT1, IFIT2, IFIT3, MX1, OAS1, PARP9, SAMD9L and TRIM22, were identified. Receiver operating characteristic (ROC) curves showed that the ten genes could discriminate pSS from controls. Gene set enrichment analysis (GSEA) showed that the enrichment of immune-related gene sets was significant in pSS patients with high expression of either biomarker. Furthermore, the association between some immunocytes and these biomarkers was identified. In the two distinct molecular patterns of pSS patients based on the expressions of these biomarkers, the proportions of immunocytes were significantly different. Our study identified shared biomarkers of multi-tissue origin and revealed their relationship with altered immune microenvironment in pSS patients. These markers not only have diagnostic implications but also provide potential immunotherapeutic targets for the clinical treatment of pSS patients.
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Affiliation(s)
- Tiantian Cai
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China; Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Jianbin Xu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Yudie Fang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Yuqing Wu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China
| | - Qiu Qin
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China.
| | - Jin-An Zhang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, People's Republic of China; Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China.
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30
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Bamunuarachchi G, Vaddadi K, Yang X, Dang Q, Zhu Z, Hewawasam S, Huang C, Liang Y, Guo Y, Liu L. MicroRNA-9-1 Attenuates Influenza A Virus Replication via Targeting Tankyrase 1. J Innate Immun 2023; 15:647-664. [PMID: 37607510 PMCID: PMC10601686 DOI: 10.1159/000532063] [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: 08/21/2022] [Accepted: 07/11/2023] [Indexed: 08/24/2023] Open
Abstract
An unstable influenza genome leads to the virus resistance to antiviral drugs that target viral proteins. Thus, identification of host factors essential for virus replication may pave the way to develop novel antiviral therapies. In this study, we investigated the roles of the poly(ADP-ribose) polymerase enzyme, tankyrase 1 (TNKS1), and the endogenous small noncoding RNA, miR-9-1, in influenza A virus (IAV) infection. Increased expression of TNKS1 was observed in IAV-infected human lung epithelial cells and mouse lungs. TNKS1 knockdown by RNA interference repressed influenza viral replication. A screen using TNKS1 3'-untranslation region (3'-UTR) reporter assays and predicted microRNAs identified that miR-9-1 targeted TNKS1. Overexpression of miR-9-1 reduced influenza viral replication in lung epithelial cells as measured by viral mRNA and protein levels as well as virus production. miR-9-1 induced type I interferon production and enhanced the phosphorylation of STAT1 in cell culture. The ectopic expression of miR-9-1 in the lungs of mice by using an adenoviral viral vector enhanced type I interferon response, inhibited viral replication, and reduced susceptibility to IAV infection. Our results indicate that miR-9-1 is an anti-influenza microRNA that targets TNKS1 and enhances cellular antiviral state.
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Affiliation(s)
- Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kishore Vaddadi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Xiaoyun Yang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Quanjin Dang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Zhengyu Zhu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Sankha Hewawasam
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yujie Guo
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
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31
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Santinelli-Pestana DV, Aikawa E, Singh SA, Aikawa M. PARPs and ADP-Ribosylation in Chronic Inflammation: A Focus on Macrophages. Pathogens 2023; 12:964. [PMID: 37513811 PMCID: PMC10386340 DOI: 10.3390/pathogens12070964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Aberrant adenosine diphosphate-ribose (ADP)-ribosylation of proteins and nucleic acids is associated with multiple disease processes such as infections and chronic inflammatory diseases. The poly(ADP-ribose) polymerase (PARP)/ADP-ribosyltransferase (ART) family members promote mono- or poly-ADP-ribosylation. Although evidence has linked PARPs/ARTs and macrophages in the context of chronic inflammation, the underlying mechanisms remain incompletely understood. This review provides an overview of literature focusing on the roles of PARP1/ARTD1, PARP7/ARTD14, PARP9/ARTD9, and PARP14/ARTD8 in macrophages. PARPs/ARTs regulate changes in macrophages during chronic inflammatory processes not only via catalytic modifications but also via non-catalytic mechanisms. Untangling complex mechanisms, by which PARPs/ARTs modulate macrophage phenotype, and providing molecular bases for the development of new therapeutics require the development and implementation of innovative technologies.
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Affiliation(s)
- Diego V. Santinelli-Pestana
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (D.V.S.-P.); (E.A.); (S.A.S.)
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (D.V.S.-P.); (E.A.); (S.A.S.)
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (D.V.S.-P.); (E.A.); (S.A.S.)
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (D.V.S.-P.); (E.A.); (S.A.S.)
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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32
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Huang J, Chen Z, Ye Y, Shao Y, Zhu P, Li X, Ma Y, Xu F, Zhou J, Wu M, Gao X, Yang Y, Zhang J, Hao C. DTX3L Enhances Type I Interferon Antiviral Response by Promoting the Ubiquitination and Phosphorylation of TBK1. J Virol 2023; 97:e0068723. [PMID: 37255478 PMCID: PMC10308958 DOI: 10.1128/jvi.00687-23] [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: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Studies already revealed that some E3 ubiquitin ligases participated in the immune response after viral infection by regulating the type I interferon (IFN) pathway. Here, we demonstrated that type I interferon signaling enhanced the translocation of ETS1 to the nucleus and the promoter activity of E3 ubiquitin ligase DTX3L (deltex E3 ubiquitin ligase 3L) after virus infection and thus increased the expression of DTX3L. Further experiments suggested that DTX3L ubiquitinated TBK1 at K30 and K401 sites on K63-linked ubiquitination pathway. DTX3L was also necessary for mediating the phosphorylation of TBK1 through binding with the tyrosine kinase SRC: both together enhanced the activation of TBK1. Therefore, DTX3L, being an important positive-feedback regulator of type I interferon, exerted a key role in antiviral response. IMPORTANCE Our present study evaluated DTX3L as an antiviral molecule by promoting IFN production and establishing an IFN-β-ETS1-DTX3L-TBK1 positive-feedback loop as a novel immunomodulatory step to enhance interferon signaling and inhibit respiratory syncytial virus (RSV) infection. Our finding enriches and complements the biological function of DTX3L and provides a new strategy to protect against lung diseases such as bronchiolitis and pneumonia that develop with RSV.
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Affiliation(s)
- Jiaqi Huang
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, People's Republic of China
| | - Zhengrong Chen
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, People's Republic of China
| | - Yunfei Ye
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Yu Shao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Peijie Zhu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Xiaoping Li
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
- Reproductive Medicine Center, the First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Yu Ma
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, People's Republic of China
| | - Fei Xu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Ji Zhou
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Mengyun Wu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Xiu Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Yi Yang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Jinping Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, People's Republic of China
| | - Chuangli Hao
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou, People's Republic of China
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Scalia P, Williams SJ, Suma A, Carnevale V. The DTX Protein Family: An Emerging Set of E3 Ubiquitin Ligases in Cancer. Cells 2023; 12:1680. [PMID: 37443713 PMCID: PMC10340142 DOI: 10.3390/cells12131680] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Until recently, Deltex (DTX) proteins have been considered putative E3 ligases, based on the presence of an E3 RING domain in their protein coding sequence. The human DTX family includes DTX1, DTX2, DTX3, DTX3L and DTX4. Despite the fact that our knowledge of this class of E3-ubiquitin ligases is still at an early stage, our understanding of their role in oncogenesis is beginning to unfold. In fact, recently published studies allow us to define specific biological scenarios and further consolidate evidence-based working hypotheses. According to the current evidence, all DTX family members are involved in the regulation of Notch signaling, suggesting a phylogenetically conserved role in the regulation of this pathway. Indeed, additional evidence reveals a wider involvement of these proteins in other signaling complexes and cancer-promoting mechanisms beyond NOTCH signaling. DTX3, in particular, had been known to express two isoform variants (DTX3a and DTX3b). The recent identification and cloning of a third isoform variant in cancer (DTX3c), and its specific involvement in EphB4 degradation in cancer cells, sheds further light on this group of proteins and their specific role in cancer. Herein, we review the cumulative knowledge of this family of E3 Ubiquitin ligases with a specific focus on the potential oncogenic role of DTX isoforms in light of the rapidly expanding findings regarding this protein family's cellular targets and regulated signaling pathways. Furthermore, using a comparative and bioinformatic approach, we here disclose a new putative motif of a member of this family which may help in understanding the biological and contextual differences between the members of these proteins.
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Affiliation(s)
- Pierluigi Scalia
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA; 93100 Caltanissetta, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Stephen J. Williams
- ISOPROG-Somatolink EPFP Research Network, Philadelphia, PA 19102, USA; 93100 Caltanissetta, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA
| | - Antonio Suma
- Institute of Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Vincenzo Carnevale
- Institute of Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Thirunavukkarasu S, Ahmed M, Rosa BA, Boothby M, Cho SH, Rangel-Moreno J, Mbandi SK, Schreiber V, Gupta A, Zuniga J, Mitreva M, Kaushal D, Scriba TJ, Khader SA. Poly(ADP-ribose) polymerase 9 mediates early protection against Mycobacterium tuberculosis infection by regulating type I IFN production. J Clin Invest 2023; 133:e158630. [PMID: 37200107 PMCID: PMC10266794 DOI: 10.1172/jci158630] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/19/2023] [Indexed: 05/20/2023] Open
Abstract
The ADP ribosyltransferases (PARPs 1-17) regulate diverse cellular processes, including DNA damage repair. PARPs are classified on the basis of their ability to catalyze poly-ADP-ribosylation (PARylation) or mono-ADP-ribosylation (MARylation). Although PARP9 mRNA expression is significantly increased in progressive tuberculosis (TB) in humans, its participation in host immunity to TB is unknown. Here, we show that PARP9 mRNA encoding the MARylating PARP9 enzyme was upregulated during TB in humans and mice and provide evidence of a critical modulatory role for PARP9 in DNA damage, cyclic GMP-AMP synthase (cGAS) expression, and type I IFN production during TB. Thus, Parp9-deficient mice were susceptible to Mycobacterium tuberculosis infection and exhibited increased TB disease, cGAS and 2'3'-cyclic GMP-AMP (cGAMP) expression, and type I IFN production, along with upregulation of complement and coagulation pathways. Enhanced M. tuberculosis susceptibility is type I IFN dependent, as blockade of IFN α receptor (IFNAR) signaling reversed the enhanced susceptibility of Parp9-/- mice. Thus, in sharp contrast to PARP9 enhancement of type I IFN production in viral infections, this member of the MAR family plays a protective role by limiting type I IFN responses during TB.
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Affiliation(s)
| | | | - Bruce A. Rosa
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Mark Boothby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sung Hoon Cho
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Javier Rangel-Moreno
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stanley K. Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Valérie Schreiber
- Biotechnology and Cell Signaling, CNRS UMR7242, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | | | - Joaquin Zuniga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Makedonka Mitreva
- McDonnell Genome Institute, and
- Division of Infectious Diseases, Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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Kumar R, Mehta D, Nayak D, Sunil S. Characterization of an Aedes ADP-Ribosylation Protein Domain and Role of Post-Translational Modification during Chikungunya Virus Infection. Pathogens 2023; 12:pathogens12050718. [PMID: 37242388 DOI: 10.3390/pathogens12050718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Poly ADP-ribose polymerases (PARPs) catalyze ADP-ribosylation, a subclass of post-translational modification (PTM). Mono-ADP-ribose (MAR) moieties bind to target molecules such as proteins and nucleic acids, and are added as part of the process which also leads to formation of polymer chains of ADP-ribose. ADP-ribosylation is reversible; its removal is carried out by ribosyl hydrolases such as PARG (poly ADP-ribose glycohydrolase), TARG (terminal ADP-ribose protein glycohydrolase), macrodomain, etc. In this study, the catalytic domain of Aedes aegypti tankyrase was expressed in bacteria and purified. The tankyrase PARP catalytic domain was found to be enzymatically active, as demonstrated by an in vitro poly ADP-ribosylation (PARylation) experiment. Using in vitro ADP-ribosylation assay, we further demonstrate that the chikungunya virus (CHIKV) nsp3 (non-structural protein 3) macrodomain inhibits ADP-ribosylation in a time-dependent way. We have also demonstrated that transfection of the CHIKV nsP3 macrodomain increases the CHIKV viral titer in mosquito cells, suggesting that ADP-ribosylation may play a significant role in viral replication.
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Affiliation(s)
- Ramesh Kumar
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore 453252, India
| | - Divya Mehta
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Debasis Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore 453252, India
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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Delgado-Rodriguez SE, Ryan AP, Daugherty MD. Recurrent Loss of Macrodomain Activity in Host Immunity and Viral Proteins. Pathogens 2023; 12:674. [PMID: 37242344 PMCID: PMC10221186 DOI: 10.3390/pathogens12050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Protein post-translational modifications (PTMs) are an important battleground in the evolutionary arms races that are waged between the host innate immune system and viruses. One such PTM, ADP-ribosylation, has recently emerged as an important mediator of host antiviral immunity. Important for the host-virus conflict over this PTM is the addition of ADP-ribose by PARP proteins and removal of ADP-ribose by macrodomain-containing proteins. Interestingly, several host proteins, known as macroPARPs, contain macrodomains as well as a PARP domain, and these proteins are both important for the host antiviral immune response and evolving under very strong positive (diversifying) evolutionary selection. In addition, several viruses, including alphaviruses and coronaviruses, encode one or more macrodomains. Despite the presence of the conserved macrodomain fold, the enzymatic activity of many of these proteins has not been characterized. Here, we perform evolutionary and functional analyses to characterize the activity of macroPARP and viral macrodomains. We trace the evolutionary history of macroPARPs in metazoans and show that PARP9 and PARP14 contain a single active macrodomain, whereas PARP15 contains none. Interestingly, we also reveal several independent losses of macrodomain enzymatic activity within mammalian PARP14, including in the bat, ungulate, and carnivore lineages. Similar to macroPARPs, coronaviruses contain up to three macrodomains, with only the first displaying catalytic activity. Intriguingly, we also reveal the recurrent loss of macrodomain activity within the alphavirus group of viruses, including enzymatic loss in insect-specific alphaviruses as well as independent enzymatic losses in two human-infecting viruses. Together, our evolutionary and functional data reveal an unexpected turnover in macrodomain activity in both host antiviral proteins and viral proteins.
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Affiliation(s)
| | | | - Matthew D. Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California—San Diego, La Jolla, CA 92093, USA
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Ran XB, Ding LW, Sun QY, Yang H, Said JW, Zhentang L, Madan V, Dakle P, Xiao JF, Loh X, Li Y, Xu L, Xiang XQ, Wang LZ, Goh BC, Lin DC, Chng WJ, Tan SY, Jha S, Koeffler HP. Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy. Cancer Res 2023; 83:922-938. [PMID: 36638333 DOI: 10.1158/0008-5472.can-21-3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite the remarkable clinical responses achieved with immune checkpoint blockade therapy, the response rate is relatively low and only a subset of patients can benefit from the treatment. Aberrant RNA accumulation can mediate IFN signaling and stimulate an immune response, suggesting that targeting RNA decay machinery might sensitize tumor cells to immunotherapy. With this in mind, we identified an RNA exoribonuclease, XRN1, as a potential therapeutic target to suppress RNA decay and stimulate antitumor immunity. Silencing of XRN1 suppressed tumor growth in syngeneic immunocompetent mice and potentiated immunotherapy efficacy, while silencing of XRN1 alone did not affect tumor growth in immunodeficient mice. Mechanistically, XRN1 depletion activated IFN signaling and the viral defense pathway; both pathways play determinant roles in regulating immune evasion. Aberrant RNA-sensing signaling proteins (RIG-I/MAVS) mediated the expression of IFN genes, as depletion of each of them blunted the elevation of antiviral/IFN signaling in XRN1-silenced cells. Analysis of pan-cancer CRISPR-screening data indicated that IFN signaling triggered by XRN1 silencing is a common phenomenon, suggesting that the effect of XRN1 silencing may be extended to multiple types of cancers. Overall, XRN1 depletion triggers aberrant RNA-mediated IFN signaling, highlighting the importance of the aberrant RNA-sensing pathway in regulating immune responses. These findings provide the molecular rationale for developing XRN1 inhibitors and exploring their potential clinical application in combination with cancer immunotherapy. SIGNIFICANCE Targeting XRN1 activates an intracellular innate immune response mediated by RNA-sensing signaling and potentiates cancer immunotherapy efficacy, suggesting inhibition of RNA decay machinery as a novel strategy for cancer treatment.
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Affiliation(s)
- Xue-Bin Ran
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jonathan W Said
- Santa Monica-University of California, Los Angeles Medical Center, California, Los Angeles
| | - Lao Zhentang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- College of life Science, Zhejiang University, Hangzhou, China
| | - Xiao-Qiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China
| | - Ling-Zhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
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Su S, You S, Wang Y, Tamukong P, Quist MJ, Grasso CS, Kim HL. PAK4 inhibition improves PD1 blockade immunotherapy in prostate cancer by increasing immune infiltration. Cancer Lett 2023; 555:216034. [PMID: 36509363 DOI: 10.1016/j.canlet.2022.216034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Antitumor immunity requires lymphocytes to localize to the tumor. Prostate cancers (PCs) are immunologically cold and tend to lack T-cell infiltration. Most advanced PCs are insensitive to PD1 blockade therapies. Using syngeneic RM1 prostate tumors, p21-activated kinase-4 (PAK4) knockdown (KD) and pharmacological inhibition was assessed in C57BL/6J mice treated with PD1 antibodies (αPD1). RNASeq was used to characterize the immune response in the tumor. Immunohistochemistry, flow cytometry, and in vivo blocking studies confirmed the role of cell surface proteins in the generation of immune responses. In The Cancer Genome Atlas, PAK4 expression was inversely correlated with immune cell infiltration. PAK4 expression was controlled by the androgen receptor and its pioneering factor, FOXA1. PAK4 KD increased CD8+ T-cell infiltration and expression of IFNγ response genes. PAK4 KD also upregulated angiogenesis and endothelial cell adhesion molecules in the tumor microenvironment, contributing to CD8+ lymphocyte recruitment. Pharmacological inhibition of PAK4 made PC more responsive to immunotherapy with αPD1. A decrease in PAK4 activity increases immune activation and vascularity, which increases CD8+ lymphocyte infiltration into the tumor. Therefore, targeting PAK4 may improve the response of human PC to immunotherapy.
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Affiliation(s)
- Shengchen Su
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Sungyong You
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Yanping Wang
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Patrick Tamukong
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Michael J Quist
- Cedars-Sinai Medical Center, Los Angeles, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Catherine S Grasso
- Cedars-Sinai Medical Center, Los Angeles, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
| | - Hyung L Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA.
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Schuller M, Zarganes-Tzitzikas T, Bennett J, De Cesco S, Fearon D, von Delft F, Fedorov O, Brennan PE, Ahel I. Discovery and Development Strategies for SARS-CoV-2 NSP3 Macrodomain Inhibitors. Pathogens 2023; 12:324. [PMID: 36839595 PMCID: PMC9965906 DOI: 10.3390/pathogens12020324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The worldwide public health and socioeconomic consequences caused by the COVID-19 pandemic highlight the importance of increasing preparedness for viral disease outbreaks by providing rapid disease prevention and treatment strategies. The NSP3 macrodomain of coronaviruses including SARS-CoV-2 is among the viral protein repertoire that was identified as a potential target for the development of antiviral agents, due to its critical role in viral replication and consequent pathogenicity in the host. By combining virtual and biophysical screening efforts, we discovered several experimental small molecules and FDA-approved drugs as inhibitors of the NSP3 macrodomain. Analogue characterisation of the hit matter and crystallographic studies confirming binding modes, including that of the antibiotic compound aztreonam, to the active site of the macrodomain provide valuable structure-activity relationship information that support current approaches and open up new avenues for NSP3 macrodomain inhibitor development.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - James Bennett
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Stephane De Cesco
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Paul E. Brennan
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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40
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ADP-Ribosylation in Antiviral Innate Immune Response. Pathogens 2023; 12:pathogens12020303. [PMID: 36839575 PMCID: PMC9964302 DOI: 10.3390/pathogens12020303] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a reversible post-translational modification catalyzed by ADP-ribosyltransferases (ARTs). ARTs transfer one or more ADP-ribose from nicotinamide adenine dinucleotide (NAD+) to the target substrate and release the nicotinamide (Nam). Accordingly, it comes in two forms: mono-ADP-ribosylation (MARylation) and poly-ADP-ribosylation (PARylation). ADP-ribosylation plays important roles in many biological processes, such as DNA damage repair, gene regulation, and energy metabolism. Emerging evidence demonstrates that ADP-ribosylation is implicated in host antiviral immune activity. Here, we summarize and discuss ADP-ribosylation modifications that occur on both host and viral proteins and their roles in host antiviral response.
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41
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Huang Z, Wang W, Xu P, Gong S, Hu Y, Liu Y, Su F, Anjum KM, Deng WM, Yang S, Liu J, Jiao R, Chen J. Drosophila Ectoderm-expressed 4 modulates JAK/STAT pathway and protects flies against Drosophila C virus infection. Front Immunol 2023; 14:1135625. [PMID: 36817462 PMCID: PMC9937023 DOI: 10.3389/fimmu.2023.1135625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Sterile alpha and HEAT/Armadillo motif-containing protein (SARM) is conserved in evolution and negatively regulates TRIF-dependent Toll signaling in mammals. The SARM protein from Litopenaeus vannamei and its Drosophila orthologue Ectoderm-expressed (Ect4) are also involved in immune defense against pathogen infection. However, the functional mechanism of the protective effect remains unclear. In this study, we show that Ect4 is essential for the viral load in flies after a Drosophila C virus (DCV) infection. Viral load is increased in Ect4 mutants resulting in higher mortality rates than wild-type. Overexpression of Ect4 leads to a suppression of virus replication and thus improves the survival rate of the animals. Ect4 is required for the viral induction of STAT-responsive genes, TotA and TotM. Furthermore, Ect4 interacts with Stat92E, affecting the tyrosine phosphorylation and nuclear translocation of Stat92E in S2 cells. Altogether, our study identifies the adaptor protein Ect4 of the Toll pathway contributes to resistance to viral infection and regulates JAK/STAT signaling pathway.
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Affiliation(s)
- Zongliang Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Pengpeng Xu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shangyu Gong
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yingshan Hu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Liu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Su
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Khalid Mahmood Anjum
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Jiyong Liu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
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42
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The DarT/DarG Toxin-Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies. Pathogens 2023; 12:pathogens12020240. [PMID: 36839512 PMCID: PMC9967889 DOI: 10.3390/pathogens12020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin-antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.
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Esteban-Cantos A, Rodríguez-Centeno J, Silla JC, Barruz P, Sánchez-Cabo F, Saiz-Medrano G, Nevado J, Mena-Garay B, Jiménez-González M, de Miguel R, Bernardino JI, Montejano R, Cadiñanos J, Marcelo C, Gutiérrez-García L, Martínez-Martín P, Wallet C, Raffi F, Rodés B, Arribas JR. Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns. EBioMedicine 2023; 88:104434. [PMID: 36640455 PMCID: PMC9842861 DOI: 10.1016/j.ebiom.2022.104434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Previous epigenome-wide association studies have shown that HIV infection can disrupt the host DNA methylation landscape. However, it remains unclear how antiretroviral therapy (ART) affects the HIV-induced epigenetic modifications. METHODS 184 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included. We compared genome-wide DNA methylation profiles in whole blood between groups adjusting for age, sex, batch effects, and DNA methylation-based estimates of leucocyte composition. FINDINGS We identified 430 differentially methylated positions (DMPs) between HIV+ pre-ART individuals and HIV-uninfected controls. In participants with HIV, ART initiation modified the DNA methylation levels at 845 CpG positions and restored 49.3% of the changes found between HIV+ pre-ART and HIV-uninfected individuals. We only found 15 DMPs when comparing DNA methylation profiles between HIV+ post-ART individuals and participants without HIV. The Gene Ontology enrichment analysis of DMPs associated with untreated HIV infection revealed an enrichment in biological processes regulating the immune system and antiviral responses. In participants with untreated HIV infection, DNA methylation levels at top HIV-related DMPs were associated with CD4/CD8 ratios and viral loads. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio. INTERPRETATION Control of HIV viraemia after 96 weeks of ART initiation partly restores the host DNA methylation changes that occurred before antiretroviral treatment of HIV infection. FUNDING NEAT-ID Foundation and Instituto de Salud Carlos III, co-funded by European Union.
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Affiliation(s)
- Andrés Esteban-Cantos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Javier Rodríguez-Centeno
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Juan C Silla
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Pilar Barruz
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Gabriel Saiz-Medrano
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julián Nevado
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Beatriz Mena-Garay
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - María Jiménez-González
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rosa de Miguel
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Jose I Bernardino
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rocío Montejano
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julen Cadiñanos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cristina Marcelo
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Lucía Gutiérrez-García
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Patricia Martínez-Martín
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cédrick Wallet
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, CHU de Bordeaux, Bordeaux, France
| | - François Raffi
- Centre Hospitalier Universitaire de Nantes and CIC 1413 INSERM, Nantes, France
| | - Berta Rodés
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
| | - José R Arribas
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
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Nakayama M, Marchi H, Dmitrieva AM, Chakraborty A, Merl-Pham J, Hennen E, Le Gleut R, Ruppert C, Guenther A, Kahnert K, Behr J, Hilgendorff A, Hauck SM, Adler H, Staab-Weijnitz CA. Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection. Front Microbiol 2023; 13:957830. [PMID: 36713229 PMCID: PMC9875134 DOI: 10.3389/fmicb.2022.957830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) collectively refers to chronic and progressive lung diseases that cause irreversible limitations in airflow. Patients with COPD are at high risk for severe respiratory symptoms upon influenza virus infection. Airway epithelial cells provide the first-line antiviral defense, but whether or not their susceptibility and response to influenza virus infection changes in COPD have not been elucidated. Therefore, this study aimed to compare the susceptibility of COPD- and control-derived airway epithelium to the influenza virus and assess protein changes during influenza virus infection by quantitative proteomics. Materials and methods The presence of human- and avian-type influenza A virus receptor was assessed in control and COPD lung sections as well as in fully differentiated primary human bronchial epithelial cells (phBECs) by lectin- or antibody-based histochemical staining. PhBECs were from COPD lungs, including cells from moderate- and severe-stage diseases, and from age-, sex-, smoking, and history-matched control lung specimens. Protein profiles pre- and post-influenza virus infection in vitro were directly compared using quantitative proteomics, and selected findings were validated by qRT-PCR and immunoblotting. Results The human-type influenza receptor was more abundant in human airways than the avian-type influenza receptor, a property that was retained in vitro when differentiating phBECs at the air-liquid interface. Proteomics of phBECs pre- and post-influenza A virus infection with A/Puerto Rico/8/34 (PR8) revealed no significant differences between COPD and control phBECs in terms of flu receptor expression, cell type composition, virus replication, or protein profile pre- and post-infection. Independent of health state, a robust antiviral response to influenza virus infection was observed, as well as upregulation of several novel influenza virus-regulated proteins, including PLSCR1, HLA-F, CMTR1, DTX3L, and SHFL. Conclusion COPD- and control-derived phBECs did not differ in cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Finally, we identified novel influenza A virus-regulated proteins in bronchial epithelial cells that might serve as potential targets to modulate the pathogenicity of infection and acute exacerbations.
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Affiliation(s)
- Misako Nakayama
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Hannah Marchi
- Core Facility Statistical Consulting, Helmholtz Zentrum München, Munich, Germany,Faculty of Business Administration and Economics, Bielefeld University, Bielefeld, Germany
| | - Anna M. Dmitrieva
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Ashesh Chakraborty
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elisabeth Hennen
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Ronan Le Gleut
- Core Facility Statistical Consulting, Helmholtz Zentrum München, Munich, Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), Giessen, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), Giessen, Germany
| | - Kathrin Kahnert
- Department of Medicine V, Ludwig Maximilian University (LMU) Munich, Member of the German Center of Lung Research, University Hospital, Munich, Germany
| | - Jürgen Behr
- Department of Medicine V, Ludwig Maximilian University (LMU) Munich, Member of the German Center of Lung Research, University Hospital, Munich, Germany
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Heiko Adler
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,*Correspondence: Heiko Adler,
| | - Claudia A. Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Claudia A. Staab-Weijnitz, ; https://orcid.org/0000-0002-1211-7834
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45
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Activities and binding partners of E3 ubiquitin ligase DTX3L and its roles in cancer. Biochem Soc Trans 2022; 50:1683-1692. [DOI: 10.1042/bst20220501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Ubiquitination is a protein post-translational modification that affects protein localisation, stability and interactions. E3 ubiquitin ligases regulate the final step of the ubiquitination reaction by recognising target proteins and mediating the ubiquitin transfer from an E2 enzyme. DTX3L is a multi-domain E3 ubiquitin ligase in which the N-terminus mediates protein oligomerisation, a middle D3 domain mediates the interaction with PARP9, a RING domain responsible for recognising E2 ∼ Ub and a DTC domain has the dual activity of ADP-ribosylating ubiquitin and mediating ubiquitination. The activity of DTX3L is known to be modulated by at least two different factors: the concentration of NAD+, which dictates if the enzyme acts as a ligase or as an ADP-ribosyltransferase, and its binding partners, which affect DTX3L activity through yet unknown mechanisms. In light of recent findings it is possible that DTX3L could ubiquitinate ADP-ribose attached to proteins. Different DTX3L–protein complexes have been found to be part of multiple signalling pathways through which they promote the adhesion, proliferation, migration and chemoresistance of e.g. lymphoma, glioma, melanoma, and prostate cancer. In this review, we have covered the literature available for the molecular functions of DTX3L especially in the context of cancer biology, different pathways it regulates and how these relate to its function as an oncoprotein.
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46
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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus. Comp Immunol Microbiol Infect Dis 2022; 90-91:101909. [PMID: 36410069 PMCID: PMC10500253 DOI: 10.1016/j.cimid.2022.101909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Intraspecific variation in host infectiousness affects disease transmission dynamics in human, domestic animal, and many wildlife host-pathogen systems including avian influenza virus (AIV); therefore, identifying host factors related to host infectiousness is important for understanding, controlling, and preventing future outbreaks. Toward this goal, we used RNA-seq data collected from low pathogenicity avian influenza virus (LPAIV)-infected blue-winged teal (Spatula discors) to determine the association between host gene expression and intraspecific variation in cloacal viral shedding magnitude, the transmissible fraction of virus. We found that host genes were differentially expressed between LPAIV-infected and uninfected birds early in the infection, host genes were differentially expressed between shed level groups at one-, three-, and five-days post-infection, host gene expression was associated with LPAIV infection patterns over time, and genes of the innate immune system had a positive linear relationship with cloacal viral shedding. This study provides important insights into host gene expression patterns associated with intraspecific LPAIV shedding variation and can serve as a foundation for future studies focused on the identification of host factors that drive or permit the emergence of high viral shedding individuals.
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Affiliation(s)
- Amanda C Dolinski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jared J Homola
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Mark D Jankowski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; US Environmental Protection Agency, Region 10, Seattle, WA 98101, USA
| | - John D Robinson
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jennifer C Owen
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; Michigan State University, Department of Large Animal Clinical Sciences, 736 Wilson Road, East Lansing, MI 48824, USA.
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47
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Bilkei‐Gorzo O, Heunis T, Marín‐Rubio JL, Cianfanelli FR, Raymond BBA, Inns J, Fabrikova D, Peltier J, Oakley F, Schmid R, Härtlova A, Trost M. The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection. EMBO J 2022; 41:e108970. [PMID: 36281581 PMCID: PMC9713710 DOI: 10.15252/embj.2021108970] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/01/2022] [Accepted: 10/06/2022] [Indexed: 01/15/2023] Open
Abstract
Phagocytosis is a key process in innate immunity and homeostasis. After particle uptake, newly formed phagosomes mature by acquisition of endolysosomal enzymes. Macrophage activation by interferon gamma (IFN-γ) increases microbicidal activity, but delays phagosomal maturation by an unknown mechanism. Using quantitative proteomics, we show that phagosomal proteins harbour high levels of typical and atypical ubiquitin chain types. Moreover, phagosomal ubiquitylation of vesicle trafficking proteins is substantially enhanced upon IFN-γ activation of macrophages, suggesting a role in regulating phagosomal functions. We identified the E3 ubiquitin ligase RNF115, which is enriched on phagosomes of IFN-γ activated macrophages, as an important regulator of phagosomal maturation. Loss of RNF115 protein or ligase activity enhanced phagosomal maturation and increased cytokine responses to bacterial infection, suggesting that both innate immune signalling from the phagosome and phagolysosomal trafficking are controlled through ubiquitylation. RNF115 knock-out mice show less tissue damage in response to S. aureus infection, indicating a role of RNF115 in inflammatory responses in vivo. In conclusion, RNF115 and phagosomal ubiquitylation are important regulators of innate immune functions during bacterial infections.
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Affiliation(s)
- Orsolya Bilkei‐Gorzo
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden,MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
| | - Tiaan Heunis
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | | | | | | | - Joseph Inns
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Daniela Fabrikova
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Fiona Oakley
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK,Newcastle Fibrosis Research GroupNewcastle UniversityNewcastle upon TyneUK
| | - Ralf Schmid
- Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK,Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, Department of Microbiology and Immunology at Institute of BiomedicineUniversity of GothenburgGothenburgSweden,MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK,Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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48
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Zhu K, Suskiewicz MJ, Hloušek-Kasun A, Meudal H, Mikoč A, Aucagne V, Ahel D, Ahel I. DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates. SCIENCE ADVANCES 2022; 8:eadd4253. [PMID: 36197986 PMCID: PMC7615817 DOI: 10.1126/sciadv.add4253] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitylation had been considered limited to protein lysine residues, but other substrates have recently emerged. Here, we show that DELTEX E3 ligases specifically target the 3' hydroxyl of the adenosine diphosphate (ADP)-ribosyl moiety that can be linked to a protein, thus generating a hybrid ADP-ribosyl-ubiquitin modification. Unlike other known hydroxyl-specific E3s, which proceed via a covalent E3~ubiqutin intermediate, DELTEX enzymes are RING E3s that stimulate a direct ubiquitin transfer from E2~ubiquitin onto a substrate. However, DELTEXes follow a previously unidentified paradigm for RING E3s, whereby the ligase not only forms a scaffold but also provides catalytic residues to activate the acceptor. Comparative analysis of known hydroxyl-ubiquitylating active sites points to the recurring use of a catalytic histidine residue, which, in DELTEX E3s, is potentiated by a glutamate in a catalytic triad-like manner. In addition, we determined the hydrolase specificity profile of this modification, identifying human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enzymes that could reverse it in cells.
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Affiliation(s)
- Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Marcin J. Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | | | - Hervé Meudal
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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49
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Liu Z, Meng M, Ding S, Zhou X, Feng K, Huang T, Cai YD. Identification of methylation signatures and rules for predicting the severity of SARS-CoV-2 infection with machine learning methods. Front Microbiol 2022; 13:1007295. [PMID: 36212830 PMCID: PMC9537378 DOI: 10.3389/fmicb.2022.1007295] [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: 07/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Patients infected with SARS-CoV-2 at various severities have different clinical manifestations and treatments. Mild or moderate patients usually recover with conventional medical treatment, but severe patients require prompt professional treatment. Thus, stratifying infected patients for targeted treatment is meaningful. A computational workflow was designed in this study to identify key blood methylation features and rules that can distinguish the severity of SARS-CoV-2 infection. First, the methylation features in the expression profile were deeply analyzed by a Monte Carlo feature selection method. A feature list was generated. Next, this ranked feature list was fed into the incremental feature selection method to determine the optimal features for different classification algorithms, thereby further building optimal classifiers. These selected key features were analyzed by functional enrichment to detect their biofunctional information. Furthermore, a set of rules were set up by a white-box algorithm, decision tree, to uncover different methylation patterns on various severity of SARS-CoV-2 infection. Some genes (PARP9, MX1, IRF7), corresponding to essential methylation sites, and rules were validated by published academic literature. Overall, this study contributes to revealing potential expression features and provides a reference for patient stratification. The physicians can prioritize and allocate health and medical resources for COVID-19 patients based on their predicted severe clinical outcomes.
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Affiliation(s)
- Zhiyang Liu
- School of Life Sciences, Changchun Sci-Tech University, Changchun, China
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - XiaoChao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Tao Huang,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- Yu-Dong Cai,
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50
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Bińkowski J, Taryma-Leśniak O, Łuczkowska K, Niedzwiedź A, Lechowicz K, Strapagiel D, Jarczak J, Davalos V, Pujol A, Esteller M, Kotfis K, Machaliński B, Parczewski M, Wojdacz TK. Epigenetic activation of antiviral sensors and effectors of interferon response pathways during SARS-CoV-2 infection. Biomed Pharmacother 2022; 153:113396. [PMID: 36076479 PMCID: PMC9271528 DOI: 10.1016/j.biopha.2022.113396] [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: 05/16/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Recent studies have shown that methylation changes identified in blood cells of COVID-19 patients have a potential to be used as biomarkers of SARS-CoV-2 infection outcomes. However, different studies have reported different subsets of epigenetic lesions that stratify patients according to the severity of infection symptoms, and more importantly, the significance of those epigenetic changes in the pathology of the infection is still not clear. We used methylomics and transcriptomics data from the largest so far cohort of COVID-19 patients from four geographically distant populations, to identify casual interactions of blood cells’ methylome in pathology of the COVID-19 disease. We identified a subset of methylation changes that is uniformly present in all COVID-19 patients regardless of symptoms. Those changes are not present in patients suffering from upper respiratory tract infections with symptoms similar to COVID-19. Most importantly, the identified epigenetic changes affect the expression of genes involved in interferon response pathways and the expression of those genes differs between patients admitted to intensive care units and only hospitalized. In conclusion, the DNA methylation changes involved in pathophysiology of SARS-CoV-2 infection, which are specific to COVID-19 patients, can not only be utilized as biomarkers in the disease management but also present a potential treatment target.
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