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Gupta A, Bohara VS, Siddegowda YB, Chaudhary N, Kumar S. Alpha-synuclein and RNA viruses: Exploring the neuronal nexus. Virology 2024; 597:110141. [PMID: 38917691 DOI: 10.1016/j.virol.2024.110141] [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: 12/28/2023] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Alpha-synuclein (α-syn), known for its pivotal role in Parkinson's disease, has recently emerged as a significant player in neurotropic RNA virus infections. Upregulation of α-syn in various viral infections has been found to impact neuroprotective functions by regulating neurotransmitter synthesis, vesicle trafficking, and synaptic vesicle recycling. This review focuses on the multifaceted role of α-syn in controlling viral replication by modulating chemoattractant properties towards microglial cells, virus-induced ER stress signaling, anti-oxidative proteins expression. Furthermore, the text underlines the α-syn-mediated regulation of interferon-stimulated genes. The review may help suggest potential therapeutic avenues for mitigating the impact of RNA viruses on the central nervous system by exploiting α-syn neuroprotective biology.
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Affiliation(s)
- Anjali Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vijay Singh Bohara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | | | - Nitin Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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2
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Morone B, Grimaldi G. PARP enzymes and mono-ADP-ribosylation: advancing the connection from interferon-signalling to cancer biology. Expert Rev Mol Med 2024; 26:e17. [PMID: 39189367 DOI: 10.1017/erm.2024.13] [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: 08/28/2024]
Abstract
ADP-ribosyltransferases of the PARP family encompass a group of enzymes with variegated regulatory functions in cells, ranging from DNA damage repair to the control of cell-cycle progression and immune response. Over the years, this knowledge has led to the use of PARP1/2 inhibitors as mainstay pharmaceutical strategies for the treatment of ovarian, pancreatic, prostate and breast cancers, holding mutations in genes encoding for proteins involved in the DNA repair mechanisms (synthetic lethality). Meanwhile, the last decade has witnessed significant progress in comprehending cellular pathways regulated by mono-ADP-ribosylation, with a huge effort in the development of novel selective compounds to inhibit those PARPs endowed with mono-ADP-ribosylation activity. This review focuses on the progress achieved in the cancer field, delving into most recent findings regarding the role of a subset of enzymes - the interferon-stimulated PARPs - in cancer progression.
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Affiliation(s)
- Barbara Morone
- Institute for Endocrinology and Experimental Oncology, National Research Council, Via Pietro Castellino 111, Napoli, Italy
| | - Giovanna Grimaldi
- Institute for Endocrinology and Experimental Oncology, National Research Council, Via Pietro Castellino 111, Napoli, Italy
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3
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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [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: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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4
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Wu X, Sun Y, Wei S, Hu H, Yang B. Identification of Potential Ferroptosis Biomarkers and Analysis of Immune Cell Infiltration in Psoriasis Using Machine Learning. Clin Cosmet Investig Dermatol 2024; 17:1281-1295. [PMID: 38835517 PMCID: PMC11149635 DOI: 10.2147/ccid.s457958] [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: 01/04/2024] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Background Ferroptosis is a type of cell death characterized by the accumulation of iron-dependent lethal lipid peroxides, which is associated with various pathophysiological processes. Psoriasis is a chronic autoimmune skin disease accompanied by abnormal immune cell infiltration and excessive production of lipid reactive oxygen species (ROS). Currently, its pathogenesis remains elusive, especially the potential role of ferroptosis in its pathophysiological process. Methods The microarrays GSE13355 (58 psoriatic skin specimens versus 122 healthy skin specimens) and the ferroptosis database were employed to identify the common differentially expressed genes (DEGs) associated with psoriasis and ferroptosis. The functions of common DEGs were investigated through functional enrichment analysis and protein-protein interaction analysis. The potential diagnostic markers for psoriasis among the common DEGs were identified using four machine-learning algorithms. DGIdb was utilized to explore potential therapeutic agents for psoriasis. Additionally, CIBERSORT was employed to investigate immune infiltration in psoriasis. Results A total of 8 common DEGs associated with psoriasis and ferroptosis were identified, which are involved in intercellular signaling and affect pathways of cell response to stress and stimulation. Four machine-learning algorithms were employed to identify poly (ADP-ribose) polymerase 12 (PARP12), frizzled homolog 7 (FZD7), and arachidonate 15-lipoxygenase (ALOX15B) among the eight common DEGs as potential diagnostic markers for psoriasis. A total of 18 drugs targeting the five common DEGs were identified as potential candidates for treating psoriasis. Additionally, significant changes were observed in the immune microenvironment of patients with psoriasis. Conclusion This study has contributed to our enhanced comprehension of ferroptosis-related genes as potential biomarkers for psoriasis diagnosis, as well as the alterations in the immune microenvironment associated with psoriasis. Our findings offer valuable insights into the diagnosis and treatment of psoriasis.
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Affiliation(s)
- Xiaoyan Wu
- Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, People's Republic of China
- Department of Dermatology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China
| | - Yuzhe Sun
- Department of Dermatology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, 510091, People's Republic of China
| | - Shuyi Wei
- Department of Dermatology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, 510091, People's Republic of China
| | - Huoyou Hu
- Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, People's Republic of China
| | - Bin Yang
- Department of Dermatology, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, People's Republic of China
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Kajimura Y, Tessari A, Orlacchio A, Thoms A, Cufaro MC, Marco FD, Amari F, Chen M, Soliman SHA, Rizzotto L, Zhang L, Amann J, Carbone DP, Ahmed A, Fiermonte G, Freitas M, Lodi A, Boccio PD, Palmieri D, Coppola V. An in vivo "turning model" reveals new RanBP9 interactions in lung macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595416. [PMID: 38826292 PMCID: PMC11142189 DOI: 10.1101/2024.05.22.595416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The biological functions of the scaffold protein Ran Binding Protein 9 (RanBP9) remain elusive in macrophages or any other cell type where this protein is expressed together with its CTLH (C-terminal to LisH) complex partners. We have engineered a new mouse model, named RanBP9-TurnX, where RanBP9 fused to three copies of the HA tag (RanBP9-3xHA) can be turned into RanBP9-V5 tagged upon Cre-mediated recombination. We created this model to enable stringent biochemical studies at cell type specific level throughout the entire organism. Here, we have used this tool crossed with LysM-Cre transgenic mice to identify RanBP9 interactions in lung macrophages. We show that RanBP9-V5 and RanBP9-3xHA can be both co-immunoprecipitated with the known members of the CTLH complex from the same whole lung lysates. However, more than ninety percent of the proteins pulled down by RanBP9-V5 differ from those pulled-down by RanBP9-HA. The lung RanBP9-V5 associated proteome includes previously unknown interactions with macrophage-specific proteins as well as with players of the innate immune response, DNA damage response, metabolism, and mitochondrial function. This work provides the first lung specific RanBP9-associated interactome in physiological conditions and reveals that RanBP9 and the CTLH complex could be key regulators of macrophage bioenergetics and immune functions.
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Wu H, Lu A, Yuan J, Yu Y, Lv C, Lu J. Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms. Cell Death Discov 2024; 10:226. [PMID: 38734665 PMCID: PMC11088682 DOI: 10.1038/s41420-024-01994-5] [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: 12/19/2023] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The functional alterations of proteins and nucleic acids mainly rely on their modifications. ADP-ribosylation is a NAD+-dependent modification of proteins and, in some cases, of nucleic acids. This modification is broadly categorized as Mono(ADP-ribosyl)ation (MARylation) or poly(ADP-ribosyl)ation (PARylation). MARylation catalyzed by mono(ADP-ribosyl) transferases (MARTs) is more common in cells and the number of MARTs is much larger than poly(ADP-ribosyl) transferases. Unlike PARylation is well-characterized, research on MARylation is at the starting stage. However, growing evidence demonstrate the cellular functions of MARylation, supporting its potential roles in human health and diseases. In this review, we outlined MARylation-associated proteins including MARTs, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. We summarized up-to-date findings about MARylation onto newly identified substrates including protein, DNA and RNA, and focused on the functions of these reactions in pathophysiological conditions as well as speculated the potential mechanisms. Furthermore, new strategies of MARylation detection and the current state of MARTs inhibitors were discussed. We also provided an outlook for future study, aiming to revealing the unknown biological properties of MARylation and its relevant mechanisms, and establish a novel therapeutic perspective in human diseases.
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Affiliation(s)
- Hao Wu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Anqi Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Jiuzhi Yuan
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yang Yu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Chongning Lv
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China
| | - Jincai Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China.
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China.
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Wazir S, Parviainen TAO, Pfannenstiel JJ, Duong MTH, Cluff D, Sowa ST, Galera-Prat A, Ferraris D, Maksimainen MM, Fehr AR, Heiskanen JP, Lehtiö L. Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication, Validating Mac1 as an Antiviral Target. J Med Chem 2024; 67:6519-6536. [PMID: 38592023 PMCID: PMC11144470 DOI: 10.1021/acs.jmedchem.3c02451] [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] [Indexed: 04/10/2024]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed. Here, we describe small-molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation-mediated innate immune responses. Three high-throughput screening hits had the same 2-amide-3-methylester thiophene scaffold. We studied the compound binding mode using X-ray crystallography, allowing us to design analogues. Compound 27 (MDOLL-0229) had an IC50 of 2.1 μM and was selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human proteins. The improved potency allowed testing of its effect on virus replication, and indeed, 27 inhibited replication of both murine hepatitis virus (MHV) prototypes CoV and SARS-CoV-2. Sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1-targeted small molecule demonstrated to inhibit coronavirus replication in a cell model.
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Affiliation(s)
- Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Tomi A. O. Parviainen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, 90014 Oulu, Finland
| | - Jessica J. Pfannenstiel
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States of America
| | - Men Thi Hoai Duong
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Daniel Cluff
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States of America
| | - Sven T. Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Dana Ferraris
- McDaniel College Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States of America
| | - Juha P. Heiskanen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, 90014 Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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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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Mustafa K, Han Y, He D, Wang Y, Niu N, Jose PA, Jiang Y, Kopp JB, Lee H, Qu P. Poly-(ADP-ribose) polymerases inhibition by olaparib attenuates activities of the NLRP3 inflammasome and of NF-κB in THP-1 monocytes. PLoS One 2024; 19:e0295837. [PMID: 38335214 PMCID: PMC10857571 DOI: 10.1371/journal.pone.0295837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 12/01/2023] [Indexed: 02/12/2024] Open
Abstract
Poly-(ADP-ribose) polymerases (PARPs) are a protein family that make ADP-ribose modifications on target genes and proteins. PARP family members contribute to the pathogenesis of chronic inflammatory diseases, including atherosclerosis, in which monocytes/macrophages play important roles. PARP inhibition is protective against atherosclerosis. However, the mechanisms by which PARP inhibition exerts this beneficial effect are not well understood. Here we show that in THP-1 monocytes, inhibition of PARP by olaparib attenuated oxidized low-density lipoprotein (oxLDL)-induced protein expressions of nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing-3 (NLRP3) inflammasome components: NLRP3, apoptosis-associated speck-like protein containing a caspase activation and recruitment domain (ASC), and caspase-1. Consistent with this effect, olaparib decreased oxLDL-enhanced interleukin (IL)-1β and IL-18 protein expression. Olaparib also decreased the oxLDL-mediated increase in mitochondrial reactive oxygen species. Similar to the effects of the NLRP3 inhibitor, MCC950, olaparib attenuated oxLDL-induced adhesion of monocytes to cultured human umbilical vein endothelial cells and reduced foam cell formation. Furthermore, olaparib attenuated the oxLDL-mediated activation of nuclear factor (NF)-κB through the oxLDL-mediated increase in IκBα phosphorylation and assembly of NF-κB subunits, demonstrated by co-immunoprecipitation of IκBα with RelA/p50 and RelB/p52 subunits. Moreover, PARP inhibition decreased oxLDL-mediated protein expression of a NF-κB target gene, VCAM1, encoding vascular cell adhesion molecule-1. This finding indicates an important role for NF-κB activity in PARP-mediated activation of the NLRP3 inflammasome. Thus, PARP inhibition by olaparib attenuates NF-κB and NLRP3 inflammasome activities, lessening monocyte cell adhesion and macrophage foam cell formation. These inhibitory effects of olaparib on NLRP3 activity potentially protect against atherosclerosis.
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Affiliation(s)
- Khamis Mustafa
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ying Han
- Department of Cardiology, Jinqiu Hospital of Liaoning Province, Shenyang, China
| | - Dan He
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Ying Wang
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Nan Niu
- Department of Cardiology, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Pedro A. Jose
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, District of Columbia, United States of America
- Department of Physiology/Pharmacology, The George Washington University School of Medicine & Health Sciences, Washington, District of Columbia, United States of America
| | - Yinong Jiang
- Department of Cardiology, The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hewang Lee
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
- Department of Medicine, The George Washington University School of Medicine & Health Sciences, Washington, District of Columbia, United States of America
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peng Qu
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
- Department of Cardiology, The Second Affiliated Hospital, Dalian Medical University, Dalian, China
- Faculty of Medicine, Dalian University of Technology, Dalian, China
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10
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Wazir S, Parviainen TAO, Pfannenstiel JJ, Duong MTH, Cluff D, Sowa ST, Galera-Prat A, Ferraris D, Maksimainen MM, Fehr AR, Heiskanen JP, Lehtiö L. Discovery of 2-amide-3-methylester thiophenes that target SARS-CoV-2 Mac1 and repress coronavirus replication, validating Mac1 as an anti-viral target. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555062. [PMID: 38234730 PMCID: PMC10793406 DOI: 10.1101/2023.08.28.555062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV-2 variants or novel CoVs. Here, we describe small molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation mediated innate immune responses. The compounds inhibiting Mac1 were discovered through high-throughput screening (HTS) using a protein FRET-based competition assay and the best hit compound had an IC50 of 14 μM. Three validated HTS hits have the same 2-amide-3-methylester thiophene scaffold and the scaffold was selected for structure-activity relationship (SAR) studies through commercial and synthesized analogs. We studied the compound binding mode in detail using X-ray crystallography and this allowed us to focus on specific features of the compound and design analogs. Compound 27 (MDOLL-0229) had an IC50 of 2.1 μM and was generally selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human ADP-ribose binding proteins. The improved potency allowed testing of its effect on virus replication and indeed, 27 inhibited replication of both MHVa prototype CoV, and SARS-CoV-2. Furthermore, sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1 targeted small molecule demonstrated to inhibit coronavirus replication in a cell model. This, together with its well-defined binding mode, makes 27 a good candidate for further hit/lead-optimization efforts.
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Affiliation(s)
- Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Tomi A. O. Parviainen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, FI-90014 Oulu, Finland
| | - Jessica J. Pfannenstiel
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Men Thi Hoai Duong
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Daniel Cluff
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Sven T. Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Dana Ferraris
- McDaniel College Department of Chemistry, 2 College Hill, Westminster, MD, USA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Juha P. Heiskanen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, FI-90014 Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
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11
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Qin C, Xie T, Yeh WW, Savas AC, Feng P. Metabolic Enzymes in Viral Infection and Host Innate Immunity. Viruses 2023; 16:35. [PMID: 38257735 PMCID: PMC10820379 DOI: 10.3390/v16010035] [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: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Metabolic enzymes are central players for cell metabolism and cell proliferation. These enzymes perform distinct functions in various cellular processes, such as cell metabolism and immune defense. Because viral infections inevitably trigger host immune activation, viruses have evolved diverse strategies to blunt or exploit the host immune response to enable viral replication. Meanwhile, viruses hijack key cellular metabolic enzymes to reprogram metabolism, which generates the necessary biomolecules for viral replication. An emerging theme arising from the metabolic studies of viral infection is that metabolic enzymes are key players of immune response and, conversely, immune components regulate cellular metabolism, revealing unexpected communication between these two fundamental processes that are otherwise disjointed. This review aims to summarize our present comprehension of the involvement of metabolic enzymes in viral infections and host immunity and to provide insights for potential antiviral therapy targeting metabolic enzymes.
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Affiliation(s)
- Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
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12
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Kerr CM, Parthasarathy S, Schwarting N, O'Connor JJ, Pfannenstiel JJ, Giri E, More S, Orozco RC, Fehr AR. PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell- and tissue-specific manner. J Virol 2023; 97:e0088523. [PMID: 37695054 PMCID: PMC10537751 DOI: 10.1128/jvi.00885-23] [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: 06/13/2023] [Accepted: 07/13/2023] [Indexed: 09/12/2023] Open
Abstract
ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD+ to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a murine hepatitis virus (MHV) Mac1 mutant virus in bone-marrow-derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and in vivo, we produced PARP12-/-mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and mice. In addition, liver pathology was also increased in A59-infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice. IMPORTANCE Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | | | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Joseph J. O'Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | | | - Emily Giri
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Sunil More
- Department of Veterinary Pathology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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13
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Zhang X, Chen B. Dermatomyositis with intrahepatic cholangiocarcinoma: a case report and data mining based on machine learning. Front Oncol 2023; 13:1206043. [PMID: 37664040 PMCID: PMC10471963 DOI: 10.3389/fonc.2023.1206043] [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: 04/14/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Cancer secondary to dermatomyositis (DM) is defined as paraneoplastic dermatomyositis, which is one of the major subtypes of DM. However, cases of DM with intrahepatic cholangiocarcinoma (ICC) are rarely reported. In the course of our clinical work, we encountered a case of a middle-aged female patient who was diagnosed with DM for 7 years and then diagnosed with ICC, and we would like to share this case. In addition, in order to further investigate the deeper mechanism of ICC associated with DM, we also analyzed the dataset related to DM and ICC in the Gene Expression Omnibus (GEO) database based on the machine learning methods and found that poly(ADP-ribose) polymerase family member 12 (PARP12) and metallothionein 1M (MT1M) were closely associated with ICC secondary to DM. They are potentially important biomarkers for predicting the occurrence of ICC in patients with DM.
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Affiliation(s)
| | - Bendong Chen
- General Hospital of Ningxia Medical University, Yinchuan, China
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14
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O’Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog 2023; 19:e1011614. [PMID: 37651466 PMCID: PMC10499221 DOI: 10.1371/journal.ppat.1011614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 catalytic activity in viral replication, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wild-type. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, the N40D mutant replicated at >1000-fold lower levels compared to the wild-type virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection. Our data validate the critical role of SARS-CoV-2 NSP3 Mac1 catalytic activity in viral replication and as a promising therapeutic target to develop antivirals.
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Affiliation(s)
- Taha Y. Taha
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Rahul K. Suryawanshi
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Irene P. Chen
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Galen J. Correy
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Maria McCavitt-Malvido
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Patrick C. O’Leary
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Manasi P. Jogalekar
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Morgan E. Diolaiti
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Gabriella R. Kimmerly
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Chia-Lin Tsou
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Ronnie Gascon
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Mauricio Montano
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Luis Martinez-Sobrido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Alan Ashworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - James S. Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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15
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Nishimura Y, Bittel AJ, Stead CA, Chen YW, Burniston JG. Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics. Mol Cell Proteomics 2023; 22:100605. [PMID: 37353005 PMCID: PMC10392138 DOI: 10.1016/j.mcpro.2023.100605] [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: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labeling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from two individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of "older" less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
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Affiliation(s)
- Yusuke Nishimura
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Adam J Bittel
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA
| | - Connor A Stead
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA.
| | - Jatin G Burniston
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
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16
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Kerr CM, Parthasarathy S, Schwarting N, O’Connor JJ, Giri E, More S, Orozco RC, Fehr AR. PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell and tissue specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545351. [PMID: 37398292 PMCID: PMC10312760 DOI: 10.1101/2023.06.16.545351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD + to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon, indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a MHV Mac1 mutant virus in bone-marrow derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and in vivo , we produced PARP12 -/- mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and in mice. In addition, liver pathology was also increased in A59 infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice. IMPORTANCE Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Here, using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Emily Giri
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Sunil More
- Department of Veterinary Pathology, Oklahoma State University, Stillwater Oklahoma 74048, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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17
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Wu X, Xu M, Geng M, Chen S, Little PJ, Xu S, Weng J. Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies. Signal Transduct Target Ther 2023; 8:220. [PMID: 37244925 DOI: 10.1038/s41392-023-01439-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 05/29/2023] Open
Abstract
The ever-increasing prevalence of noncommunicable diseases (NCDs) represents a major public health burden worldwide. The most common form of NCD is metabolic diseases, which affect people of all ages and usually manifest their pathobiology through life-threatening cardiovascular complications. A comprehensive understanding of the pathobiology of metabolic diseases will generate novel targets for improved therapies across the common metabolic spectrum. Protein posttranslational modification (PTM) is an important term that refers to biochemical modification of specific amino acid residues in target proteins, which immensely increases the functional diversity of the proteome. The range of PTMs includes phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, neddylation, glycosylation, palmitoylation, myristoylation, prenylation, cholesterylation, glutathionylation, S-nitrosylation, sulfhydration, citrullination, ADP ribosylation, and several novel PTMs. Here, we offer a comprehensive review of PTMs and their roles in common metabolic diseases and pathological consequences, including diabetes, obesity, fatty liver diseases, hyperlipidemia, and atherosclerosis. Building upon this framework, we afford a through description of proteins and pathways involved in metabolic diseases by focusing on PTM-based protein modifications, showcase the pharmaceutical intervention of PTMs in preclinical studies and clinical trials, and offer future perspectives. Fundamental research defining the mechanisms whereby PTMs of proteins regulate metabolic diseases will open new avenues for therapeutic intervention.
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Affiliation(s)
- Xiumei Wu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China
| | - Mengyun Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mengya Geng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Shuo Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Peter J Little
- School of Pharmacy, University of Queensland, Pharmacy Australia Centre of Excellence, Woolloongabba, QLD, 4102, Australia
- Sunshine Coast Health Institute and School of Health and Behavioural Sciences, University of the Sunshine Coast, Birtinya, QLD, 4575, Australia
| | - Suowen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jianping Weng
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, 510000, Guangzhou, China.
- Bengbu Medical College, Bengbu, 233000, China.
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18
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, O’Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti ME, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537104. [PMID: 37131711 PMCID: PMC10153184 DOI: 10.1101/2023.04.18.537104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the therapeutic potential of Mac1 inhibition, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wildtype. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, N40D replicated at >1000-fold lower levels compared to the wildtype virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection and showed no signs of lung pathology. Our data validate the SARS-CoV-2 NSP3 Mac1 domain as a critical viral pathogenesis factor and a promising target to develop antivirals.
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Affiliation(s)
| | | | - Irene P. Chen
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
| | - Galen J. Correy
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | | | | | | | | | | | | | | | - Nevan J. Krogan
- University of California San Francisco, San Francisco, CA 94158
| | - Alan Ashworth
- University of California San Francisco, San Francisco, CA 94158
| | - James S. Fraser
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158
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19
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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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20
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IFN-Induced PARPs—Sensors of Foreign Nucleic Acids? Pathogens 2023; 12:pathogens12030457. [PMID: 36986379 PMCID: PMC10057411 DOI: 10.3390/pathogens12030457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Cells have developed different strategies to cope with viral infections. Key to initiating a defense response against viruses is the ability to distinguish foreign molecules from their own. One central mechanism is the perception of foreign nucleic acids by host proteins which, in turn, initiate an efficient immune response. Nucleic acid sensing pattern recognition receptors have evolved, each targeting specific features to discriminate viral from host RNA. These are complemented by several RNA-binding proteins that assist in sensing of foreign RNAs. There is increasing evidence that the interferon-inducible ADP-ribosyltransferases (ARTs; PARP9—PARP15) contribute to immune defense and attenuation of viruses. However, their activation, subsequent targets, and precise mechanisms of interference with viruses and their propagation are still largely unknown. Best known for its antiviral activities and its role as RNA sensor is PARP13. In addition, PARP9 has been recently described as sensor for viral RNA. Here we will discuss recent findings suggesting that some PARPs function in antiviral innate immunity. We expand on these findings and integrate this information into a concept that outlines how the different PARPs might function as sensors of foreign RNA. We speculate about possible consequences of RNA binding with regard to the catalytic activities of PARPs, substrate specificity and signaling, which together result in antiviral activities.
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21
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Wang R, Xu J, Tang Y, Wang Y, Zhao J, Ding L, Peng Y, Zhang Z. Transcriptome-wide analysis reveals the coregulation of RNA-binding proteins and alternative splicing genes in the development of atherosclerosis. Sci Rep 2023; 13:1764. [PMID: 36720950 PMCID: PMC9889815 DOI: 10.1038/s41598-022-26556-6] [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: 08/02/2022] [Accepted: 12/16/2022] [Indexed: 02/02/2023] Open
Abstract
RNA-binding proteins (RBPs) are involved in the regulation of RNA splicing, stability, and localization. How RBPs control the development of atherosclerosis, is not fully understood. To explore the relevant RNA-binding proteins (RBPs) and alternative splicing events (ASEs) in atherosclerosis. We made a comprehensive work to integrate analyses of differentially expressed genes, including differential RBPs, and variable splicing characteristics related to different stages of atherosclerosis in dataset GSE104140. A total of 3712 differentially expressed genes (DEGs) were identified, including 2921 upregulated genes and 791 downregulated genes. Further analysis screened out 54 RBP genes, and 434 AS genes overlapped DEGs. We selected high expression ten RBP genes (SAMHD1, DDX60 L, TLR7, RBM47, MYEF2, RNASE6, PARP12, APOBEC3G, SMAD9, and RNASE1) for co-expression analysis. Meanwhile, we found seven regulated alternative splicing genes (RASGs) (ABI1, FXR1, CHID1, PLEC, PRKACB, BNIP2, PPP3CB) that could be regulated by RBPs. The co-expression network was used to further elucidate the regulatory and interaction relationship between RBPs and AS genes. Apoptotic process and innate immune response, revealed by the functional enrichment analysis of RASGs regulated by RBPs were closely related to atherosclerosis. In addition, 26 of the 344 alternative splicing genes regulated by the above 10 RBPs were transcription factors (TFs), We selected high expression nine TFs (TFDP1, RBBP7, STAT2, CREB5, ERG, ELF1, HMGN3, BCLAF1, and ZEB2) for co-expression analysis. The target genes of these TFs were mainly enriched in inflammatory and immune response pathways that were associated with atherosclerosis. indicating that AS abnormalities of these TFs may have a function in atherosclerosis. Furthermore, the expression of differentially expressed RBPs and the alternative splicing events of AS genes was validated by qRT-PCR in umbilical vein endothelial cells (HUVEC). The results showed that RBM47 were remarkedly difference in HUVEC treated with ox-LDL and the splicing ratio of AS in BCLAF1which is regulated by RBM47 significantly changed. In conclusion, the differentially expressed RBPs identified in our analysis may play important roles in the development of atherosclerosis by regulating the AS of these TF genes.
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Affiliation(s)
- Runqing Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Jin Xu
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yuning Tang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Department of Cardiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Yongxiang Wang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Jing Zhao
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China.,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Liqiong Ding
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yu Peng
- Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zheng Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, China. .,Gansu Key Laboratory of Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China. .,Gansu Clinical Medical Research Center for Cardiovascular Diseases, The First Hospital of Lanzhou University, Lanzhou, Gansu, China. .,Heart Center, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.
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22
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Hu F, Li C, Ye Y, Lu X, Alimujiang M, Bai N, Sun J, Ma X, Li X, Yang Y. PARP12 is required for mitochondrial function maintenance in thermogenic adipocytes. Adipocyte 2022; 11:379-388. [PMID: 35916471 PMCID: PMC9351573 DOI: 10.1080/21623945.2022.2091206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
PARP12 is a member of poly-ADP-ribosyl polymerase (PARPs), which has been characterized for its antiviral function. Yet its physiological implication in adipocytes remains unknown. Here, we report a central function of PARP12 in thermogenic adipocytes. We show that PARP12 is highly expressed in brown adipose tissue and is mainly localized to the mitochondria. Knockdown of PARP12 in vitro reduced UCP1 expression. In parallel, the deficiency of PARP12 reduced mitochondrial respiration in adipocytes, while overexpression of PARP12 reversed these effects.
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Affiliation(s)
- Fan Hu
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Chang Li
- Department of Endocrinology, Seventh People's Hospital Affiliated to Shanghai University of TCM, Shanghai, China
| | - Yafen Ye
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Xuhong Lu
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Miriayi Alimujiang
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Ningning Bai
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Jingjing Sun
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Xiaojing Ma
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Xiaohua Li
- Department of Endocrinology, Seventh People's Hospital Affiliated to Shanghai University of TCM, Shanghai, China
| | - Ying Yang
- Shanghai Clinical Center for Diabetes, Shanghai Key Clinical Center for Metabolic Disease, Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
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23
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Weixler L, Ikenga NJ, Voorneveld J, Aydin G, Bolte TMHR, Momoh J, Bütepage M, Golzmann A, Lüscher B, Filippov DV, Žaja R, Feijs KLH. Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used. Life Sci Alliance 2022; 6:6/1/e202201455. [PMID: 36368907 PMCID: PMC9652768 DOI: 10.26508/lsa.202201455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
The modification of substrates with ADP-ribose (ADPr) is important in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it is unknown whether they recognise ADPr, specific amino acid-ADPr linkages, or ADPr with the surrounding protein backbone. We first optimised methods to prepare extracts containing ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the reactivity of available reagents with diverse ADP-ribosylated protein and RNA substrates and observed that not all reagents are equally suited for all substrates. Next, we determined cross-reactivity with adenylylated RNA, AMPylated proteins, and metabolites, including NADH, which are detected by some reagents. Lastly, we analysed ADP-ribosylation using confocal microscopy, where depending on the fixation method, either mitochondrion, nucleus, or nucleolus is stained. This study allows future work dissecting the function of ADP-ribosylation in cells, both on protein and on RNA substrates, as we optimised sample preparation methods and have defined the reagents suitable for specific methods and substrates.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Nonso Josephat Ikenga
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Gülcan Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Timo MHR Bolte
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Alexandra Golzmann
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Karla LH Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany,Correspondence: ;
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24
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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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25
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Abstract
Metabolic adaptation to viral infections critically determines the course and manifestations of disease. At the systemic level, a significant feature of viral infection and inflammation that ensues is the metabolic shift from anabolic towards catabolic metabolism. Systemic metabolic sequelae such as insulin resistance and dyslipidaemia represent long-term health consequences of many infections such as human immunodeficiency virus, hepatitis C virus and severe acute respiratory syndrome coronavirus 2. The long-held presumption that peripheral and tissue-specific 'immune responses' are the chief line of defence and thus regulate viral control is incomplete. This Review focuses on the emerging paradigm shift proposing that metabolic engagements and metabolic reconfiguration of immune and non-immune cells following virus recognition modulate the natural course of viral infections. Early metabolic footprints are likely to influence longer-term disease manifestations of infection. A greater appreciation and understanding of how local biochemical adjustments in the periphery and tissues influence immunity will ultimately lead to interventions that curtail disease progression and identify new and improved prognostic biomarkers.
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Affiliation(s)
- Clovis S Palmer
- Division of Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA.
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26
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Weixler L, Feijs KLH, Zaja R. ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs. Nucleic Acids Res 2022; 50:9426-9441. [PMID: 36018800 PMCID: PMC9458441 DOI: 10.1093/nar/gkac711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Abstract
RNA function relies heavily on posttranscriptional modifications. Recently, it was shown that certain PARPs and TRPT1 can ADP-ribosylate RNA in vitro. Traditionally, intracellular ADP-ribosylation has been considered mainly as a protein posttranslational modification. To date, it is not clear whether RNA ADP-ribosylation occurs in cells. Here we present evidence that different RNA species are ADP-ribosylated in human cells. The modification of cellular RNA is mediated by several transferases such as TRPT1, PARP10, PARP11, PARP12 and PARP15 and is counteracted by different hydrolases including TARG1, PARG and ARH3. In addition, diverse cellular stressors can modulate the content of ADP-ribosylated RNA in cells. We next investigated potential consequences of ADP-ribosylation for RNA and found that ADPr-capped mRNA is protected against XRN1 mediated degradation but is not translated. T4 RNA ligase 1 can ligate ADPr-RNA in absence of ATP, resulting in the incorporation of an abasic site. We thus provide the first evidence of RNA ADP-ribosylation in mammalian cells and postulate potential functions of this novel RNA modification.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen 52074, Germany
| | - Karla L H Feijs
- Correspondence may also be addressed to Karla L.H. Feijs. Tel: +49 2418080692; Fax: +49 2418082427;
| | - Roko Zaja
- To whom correspondence should be addressed. Tel: +49 2418037944; Fax: +49 2418082427;
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27
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Luo L, Keyomarsi K. PARP inhibitors as single agents and in combination therapy: the most promising treatment strategies in clinical trials for BRCA-mutant ovarian and triple-negative breast cancers. Expert Opin Investig Drugs 2022; 31:607-631. [PMID: 35435784 PMCID: PMC9296104 DOI: 10.1080/13543784.2022.2067527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Poly (ADP-ribose) polymerase inhibitors (PARPis) are an exciting class of agents that have shown efficacy, particularly for BRCA-mutant triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC). However, most patients who receive PARPi as their standard of care therapy inevitably develop resistance and this underscores the need to identify additional targets that can circumvent such resistance. Combination treatment strategies have been developed in preclinical and clinical studies to address the challenges of efficacy and resistance. AREAS COVERED This review examines completed or ongoing clinical trials of PARPi mono- and combination therapies. PARPi monotherapy in HER2 negative breast (HR+ and TNBC subtypes) and ovarian cancer is a focal point. The authors propose potential strategies that might overcome resistance to PARPi and discuss key questions and future directions. EXPERT OPINION While the advent of PARPis has significantly improved the treatment of tumors with defects in DNA damage and repair pathways, careful patient selection will be essential to enhance these treatments. The identification of molecular biomarkers to predict disease response and progression is an endeavor.
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Affiliation(s)
- Linjie Luo
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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28
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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29
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Sindbis Macrodomain Poly-ADP-Ribose Hydrolase Activity Is Important for Viral RNA Synthesis. J Virol 2022; 96:e0151621. [PMID: 35297669 DOI: 10.1128/jvi.01516-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ADP-ribosylation is a highly dynamic posttranslational modification frequently studied in stress response pathways with recent attention given to its role in response to viral infection. Notably, the alphaviruses encode catalytically active macrodomains capable of ADP-ribosylhydrolase (ARH) activities, implying a role in remodeling the cellular ADP-ribosylome. This report decouples mono- and poly-ARH contributions to macrodomain function using a newly engineered Sindbis virus (SINV) mutant with attenuated poly-ARH activity. Our findings indicate that viral poly-ARH activity is uniquely required for high titer replication in mammalian systems. Despite translating incoming genomic RNA as efficiently as WT virus, mutant viruses have a reduced capacity to establish productive infection, offering a more complete understanding of the kinetics and role of the alphavirus macrodomain with important implications for broader ADP-ribosyltransferase biology. IMPORTANCE Viral macrodomains have drawn attention in recent years due to their high degree of conservation in several virus families (e.g., coronaviruses and alphaviruses) and their potential druggability. These domains erase mono- or poly-ADP-ribose, posttranslational modifications written by host poly-ADP-ribose polymerase (PARP) proteins, from undetermined host or viral proteins to enhance replication. Prior work determined that efficient alphavirus replication requires catalytically active macrodomains; however, which form of the modification requires removal and from which protein(s) had not been determined. Here, we present evidence for the specific requirement of poly-ARH activity to ensure efficient productive infection and virus replication.
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30
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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31
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PKD-dependent PARP12-catalyzed mono-ADP-ribosylation of Golgin-97 is required for E-cadherin transport from Golgi to plasma membrane. Proc Natl Acad Sci U S A 2022; 119:2026494119. [PMID: 34969853 PMCID: PMC8740581 DOI: 10.1073/pnas.2026494119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a posttranslational modification involved in key regulatory events catalyzed by ADP-ribosyltransferases (ARTs). Substrate identification and localization of the mono-ADP-ribosyltransferase PARP12 at the trans-Golgi network (TGN) hinted at the involvement of ARTs in intracellular traffic. We find that Golgin-97, a TGN protein required for the formation and transport of a specific class of basolateral cargoes (e.g., E-cadherin and vesicular stomatitis virus G protein [VSVG]), is a PARP12 substrate. PARP12 targets an acidic cluster in the Golgin-97 coiled-coil domain essential for function. Its mutation or PARP12 depletion, delays E-cadherin and VSVG export and leads to a defect in carrier fission, hence in transport, with consequent accumulation of cargoes in a trans-Golgi/Rab11-positive intermediate compartment. In contrast, PARP12 does not control the Golgin-245-dependent traffic of cargoes such as tumor necrosis factor alpha (TNFα). Thus, the transport of different basolateral proteins to the plasma membrane is differentially regulated by Golgin-97 mono-ADP-ribosylation by PARP12. This identifies a selective regulatory mechanism acting on the transport of Golgin-97- vs. Golgin-245-dependent cargoes. Of note, PARP12 enzymatic activity, and consequently Golgin-97 mono-ADP-ribosylation, depends on the activation of protein kinase D (PKD) at the TGN during traffic. PARP12 is directly phosphorylated by PKD, and this is essential to stimulate PARP12 catalytic activity. PARP12 is therefore a component of the PKD-driven regulatory cascade that selectively controls a major branch of the basolateral transport pathway. We propose that through this mechanism, PARP12 contributes to the maintenance of E-cadherin-mediated cell polarity and cell-cell junctions.
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NAD+-consuming enzymes in immune defense against viral infection. Biochem J 2021; 478:4071-4092. [PMID: 34871367 PMCID: PMC8718269 DOI: 10.1042/bcj20210181] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic reminds us that in spite of the scientific progress in the past century, there is a lack of general antiviral strategies. In analogy to broad-spectrum antibiotics as antibacterial agents, developing broad spectrum antiviral agents would buy us time for the development of vaccines and treatments for future viral infections. In addition to targeting viral factors, a possible strategy is to understand host immune defense mechanisms and develop methods to boost the antiviral immune response. Here we summarize the role of NAD+-consuming enzymes in the immune defense against viral infections, with the hope that a better understanding of this process could help to develop better antiviral therapeutics targeting these enzymes. These NAD+-consuming enzymes include PARPs, sirtuins, CD38, and SARM1. Among these, the antiviral function of PARPs is particularly important and will be a focus of this review. Interestingly, NAD+ biosynthetic enzymes are also implicated in immune responses. In addition, many viruses, including SARS-CoV-2 contain a macrodomain-containing protein (NSP3 in SARS-CoV-2), which serves to counteract the antiviral function of host PARPs. Therefore, NAD+ and NAD+-consuming enzymes play crucial roles in immune responses against viral infections and detailed mechanistic understandings in the future will likely facilitate the development of general antiviral strategies.
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Masood KI, Yameen M, Ashraf J, Shahid S, Mahmood SF, Nasir A, Nasir N, Jamil B, Ghanchi NK, Khanum I, Razzak SA, Kanji A, Hussain R, E Rottenberg M, Hasan Z. Upregulated type I interferon responses in asymptomatic COVID-19 infection are associated with improved clinical outcome. Sci Rep 2021; 11:22958. [PMID: 34824360 PMCID: PMC8617268 DOI: 10.1038/s41598-021-02489-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/15/2021] [Indexed: 12/23/2022] Open
Abstract
Understanding key host protective mechanisms against SARS-CoV-2 infection can help improve treatment modalities for COVID-19. We used a blood transcriptome approach to study biomarkers associated with differing severity of COVID-19, comparing severe and mild Symptomatic disease with Asymptomatic COVID-19 and uninfected Controls. There was suppression of antigen presentation but upregulation of inflammatory and viral mRNA translation associated pathways in Symptomatic as compared with Asymptomatic cases. In severe COVID-19, CD177 a neutrophil marker, was upregulated while interferon stimulated genes (ISGs) were downregulated. Asymptomatic COVID-19 cases displayed upregulation of ISGs and humoral response genes with downregulation of ICAM3 and TLR8. Compared across the COVID-19 disease spectrum, we found type I interferon (IFN) responses to be significantly upregulated (IFNAR2, IRF2BP1, IRF4, MAVS, SAMHD1, TRIM1), or downregulated (SOCS3, IRF2BP2, IRF2BPL) in Asymptomatic as compared with mild and severe COVID-19, with the dysregulation of an increasing number of ISGs associated with progressive disease. These data suggest that initial early responses against SARS-CoV-2 may be effectively controlled by ISGs. Therefore, we hypothesize that treatment with type I interferons in the early stage of COVID-19 may limit disease progression by limiting SARS-CoV-2 in the host.
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Affiliation(s)
- Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Javeria Ashraf
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Saba Shahid
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | | | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | | | | | - Najia Karim Ghanchi
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | | | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Rabia Hussain
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan
| | - Martin E Rottenberg
- Department of Microbiology and Tumor Cell Biology, Karolinska Institute, Solna, Sweden
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, P.O. Box 3500, Karachi, 75400, Pakistan.
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Boehi F, Manetsch P, Hottiger MO. Interplay between ADP-ribosyltransferases and essential cell signaling pathways controls cellular responses. Cell Discov 2021; 7:104. [PMID: 34725336 PMCID: PMC8560908 DOI: 10.1038/s41421-021-00323-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Signaling cascades provide integrative and interactive frameworks that allow the cell to respond to signals from its environment and/or from within the cell itself. The dynamic regulation of mammalian cell signaling pathways is often modulated by cascades of protein post-translational modifications (PTMs). ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases and manifests as mono- (MARylation) or poly- (PARylation) ADP-ribosylation depending on the addition of one or multiple ADP-ribose units to protein substrates. ADP-ribosylation has recently emerged as an important cell regulator that impacts a plethora of cellular processes, including many intracellular signaling events. Here, we provide an overview of the interplay between the intracellular diphtheria toxin-like ADP-ribosyltransferase (ARTD) family members and five selected signaling pathways (including NF-κB, JAK/STAT, Wnt-β-catenin, MAPK, PI3K/AKT), which are frequently described to control or to be controlled by ADP-ribosyltransferases and how these interactions impact the cellular responses.
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Affiliation(s)
- Flurina Boehi
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Cancer Biology PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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CD20 positive CD8 T cells are a unique and transcriptionally-distinct subset of T cells with distinct transmigration properties. Sci Rep 2021; 11:20499. [PMID: 34654826 PMCID: PMC8520003 DOI: 10.1038/s41598-021-00007-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
The presence of T cells that are dimly positive for the B cell marker CD20 is well-established in autoimmunity and correlates with disease severity in various diseases. Further, we previously identified that the level of CD20-positive T cells was three-fourfold elevated in ascites fluid of ovarian carcinoma patients, together suggesting a role in both autoimmunity and cancer. In this respect, treatment of autoimmune patients with the CD20-targeting antibody Rituximab has also been shown to target and deplete CD20-positive T cells, previously identified as IFN-gamma producing, low proliferative, CD8 cytotoxic T cells with an effector memory (EM) differentiation state. However, the exact phenotype and relevance of CD20-positive T cells remains unclear. Here, we set out to identify the transcriptomic profile of CD20-positive T cells using RNA sequencing. Further, to gain insight into potential functional properties of CD20 expression in T cells, CD20 was ectopically expressed on healthy human T cells and phenotypic, functional, migratory and adhesive properties were determined in vitro and in vivo. Together, these assays revealed a reduced transmigration and an enhanced adhesive profile combined with an enhanced activation status for CD20-positive T cells.
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Hoch NC. Host ADP-ribosylation and the SARS-CoV-2 macrodomain. Biochem Soc Trans 2021; 49:1711-1721. [PMID: 34351418 PMCID: PMC8421052 DOI: 10.1042/bst20201212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022]
Abstract
The COVID-19 pandemic has prompted intense research efforts into elucidating mechanisms of coronavirus pathogenesis and to propose antiviral interventions. The interferon (IFN) response is the main antiviral component of human innate immunity and is actively suppressed by several non-structural SARS-CoV-2 proteins, allowing viral replication within human cells. Differences in IFN signalling efficiency and timing have emerged as central determinants of the variability of COVID-19 disease severity between patients, highlighting the need for an improved understanding of host-pathogen interactions that affect the IFN response. ADP-ribosylation is an underexplored post-translational modification catalyzed by ADP-ribosyl transferases collectively termed poly(ADP-ribose) polymerases (PARPs). Several human PARPs are induced by the IFN response and participate in antiviral defences by regulating IFN signalling itself, modulating host processes such as translation and protein trafficking, as well as directly modifying and inhibiting viral target proteins. SARS-CoV-2 and other viruses encode a macrodomain that hydrolyzes ADP-ribose modifications, thus counteracting antiviral PARP activity. This mini-review provides a brief overview of the known targets of IFN-induced ADP-ribosylation and the functions of viral macrodomains, highlighting several open questions in the field.
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Affiliation(s)
- Nicolas C. Hoch
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
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37
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Zhu H, Tang YD, Zhan G, Su C, Zheng C. The Critical Role of PARPs in Regulating Innate Immune Responses. Front Immunol 2021; 12:712556. [PMID: 34367175 PMCID: PMC8341640 DOI: 10.3389/fimmu.2021.712556] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022] Open
Abstract
Poly (adenosine diphosphate-ribose) polymerases (PARPs) are a family of proteins responsible for transferring ADP-ribose groups to target proteins to initiate the ADP-ribosylation, a highly conserved and fundamental post-translational modification in all organisms. PARPs play important roles in various cellular functions, including regulating chromatin structure, transcription, replication, recombination, and DNA repair. Several studies have recently converged on the widespread involvement of PARPs and ADP-Ribosylation reaction in mammalian innate immunity. Here, we provide an overview of the emerging roles of PARPs family and ADP-ribosylation in regulating the host's innate immune responses involved in cancers, pathogenic infections, and inflammations, which will help discover and design new molecular targets for cancers, pathogenic infections, and inflammations.
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Affiliation(s)
- Huifang Zhu
- Neonatal/Pediatric Intensive Care Unit, Children’s Medical Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guoqing Zhan
- Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, China
| | - Chenhe Su
- The Wistar Institute, Philadelphia, PA, United States
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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Lee S, Lee YS, Choi Y, Son A, Park Y, Lee KM, Kim J, Kim JS, Kim VN. The SARS-CoV-2 RNA interactome. Mol Cell 2021; 81:2838-2850.e6. [PMID: 33989516 PMCID: PMC8075806 DOI: 10.1016/j.molcel.2021.04.022] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/26/2021] [Accepted: 04/20/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its abilities to repurpose host RNA-binding proteins (RBPs) and to evade antiviral RBPs. To uncover the SARS-CoV-2 RNA interactome, we here develop a robust ribonucleoprotein (RNP) capture protocol and identify 109 host factors that directly bind to SARS-CoV-2 RNAs. Applying RNP capture on another coronavirus, HCoV-OC43, revealed evolutionarily conserved interactions between coronaviral RNAs and host proteins. Transcriptome analyses and knockdown experiments delineated 17 antiviral RBPs, including ZC3HAV1, TRIM25, PARP12, and SHFL, and 8 proviral RBPs, such as EIF3D and CSDE1, which are responsible for co-opting multiple steps of the mRNA life cycle. This also led to the identification of LARP1, a downstream target of the mTOR signaling pathway, as an antiviral host factor that interacts with the SARS-CoV-2 RNAs. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions.
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Affiliation(s)
- Sungyul Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young-Suk Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Youngran Park
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyung-Min Lee
- International Vaccine Institute, Seoul, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
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39
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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40
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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Gonçalves-Carneiro D, Takata MA, Ong H, Shilton A, Bieniasz PD. Origin and evolution of the zinc finger antiviral protein. PLoS Pathog 2021; 17:e1009545. [PMID: 33901262 PMCID: PMC8102003 DOI: 10.1371/journal.ppat.1009545] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 01/24/2023] Open
Abstract
The human zinc finger antiviral protein (ZAP) recognizes RNA by binding to CpG dinucleotides. Mammalian transcriptomes are CpG-poor, and ZAP may have evolved to exploit this feature to specifically target non-self viral RNA. Phylogenetic analyses reveal that ZAP and its paralogue PARP12 share an ancestral gene that arose prior to extensive eukaryote divergence, and the ZAP lineage diverged from the PARP12 lineage in tetrapods. Notably, the CpG content of modern eukaryote genomes varies widely, and ZAP-like genes arose subsequent to the emergence of CpG-suppression in vertebrates. Human PARP12 exhibited no antiviral activity against wild type and CpG-enriched HIV-1, but ZAP proteins from several tetrapods had antiviral activity when expressed in human cells. In some cases, ZAP antiviral activity required a TRIM25 protein from the same or related species, suggesting functional co-evolution of these genes. Indeed, a hypervariable sequence in the N-terminal domain of ZAP contributed to species-specific TRIM25 dependence in antiviral activity assays. Crosslinking immunoprecipitation coupled with RNA sequencing revealed that ZAP proteins from human, mouse, bat and alligator exhibit a high degree of CpG-specificity, while some avian ZAP proteins appear more promiscuous. Together, these data suggest that the CpG- rich RNA directed antiviral activity of ZAP-related proteins arose in tetrapods, subsequent to the onset of CpG suppression in certain eukaryote lineages, with subsequent species-specific adaptation of cofactor requirements and RNA target specificity. To control viral infections, cells have evolved a variety of mechanisms that detect, modify and sometimes eliminate viral components. One of such mechanism is the Zinc Finger Antiviral Protein (ZAP) which binds RNA sequences that are rich in elements composed of a cytosine followed by a guanine. Selection of viral RNA can only be achieved because such elements are sparse in RNAs encoded by human genes. Here, we traced the molecular evolution of ZAP. We found that ZAP and a closely related gene, PARP12, originated from the same ancestral gene that existed in a predecessor of vertebrates and invertebrates. We found that ZAP proteins from mammals, birds and reptiles have antiviral activity but only in the presence of a co-factor, TRIM25, from the same species. ZAP proteins from birds were particularly interesting since they demonstrated a broader antiviral activity, primarily driven by relaxed requirement for cytosine-guanine. Our findings suggest that viruses that infect birds–which are important vectors for human diseases–are under differential selective pressures and this property may influence the outcome of interspecies transmission.
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Affiliation(s)
- Daniel Gonçalves-Carneiro
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Matthew A. Takata
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Heley Ong
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Amanda Shilton
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York City, New York, United States of America
- * E-mail:
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Demény MA, Virág L. The PARP Enzyme Family and the Hallmarks of Cancer Part 2: Hallmarks Related to Cancer Host Interactions. Cancers (Basel) 2021; 13:2057. [PMID: 33923319 PMCID: PMC8123211 DOI: 10.3390/cancers13092057] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
Poly (ADP-ribose) polymerases (PARPs) modify target proteins with a single ADP-ribose unit or with a poly (ADP-ribose) (PAR) polymer. PARP inhibitors (PARPis) recently became clinically available for the treatment of BRCA1/2 deficient tumors via the synthetic lethality paradigm. This personalized treatment primarily targets DNA damage-responsive PARPs (PARP1-3). However, the biological roles of PARP family member enzymes are broad; therefore, the effects of PARPis should be viewed in a much wider context, which includes complex effects on all known hallmarks of cancer. In the companion paper (part 1) to this review, we presented the fundamental roles of PARPs in intrinsic cancer cell hallmarks, such as uncontrolled proliferation, evasion of growth suppressors, cell death resistance, genome instability, replicative immortality, and reprogrammed metabolism. In the second part of this review, we present evidence linking PARPs to cancer-associated inflammation, anti-cancer immune response, invasion, and metastasis. A comprehensive overview of the roles of PARPs can facilitate the identification of novel cancer treatment opportunities and barriers limiting the efficacy of PARPi compounds.
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Affiliation(s)
- Máté A. Demény
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, 4032 Debrecen, Hungary
| | - László Virág
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, 4032 Debrecen, Hungary
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43
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Malgras M, Garcia M, Jousselin C, Bodet C, Lévêque N. The Antiviral Activities of Poly-ADP-Ribose Polymerases. Viruses 2021; 13:v13040582. [PMID: 33808354 PMCID: PMC8066025 DOI: 10.3390/v13040582] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The poly-adenosine diphosphate (ADP)-ribose polymerases (PARPs) are responsible for ADP-ribosylation, a reversible post-translational modification involved in many cellular processes including DNA damage repair, chromatin remodeling, regulation of translation and cell death. In addition to these physiological functions, recent studies have highlighted the role of PARPs in host defenses against viruses, either by direct antiviral activity, targeting certain steps of virus replication cycle, or indirect antiviral activity, via modulation of the innate immune response. This review focuses on the antiviral activity of PARPs, as well as strategies developed by viruses to escape their action.
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Affiliation(s)
- Mathilde Malgras
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Magali Garcia
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Clément Jousselin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
| | - Charles Bodet
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
| | - Nicolas Lévêque
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines, Université de Poitiers, 86073 Poitiers, France; (M.M.); (M.G.); (C.J.); (C.B.)
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, 86021 Poitiers, France
- Correspondence: nicolas.lévê; Tel.: +33-(0)5-49-44-38-17
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Hopp AK, Hottiger MO. Uncovering the Invisible: Mono-ADP-ribosylation Moved into the Spotlight. Cells 2021; 10:680. [PMID: 33808662 PMCID: PMC8003356 DOI: 10.3390/cells10030680] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD+)-dependent post-translational modification that is found on proteins as well as on nucleic acids. While ARTD1/PARP1-mediated poly-ADP-ribosylation has extensively been studied in the past 60 years, comparably little is known about the physiological function of mono-ADP-ribosylation and the enzymes involved in its turnover. Promising technological advances have enabled the development of innovative tools to detect NAD+ and NAD+/NADH (H for hydrogen) ratios as well as ADP-ribosylation. These tools have significantly enhanced our current understanding of how intracellular NAD dynamics contribute to the regulation of ADP-ribosylation as well as to how mono-ADP-ribosylation integrates into various cellular processes. Here, we discuss the recent technological advances, as well as associated new biological findings and concepts.
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Affiliation(s)
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland;
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Yang E, Li MMH. All About the RNA: Interferon-Stimulated Genes That Interfere With Viral RNA Processes. Front Immunol 2020; 11:605024. [PMID: 33362792 PMCID: PMC7756014 DOI: 10.3389/fimmu.2020.605024] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Interferon (IFN) signaling induces the expression of a wide array of genes, collectively referred to as IFN-stimulated genes (ISGs) that generally function to inhibit viral replication. RNA viruses are frequently targeted by ISGs through recognition of viral replicative intermediates and molecular features associated with viral genomes, or the lack of molecular features associated with host mRNAs. The ISGs reviewed here primarily inhibit viral replication in an RNA-centric manner, working to sense, degrade, or repress expression of viral RNA. This review focuses on dissecting how these ISGs exhibit multiple antiviral mechanisms, often through use of varied co-factors, highlighting the complexity of the type I IFN response. Specifically, these ISGs can mediate antiviral effects through viral RNA degradation, viral translation inhibition, or both. While the OAS/RNase L pathway globally degrades RNA and arrests translation, ISG20 and ZAP employ targeted RNA degradation and translation inhibition to block viral replication. Meanwhile, SHFL targets translation by inhibiting -1 ribosomal frameshifting, which is required by many RNA viruses. Finally, a number of E3 ligases inhibit viral transcription, an attractive antiviral target during the lifecycle of negative-sense RNA viruses which must transcribe their genome prior to translation. Through this review, we aim to provide an updated perspective on how these ISGs work together to form a complex network of antiviral arsenals targeting viral RNA processes.
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Affiliation(s)
- Emily Yang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melody M. H. Li
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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Syed Lal Badshah, Ullah A, Syed S. The Role of Zinc-Finger Antiviral Proteins in Immunity against Viruses. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2020. [DOI: 10.3103/s0891416820020020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12:v12090984. [PMID: 32899736 PMCID: PMC7552005 DOI: 10.3390/v12090984] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Cells have evolved highly specialized sentinels that detect viral infection and elicit an antiviral response. Among these, the stress-sensing protein kinase R, which is activated by double-stranded RNA, mediates suppression of the host translation machinery as a strategy to limit viral replication. Non-translating mRNAs rapidly condensate by phase separation into cytosolic stress granules, together with numerous RNA-binding proteins and components of signal transduction pathways. Growing evidence suggests that the integrated stress response, and stress granules in particular, contribute to antiviral defense. This review summarizes the current understanding of how stress and innate immune signaling act in concert to mount an effective response against virus infection, with a particular focus on the potential role of stress granules in the coordination of antiviral signaling cascades.
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Affiliation(s)
- Nina Eiermann
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Katharina Haneke
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Zhaozhi Sun
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; (N.E.); (K.H.); (G.S.)
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), University of Heidelberg, 69120 Heidelberg, Germany;
- Correspondence:
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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Abraham R, McPherson RL, Dasovich M, Badiee M, Leung AKL, Griffin DE. Both ADP-Ribosyl-Binding and Hydrolase Activities of the Alphavirus nsP3 Macrodomain Affect Neurovirulence in Mice. mBio 2020; 11:e03253-19. [PMID: 32047134 PMCID: PMC7018654 DOI: 10.1128/mbio.03253-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/06/2020] [Indexed: 12/13/2022] Open
Abstract
Macrodomain (MD), a highly conserved protein fold present in a subset of plus-strand RNA viruses, binds to and hydrolyzes ADP-ribose (ADPr) from ADP-ribosylated proteins. ADPr-binding by the alphavirus nonstructural protein 3 (nsP3) MD is necessary for the initiation of virus replication in neural cells, whereas hydrolase activity facilitates replication complex amplification. To determine the importance of these activities for pathogenesis of alphavirus encephalomyelitis, mutations were introduced into the nsP3 MD of Sindbis virus (SINV), and the effects on ADPr binding and hydrolase activities, virus replication, immune responses, and disease were assessed. Elimination of ADPr-binding and hydrolase activities (G32E) severely impaired in vitro replication of SINV in neural cells and in vivo replication in the central nervous systems of 2-week-old mice with reversion to wild type (WT) (G) or selection of a less compromising change (S) during replication. SINVs with decreased binding and hydrolase activities (G32S and G32A) or with hydrolase deficiency combined with better ADPr-binding (Y114A) were less virulent than WT virus. Compared to the WT, the G32S virus replicated less well in both the brain and spinal cord, induced similar innate responses, and caused less severe disease with full recovery of survivors, whereas the Y114A virus replicated well, induced higher expression of interferon-stimulated and NF-κB-induced genes, and was cleared more slowly from the spinal cord with persistent paralysis in survivors. Therefore, MD function was important for neural cell replication both in vitro and in vivo and determined the outcome from alphavirus encephalomyelitis in mice.IMPORTANCE Viral encephalomyelitis is an important cause of long-term disability, as well as acute fatal disease. Identifying viral determinants of outcome helps in assessing disease severity and developing new treatments. Mosquito-borne alphaviruses infect neurons and cause fatal disease in mice. The highly conserved macrodomain of nonstructural protein 3 binds and can remove ADP-ribose (ADPr) from ADP-ribosylated proteins. To determine the importance of these functions for virulence, recombinant mutant viruses were produced. If macrodomain mutations eliminated ADPr-binding or hydrolase activity, viruses did not grow. If the binding and hydrolase activities were impaired, the viruses grew less well than the wild-type virus, induced similar innate responses, and caused less severe disease, and most of the infected mice recovered. If binding was improved, but hydrolase activity was decreased, the virus replicated well and induced greater innate responses than did the WT, but clearance from the nervous system was impaired, and mice remained paralyzed. Therefore, macrodomain function determined the outcome of alphavirus encephalomyelitis.
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Affiliation(s)
- Rachy Abraham
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Robert L McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mohsen Badiee
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Diane E Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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Kim DS, Challa S, Jones A, Kraus WL. PARPs and ADP-ribosylation in RNA biology: from RNA expression and processing to protein translation and proteostasis. Genes Dev 2020; 34:302-320. [PMID: 32029452 PMCID: PMC7050490 DOI: 10.1101/gad.334433.119] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Kim et al. discuss the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. ADP-ribosylation (ADPRylation) is a posttranslational modification of proteins discovered nearly six decades ago, but many important questions remain regarding its molecular functions and biological roles, as well as the activity of the ADP-ribose (ADPR) transferase enzymes (PARP family members) that catalyze it. Growing evidence indicates that PARP-mediated ADPRylation events are key regulators of the protein biosynthetic pathway, leading from rDNA transcription and ribosome biogenesis to mRNA synthesis, processing, and translation. In this review we describe the role of PARP proteins and ADPRylation in all facets of this pathway. PARP-1 and its enzymatic activity are key regulators of rDNA transcription, which is a critical step in ribosome biogenesis. An emerging role of PARPs in alternative splicing of mRNAs, as well as direct ADPRylation of mRNAs, highlight the role of PARP members in RNA processing. Furthermore, PARP activity, stimulated by cellular stresses, such as viral infections and ER stress, leads to the regulation of mRNA stability and protein synthesis through posttranscriptional mechanisms. Dysregulation of PARP activity in these processes can promote disease states. Collectively, these results highlight the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. Future studies in these areas will yield new insights into the fundamental mechanisms and a broader utility for PARP-targeted therapeutic agents.
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Affiliation(s)
- Dae-Seok Kim
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Aarin Jones
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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