1
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García-delaTorre P, Rivero-Segura NA, Sánchez-García S, Becerril-Rojas K, Sandoval-Rodriguez FE, Castro-Morales D, Cruz-Lopez M, Vazquez-Moreno M, Rincón-Heredia R, Ramirez-Garcia P, Gomez-Verjan JC. GrimAge is elevated in older adults with mild COVID-19 an exploratory analysis. GeroScience 2024; 46:3511-3524. [PMID: 38358578 PMCID: PMC11226692 DOI: 10.1007/s11357-024-01095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 has been contained; however, the side effects associated with its infection continue to be a challenge for public health, particularly for older adults. On the other hand, epigenetic status contributes to the inter-individual health status and is associated with COVID-19 severity. Nevertheless, current studies focus only on severe COVID-19. Considering that most of the worldwide population developed mild COVID-19 infection. In the present exploratory study, we aim to analyze the association of mild COVID-19 with epigenetic ages (HorvathAge, HannumAge, GrimAge, PhenoAge, SkinAge, and DNAmTL) and clinical variables obtained from a Mexican cohort of older adults. We found that all epigenetic ages significantly differ from the chronological age, but only GrimAge is elevated. Additionally, both the intrinsic epigenetic age acceleration (IEAA) and the extrinsic epigenetic age acceleration (EEAA) are accelerated in all patients. Moreover, we found that immunological estimators and DNA damage were associated with PhenoAge, SkinBloodHorvathAge, and HorvathAge, suggesting that the effects of mild COVID-19 on the epigenetic clocks are mainly associated with inflammation and immunology changes. In conclusion, our results show that the effects of mild COVID-19 on the epigenetic clock are mainly associated with the immune system and an increase in GrimAge, IEAA, and EEAA.
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Affiliation(s)
- Paola García-delaTorre
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | | | - Sergio Sánchez-García
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | | | | | - Diana Castro-Morales
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Miguel Cruz-Lopez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Ruth Rincón-Heredia
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Perla Ramirez-Garcia
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico.
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2
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Petersen JM, Burgess AL, van Oers MM, Herniou EA, Bojko J. Nudiviruses in free-living and parasitic arthropods: evolutionary taxonomy. Trends Parasitol 2024:S1471-4922(24)00167-3. [PMID: 39019701 DOI: 10.1016/j.pt.2024.06.009] [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: 04/24/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024]
Abstract
The nudiviruses (family: Nudiviridae) are large double-stranded DNA (dsDNA) viruses that infect insects and crustaceans, and have most recently been identified from ectoparasitic members (fleas and lice). This virus family was created in 2014 and has since been expanded via the discovery of multiple novel viral candidates or accepted members, sparking the need for a new taxonomic and evolutionary overview. Using current information (including data from public databases), we construct a new comprehensive phylogeny, encompassing 49 different nudiviruses. We use this novel phylogeny to propose a new taxonomic structure of the Nudiviridae by suggesting two new viral genera (Zetanudivirus and Etanudivirus), from ectoparasitic lice. We detail novel emerging relationships between nudiviruses and their hosts, considering their evolutionary history and ecological role.
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Affiliation(s)
- Jirka Manuel Petersen
- Laboratory of Virology, Wageningen University and Research, 6708, PB, Wageningen, The Netherlands; Institut de Recherche sur la Biologie de l'Insecte, UMR7261 CNRS - Université de Tours, 37200 Tours, France.
| | - Amy L Burgess
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK; National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, 6708, PB, Wageningen, The Netherlands
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR7261 CNRS - Université de Tours, 37200 Tours, France
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK; National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK.
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3
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Du J, Zhang J, Liu D, Gao L, Liao H, Chu L, Lin J, Li W, Meng X, Zou F, Cai S, Zou M, Dong H. 1G6-D7 Inhibits Homologous Recombination Repair by Targeting Extracellular HSP90α to Promote Apoptosis in Non-Small Cell Lung Cancer. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38899512 DOI: 10.1002/tox.24356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Despite recent advances in treatment, non-small cell lung cancer (NSCLC) continues to have a high mortality rate. Currently, NSCLC pathogenesis requires further investigation, and therapeutic drugs are still under development. Homologous recombination repair (HRR) repairs severe DNA double-strand breaks. Homologous recombination repair deficiency (HRD) occurs when HRR is impaired and causes irreparable double-strand DNA damage, leading to genomic instability and increasing the risk of cancer development. Poly(ADP-ribose) polymerase (PARP) inhibitors can effectively treat HRD-positive tumors. Extracellular heat shock protein 90α (eHSP90α) is highly expressed in hypoxic environments and inhibits apoptosis, thereby increasing cellular tolerance. Here, we investigated the relationship between eHSP90α and HRR in NSCLC. DNA damage models were established in NSCLC cell lines (A549 and H1299). The activation of DNA damage and HRR markers, apoptosis, proliferation, and migration were investigated. In vivo tumor models were established using BALB/c nude mice and A549 cells. We found that human recombinant HSP90α stimulation further activated HRR and reduced DNA damage extent; however, eHSP90α monoclonal antibody, 1G6-D7, effectively inhibited HRR. HRR inhibition and increased apoptosis were observed after LRP1 knockdown; this effect could not be reversed with hrHSP90α addition. The combined use of 1G6-D7 and olaparib caused significant apoptosis and HRR inhibition in vitro and demonstrated promising anti-tumor effects in vivo. Extracellular HSP90α may be involved in HRR in NSCLC through LRP1. The combined use of 1G6-D7 and PARP inhibitors may exert anti-tumor effects by inhibiting DNA repair and further inducing apoptosis of NSCLC cells.
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Affiliation(s)
- Jiangzhou Du
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinming Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongyu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Gao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hua Liao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lanhe Chu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Li
- Department of Dermatology, The USC-Norris Comprehensive Cancer Center, University of Southern California Keck Medical Center, California, Los Angeles, USA
| | - Xiaojing Meng
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fei Zou
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shaoxi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengchen Zou
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hangming Dong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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4
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Lin YC, Lu M, Cai W, Hu WS. Comparative transcriptomic and proteomic kinetic analysis of adeno-associated virus production systems. Appl Microbiol Biotechnol 2024; 108:385. [PMID: 38896252 PMCID: PMC11186941 DOI: 10.1007/s00253-024-13203-5] [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: 02/29/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is a major gene delivery vehicle. We have constructed a stable rAAV producer cell line by integrating essential rAAV genome, viral and helper genes into the genome of HEK293 cell under the control of inducible promoters. Upon induction, the cell line produces transducing rAAV. To gain insight into enhancing rAAV productivity and vector quality, we performed a comparative transcriptomic and proteomic analysis of our synthetic cell line GX2 and two wild-type AAV (wtAAV) production systems, one by virus co-infection and the other by multi-plasmid transfection. The three systems had different kinetics in viral component synthesis but generated comparable copies of AAV genomes; however, the capsid titer of GX2 was an order of magnitude lower compared to those two wtAAV systems, indicating that its capsid production may be insufficient. The genome packaging efficiency was also lower in GX2 despite it produced higher levels of Rep52 proteins than either wtAAV systems, suggesting that Rep52 protein expression may not limit genome packaging. In the two wtAAV systems, VP were the most abundant AAV proteins and their levels continued to increase, while GX2 had high level of wasteful cargo gene expression. Furthermore, upregulated inflammation, innate immune responses, and MAPK signaling, as well as downregulated mitochondrial functions, were commonly observed in either rAAV or wtAAV systems. Overall, this comparative multi-omics study provided rich insights into host cell and viral factors that are potential targets for genetic and process intervention to enhance the productivity of synthetic rAAV producer cell lines. KEY POINTS: • wtAAV infection was more efficient in producing full viral particles than the synthetic cell GX2. • Capsid protein synthesis, genome replication, and packaging may limit rAAV production in GX2. • wtAAV infection and rAAV production in GX2 elicited similar host cell responses.
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Affiliation(s)
- Yu-Chieh Lin
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue S.E, Minneapolis, MN, 55455-0132, USA
| | - Min Lu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue S.E, Minneapolis, MN, 55455-0132, USA
| | - Wen Cai
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue S.E, Minneapolis, MN, 55455-0132, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue S.E, Minneapolis, MN, 55455-0132, USA.
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5
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Packard JE, Kumar N, Weitzman MD, Dembowski JA. Identifying Protein Interactions with Viral DNA Genomes during Virus Infection. Viruses 2024; 16:845. [PMID: 38932138 PMCID: PMC11209293 DOI: 10.3390/v16060845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/28/2024] Open
Abstract
Viruses exploit the host cell machinery to enable infection and propagation. This review discusses the complex landscape of DNA virus-host interactions, focusing primarily on herpesviruses and adenoviruses, which replicate in the nucleus of infected cells, and vaccinia virus, which replicates in the cytoplasm. We discuss experimental approaches used to discover and validate interactions of host proteins with viral genomes and how these interactions impact processes that occur during infection, including the host DNA damage response and viral genome replication, repair, and transcription. We highlight the current state of knowledge regarding virus-host protein interactions and also outline emerging areas and future directions for research.
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Affiliation(s)
- Jessica E. Packard
- Department of Biological Sciences, School of Science and Engineering, Duquesne University, Pittsburgh, PA 15282, USA
| | - Namrata Kumar
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew D. Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jill A. Dembowski
- Department of Biological Sciences, School of Science and Engineering, Duquesne University, Pittsburgh, PA 15282, USA
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6
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Pastor F, Charles E, Belmudes L, Chabrolles H, Cescato M, Rivoire M, Burger T, Passot G, Durantel D, Lucifora J, Couté Y, Salvetti A. Deciphering the phospho-signature induced by hepatitis B virus in primary human hepatocytes. Front Microbiol 2024; 15:1415449. [PMID: 38841065 PMCID: PMC11150682 DOI: 10.3389/fmicb.2024.1415449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Phosphorylation is a major post-translation modification (PTM) of proteins which is finely tuned by the activity of several hundred kinases and phosphatases. It controls most if not all cellular pathways including anti-viral responses. Accordingly, viruses often induce important changes in the phosphorylation of host factors that can either promote or counteract viral replication. Among more than 500 kinases constituting the human kinome only few have been described as important for the hepatitis B virus (HBV) infectious cycle, and most of them intervene during early or late infectious steps by phosphorylating the viral Core (HBc) protein. In addition, little is known on the consequences of HBV infection on the activity of cellular kinases. The objective of this study was to investigate the global impact of HBV infection on the cellular phosphorylation landscape early after infection. For this, primary human hepatocytes (PHHs) were challenged or not with HBV, and a mass spectrometry (MS)-based quantitative phosphoproteomic analysis was conducted 2- and 7-days post-infection. The results indicated that while, as expected, HBV infection only minimally modified the cell proteome, significant changes were observed in the phosphorylation state of several host proteins at both time points. Gene enrichment and ontology analyses of up- and down-phosphorylated proteins revealed common and distinct signatures induced by infection. In particular, HBV infection resulted in up-phosphorylation of proteins involved in DNA damage signaling and repair, RNA metabolism, in particular splicing, and cytoplasmic cell-signaling. Down-phosphorylated proteins were mostly involved in cell signaling and communication. Validation studies carried out on selected up-phosphorylated proteins, revealed that HBV infection induced a DNA damage response characterized by the appearance of 53BP1 foci, the inactivation of which by siRNA increased cccDNA levels. In addition, among up-phosphorylated RNA binding proteins (RBPs), SRRM2, a major scaffold of nuclear speckles behaved as an antiviral factor. In accordance with these findings, kinase prediction analysis indicated that HBV infection upregulates the activity of major kinases involved in DNA repair. These results strongly suggest that HBV infection triggers an intrinsic anti-viral response involving DNA repair factors and RBPs that contribute to reduce HBV replication in cell culture models.
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Affiliation(s)
- Florentin Pastor
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Emilie Charles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Lucid Belmudes
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Hélène Chabrolles
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Marion Cescato
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | | | - Thomas Burger
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Guillaume Passot
- Service de Chirurgie Générale et Oncologique, Hôpital Lyon Sud, Hospices Civils de Lyon Et CICLY, EA3738, Université Claude Bernard Lyon, Lyon, France
| | - David Durantel
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Julie Lucifora
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, UA13 BGE, CEA, CNRS, FR2048, Grenoble, France
| | - Anna Salvetti
- International Center for Research in Infectiology (CIRI), INSERM U1111, Université Claude Bernard Lyon, CNRS, UMR5308, ENS, Lyon, France
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7
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Yarahmadi A, Zare M, Aghayari M, Afkhami H, Jafari GA. Therapeutic bacteria and viruses to combat cancer: double-edged sword in cancer therapy: new insights for future. Cell Commun Signal 2024; 22:239. [PMID: 38654309 PMCID: PMC11040964 DOI: 10.1186/s12964-024-01622-w] [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: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Cancer, ranked as the second leading cause of mortality worldwide, leads to the death of approximately seven million people annually, establishing itself as one of the most significant health challenges globally. The discovery and identification of new anti-cancer drugs that kill or inactivate cancer cells without harming normal and healthy cells and reduce adverse effects on the immune system is a potential challenge in medicine and a fundamental goal in Many studies. Therapeutic bacteria and viruses have become a dual-faceted instrument in cancer therapy. They provide a promising avenue for cancer treatment, but at the same time, they also create significant obstacles and complications that contribute to cancer growth and development. This review article explores the role of bacteria and viruses in cancer treatment, examining their potential benefits and drawbacks. By amalgamating established knowledge and perspectives, this review offers an in-depth examination of the present research landscape within this domain and identifies avenues for future investigation.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Mitra Zare
- Department of Microbiology, Faculty of Sciences, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Masoomeh Aghayari
- Department of Microbiology, Faculty of Sciences, Urmia Branch, Islamic Azad University, Urmia, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.
| | - Gholam Ali Jafari
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
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8
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Işıksaçan N, Adaş G, Kasapoğlu P, Çukurova Z, Yılmaz R, Kurt Yaşar K, Irmak Koyuncu D, Tuncel FC, Şahingöz Erdal G, Gedikbaşı A, Pehlivan S, Karaoz E. The effect of mesenchymal stem cells administration on DNA repair gene expressions in critically ill COVID-19 patients: prospective controlled study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-16. [PMID: 38459810 DOI: 10.1080/15257770.2024.2327478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
When the studies are evaluated, immunomodulatory effect of MSCs, administration in critically ill patients, obstacle situations in use and side effects, pulmonary fibrosis prevention, which stem cells and their products, regeneration effect, administration route, and dosage are listed under the main heading like. The effect of MSC administration on DNA repair genes in COVID-19 infection is unknown. Our aim is to determine the effect of mesenchymal stem cells (MSCs) therapy applied in critically ill patients with coronavirus infection on DNA repair pathways and genes associated with those pathways. Patients (n = 30) divided into two equal groups. Group-1: Patients in a critically ill condition, Group-2: Patients in critically ill condition and transplanted MSCs. The mechanism was investigated in eleven genes of five different pathways; Base excision repair: PARP1, Nucleotide excision repair (NER): RAD23B and ERCC1, Homologous recombinational repair (HR): ATM, RAD51, RAD52 and WRN, Mismatch repair (MMR): MLH1, MSH2, and MSH6, Direct reversal repair pathway: MGMT. It was found that MSCs application had a significant effect on 6 genes located in 3 different DNA damage response pathways. These are NER pathway genes; RAD23 and ERCC1, HR pathway genes; ATM and RAD51, MMR pathway genes; MSH2 and MSH6 (p < 0.05). Two main points were shown. First, as a result of cellular damage in critical patients with COVID-19, DNA damage occurs and then DNA repair pathways and genes are activated in reaction to this situation. Second, administration of MSC to patients with COVID-19 infection plays a positive role by increasing the expression of DNA repair genes located in DNA damage pathways.
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Affiliation(s)
- Nilgün Işıksaçan
- Department of Biochemistry, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gökhan Adaş
- Stem Cell And Gene Therapies Application And Research Center, Department Of Surgery, Bakırköy Dr. Sadi Konuk Training And Research Hospital, University Of Health Sciences, Istanbul, Turkey
| | - Pınar Kasapoğlu
- Department of Biochemistry, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Zafer Çukurova
- Department of Anesthesia and Intensive Care, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Rabia Yılmaz
- Department of Anesthesia and Intensive Care, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Kadriye Kurt Yaşar
- Department of Infectious Disease, Istanbul Bakırköy Dr.Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Duygu Irmak Koyuncu
- Center of Stem Cells and Tissue Engineering Research & Practice, Istinye University, Istanbul, Turkey
| | - Fatima Ceren Tuncel
- Department of Medical Biology Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Gülçin Şahingöz Erdal
- Department of Oncology, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Asuman Gedikbaşı
- Department of Pediatric Basic Science, Division of Medical Genetics, Institute of Child Health, Istanbul University, Istanbul, Turkey
| | - Sacide Pehlivan
- Department of Medical Biology Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Erdal Karaoz
- Department of Histology & Embrology, Faculty of Medicine, Istinye University, LIV Hospital, Center of Regenerative Medicine and Stem Cell Manufacturing, Istanbul, Turkey
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9
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Aghajani Mir M. Vault RNAs (vtRNAs): Rediscovered non-coding RNAs with diverse physiological and pathological activities. Genes Dis 2024; 11:772-787. [PMID: 37692527 PMCID: PMC10491885 DOI: 10.1016/j.gendis.2023.01.014] [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: 07/26/2022] [Accepted: 01/16/2023] [Indexed: 04/05/2023] Open
Abstract
The physicochemical characteristics of RNA admit non-coding RNAs to perform a different range of biological acts through various mechanisms and are involved in regulating a diversity of fundamental processes. Notably, some reports of pathological conditions have proved abnormal expression of many non-coding RNAs guides the ailment. Vault RNAs are a class of non-coding RNAs containing stem regions or loops with well-conserved sequence patterns that play a fundamental role in the function of vault particles through RNA-ligand, RNA-RNA, or RNA-protein interactions. Taken together, vault RNAs have been proposed to be involved in a variety of functions such as cell proliferation, nucleocytoplasmic transport, intracellular detoxification processes, multidrug resistance, apoptosis, and autophagy, and serve as microRNA precursors and signaling pathways. Despite decades of investigations devoted, the biological function of the vault particle or the vault RNAs is not yet completely cleared. In this review, the current scientific assertions of the vital vault RNAs functions were discussed.
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Affiliation(s)
- Mahsa Aghajani Mir
- Deputy of Research and Technology, Health Research Institute, Babol University of Medical Sciences, Babol 47176-4774, Iran
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10
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Wang Y, Fu Q, Park SY, Lee YS, Park SY, Lee DY, Yoon S. Decoding cellular mechanism of recombinant adeno-associated virus (rAAV) and engineering host-cell factories toward intensified viral vector manufacturing. Biotechnol Adv 2024; 71:108322. [PMID: 38336188 DOI: 10.1016/j.biotechadv.2024.108322] [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: 06/11/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is one of the prominent gene delivery vehicles that has opened promising opportunities for novel gene therapeutic approaches. However, the current major viral vector production platform, triple transfection in mammalian cells, may not meet the increasing demand. Thus, it is highly required to understand production bottlenecks from the host cell perspective and engineer the cells to be more favorable and tolerant to viral vector production, thereby effectively enhancing rAAV manufacturing. In this review, we provided a comprehensive exploration of the intricate cellular process involved in rAAV production, encompassing various stages such as plasmid entry to the cytoplasm, plasmid trafficking and nuclear delivery, rAAV structural/non-structural protein expression, viral capsid assembly, genome replication, genome packaging, and rAAV release/secretion. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production is summarized for each stage. The control strategies from the perspectives of host cell and materials (e.g., AAV plasmids) are proposed as our insights based on the characterization of molecular features and our existing knowledge of the AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.
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Affiliation(s)
- Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America.
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11
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Sun H, Wang T, Liu S, Tang X, Sun J, Liu X, Zhao Y, Shen P, Zhang Y. Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones. MICROBIOME 2024; 12:27. [PMID: 38350953 PMCID: PMC10865565 DOI: 10.1186/s40168-024-01759-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/07/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Seagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors. RESULTS Significant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones. CONCLUSIONS Our findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration. Video Abstract.
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Affiliation(s)
- Hao Sun
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Tianyu Wang
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Shuai Liu
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Guangzhou, 510301, China
| | - Jie Sun
- Fisheries College, Ocean University of China, Qingdao, 266003, China
| | - Xuerui Liu
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Ye Zhao
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Pingping Shen
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Yanying Zhang
- School of Ocean, Yantai University, Yantai, 264005, China.
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12
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Collin V, Biquand É, Tremblay V, Lavoie ÉG, Blondeau A, Gravel A, Galloy M, Lashgari A, Dessapt J, Côté J, Flamand L, Fradet-Turcotte A. The immediate-early protein 1 of human herpesvirus 6B interacts with NBS1 and inhibits ATM signaling. EMBO Rep 2024; 25:725-744. [PMID: 38177923 PMCID: PMC10897193 DOI: 10.1038/s44319-023-00035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Viral infection often trigger an ATM serine/threonine kinase (ATM)-dependent DNA damage response in host cells that suppresses viral replication. Viruses evolved different strategies to counteract this antiviral surveillance system. Here, we report that human herpesvirus 6B (HHV-6B) infection causes genomic instability by suppressing ATM signaling in host cells. Expression of immediate-early protein 1 (IE1) phenocopies this phenotype and blocks homology-directed double-strand break repair. Mechanistically, IE1 interacts with NBS1, and inhibits ATM signaling through two distinct domains. HHV-6B seems to efficiently inhibit ATM signaling as further depletion of either NBS1 or ATM do not significantly boost viral replication in infected cells. Interestingly, viral integration of HHV-6B into the host's telomeres is not strictly dependent on NBS1, challenging current models where integration occurs through homology-directed repair. Given that spontaneous IE1 expression has been detected in cells of subjects with inherited chromosomally-integrated form of HHV-6B (iciHHV-6B), a condition associated with several health conditions, our results raise the possibility of a link between genomic instability and the development of iciHHV-6-associated diseases.
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Affiliation(s)
- Vanessa Collin
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Élise Biquand
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
- INSERM, Centre d'Étude des Pathologies Respiratoires (CEPR), UMR 1100, Université de Tours, Tours, France
| | - Vincent Tremblay
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Élise G Lavoie
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Andréanne Blondeau
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Annie Gravel
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Maxime Galloy
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Anahita Lashgari
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Julien Dessapt
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Jacques Côté
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada
| | - Louis Flamand
- Division of Infectious Disease and Immunity, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1V 4G2, Canada.
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
| | - Amélie Fradet-Turcotte
- Oncology Division, Centre Hospitalier Universitaire (CHU) de Québec-Université Laval Research Center, Quebec City, QC, G1R 2J6, Canada.
- Department of Molecular biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada.
- Université Laval Cancer Research Center, Université Laval, Quebec City, QC, G1R 3S3, Canada.
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13
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Du Q, Zhu L, Zhong J, Wei X, Zhang Q, Shi T, Han C, Yin X, Chen X, Tong D, Huang Y. Porcine circovirus type 2 infection promotes the SUMOylation of nucleophosmin-1 to facilitate the viral circular single-stranded DNA replication. PLoS Pathog 2024; 20:e1012014. [PMID: 38394330 PMCID: PMC10917307 DOI: 10.1371/journal.ppat.1012014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/06/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
The mechanism of genome DNA replication in circular single-stranded DNA viruses is currently a mystery, except for the fact that it undergoes rolling-circle replication. Herein, we identified SUMOylated porcine nucleophosmin-1 (pNPM1), which is previously reported to be an interacting protein of the viral capsid protein, as a key regulator that promotes the genome DNA replication of porcine single-stranded DNA circovirus. Upon porcine circovirus type 2 (PCV2) infection, SUMO2/3 were recruited and conjugated with the K263 site of pNPM1's C-terminal domain to SUMOylate pNPM1, subsequently, the SUMOylated pNPM1 were translocated in nucleoli to promote the replication of PCV2 genome DNA. The mutation of the K263 site reduced the SUMOylation levels of pNPM1 and the nucleolar localization of pNPM1, resulting in a decrease in the level of PCV2 DNA replication. Meanwhile, the mutation of the K263 site prevented the interaction of pNPM1 with PCV2 DNA, but not the interaction of pNPM1 with PCV2 Cap. Mechanistically, PCV2 infection increased the expression levels of Ubc9, the only E2 enzyme involved in SUMOylation, through the Cap-mediated activation of ERK signaling. The upregulation of Ubc9 promoted the interaction between pNPM1 and TRIM24, a potential E3 ligase for SUMOylation, thereby facilitating the SUMOylation of pNPM1. The inhibition of ERK activation could significantly reduce the SUMOylation levels and the nucleolar localization of pNPM1, as well as the PCV2 DNA replication levels. These results provide new insights into the mechanism of circular single-stranded DNA virus replication and highlight NPM1 as a potential target for inhibiting PCV2 replication.
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Affiliation(s)
- Qian Du
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province, Yangling, China
| | - Lei Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jianhui Zhong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xueqi Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qi Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Tengfei Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Cong Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xinhuan Yin
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, Sweden
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province, Yangling, China
| | - Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Ministry of Education, Yangling, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agriculture and Rural Affairs, Yangling, China
- Engineering Research Center of Efficient New Vaccines for Animals, Universities of Shaanxi Province, Yangling, China
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14
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Sandoval C, Nisson K, Fregoso OI. HIV-1 Vpr-induced DNA damage activates NF-κB through ATM-NEMO independent of cell cycle arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.23.541990. [PMID: 37292767 PMCID: PMC10245860 DOI: 10.1101/2023.05.23.541990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lentiviral accessory genes enhance replication through diverse mechanisms. HIV-1 accessory protein Vpr modulates the host DNA damage response (DDR) at multiple steps through DNA damage, cell cycle arrest, the degradation of host proteins, and both the activation and repression of DDR signaling. Vpr also alters host and viral transcription; however, the connection between Vpr-mediated DDR modulation and transcriptional activation remains unclear. Here, we determined the cellular consequences of Vpr-induced DNA damage using Vpr mutants that allow us to separate the ability of Vpr to induce DNA damage from cell cycle arrest and other DDR phenotypes including host protein degradation and repression of DDR. RNA-sequencing of cells expressing Vpr or Vpr mutants identified that Vpr alters cellular transcription through mechanisms both dependent and independent of cell cycle arrest. In tissue-cultured U2OS cells and primary human monocyte-derived macrophages (MDMs), Vpr-induced DNA damage activates the ATM-NEMO pathway and alters cellular transcription via NF-κB/RelA signaling. HIV-1 infection of primary MDMs validated Vpr-dependent NF-κB transcriptional activation during infection. Both virion delivered and de novo expressed Vpr induced DNA damage and activated ATM-NEMO dependent NF-κB transcription, suggesting that engagement of the DDR and transcriptional reprogramming can occur during early and late stages of viral replication. Together, our data identifies a mechanism by which Vpr activates NF-κB through DNA damage and the ATM-NEMO pathway, which occur independent of cell cycle arrest. We propose this is essential to overcoming restrictive environments, such as in macrophages, to enhance viral transcription and replication.
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Affiliation(s)
- Carina Sandoval
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Karly Nisson
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Oliver I. Fregoso
- Molecular Biology Institute, University of California, Los Angeles, California, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
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15
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Li C, Zhang P, Hong PP, Niu GJ, Wang XP, Zhao XF, Wang JX. White spot syndrome virus hijacks host PP2A-FOXO axes to promote its propagation. Int J Biol Macromol 2024; 256:128333. [PMID: 38007022 DOI: 10.1016/j.ijbiomac.2023.128333] [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: 06/23/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Abstract
Viruses have developed superior strategies to escape host defenses or exploit host components and enable their infection. The forkhead box transcription factor O family proteins (FOXOs) are reportedly utilized by human cytomegalovirus during their reactivation in mammals, but if FOXOs are exploited by viruses during their infection remains unclear. In the present study, we found that the FOXO of kuruma shrimp (Marsupenaeus japonicus) was hijacked by white spot syndrome virus (WSSV) during infection. Mechanistically, the expression of leucine carboxyl methyl transferase 1 (LCMT1) was up-regulated during the early stages of WSSV infection, which activated the protein phosphatase 2A (PP2A) by methylation, leading to dephosphorylation of FOXO and translocation into the nucleus. The FOXO directly promoted transcription of the immediate early gene, wsv079 of WSSV, which functioned as a transcriptional activator to initiate the expression of viral early and late genes. Thus, WSSV utilized the host LCMT1-PP2A-FOXO axis to promote its replication during the early infection stage. We also found that, during the late stages of WSSV infection, the envelope protein of WSSV (VP26) promoted PP2A activity by directly binding to FOXO and the regulatory subunit of PP2A (B55), which further facilitated FOXO dephosphorylation and WSSV replication via the VP26-PP2A-FOXO axis in shrimp. Overall, this study reveals novel viral strategies by which WSSV hijacks host LCMT1-PP2A-FOXO or VP26-PP2A-FOXO axes to promote its propagation, and provides clinical targets for WSSV control in shrimp aquaculture.
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Affiliation(s)
- Cang Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Peng Zhang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Pan-Pan Hong
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Guo-Juan Niu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiao-Pei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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16
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Yu H, Chen H, Li N, Yang CJ, Xiao HY, Chen G, Huang GH. Flexible changes to the Heliothis virescens ascovirus 3h (HvAV-3h) virion components affect pathogenicity against different host larvae species. Microbiol Spectr 2023; 11:e0248823. [PMID: 37943038 PMCID: PMC10714839 DOI: 10.1128/spectrum.02488-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Different pathogenic processes of a virus in different hosts are related to the host individual differences, which makes the virus undergoes different survival pressures. Here, we found that the virions of an insect virus, Heliothis virescens ascovirus 3h (HvAV-3h), had different protein composition when they were purified from different host larval species. These "adaptive changes" of the virions were analyzed in detail in this study, which mainly included the differences of the protein composition of virions and the differences in affinity between virions and different host proteins. The results of this study revealed the flexible changes of viruses to help themselves adapt to different hosts. Also, these interesting findings can provide new insights to improve our understanding of virus adaptability and virulence differentiation caused by the adaptation process.
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Affiliation(s)
- Huan Yu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Hong Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Ni Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Chang-Jin Yang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
- Agriculture and Rural Bureau of Xinhuang Dong Autonomous County, Huaihua, Hunan, China
| | - Hua-Yan Xiao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Gong Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Hua Huang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
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17
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Tapryal N, Chakraborty A, Saha K, Islam A, Pan L, Hosoki K, Sayed IM, Duran JM, Alcantara J, Castillo V, Tindle C, Sarker AH, Wakamiya M, Cardenas VJ, Sharma G, Crotty Alexander LE, Sur S, Sahoo D, Ghosh G, Das S, Ghosh P, Boldogh I, Hazra TK. The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection. Nat Commun 2023; 14:8169. [PMID: 38071370 PMCID: PMC10710473 DOI: 10.1038/s41467-023-43938-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
SARS-CoV-2 infection-induced aggravation of host innate immune response not only causes tissue damage and multiorgan failure in COVID-19 patients but also induces host genome damage and activates DNA damage response pathways. To test whether the compromised DNA repair capacity of individuals modulates the severity of COVID-19 infection, we analyze DNA repair gene expression in publicly available patient datasets and observe a lower level of the DNA glycosylase NEIL2 in the lungs of severely infected COVID-19 patients. This observation of lower NEIL2 levels is further validated in infected patients, hamsters and ACE2 receptor-expressing human A549 (A549-ACE2) cells. Furthermore, delivery of recombinant NEIL2 in A549-ACE2 cells shows decreased expression of proinflammatory genes and viral E-gene, as well as lowers the yield of viral progeny compared to mock-treated cells. Mechanistically, NEIL2 cooperatively binds to the 5'-UTR of SARS-CoV-2 genomic RNA to block viral protein synthesis. Collectively, these data strongly suggest that the maintenance of basal NEIL2 levels is critical for the protective response of hosts to viral infection and disease.
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Affiliation(s)
- Nisha Tapryal
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kaushik Saha
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92037, USA
- Department of Biological Sciences, School of Engineering and Sciences, SRM University-AP, Guntur District, Andhra Pradesh, 522240, India
| | - Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Koa Hosoki
- Department of Medicine, Immunology Allergy and Rheumatology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California, San Diego, CA, 92093, USA
- Department of Biomedical and Nutritional Science, University of Massachusetts-Lowell, Lowell, MA, 01854, USA
| | - Jason M Duran
- Department of Internal Medicine, Division of Cardiology, UC San Diego Medical Center, La Jolla, CA, 92037, USA
| | - Joshua Alcantara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Vanessa Castillo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Altaf H Sarker
- Department of Cancer and DNA Damage Responses, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Maki Wakamiya
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Victor J Cardenas
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Gulshan Sharma
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | | | - Sanjiv Sur
- Department of Medicine, Immunology Allergy and Rheumatology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Debashis Sahoo
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92037, USA.
| | - Soumita Das
- Department of Pathology, University of California, San Diego, CA, 92093, USA.
- Department of Biomedical and Nutritional Science, University of Massachusetts-Lowell, Lowell, MA, 01854, USA.
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California, San Diego, CA, 92093, USA.
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Tapas K Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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18
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Studstill CJ, Mac M, Moody CA. Interplay between the DNA damage response and the life cycle of DNA tumor viruses. Tumour Virus Res 2023; 16:200272. [PMID: 37918513 PMCID: PMC10685005 DOI: 10.1016/j.tvr.2023.200272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023] Open
Abstract
Approximately 20 % of human cancers are associated with virus infection. DNA tumor viruses can induce tumor formation in host cells by disrupting the cell's DNA replication and repair mechanisms. Specifically, these viruses interfere with the host cell's DNA damage response (DDR), which is a complex network of signaling pathways that is essential for maintaining the integrity of the genome. DNA tumor viruses can disrupt these pathways by expressing oncoproteins that mimic or inhibit various DDR components, thereby promoting genomic instability and tumorigenesis. Recent studies have highlighted the molecular mechanisms by which DNA tumor viruses interact with DDR components, as well as the ways in which these interactions contribute to viral replication and tumorigenesis. Understanding the interplay between DNA tumor viruses and the DDR pathway is critical for developing effective strategies to prevent and treat virally associated cancers. In this review, we discuss the current state of knowledge regarding the mechanisms by which human papillomavirus (HPV), merkel cell polyomavirus (MCPyV), Kaposi's sarcoma-associated herpesvirus (KSHV), and Epstein-Barr virus (EBV) interfere with DDR pathways to facilitate their respective life cycles, and the consequences of such interference on genomic stability and cancer development.
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Affiliation(s)
- Caleb J Studstill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Michelle Mac
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Cary A Moody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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19
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Youssef ASED, Zekri ARN, Mohanad M, Loutfy SA, Abdel Fattah NF, Elberry MH, El Leithy AA, El-Touny A, Rabie AS, Shalaby M, Hanafy A, Lotfy MM, El-Sisi ER, El-Sayyad GS, Nassar A. Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus. Clin Exp Med 2023; 23:5063-5088. [PMID: 37804357 PMCID: PMC10725364 DOI: 10.1007/s10238-023-01207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
This study aimed to identify BRCA1/2 mutational patterns in the tissue and blood of Egyptian colorectal cancer (CRC) patients and to study the possible correlation of this mutational pattern with Human papillomavirus (HPV) infection. Eighty-two colonoscopic biopsies and forty-six blood samples were collected from Egyptian CRC patients, as well as blood samples of age and sex-matched healthy controls (n = 43) were enrolled. The libraries were performed using Qiaseq Human BRCA1 and BRCA2 targeted DNA panel and sequenced via Ion proton sequencer. Also, the CRC tissues were subjected to conventional PCR targeting the HPV Late 1 (L1) region. Our analysis revealed that the BRCA-DNA damage pathway had been altered in more than 65% of the CRC patients. Comparing tissue and blood samples from CRC patients, 25 somatic mutations were found exclusively in tissue, while 41 germline mutations were found exclusively in blood. Additionally, we identified 23 shared BRCA1/2 pathogenic (PVs) mutations in both blood and tissue samples, with a significantly higher frequency in blood samples compared to tissue samples. The most affected exon in BRCA1 was exon 10, while the most affected exons in BRCA2 were 11, 14, 18, 24, and 27 exons. Notably, we revealed an ethnic-related cluster of polymorphism variants in our population closely related to South Asian and African ethnicities. Novel PVs were identified and submitted to the ClinVar database. HPV was found in 23.8% of the CRC tissues, and 54% of HPV-positive cases had somatic BRCA1/2 PVs. The results of this research point to a possible connection between infection with HPV and BRCA1/2 mutations in the occurrence of colorectal cancer in the Egyptian population, which has a mixed ethnic background. Our data also indicate that liquid biopsy (blood samples) may be more representative than tissue samples for detecting BRCA1/2 mutations. These findings may have implications for cancer screening and the development of personalized, targeted therapies, such as PARP inhibitors, which can effectively target BRCA1/2 mutations.
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Affiliation(s)
- Amira Salah El-Din Youssef
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Abdel Rahman N Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa Mohanad
- Department of Biochemistry, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center (NTRC), The British University in Egypt (BUE), El-Shorouk City, Suez Desert Road, P. O. Box 43, Cairo, Egypt
| | - Nasra F Abdel Fattah
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mostafa H Elberry
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Asmaa A El Leithy
- Department of Medical Biotechnology, College of Biotechnology, Misr University for Science and Technology, Giza, Egypt
| | - Ahmed El-Touny
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ahmed Samy Rabie
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed Shalaby
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ayman Hanafy
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mai M Lotfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Enas R El-Sisi
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Gharieb S El-Sayyad
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, Egypt.
- Drug Microbiology Lab., Drug Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Auhood Nassar
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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20
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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21
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Zhao S, Li Y, Chen G, Wang X, Chen N, Wu X. Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection. Genome Res 2023; 33:gr.277931.123. [PMID: 37871969 PMCID: PMC10760458 DOI: 10.1101/gr.277931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
As influential regulatory elements in the genome, enhancers control gene expression under specific cellular conditions, and such connections are dynamic under different conditions. However, because of the lack of a genome-wide enhancer-gene connection map, the roles and regulatory pattern of enhancers were poorly investigated in insects, and the dynamic changes of enhancer contacts and functions under different conditions remain elusive. Here, combining Hi-C, ATAC-seq, and H3K27ac ChIP-seq data, we generate the genome-wide enhancer-gene map of silkworm and identify super-enhancers with a role in regulating the expression of vital genes related to cell state maintenance through a sophisticated interaction network. Additionally, a radical attenuation of chromatin interactions is found after infection of Bombyx mori nucleopolyhedrovirus (BmNPV), the main pathogen of silkworm, which directly rearranges the enhancer contacts. Such a rearrangement disturbs the intrinsic enhancer-gene connections in several antiviral genes, resulting in reduced expression of these genes, which accelerates viral infection. Overall, our results reveal the regulatory role of super-enhancers and shed new light on the mechanisms and dynamic changes of the genome-wide enhancer regulatory network.
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Affiliation(s)
- Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Yuedong Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xingyang Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Nan Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
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22
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Fu Q, Polanco A, Lee YS, Yoon S. Critical challenges and advances in recombinant adeno-associated virus (rAAV) biomanufacturing. Biotechnol Bioeng 2023; 120:2601-2621. [PMID: 37126355 DOI: 10.1002/bit.28412] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/27/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Gene therapy is a promising therapeutic approach for genetic and acquired diseases nowadays. Among DNA delivery vectors, recombinant adeno-associated virus (rAAV) is one of the most effective and safest vectors used in commercial drugs and clinical trials. However, the current yield of rAAV biomanufacturing lags behind the necessary dosages for clinical and commercial use, which embodies a concentrated reflection of low productivity of rAAV from host cells, difficult scalability of the rAAV-producing bioprocess, and high levels of impurities materialized during production. Those issues directly impact the price of gene therapy medicine in the market, limiting most patients' access to gene therapy. In this context, the current practices and several critical challenges associated with rAAV gene therapy bioprocesses are reviewed, followed by a discussion of recent advances in rAAV-mediated gene therapy and other therapeutic biological fields that could improve biomanufacturing if these advances are integrated effectively into the current systems. This review aims to provide the current state-of-the-art technology and perspectives to enhance the productivity of rAAV while reducing impurities during production of rAAV.
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Affiliation(s)
- Qiang Fu
- Department of Biomedical Engineering and Biotechnology, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Ashli Polanco
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
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23
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Veschetti L, Treccani M, De Tomi E, Malerba G. Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects? Int J Mol Sci 2023; 24:11437. [PMID: 37511197 PMCID: PMC10380557 DOI: 10.3390/ijms241411437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan.
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Affiliation(s)
| | | | | | - Giovanni Malerba
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (M.T.); (E.D.T.)
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24
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Li G, Jin Y, Chen B, Lin A, Wang E, Xu F, Hu G, Xiao C, Liu H, Hou X, Zhang B, Song J. Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations. Cancers (Basel) 2023; 15:3555. [PMID: 37509218 PMCID: PMC10376985 DOI: 10.3390/cancers15143555] [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: 05/10/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.
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Affiliation(s)
- Gangping Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yu Jin
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Baolong Chen
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen 361115, China
| | - Aiqiang Lin
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen 361115, China
| | - Erchuan Wang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Fenghua Xu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Gengcheng Hu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chuanxing Xiao
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen 361115, China
| | - Hongli Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bangzhou Zhang
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Jun Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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25
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Larsen CIS, Majumder K. The Autonomous Parvovirus Minute Virus of Mice Localizes to Cellular Sites of DNA Damage Using ATR Signaling. Viruses 2023; 15:1243. [PMID: 37376543 DOI: 10.3390/v15061243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Minute Virus of Mice (MVM) is an autonomous parvovirus of the Parvoviridae family that replicates in mouse cells and transformed human cells. MVM genomes localize to cellular sites of DNA damage with the help of their essential non-structural phosphoprotein NS1 to establish viral replication centers. MVM replication induces a cellular DNA damage response that is mediated by signaling through the ATM kinase pathway, while inhibiting induction of the ATR kinase signaling pathway. However, the cellular signals regulating virus localization to cellular DNA damage response sites has remained unknown. Using chemical inhibitors to DNA damage response proteins, we have discovered that NS1 localization to cellular DDR sites is independent of ATM or DNA-PK signaling but is dependent on ATR signaling. Pulsing cells with an ATR inhibitor after S-phase entry leads to attenuated MVM replication. These observations suggest that the initial localization of MVM to cellular DDR sites depends on ATR signaling before it is inactivated by vigorous virus replication.
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Affiliation(s)
- Clairine I S Larsen
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Kinjal Majumder
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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26
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Zheng R, Chen D, Su J, Lai J, Wang C, Chen H, Ning Z, Liu X, Tian X, Li Y, Zhu B. Inhibition of HAdV-14 induced apoptosis by selenocystine through ROS-mediated PARP and p53 signaling pathways. J Trace Elem Med Biol 2023; 79:127213. [PMID: 37244045 DOI: 10.1016/j.jtemb.2023.127213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/10/2022] [Accepted: 05/17/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Human Adenovirus (HAdV) can cause severe respiratory symptoms in people with low immunity and there is no targeted treatment for adenovirus infection. Anti-adenoviral drugs have high clinical significance for inhibiting adenovirus infection. Selenium (Se) plays an important role in anti-oxidation, redox signal transduction, and redox homeostasis. The excellent biological activity of Se is mainly achieved by being converted into selenocystine (SeC). Se participates in the active sites of various selenoproteins in the form of SeC. The ability of SeC to resist the virus has raised high awareness due to its unique antioxidative activity in recent years. The antiviral ability of the SeC was determined by detecting the infection rate of the virus in the cells. METHODS The experiment mainly investigated the antiviral mechanism of SeC by locating the virus in the cell, detecting the generation of ROS, observing the DNA status of the cell, and monitoring the mitochondrial membrane potential. RESULTS In the present study, SeC was designed to resist A549 cells infections caused by HAdV-14. SeC could prevent HAdV-14 from causing cell apoptosis-related to DNA damage. SeC significantly inhibited ROS generation and protect the cells from oxidative damage induced by ROS against HAdV-14. SeC induced the increase of antiviral cytokines such as IL-6 and IL-8 by activating the Jak2 signaling pathway, and repaired DNA lesions by suppressing ATR, p53, and PARP signaling pathways. CONCLUSION SeC might provide an effective selenium species with antiviral properties for the therapies against HAdV-14.
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Affiliation(s)
- Ruilin Zheng
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Danyang Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Jingyao Su
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Jia Lai
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Chenyang Wang
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Haitian Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Zhihui Ning
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Xia Liu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Yinghua Li
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China.
| | - Bing Zhu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, Guangdong, China.
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27
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Lu J, Liu W, Chen XZ, Wang Y, Ying T, Qiao L, Liu YJ, Liu B. Temporal proteomic profiling reveals functional pathways in vaccinia virus-induced cell migration. Front Microbiol 2023; 14:1185960. [PMID: 37303799 PMCID: PMC10249495 DOI: 10.3389/fmicb.2023.1185960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Viral diseases have always been intricate and persistent issues throughout the world and there is a lack of holistic discoveries regarding the molecular dysregulations of virus-host interactions. The temporal proteomics strategy can identify various differentially expressed proteins and offer collaborated interaction networks under pathological conditions. Method Herein, temporal proteomics at various hours post infection of Vero cells were launched to uncover molecular alternations during vaccinia virus (VACV)-induced cell migration. Different stages of infection were included to differentiate gene ontologies and critical pathways at specific time points of infection via bioinformatics. Results Bioinformatic results showed functional and distinct ontologies and pathways at different stages of virus infection. The enrichment of interaction networks and pathways verified the significances of the regulation of actin cytoskeleton and lamellipodia during VACV-induced fast cell motility. Discussion The current results offer a systematic proteomic profiling of molecular dysregulations at different stages of VACV infection and potential biomedical targets for treating viral diseases.
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Affiliation(s)
- Jiayin Lu
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Wei Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Xue-Zhu Chen
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Yiwen Wang
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Yan-Jun Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), State Key Lab of Molecular Engineering of Polymers, Fudan University, Shanghai, China
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28
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Costanzo M, De Giglio MAR, Roviello GN. Deciphering the Relationship between SARS-CoV-2 and Cancer. Int J Mol Sci 2023; 24:ijms24097803. [PMID: 37175509 PMCID: PMC10178366 DOI: 10.3390/ijms24097803] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Some viruses are known to be associated with the onset of specific cancers. These microorganisms, oncogenic viruses or oncoviruses, can convert normal cells into cancer cells by modulating the central metabolic pathways or hampering genomic integrity mechanisms, consequently inhibiting the apoptotic machinery and/or enhancing cell proliferation. Seven oncogenic viruses are known to promote tumorigenesis in humans: human papillomavirus (HPV), hepatitis B and C viruses (HBV, HCV), Epstein-Barr virus (EBV), human T-cell leukemia virus 1 (HTLV-1), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV). Recent research indicates that SARS-CoV-2 infection and COVID-19 progression may predispose recovered patients to cancer onset and accelerate cancer development. This hypothesis is based on the growing evidence regarding the ability of SARS-CoV-2 to modulate oncogenic pathways, promoting chronic low-grade inflammation and causing tissue damage. Herein, we summarize the main relationships known to date between virus infection and cancer, providing a summary of the proposed biochemical mechanisms behind the cellular transformation. Mechanistically, DNA viruses (such as HPV, HBV, EBV, and MCPyV) encode their virus oncogenes. In contrast, RNA viruses (like HCV, HTLV-1) may encode oncogenes or trigger host oncogenes through cis-/-trans activation leading to different types of cancer. As for SARS-CoV-2, its role as an oncogenic virus seems to occur through the inhibition of oncosuppressors or controlling the metabolic and autophagy pathways in the infected cells. However, these effects could be significant in particular scenarios like those linked to severe COVID-19 or long COVID. On the other hand, looking at the SARS-CoV-2─cancer relationship from an opposite perspective, oncolytic effects and anti-tumor immune response were triggered by SARS-CoV-2 infection in some cases. In summary, our work aims to recall comprehensive attention from the scientific community to elucidate the effects of SARS-CoV-2 and, more in general, β-coronavirus infection on cancer susceptibility for cancer prevention or supporting therapeutic approaches.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Via G. Salvatore 486, 80145 Naples, Italy
| | | | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
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Xu W, Yan P, Zhou Z, Yao J, Pan H, Jiang L, Bo Z, Ni B, Sun M, Gao S, Huan C. HDAC6 Triggers the ATM-Dependent DNA Damage Response To Promote PRV Replication. Microbiol Spectr 2023; 11:e0213222. [PMID: 36951571 PMCID: PMC10101138 DOI: 10.1128/spectrum.02132-22] [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: 06/07/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
Pseudorabies virus (PRV) infection is modulated by various cellular host factors. In this study, we investigated the role of histone deacetylase 6 (HDAC6) in this process. We determined HDAC6 expression in vitro and performed gene knockout, pharmacological inhibition analyses, immunofluorescence assays, and statistical analyses. We found that the pharmacological and genetic inhibition of HDAC6 significantly decreased PRV replication, whereas its overexpression promoted PRV replication. Additionally, we demonstrated that PRV infection can induce the phosphorylation of histone H2AX and lead to DNA damage response (DDR), and the ataxia telangiectasia mutated (ATM) inhibitor KU55933 inhibits DDR and PRV infection. Mechanistically, the HDAC6 inhibitor tubacin and HDAC6 knockout can decrease DDR. The results of this study suggested that HDAC6 may be a crucial factor in PRV-induced ATM-dependent DDR to promote PRV replication. IMPORTANCE Pseudorabies virus (PRV) is a member of the subfamily Alphaherpesvirinae of the family Herpesviridae. PRV infection in swine can lead to high morbidity and mortality of swine, causing huge economic losses. In particular, PRV variants can cause severe damage to the nervous and respiratory systems of humans, revealing that PRV may be a potential zoonotic pathogen. Vaccines for PRV have been developed that can delay or reduce the epidemic, but they currently cannot eliminate this disease completely. Therefore, studies should investigate new targets for the prevention and control of PRV infection. In this study, we demonstrated that HDAC6 can induce ataxia telangiectasia mutated-dependent DNA damage response to foster PRV replication, indicating that HDAC6 is a therapeutic target for PRV infection.
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Affiliation(s)
- Weiyin Xu
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Ping Yan
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Ziyan Zhou
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Jingting Yao
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Haochun Pan
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Luyao Jiang
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Zongyi Bo
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Bo Ni
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Mingxia Sun
- Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Song Gao
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Changchao Huan
- Institute of Agricultural Science and Technology Development, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- Key Laboratory of Avian Bioproduct Development, Ministry of Agriculture and Rural Affairs, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
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Apoptosis or Antiapoptosis? Interrupted Regulated Cell Death of Host Cells by Ascovirus Infection In Vitro. mBio 2023; 14:e0311922. [PMID: 36744941 PMCID: PMC9973268 DOI: 10.1128/mbio.03119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ascoviruses are insect-specific viruses thought to utilize the cellular apoptotic processes of host larvae to produce numerous virion-containing vesicles. In this study, we first determined the biochemical characteristics of ascovirus-infected, in vitro-cultured insect cells and the possible antiapoptotic capacity of ascovirus-infected insect cells. The results indicated that the ascovirus infection in the first 24 h was different from the infection from 48 h to the later infection stages. In the early infection stage, the Spodoptera exigua host cells had high membrane permeability and cleaved gasdermin D (GSDMD) but uncleaved Casp-6 (SeCasp-6). In contrast, the later infection stage had no such increased membrane permeability and had cleaved SeCasp-6. Four different chemicals were used to induce apoptosis at different stages of ascovirus infection: hydrogen peroxide (H2O2) and actinomycin D (ActD) had similar effects on the ascovirus-infected cells, whereas cMYC inhibitors and tumor necrosis factor alpha (TNF-α) plus SM-164 apoptosis inducers (T/S) had similar effects on infected cells. The former two inducers inhibited viral DNA replication in most situations, while the latter two inducers inhibited viral DNA replication in the early stage of infection but promoted viral DNA replication in the later infection stage. Furthermore, immunoblotting assays verified that T/S treatment could increase the expression levels of viral major capsid protein (MCP) and the host inhibitor of apoptosis protein (SeIAP). Coimmunoprecipitation assays revealed interaction between SeIAP and SeCasps, but this interaction was disturbed in ascovirus-infected cells. This study details the in vitro infection process of ascovirus, indicating the utilization of pyroptosis for antiapoptosis cytopathology. IMPORTANCE Clarifying the relationship between different types of viral infections and host regulation of cell death (RCD) can provide insights into the interaction between viruses and host cells. Ascoviruses are insect-specific viruses with apoptosis-utilizing-like infection cytopathology. However, RCD does not only include apoptosis, and while in our previous transmission electron microscopic observations, ascovirus-infected cells did not show typical apoptotic characteristics (unpublished data), in this study, they did show increased membrane permeability. These results indicate that the cytopathology of ascovirus infection is a complex process in which the virus manipulates host RCD. The RCD of insect cells is quite different from that of mammals, and studies on the former are many fewer than those on the latter, especially in the case of RCD in lepidopteran insects. Our results will lay a foundation for understanding the RCD of lepidopteran insects and its function in the process of insect virus infection.
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Robin S, Legeai F, Jouan V, Ogliastro M, Darboux I. Genome-wide identification of lncRNAs associated with viral infection in Spodoptera frugiperda. J Gen Virol 2023; 104. [PMID: 36757871 DOI: 10.1099/jgv.0.001827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The role of lncRNAs in immune defence has been demonstrated in many multicellular and unicellular organisms. However, investigation of the identification and characterization of long non-coding RNAs (lncRNAs) involved in the insect immune response is still limited. In this study, we used RNA sequencing (RNA-seq) to investigate the expression profiles of lncRNAs and mRNAs in the fall armyworm Spodoptera frugiperda in response to virus infection. To assess the tissue- and virus-specificity of lncRNAs, we analysed and compared their expression profiles in haemocytes and fat body of larvae infected with two entomopathogenic viruses with different lifestyles, i.e. the polydnavirus HdIV (Hyposoter didymator IchnoVirus) and the densovirus JcDV (Junonia coenia densovirus). We identified 1883 candidate lncRNAs, of which 529 showed differential expression following viral infection. Expression profiles differed considerably between samples, indicating that many differentially expressed (DE) lncRNAs showed virus- and tissue-specific expression patterns. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and target prediction analyses indicated that DE-LncRNAs were mainly enriched in metabolic process, DNA replication and repair, immune response, metabolism of insect hormone and cell adhesion. In addition, we identified three DE-lncRNAs potentially acting as microRNA host genes, suggesting that they participate in gene regulation by producing miRNAs in response to virus infection. This study provides a catalogue of lncRNAs expressed in two important immune tissues and potential insight into their roles in the antiviral defence in S. frugiperda. The results may help future in-depth functional studies to better understand the biological function of lncRNAs in interaction between viruses and the fall armyworm.
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Affiliation(s)
- Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, University of Rennes, Rennes, France.,University of Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Véronique Jouan
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Mylène Ogliastro
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
| | - Isabelle Darboux
- INRAE, University of Montpellier, UMR Diversité, Génomes & Interactions Microorganismes-Insectes (DGIMI), Montpellier, France
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Fan J, Lv X, Yang S, Geng S, Yang J, Zhao Y, Zhang Z, Liu Z, Guan G, Luo J, Zeng Q, Yin H, Niu Q. OGG1 inhibition suppresses African swine fever virus replication. Virol Sin 2023; 38:96-107. [PMID: 36435451 PMCID: PMC10006199 DOI: 10.1016/j.virs.2022.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 11/26/2022] Open
Abstract
African swine fever virus (ASFV) is an important pathogen that causes a highly contagious and lethal disease in swine, for which neither a vaccine nor treatment is available. The DNA repair enzyme 8-oxoguanine DNA glycosylase 1 (OGG1), which excises the oxidative base lesion 8-oxo-7,8-dihydroguanine (8-oxoG), has been linked to the pathogenesis of different diseases associated with viral infections. However, the role of OGG1-base excision repair (BER) in ASFV infection has been poorly investigated. Our study aimed to characterize the alteration of host reactive oxygen species (ROS) and OGG1 and to analyse the role of OGG1 in ASFV infection. We found that ASFV infection induced high levels and dynamic changes in ROS and 8-oxoG and consistently increased the expression of OGG1. Viral yield, transcription level, and protein synthesis were reduced in ASFV-infected primary alveolar macrophages (PAMs) treated by TH5487 or SU0268 inhibiting OGG1. The expression of BER pathway associated proteins of ASFV was also suppressed in OGG1-inhibited PAMs. Furthermore, OGG1 was found to negatively regulate interferon β (IFN-β) production during ASFV infection and IFN-β could be activated by OGG1 inhibition with TH5487 and SU0268, which blocked OGG1 binding to 8-oxoG. Additionally, the interaction of OGG1 with viral MGF360-14-L protein could disturb IFN-β production to further affect ASFV replication. These results suggest that OGG1 plays the crucial role in successful viral infection and OGG1 inhibitors SU0268 or TH5487 could be used as antiviral agents for ASFV infection.
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Affiliation(s)
- Jie Fan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Xinqian Lv
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Saixia Yang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Shuxian Geng
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China; African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jifei Yang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yaru Zhao
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Zhonghui Zhang
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Zhijie Liu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Guiquan Guan
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jianxun Luo
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Qiaoying Zeng
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Hong Yin
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Qingli Niu
- African Swine Fever Regional Laboratory of China (Lanzhou), State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
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Singh Raman A, Muhammad AA, Singh H, Singh T, Mkhize Z, Jain P, Singh SK, Bahadur I, Singh P. A Review on Interactions between Amino Acids and Surfactants as Well as Their Impact on Corrosion Inhibition. ACS OMEGA 2022; 7:47471-47489. [PMID: 36591120 PMCID: PMC9798777 DOI: 10.1021/acsomega.2c03629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Amino acid-surfactant interactions are central to numerous studies because of their increased effectiveness in chemical, biological, household and industrial use. This review will focus on the impact and effect of the physicochemical properties, temperature, pH, and surfactant chain length of the amino acid for detailed exploration of amino acids and surfactants in aqueous medium. The impact of cosolvent on self-aggregation, critical micelle concentration (CMC), and binding affinity with other biomolecules, as well as amino acid-surfactant interactions, are the epicenters. The results show that increasing the temperature causes negative enthalpy for ionic surfactants and micellization, implying that micellization and amino acids are thermodynamically spontaneous and exothermic, accompanied by positive entropy. As these physicochemical studies are additive, the amino acid and ionic surfactant interactions provide clues on protein unfolding and denaturation under different media, which further changes with a change in physiological conditions like pH, cosolvent, chain length, and temperature. On varying the pH, the net charge of the amino acid also changes and, subsequently, the binding efficiency of the amino acids to the surfactants. The presence of cosolvent causes a lowering in the hydrophobic chain, which changes the surfactant's CMC. At a reduced CMC, the hydrophobic characteristic of amino acid-surfactant associations is amplified, leading to rapid denaturation of proteins that act as propulsion under the influence of extended chain surfactants. Amino acids are one of the most intriguing classes of chemicals that produce high inhibitory efficacy. Amino acids are also a component of proteins and therefore, found in a significant part of the human body, further making them a promising candidate as corrosion inhibitors. In this review article, authors have also focused on the collection and investigation for application of amino acid-surfactant interactions in corrosion inhibition. Various predictive studies/in silico studies are also reported by many research groups, such as density functional theory (DFT) calculations and molecular dynamics simulations to obtain tentative electronic, structural, and physiochemical characteristics like energies of the highest occupied molecular orbitals and lowest unoccupied molecular orbitals, binding energy, Gibb's free energy, electronegativity, polarizability, and entropy. In silico studies are helpful for the mechanism predictions of the process occurring on metal surfaces.
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Affiliation(s)
| | - Amina Abdullahi Muhammad
- Department
of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara144411, Punjab, India
| | - Harpreet Singh
- Department
of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Phagwara144411, Punjab, India
| | - Thishana Singh
- College
of Agriculture, Engineering and Science, School of Chemistry and Physics, University of KwaZulu-Natal, Durban4000, South Africa
| | - Zimbili Mkhize
- Department
of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho2735, South Africa
| | - Pallavi Jain
- Department
of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, NCR Campus, Modinagar, Ghaziabad603203, UP, India
| | | | - Indra Bahadur
- Department
of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho2735, South Africa
| | - Prashant Singh
- Department
of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi110021, India
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Sulfolobus islandicus Employs Orc1-2-Mediated DNA Damage Response in Defense against Infection by SSV2. J Virol 2022; 96:e0143822. [PMID: 36448807 PMCID: PMC9769372 DOI: 10.1128/jvi.01438-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
All living organisms have evolved DNA damage response (DDR) strategies in coping with threats to the integrity of their genome. In response to DNA damage, Sulfolobus islandicus activates its DDR network in which Orc1-2, an ortholog of the archaeal Orc1/Cdc6 superfamily proteins, plays a central regulatory role. Here, we show that pretreatment with UV irradiation reduced virus genome replication in S. islandicus infected with the fusellovirus SSV2. Like treatment with UV or the DNA-damaging agent 4-nitroquinoline-1-oxide (NQO), infection with SSV2 facilitated the expression of orc1-2 and significantly raised the cellular level of Orc1-2. The inhibitory effect of UV irradiation on the virus DNA level was no longer apparent in the infected culture of an S. islandicus orc1-2 deletion mutant strain. On the other hand, the overexpression of orc1-2 decreased virus genomic DNA by ~102-fold compared to that in the parent strain. Furthermore, as part of the Orc1-2-mediated DDR response genes for homologous recombination repair (HRR), cell aggregation and intercellular DNA transfer were upregulated, whereas genes for cell division were downregulated. However, the HRR pathway remained functional in host inhibition of SSV2 genome replication in the absence of UpsA, a subunit of pili essential for intercellular DNA transfer. In agreement with this finding, lack of the general transcriptional activator TFB3, which controls the expression of the ups genes, only moderately affected SSV2 genome replication. Our results demonstrate that infection of S. islandicus by SSV2 triggers the host DDR pathway that, in return, suppresses virus genome replication. IMPORTANCE Extremophiles thrive in harsh habitats and thus often face a daunting challenge to the integrity of their genome. How these organisms respond to virus infection when their genome is damaged remains unclear. We found that the thermophilic archaeon Sulfolobus islandicus became more inhibitory to genome replication of the virus SSV2 after preinfection UV irradiation than without the pretreatment. On the other hand, like treatment with UV or other DNA-damaging agents, infection of S. islandicus by SSV2 triggers the activation of Orc1-2-mediated DNA damage response, including the activation of homologous recombination repair, cell aggregation and DNA import, and the repression of cell division. The inhibitory effect of pretreatment with UV irradiation on SSV2 genome replication was no longer observed in an S. islandicus mutant lacking Orc1-2. Our results suggest that DNA damage response is employed by S. islandicus as a strategy to defend against virus infection.
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Erickson JR, Kalejta RF, Friesen PD. Ataxia Telangiectasia-Mutated Is Activated but Not Required for Productive Autographa californica Multiple Nucleopolyhedrovirus Infection. J Virol 2022; 96:e0126922. [PMID: 36314821 PMCID: PMC9682986 DOI: 10.1128/jvi.01269-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
Multiplication of the invertebrate DNA baculoviruses activates the host DNA damage response (DDR), which promotes virus DNA replication. DDR signaling is initiated by the host insect's phosphatidylinositol-3 kinase-related kinases (PIKKs), including ataxia telangiectasia-mutated kinase (ATM). Like other PIKKs, ATM phosphorylates an array of host DDR proteins at serine/threonine glutamine (S/TQ) motifs, the result of which leads to cell cycle arrest, DNA repair, or apoptosis. To define the role of host PIKKs in baculovirus replication, we compared replication levels of the baculovirus prototype species Autographa californica multiple nucleopolyhedrovirus in permissive Spodoptera frugiperda (SF21) cells with and without ATM function. Caffeine, which inhibits multiple DDR kinases, and the ATM-specific inhibitors KU-55933 and KU-60019 each prevented phosphorylation of Spodoptera histone H2AX (SfH2AX), a recognized indicator of ATM activity. However, only caffeine reduced autographa californica multiple nucleopolyhedrovirus (AcMNPV)-induced bulk phosphorylation of S/TQ protein motifs. Furthermore, only caffeine, not KU-55933 or KU-60019, reduced AcMNPV yields, suggesting a limited role for ATM. To investigate further, we identified and edited the Spodoptera ATM gene (sfatm). Consistent with ATM's known functions, CRISPR/Cas9-mediated knockout of sfatm eliminated DNA damage-induced phosphorylation of DDR marker SfH2AX in SF21 cells. However, loss of sfatm failed to affect the levels of AcMNPV multiplication. These findings suggested that in the absence of the kinase SfATM, another caffeine-sensitive host DDR kinase promotes S/TQ phosphorylation and baculovirus multiplication. Thus, baculoviruses activate and utilize the host insect DDR in an ATM-independent manner. IMPORTANCE The DDR, while necessary for the maintenance and fidelity of the host genome, represents an important cellular response to viral infection. The prolific DNA baculoviruses activate and manipulate the invertebrate DDR by using mechanisms that positively impact virus multiplication, including virus DNA replication. As the key DDR initiator kinase, ATM was suspected to play a critical role in this host response. However, we show here that baculovirus AcMNPV activates an ATM-independent DDR. By identifying the insect host ATM ortholog (Spodoptera frugiperda SfATM) and evaluating genetic knockouts, we show that SfATM is dispensable for AcMNPV activation of the DDR and for virus replication. Thus, another PIKK, possibly the closely related kinase ATR (ATM- and Rad3-related kinase), is responsible for efficient baculovirus multiplication. These findings better define the host pathways used by invertebrates to engage viral pathogens, including DNA viruses.
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Affiliation(s)
- Jared R. Erickson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert F. Kalejta
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Paul D. Friesen
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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36
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The Role of DNA Damage and Repair in Idiopathic Pulmonary Fibrosis. Antioxidants (Basel) 2022; 11:antiox11112292. [PMID: 36421478 PMCID: PMC9687113 DOI: 10.3390/antiox11112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The mortality rate of idiopathic pulmonary fibrosis (IPF) increases yearly due to ineffective treatment. Given that the lung is exposed to the external environment, it is likely that oxidative stress, especially the stimulation of DNA, would be of particular importance in pulmonary fibrosis. DNA damage is known to play an important role in idiopathic pulmonary fibrosis initiation, so DNA repair systems targeting damage are also crucial for the survival of lung cells. Although many contemporary reports have summarized the role of individual DNA damage and repair pathways in their hypotheses, they have not focused on idiopathic pulmonary fibrosis. This review, therefore, aims to provide a concise overview for researchers to understand the pathways of DNA damage and repair and their roles in IPF.
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Hao Y, Yang J, Yang B, Zhang T, Shi X, Yang X, Zhang D, Zhao D, Yan W, Chen L, Liu X, Zheng H, Zhang K. Identification and analysis of the interaction network of African swine fever virus D1133L with host proteins. Front Microbiol 2022; 13:1037346. [PMID: 36406406 PMCID: PMC9673173 DOI: 10.3389/fmicb.2022.1037346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
African swine fever (ASF) is a contagious and lethal hemorrhagic disease in pigs; its spread results in huge economic losses to the global pig industry. ASF virus (ASFV) is a large double-stranded DNA virus encoding >150 open reading frames. Among them, ASFV-encoded D1133L was predicted to be a helicase but its specific function remains unknown. Since virus-host protein interactions are key to understanding viral protein function, we used co-immunoprecipitation combined with liquid chromatography-mass spectrometry to investigate D1133L. This study describes the interaction network of ASFV D1133L protein in porcine kidney PK-15 cells. Overall, 1,471 host proteins that potentially interact with D1133L are identified. Based on these host proteins, a protein–protein network was constructed. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that cellular D1133L-interacted proteins are involved in the ribosome, spliceosome, RNA transport, oxidative phosphorylation, proteasome, and DNA replication. Vimentin (VIM), tripartite motif-containing protein 21 (TRIM21), and Tu translation elongation factor (TUFM) were confirmed to interact with D1133L in vitro. VIM or TRIM21 overexpression significantly promoted ASFV replication, but TUFM overexpression significantly inhibited ASFV replication. These results help elucidate the specific functions of D1133L and the potential mechanisms underlying ASFV replication.
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Wardlaw CP, Petrini JHJ. ISG15 conjugation to proteins on nascent DNA mitigates DNA replication stress. Nat Commun 2022; 13:5971. [PMID: 36216822 PMCID: PMC9550767 DOI: 10.1038/s41467-022-33535-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
The pathways involved in suppressing DNA replication stress and the associated DNA damage are critical to maintaining genome integrity. The Mre11 complex is unique among double strand break (DSB) repair proteins for its association with the DNA replication fork. Here we show that Mre11 complex inactivation causes DNA replication stress and changes in the abundance of proteins associated with nascent DNA. One of the most highly enriched proteins at the DNA replication fork upon Mre11 complex inactivation was the ubiquitin like protein ISG15. Mre11 complex deficiency and drug induced replication stress both led to the accumulation of cytoplasmic DNA and the subsequent activation of innate immune signaling via cGAS-STING-Tbk1. This led to ISG15 induction and protein ISGylation, including constituents of the replication fork. ISG15 plays a direct role in preventing replication stress. Deletion of ISG15 was associated with replication fork stalling, tonic ATR activation, genomic aberrations, and sensitivity to aphidicolin. These data reveal a previously unrecognized role for ISG15 in mitigating DNA replication stress and promoting genomic stability.
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Affiliation(s)
- Christopher P Wardlaw
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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Zhang W, Guo J, Chen Q. Role of PARP-1 in Human Cytomegalovirus Infection and Functional Partners Encoded by This Virus. Viruses 2022; 14:2049. [PMID: 36146855 PMCID: PMC9501325 DOI: 10.3390/v14092049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous pathogen that threats the majority of the world's population. Poly (ADP-ribose) polymerase 1 (PARP-1) and protein poly (ADP-ribosyl)ation (PARylation) regulates manifold cellular functions. The role of PARP-1 and protein PARylation in HCMV infection is still unknown. In the present study, we found that the pharmacological and genetic inhibition of PARP-1 attenuated HCMV replication, and PARG inhibition favors HCMV replication. PARP-1 and its enzymatic activity were required for efficient HCMV replication. HCMV infection triggered the activation of PARP-1 and induced the translocation of PARP-1 from nucleus to cytoplasm. PARG was upregulated in HCMV-infected cells and this upregulation was independent of viral DNA replication. Moreover, we found that HCMV UL76, a true late protein of HCMV, inhibited the overactivation of PARP-1 through direct binding to the BRCT domain of PARP-1. In addition, UL76 also physically interacted with poly (ADP-ribose) (PAR) polymers through the RG/RGG motifs of UL76 which mediates its recruitment to DNA damage sites. Finally, PARP-1 inhibition or depletion potentiated HCMV-triggered induction of type I interferons. Our results uncovered the critical role of PARP-1 and PARP-1-mediated protein PARylation in HCMV replication.
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Affiliation(s)
| | | | - Qiang Chen
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan 430071, China
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40
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DNA Damage Response Differentially Affects BoHV-1 Gene Transcription in Cell Type-Dependent Manners. Biomedicines 2022; 10:biomedicines10092282. [PMID: 36140380 PMCID: PMC9496131 DOI: 10.3390/biomedicines10092282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine herpesvirus 1 (BoHV-1), an important pathogen of cattle, is also a promising oncolytic virus. Recent studies have demonstrated that the virus infection induces DNA damage and DNA damage response (DDR), potentially accounting for virus infection-induced cell death and oncolytic effects. However, whether the global DDR network affects BoHV-1 productive infection remains to be elucidated. In this study, we show that global DDR induced by ultraviolet (UV) irradiation prior to BoHV-1 infection differentially affected transcription of immediate early (IE) genes, such as infected cell protein 0 (bICP0) and bICP22, in a cell-type-dependent manner. In addition, UV-induced DDR may affect the stabilization of viral protein levels, such as glycoprotein C (gC) and gD, because the variation in mRNA levels of gC and gD as a consequence of UV treatment were not in line with the variation in individual protein levels. The virus productive infection also affects UV-primed DDR signaling, as demonstrated by the alteration of phosphorylated histone H2AX (γH2AX) protein levels and γH2AX formation following virus infection. Taken together, for the first time, we evidenced the interplay between UV-primed global DDR and BoHV-1 productive infection. UV-primed global DDR differentially modulates the transcription of virus genes and stabilization of virus protein. Vice versa, the virus infection may affect UV-primed DDR signaling.
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Epstein-Barr virus protein BKRF4 restricts nucleosome assembly to suppress host antiviral responses. Proc Natl Acad Sci U S A 2022; 119:e2203782119. [PMID: 36067323 PMCID: PMC9477414 DOI: 10.1073/pnas.2203782119] [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: 11/18/2022] Open
Abstract
Inhibition of host DNA damage response (DDR) is a common mechanism used by viruses to manipulate host cellular machinery and orchestrate viral life cycles. Epstein-Barr virus tegument protein BKRF4 associates with cellular chromatin to suppress host DDR signaling, but the underlying mechanism remains elusive. Here, we identify a BKRF4 histone binding domain (residues 15-102, termed BKRF4-HBD) that can accumulate at the DNA damage sites to disrupt 53BP1 foci formation. The high-resolution structure of the BKRF4-HBD in complex with a human H2A-H2B dimer shows that BKRF4-HBD interacts with the H2A-H2B dimer via the N-terminal region (NTR), the DWP motif (residues 80-86 containing D81, W84, P86), and the C-terminal region (CTR). The "triple-anchor" binding mode confers BKRF4-HBD the ability to associate with the partially unfolded nucleosomes, promoting the nucleosome disassembly. Importantly, disrupting the BKRF4-H2A-H2B interaction impairs the binding between BKRF4-HBD and nucleosome in vitro and inhibits the recruitment of BKRF4-HBD to DNA breaks in vivo. Together, our study reveals the structural basis of BKRF4 bindings to the partially unfolded nucleosome and elucidates an unconventional mechanism of host DDR signal attenuation.
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Spirin P, Shyrokova E, Vedernikova V, Lebedev T, Prassolov V. Emetine in Combination with Chloroquine Induces Oncolytic Potential of HIV-1-Based Lentiviral Particles. Cells 2022; 11:cells11182829. [PMID: 36139404 PMCID: PMC9497060 DOI: 10.3390/cells11182829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Chloroquine and Emetine are drugs used to treat human parasitic infections. In addition, it has been shown that these drugs have an antiviral effect. Both drugs were also found to cause a suppressive effect on the growth of cancer cells of different origins. Here, using the replication-deficient HIV-1-based lentiviral vector particles, we evaluated the ability of the combination of these drugs to reduce viral transduction efficiency. We showed that these drugs act synergistically to decrease cancer cell growth when added in combination with medium containing lentiviral particles. We found that the combination of these drugs with lentiviral particles decreases the viability of treated cells. Taken together, we state the oncolytic potential of the medium containing HIV-1-based particles provoked by the combination of Chloroquine and Emetine.
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Affiliation(s)
- Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Correspondence:
| | - Elena Shyrokova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Valeria Vedernikova
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Timofey Lebedev
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
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43
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Hafez Ghoran S, Calcaterra A, Abbasi M, Taktaz F, Nieselt K, Babaei E. Curcumin-Based Nanoformulations: A Promising Adjuvant towards Cancer Treatment. Molecules 2022; 27:molecules27165236. [PMID: 36014474 PMCID: PMC9414608 DOI: 10.3390/molecules27165236] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/10/2022] [Accepted: 08/13/2022] [Indexed: 02/06/2023] Open
Abstract
Throughout the United States, cancer remains the second leading cause of death. Traditional treatments induce significant medical toxic effects and unpleasant adverse reactions, making them inappropriate for long-term use. Consequently, anticancer-drug resistance and relapse are frequent in certain situations. Thus, there is an urgent necessity to find effective antitumor medications that are specific and have few adverse consequences. Curcumin is a polyphenol derivative found in the turmeric plant (Curcuma longa L.), and provides chemopreventive, antitumor, chemo-, and radio-sensitizing properties. In this paper, we summarize the new nano-based formulations of polyphenolic curcumin because of the growing interest in its application against cancers and tumors. According to recent studies, the use of nanoparticles can overcome the hydrophobic nature of curcumin, as well as improving its stability and cellular bioavailability in vitro and in vivo. Several strategies for nanocurcumin production have been developed, each with its own set of advantages and unique features. Because the majority of the curcumin-based nanoformulation evidence is still in the conceptual stage, there are still numerous issues impeding the provision of nanocurcumin as a possible therapeutic option. To support the science, further work is necessary to develop curcumin as a viable anti-cancer adjuvant. In this review, we cover the various curcumin nanoformulations and nanocurcumin implications for therapeutic uses for cancer, as well as the current state of clinical studies and patents. We further address the knowledge gaps and future research orientations required to develop curcumin as a feasible treatment candidate.
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Affiliation(s)
- Salar Hafez Ghoran
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran 16666-63111, Iran
- Medicinal Plant Breeding and Development Research Institute, University of Kurdistan, Sanandaj 66177-15175, Iran
- Correspondence: (S.H.G.); or (E.B.); Tel.: +98-9144425047 (S.H.G.); Tel.: +98-4133392686 (E.B.)
| | - Andrea Calcaterra
- Department of Chemistry and Technology of Drugs, Sapienza–University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz 71336-54361, Iran
| | - Fatemeh Taktaz
- Department of Biology, Faculty of Sciences, University of Hakim Sabzevari, Sabzevar 96179-76487, Iran
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Kay Nieselt
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Esmaeil Babaei
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz 51666-16471, Iran
- Correspondence: (S.H.G.); or (E.B.); Tel.: +98-9144425047 (S.H.G.); Tel.: +98-4133392686 (E.B.)
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Mekawy AS, Alaswad Z, Ibrahim AA, Mohamed AA, AlOkda A, Elserafy M. The consequences of viral infection on host DNA damage response: a focus on SARS-CoVs. J Genet Eng Biotechnol 2022; 20:104. [PMID: 35829826 PMCID: PMC9277982 DOI: 10.1186/s43141-022-00388-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022]
Abstract
DNA damage and genome instability in host cells are introduced by many viruses during their life cycles. Severe acute respiratory syndrome coronaviruses (SARS-CoVs) manipulation of DNA damage response (DDR) is an important area of research that is still understudied. Elucidation of the direct and indirect interactions between SARS-CoVs and DDR not only provides important insights into how the viruses exploit DDR pathways in host cells but also contributes to our understanding of their pathogenicity. Here, we present the known interactions of both SARS-CoV and SARS-CoV-2 with DDR pathways of the host cells, to further understand the consequences of infection on genome integrity. Since this area of research is in its early stages, we try to connect the unlinked dots to speculate and propose different consequences on DDR mechanisms. This review provides new research scopes that can be further investigated in vitro and in vivo, opening new avenues for the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Asmaa S Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Aya A Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed A Mohamed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Abdelrahman AlOkda
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.,Metabolic Disorders and Complications Program and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt. .,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
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45
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Hashimoto H, Hara K, Hishiki A. Structural basis for molecular interactions on the eukaryotic DNA sliding clamps PCNA and RAD9-RAD1-HUS1. J Biochem 2022; 172:189-196. [PMID: 35731009 DOI: 10.1093/jb/mvac053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
DNA sliding clamps are widely conserved in all living organisms and play crucial roles in DNA replication and repair. Each DNA sliding clamp is a doughnut-shaped protein with a quaternary structure that encircles the DNA strand and recruits various factors involved in DNA replication and repair, thereby stimulating their biological functions. Eukaryotes have two types of DNA sliding clamp, proliferating cell nuclear antigen (PCNA) and RAD9-RAD1-HUS1 (9-1-1). The homo-trimer PCNA physically interacts with multiple proteins containing a PIP-box and/or APIM. The two motifs bind to PCNA by a similar mechanism; in addition, the bound PCNA structure is similar, implying a universality of PCNA interactions. In contrast to PCNA, 9-1-1 is a hetero-trimer composed of RAD9, RAD1, and HUS1 subunits. Although 9-1-1 forms a trimeric ring structure similar to PCNA, the C-terminal extension of the RAD9 is intrinsically unstructured. Based on the structural similarity between PCNA and 9-1-1, the mechanism underlying the interaction of 9-1-1 with its partners was thought to be analogous to that of PCNA. Unexpectedly, however, the recent structure of the 9-1-1 ring bound to a partner has revealed a novel interaction distinct from that of PCNA, potentially providing a new principle for molecular interactions on DNA sliding clamps.
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Affiliation(s)
- Hiroshi Hashimoto
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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The small nonstructural protein NP1 of human bocavirus 1 directly interacts with Ku70 and RPA70 and facilitates viral DNA replication. PLoS Pathog 2022; 18:e1010578. [PMID: 35653410 PMCID: PMC9197078 DOI: 10.1371/journal.ppat.1010578] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/14/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Human bocavirus 1 (HBoV1), a member of the genus Bocaparvovirus of the family Parvoviridae, causes acute respiratory tract infections in young children. Well-differentiated pseudostratified human airway epithelium cultured at an air-liquid interface (HAE-ALI) is an ideal in vitro culture model to study HBoV1 infection. Unique to other parvoviruses, bocaparvoviruses express a small nonstructured protein NP1 of ~25 kDa from an open reading frame (ORF) in the center of the viral genome. NP1 plays an important role in viral DNA replication and pre-mRNA processing. In this study, we performed an affinity purification assay to identify HBoV1 NP1-inteacting proteins. We identified that Ku70 and RPA70 directly interact with the NP1 at a high binding affinity, characterized with an equilibrium dissociation constant (KD) of 95 nM and 122 nM, respectively. Furthermore, we mapped the key NP1-interacting domains of Ku70 at aa266-439 and of RPA70 at aa181-422. Following a dominant negative strategy, we revealed that the interactions of Ku70 and RPA70 with NP1 play a significant role in HBoV1 DNA replication not only in an in vitro viral DNA replication assay but also in HBoV1-infected HAE-ALI cultures. Collectively, our study revealed a novel mechanism by which HBoV1 NP1 enhances viral DNA replication through its direct interactions with Ku70 and RPA70.
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Jiang Y, Yang B, Liu X, Tian X, Wang Q, Wang B, Zhang Q, Yu W, Qi X, Jiang Y, Hsiang T. A Satellite dsRNA Attenuates the Induction of Helper Virus-Mediated Symptoms in Aspergillus flavus. Front Microbiol 2022; 13:895844. [PMID: 35711767 PMCID: PMC9195127 DOI: 10.3389/fmicb.2022.895844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus flavus is an important fungal pathogen of animals and plants. Previously, we reported a novel partitivirus, Aspergillus flavus partitivirus 1 (AfPV1), infecting A. flavus. In this study, we obtained a small double-stranded (ds) RNA segment (734 bp), which is a satellite RNA of the helper virus, AfPV1. The presence of AfPV1 altered the colony morphology, decreased the number of conidiophores, created significantly larger vacuoles, and caused more sensitivity to osmotic, oxidative, and UV stresses in A. flavus, but the small RNA segment could attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus. Moreover, AfPV1 infection reduced the pathogenicity of A. flavus in corn (Zea mays), honeycomb moth (Galleria mellonella), mice (Mus musculus), and the adhesion of conidia to host epithelial cells, and increased conidial death by macrophages. However, the small RNA segment could also attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus, perhaps by reducing the genomic accumulation of the helper virus AfPV1 in A. flavus. We used this model to investigate transcriptional genes regulated by AfPV1 and the small RNA segment in A. flavus, and their role in generating different phenotypes. We found that the pathways of the genes regulated by AfPV1 in its host were similar to those of retroviral viruses. Therefore, some pathways may be of benefit to non-retroviral viral integration or endogenization into the genomes of its host. Moreover, some potential antiviral substances were also found in A. flavus using this system.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Yang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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48
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Hazra T, Tapryal N, Chakraborty A, Rayavara K, Wakamiya M, Islam A, Pan L, Hsu J, Tat V, Maruyama J, Hosoki K, Sayed I, Alcantara J, Castillo V, Tindle C, Sarker A, Cardenas V, Sharma G, Alexander LC, Sur S, Ghosh G, Paessler S, Sahoo D, Ghosh P, Das S, Boldogh I, Tseng CT. The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. RESEARCH SQUARE 2022:rs.3.rs-1690354. [PMID: 35665009 PMCID: PMC9164514 DOI: 10.21203/rs.3.rs-1690354/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Compromised DNA repair capacity of individuals could play a critical role in the severity of SARS-CoV-2 infection-induced COVID-19. We therefore analyzed the expression of DNA repair genes in publicly available transcriptomic datasets of COVID-19 patients and found that the level of NEIL2, an oxidized base specific mammalian DNA glycosylase, is particularly low in the lungs of COVID-19 patients displaying severe symptoms. Downregulation of pulmonary NEIL2 in CoV-2-permissive animals and postmortem COVID-19 patients validated these results. To investigate the potential roles of NEIL2 in CoV-2 pathogenesis, we infected Neil2-null (Neil2-/-) mice with a mouse-adapted CoV-2 strain and found that Neil2-/- mice suffered more severe viral infection concomitant with increased expression of proinflammatory genes, which resulted in an enhanced mortality rate of 80%, up from 20% for the age matched Neil2+/+ cohorts. We also found that infected animals accumulated a significant amount of damage in their lung DNA. Surprisingly, recombinant NEIL2 delivered into permissive A549-ACE2 cells significantly decreased viral replication. Toward better understanding the mechanistic basis of how NEIL2 plays such a protective role against CoV-2 infection, we determined that NEIL2 specifically binds to the 5'-UTR of SARS-CoV-2 genomic RNA and blocks protein synthesis. Together, our data suggest that NEIL2 plays a previously unidentified role in regulating CoV-2-induced pathogenesis, via inhibiting viral replication and preventing exacerbated proinflammatory responses, and also via its well-established role of repairing host genome damage.
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Affiliation(s)
- Tapas Hazra
- The University of Texas Medical Branch at Galveston
| | | | | | | | | | | | - Lang Pan
- The University of Texas Medical Branch at Galveston
| | - Jason Hsu
- The University of Texas Medical Branch
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Chen Y, Huang M, Zhu J, Xu L, Cheng W, Lu X, Yan F. Identification of a DNA Damage Response and Repair-Related Gene-Pair Signature for Prognosis Stratification Analysis in Hepatocellular Carcinoma. Front Pharmacol 2022; 13:857060. [PMID: 35496321 PMCID: PMC9038539 DOI: 10.3389/fphar.2022.857060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Nowadays, although the cause of hepatocellular carcinoma (HCC) mortality and recurrence remains at a high level, the 5-year survival rate is still very low. The DNA damage response and repair (DDR) pathway may affect HCC patients’ survival by influencing tumor development and therapeutic response. It is necessary to identify a prognostic DDR-related gene signature to predict the outcome of patients. Methods: Level 3 mRNA expression and clinical information were extracted from the TCGA website. The GSE14520 datasets, ICGC-LIRI datasets, and a Chinese HCC cohort were served as validation sets. Univariate Cox regression analysis and LASSO-penalized Cox regression analysis were performed to construct the DDR-related gene pair (DRGP) signature. Kaplan–Meier survival curves and time-dependent receiver operating characteristic (ROC) analysis curves were calculated to determine the predictive ability of this prognostic model. Then, a prognostic nomogram was established to help clinical management. We investigated the difference in biological processes between HRisk and LRisk by conducting several enrichment analyses. The TIDE algorithm and R package “pRRophetic” were applied to estimate the immunotherapeutic and chemotherapeutic response. Results: We constructed the prognostic signature based on 23 DDR-related gene pairs. The patients in the training datasets were divided into HRisk and LRisk groups at median cut-off. The HRisk group had significantly poorer OS than the LRisk group, and the signature was an independent prognostic indicator in HCC. Furthermore, a nomogram of the riskscore combined with TNM stage was constructed and detected by the calibration curve and decision curve. The LRisk group was associated with higher expression of HBV oncoproteins and metabolism pathways, while DDR-relevant pathways and cell cycle process were enriched in the HRisk group. Moreover, patients in the LRisk group may be more beneficial from immunotherapy. We also found that TP53 gene was more frequently mutated in the HRisk group. As for chemotherapeutic drugs commonly used in HCC, the HRisk group was highly sensitive to 5-fluorouracil, while the LRisk group presented with a significantly higher response to gefitinib and gemcitabine. Conclusion: Overall, we developed a novel DDR-related gene pair signature and nomogram to assist in predicting survival outcomes and clinical treatment of HCC patients. It also helps understand the underlying mechanisms of different DDR patterns in HCC.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mengjia Huang
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Junkai Zhu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Li Xu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenxuan Cheng
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaofan Lu
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangrong Yan
- State Key Laboratory of Natural Medicines, Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, China
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Wang F, Zhao M, Chang B, Zhou Y, Wu X, Ma M, Liu S, Cao Y, Zheng M, Dang Y, Xu J, Chen L, Liu T, Tang F, Ren Y, Xu Z, Mao Z, Huang K, Luo M, Li J, Liu H, Ge B. Cytoplasmic PARP1 links the genome instability to the inhibition of antiviral immunity through PARylating cGAS. Mol Cell 2022; 82:2032-2049.e7. [PMID: 35460603 DOI: 10.1016/j.molcel.2022.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/10/2021] [Accepted: 03/25/2022] [Indexed: 12/22/2022]
Abstract
Virus infection modulates both host immunity and host genomic stability. Poly(ADP-ribose) polymerase 1 (PARP1) is a key nuclear sensor of DNA damage, which maintains genomic integrity, and the successful application of PARP1 inhibitors for clinical anti-cancer therapy has lasted for decades. However, precisely how PARP1 gains access to cytoplasm and regulates antiviral immunity remains unknown. Here, we report that DNA virus induces a reactive nitrogen species (RNS)-dependent DNA damage and activates DNA-dependent protein kinase (DNA-PK). Activated DNA-PK phosphorylates PARP1 on Thr594, thus facilitating the cytoplasmic translocation of PARP1 to inhibit the antiviral immunity both in vitro and in vivo. Mechanistically, cytoplasmic PARP1 interacts with and directly PARylates cyclic GMP-AMP synthase (cGAS) on Asp191 to inhibit its DNA-binding ability. Together, our findings uncover an essential role of PARP1 in linking virus-induced genome instability with inhibition of host immunity, which is of relevance to cancer, autoinflammation, and other diseases.
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Affiliation(s)
- Fei Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Mengmeng Zhao
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Boran Chang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilong Zhou
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiangyang Wu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China
| | - Siyu Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China
| | - Yajuan Cao
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Mengge Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Yifang Dang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Junfang Xu
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Li Chen
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University School of Medicine, Shanghai 200433, China
| | - Tianhao Liu
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University School of Medicine, Shanghai 200433, China
| | - Fen Tang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China
| | - Yefei Ren
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China
| | - Zhu Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kai Huang
- Department of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Clinical Center for Human Genomic Research, Union Hospital, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Minhua Luo
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Haipeng Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University School of Medicine, Shanghai 200433, China.
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai 200072, China; Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
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