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Wu Y, Sun A, Yang Q, Wang M, Tian B, Yang Q, Jia R, Chen S, Ou X, Huang J, Sun D, Zhu D, Liu M, Zhang S, Zhao XX, He Y, Wu Z, Cheng A. An alpha-herpesvirus employs host HEXIM1 to promote viral transcription. J Virol 2024; 98:e0139223. [PMID: 38363111 PMCID: PMC10949456 DOI: 10.1128/jvi.01392-23] [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: 11/07/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Although it is widely accepted that herpesviruses utilize host RNA polymerase II (RNAPII) to transcribe viral genes, the mechanism of utilization varies significantly among herpesviruses. With the exception of herpes simplex virus 1 (HSV-1) in alpha-herpesviruses, the mechanism by which RNAPII transcribes viral genes in the remaining alpha-herpesviruses has not been reported. In this study, we investigated the transcriptional mechanism of an avian alpha-herpesvirus, Anatid herpesvirus 1 (AnHV-1). We discovered for the first time that hexamethylene-bis-acetamide-inducing protein 1 (HEXIM1), a major inhibitor of positive elongation factor B (P-TEFb), was significantly upregulated during AnHV-1 infection, and its expression was dynamically regulated throughout the progression of the disease. However, the expression level of HEXIM1 remained stable before and after HSV-1 infection. Excessive HEXIM1 assists AnHV-1 in progeny virus production, gene expression, and RNA polymerase II recruitment by promoting the formation of more inactive P-TEFb and the loss of RNAPII S2 phosphorylation. Conversely, the expression of some host survival-related genes, such as SOX8, CDK1, MYC, and ID2, was suppressed by HEXIM1 overexpression. Further investigation revealed that the C-terminus of the AnHV-1 US1 gene is responsible for the upregulation of HEXIM1 by activating its promoter but not by interacting with P-TEFb, which is the mechanism adopted by its homologs, HSV-1 ICP22. Additionally, the virus proliferation deficiency caused by US1 deletion during the early infection stage could be partially rescued by HEXIM1 overexpression, suggesting that HEXIM1 is responsible for AnHV-1 gaining transcription advantages when competing with cells. Taken together, this study revealed a novel HEXIM1-dependent AnHV-1 transcription mechanism, which has not been previously reported in herpesvirus or even DNA virus studies.IMPORTANCEHexamethylene-bis-acetamide-inducing protein 1 (HEXIM1) has been identified as an inhibitor of positive transcriptional elongation factor b associated with cancer, AIDS, myocardial hypertrophy, and inflammation. Surprisingly, no previous reports have explored the role of HEXIM1 in herpesvirus transcription. This study reveals a mechanism distinct from the currently known herpesvirus utilization of RNA polymerase II, highlighting the dependence on high HEXIM1 expression, which may be a previously unrecognized facet of the host shutoff manifested by many DNA viruses. Moreover, this discovery expands the significance of HEXIM1 in pathogen infection. It raises intriguing questions about whether other herpesviruses employ similar mechanisms to manipulate HEXIM1 and if this molecular target can be exploited to limit productive replication. Thus, this discovery not only contributes to our understanding of herpesvirus infection regulation but also holds implications for broader research on other herpesviruses, even DNA viruses.
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Affiliation(s)
- Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Anyang Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Qiqi Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Xin-Xin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Yu He
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Zhen Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Science & Technology Department of Sichuan Province, International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, China
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Guo M, Yao Z, Jiang C, Songyang Z, Gan L, Xiong Y. Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection. Front Immunol 2023; 14:1161522. [PMID: 37063858 PMCID: PMC10102373 DOI: 10.3389/fimmu.2023.1161522] [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: 02/08/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
BackgroundsHepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive.MethodsWe applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization.ResultsWe found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure.ConclusionOur work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhicheng Yao
- Department of General Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chen Jiang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lian Gan
- Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Lian Gan, ; Yuanyan Xiong,
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Lian Gan, ; Yuanyan Xiong,
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Pan L, Li M, Zhang X, Xia Y, Mian AM, Wu H, Sun Y, Qiu HJ. Establishment of an In Vitro Model of Pseudorabies Virus Latency and Reactivation and Identification of Key Viral Latency-Associated Genes. Viruses 2023; 15:v15030808. [PMID: 36992518 PMCID: PMC10056777 DOI: 10.3390/v15030808] [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: 02/25/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Alphaherpesviruses infect humans and most animals. They can cause severe morbidity and mortality. The pseudorabies virus (PRV) is a neurotropic alphaherpesvirus that can infect most mammals. The PRV persists in the host by establishing a latent infection, and stressful stimuli can induce the latent viruses to reactivate and cause recurrent diseases. The current strategies of antiviral drug therapy and vaccine immunization are ineffective in eliminating these viruses from the infected host. Moreover, overspecialized and complex models are also a major obstacle to the elucidation of the mechanisms involved in the latency and reactivation of the PRV. Here, we present a streamlined model of the latent infection and reactivation of the PRV. A latent infection established in N2a cells infected with the PRV at a low multiplicity of infection (MOI) and maintained at 42 °C. The latent PRV was reactivated when the infected cells were transferred to 37 °C for 12 to 72 h. When the above process was repeated with a UL54-deleted PRV mutant, it was observed that the UL54 deletion did not affect viral latency. However, viral reactivation was limited and delayed. This study establishes a powerful and streamlined model to simulate PRV latency and reveals the potential role of temperature in PRV reactivation and disease. Meanwhile, the key role of the early gene UL54 in the latency and reactivation of PRV was initially elucidated.
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Affiliation(s)
- Li Pan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
| | - Mingzhi Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
- School of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xinyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Yu Xia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
- School of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Assad Moon Mian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
| | - Hongxia Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
| | - Yuan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
- School of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin 150069, China
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
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Boftsi M, Whittle FB, Wang J, Shepherd P, Burger LR, Kaifer KA, Lorson CL, Joshi T, Pintel DJ, Majumder K. The adeno-associated virus 2 (AAV2) genome and rep 68/78 proteins interact with cellular sites of DNA damage. Hum Mol Genet 2021; 31:985-998. [PMID: 34652429 DOI: 10.1093/hmg/ddab300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/20/2021] [Accepted: 10/11/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear DNA viruses simultaneously access cellular factors that aid their life cycle while evading inhibitory factors by localizing to distinct nuclear sites. Adeno-Associated Viruses (AAVs), which are Dependoviruses in the family Parvovirinae, are non-enveloped icosahedral viruses, that have been developed as recombinant AAV vectors (rAAV) to express transgenes. AAV2 expression and replication occur in nuclear viral replication centers (VRCs), which relies on cellular replication machinery as well as coinfection by helper viruses such as adenoviruses or herpesviruses, or exogenous DNA damage to host cells. AAV2 infection induces a complex cellular DNA damage response (DDR), either in response to viral DNA or viral proteins expressed in the host nucleus during infection, where VRCs colocalize with DDR proteins. We have previously developed a modified iteration of a viral chromosome conformation capture (V3C-seq) assay to show that the autonomous parvovirus Minute Virus of Mice (MVM) localizes to cellular sites of DNA damage to establish and amplify its replication. Similar V3C-seq assays to map AAV2 show that the AAV2 genome colocalized with cellular sites of DNA damage under both non-replicating and replicating conditions. The AAV2 non-structural protein Rep 68/78, also localized to cellular DDR sites during both non-replicating and replicating infections, and also when ectopically expressed. Ectopically expressed Rep could be efficiently re-localized to DDR sites induced by micro-irradiation. Recombinant AAV2 gene therapy vector genomes derived from AAV2 localized to sites of cellular DNA damage to a lesser degree, suggesting that the Inverted Terminal Repeat (ITR) origins of replication were insufficient for targeting.
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Affiliation(s)
- Maria Boftsi
- Pathobiology Area Graduate Program.,Christopher S. Bond Life Sciences Center
| | | | - Juexin Wang
- Christopher S. Bond Life Sciences Center.,Department of Electrical Engineering and Computer Science
| | | | | | - Kevin A Kaifer
- Christopher S. Bond Life Sciences Center.,Department of Veterinary Pathobiology, College of Veterinary Medicine
| | - Christian L Lorson
- Christopher S. Bond Life Sciences Center.,Department of Veterinary Pathobiology, College of Veterinary Medicine
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center.,Department of Electrical Engineering and Computer Science.,MU Informatics Institute.,Department of Health Management and Informatics
| | - David J Pintel
- Christopher S. Bond Life Sciences Center.,Molecular Microbiology and Immunology, University of Missouri-Columbia, School of Medicine, Columbia, MO USA 65211
| | - Kinjal Majumder
- Institute for Molecular Virology.,McArdle Laboratory for Cancer Research.,University of Wisconsin-Carbone Cancer Center
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