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Cury S, Oliveira J, Biagi-Júnior C, Silva Jr W, Reis P, Cabral-Marques O, Hasimoto E, Freire P, Carvalho R. Transcriptional profiles and common genes link lung cancer with the development and severity of COVID-19. Gene 2023; 852:147047. [PMID: 36379381 PMCID: PMC9659360 DOI: 10.1016/j.gene.2022.147047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
Abstract
Lung cancer patients with COVID-19 present an increased risk of developing severe disease and, consequently, have poor outcomes. Determining SARS-CoV-2-host interactome in lung cancer cells and tissues, infected or uninfected with SARS-CoV-2, may reveal molecular mechanisms associated with COVID-19 development and severity in lung cancer patients. Here, we integrated transcriptome data of lung tumors from patients with small- or non-small cell lung cancer (SCLC and NSCLC) and normal lung and lung cancer cells infected with SARS-CoV-2. We aimed to characterize molecular mechanisms potentially associated with COVID-19 development and severity in lung cancer patients and to predict the SARS-CoV-2-host cell interactome. We found that the gene expression profiles of lung cell lines infected with SARS-CoV-2 resemble more primary lung tumors than non-malignant lung tissues. In addition, the transcriptomic-based interactome analysis of SCLC and NSCLC revealed increased expression of cancer genes BRCA1 and CENPF, whose proteins are known or predicted to interact with the SARS-CoV-2 spike glycoprotein and helicase, respectively. We also found that TRIB3, a gene coding a putative host-SARS-CoV-2 interacting protein associated with COVID-19 infection, is co-expressed with the up-regulated genes MTHFD2, ADM2, and GPT2 in all tested conditions. Our analysis identified biological processes such as amino acid metabolism and angiogenesis and 22 host mediators of SARS-CoV-2 infection and replication that may contribute to the development and severity of COVID-19 in lung cancers.
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Affiliation(s)
- S.S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - J.S. Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - C.A.O. Biagi-Júnior
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - W.A. Silva Jr
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, Brazil,Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil,Institute for Cancer Research (IPEC), Guarapuava, PR, Brazil
| | - P.P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - O. Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - E.N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - P.P. Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
| | - R.F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP, Brazil,Lead Contact,Corresponding authors at: Department of Immunology, Institute of Biomedical Sciences - University of São Paulo, Lineu Prestes Avenue, 1730 São Paulo, Brazil (P.P. Freire). Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), CEP: 18.618-689, Botucatu, São Paulo, Brazil (R.F. Carvalho)
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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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Yeh YHJ, Jenike KM, Calvi RM, Chiarella J, Hoh R, Deeks SG, Ho YC. Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation. J Clin Invest 2021; 130:4969-4984. [PMID: 32573496 DOI: 10.1172/jci137371] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Despite effective antiretroviral therapy, HIV-1-infected cells continue to produce viral antigens and induce chronic immune exhaustion. We propose to identify HIV-1-suppressing agents that can inhibit HIV-1 reactivation and reduce HIV-1-induced immune activation. Using a newly developed dual-reporter system and a high-throughput drug screen, we identified FDA-approved drugs that can suppress HIV-1 reactivation in both cell line models and CD4+ T cells from virally suppressed HIV-1-infected individuals. We identified 11 cellular pathways required for HIV-1 reactivation as druggable targets. Using differential expression analysis, gene set enrichment analysis, and exon-intron landscape analysis, we examined the impact of drug treatment on the cellular environment at a genome-wide level. We identified what we believe to be a new function of a JAK inhibitor, filgotinib, that suppresses HIV-1 splicing. First, filgotinib preferentially suppresses spliced HIV-1 RNA transcription. Second, filgotinib suppresses HIV-1-driven aberrant cancer-related gene expression at the integration site. Third, we found that filgotinib suppresses HIV-1 transcription by inhibiting T cell activation and by modulating RNA splicing. Finally, we found that filgotinib treatment reduces the proliferation of HIV-1-infected cells. Overall, the combination of a drug screen and transcriptome analysis provides systematic understanding of cellular targets required for HIV-1 reactivation and drug candidates that may reduce HIV-1-related immune activation.
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Affiliation(s)
- Yang-Hui Jimmy Yeh
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katharine M Jenike
- Human Genetics PhD Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rachela M Calvi
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebecca Hoh
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, UCSF, San Francisco, California, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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Liu C, Qiao Y, Xu L, Wu J, Mei Q, Zhang X, Wang K, Li Q, Jia X, Sun H, Wu J, Sun W, Fu S. Association between polymorphisms in MRE11 and HIV-1 susceptibility and AIDS progression in a northern Chinese MSM population. J Antimicrob Chemother 2020; 74:2009-2018. [PMID: 30989233 DOI: 10.1093/jac/dkz132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 02/28/2019] [Accepted: 03/06/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Previous studies reported that DNA damage repair (DDR) genes may play an important role in HIV-1 infection. The MRE11 gene, a member of the MRN complex, plays an essential part in the homologous recombination pathway, which is one of the classical DDR pathways. Previous reports have demonstrated that MRE11 has an effect on HIV-1 replication. However, the role of SNPs in the MRE11 gene and their impact on HIV-1 infection and AIDS progression remain unknown. METHODS In this study, 434 MSM HIV-1-infected patients in northern China and 431 age-matched healthy controls were enrolled. Five SNPs (rs2155209, rs10831234, rs13447720, rs601341 and rs11020803) at the MRE11 gene were genotyped. Another series of cases (409 MSM HIV-1-infected patients) and controls (403 age-matched healthy males) were recruited as the validation set. RESULTS In our study, rs10831234 showed differences in allele frequencies between cases and controls (P = 0.005). Additionally, there was an association between rs10831234 and HIV-1 infection susceptibility in dominant and additive models (P = 0.005 and P = 0.006, respectively). All significant associations were replicated in the validation set, and the associations were still significant after Bonferroni correction for multiple testing when the two data sets were combined. Furthermore, in haplotype association analyses between the case and control groups, the frequencies of the haplotypes Crs11020803Crs10831234 and Trs11020803Trs10831234 showed significant differences (P = 0.0181 and P = 0.0068, respectively). CONCLUSIONS We demonstrated that the MRE11 rs10831234-T allele may confer increased risk of HIV-1 infection.
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Affiliation(s)
- Chang Liu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Jiawei Wu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Qingbu Mei
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Kaili Wang
- Infectious Disease Hospital of Heilongjiang Province, Harbin, China
| | - Qiuyan Li
- Editorial Department of International Journal of Genetics, Harbin Medical University, Harbin, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, China.,Key Laboratory of Medical Genetics, (Harbin Medical University), Heilongjiang Higher Education Institutions, 157 Baojian Road, Nangang District, Harbin, China
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Characterizing the antiviral effect of an ATR inhibitor on human immunodeficiency virus type 1 replication. Arch Virol 2020; 165:683-690. [PMID: 32002668 DOI: 10.1007/s00705-020-04531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/18/2020] [Indexed: 10/25/2022]
Abstract
In the search for new antiviral therapies against human immunodeficiency virus type 1 (HIV-1), several cellular targets are being investigated. Ataxia telangiectasia and Rad3-related protein (ATR) has been implicated in HIV-1 replication, namely during retroviral DNA integration. We studied the effect of the ATR inhibitor ETP-46464 on HIV-1 replication in peripheral blood mononuclear cells (PBMCs) and in the persistently HIV-1-infected cell line H61-D. After treatment with ETP-46464, a significant decrease in virus production was observed in both cell systems. Quantification of viral DNA forms in the acutely infected PBMCs suggests that inhibition could take place in the early phase of the viral life cycle before viral DNA integration. Moreover, after treatment of H61-D cells with 3'-azido-3'-deoxythymidine (AZT), which blocks new reverse transcription events, ETP-46464 decreased viral production, suggesting that inhibition of viral replication occurred in the late phase of the life cycle after viral DNA integration. A decrease in virus production after transfection of 293T cells with an HIV-1 infectious molecular clone also suggested that the effect of ETP-46464 is exerted at a post-integration step. We propose that ETP-46464 produces its inhibitory effect on HIV-1 replication by acting in both the early and late phases of the retroviral replication cycle. Thus, ATR could represent a new target for inhibition of HIV-1 replication.
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6
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Sengodan SK, K H S, Nadhan R, Srinivas P. Regulation of epithelial to mesenchymal transition by BRCA1 in breast cancer. Crit Rev Oncol Hematol 2018; 123:74-82. [PMID: 29482782 DOI: 10.1016/j.critrevonc.2018.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/06/2017] [Accepted: 01/17/2018] [Indexed: 12/13/2022] Open
Abstract
Reports till its discovery has proven multiple facets of Breast Cancer type 1 susceptibility gene (BRCA1) from nucleus to cytoplasm; from DNA repair to drug resistance; from Homologous Recombination (HR) to Ubiquitination; from breast to brain; from cancer to HIV and many of the roles are still unexplored. One of the recent attractions of BRCA1 is its role in regulating breast cancer metastasis though the exact mechanism is poorly understood. In this review, we will discuss the molecular interactions between BRCA1 and the key molecules of Epithelial to Mesenchymal Transition (EMT) associated with metastasis, its associated drug resistance and the possible treatment strategy for BRCA1 mutated breast cancer.
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Affiliation(s)
- Satheesh Kumar Sengodan
- Cancer Research Program 5, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram 695 014, Kerala, India
| | - Sreelatha K H
- Cancer Research Program 5, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram 695 014, Kerala, India
| | - Revathy Nadhan
- Cancer Research Program 5, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram 695 014, Kerala, India
| | - Priya Srinivas
- Cancer Research Program 5, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram 695 014, Kerala, India.
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Nair M, Sagar V, Pilakka-Kanthikeel S. Gene-expression reversal of lncRNAs and associated mRNAs expression in active vs latent HIV infection. Sci Rep 2016; 6:34862. [PMID: 27756902 PMCID: PMC5069461 DOI: 10.1038/srep34862] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/15/2016] [Indexed: 01/09/2023] Open
Abstract
Interplay between lncRNAs and mRNAs is rapidly emerging as a key epigenetic mechanism in controlling various cell functions. HIV can actively infect and/or can persist latently for years by manipulating host epigenetics; however, its molecular essence remains undiscovered in entirety. Here for the first time, we delineate the influence of HIV on global lncRNAs expression in monocytic cells lines. Our analysis revealed the expression modulation of nearly 1060 such lncRNAs which are associated with differentially expressed mRNAs in active and latent infection. This suggests a greater role of lncRNAs in regulating transcriptional and post-transcriptional gene expression during HIV infection. The differentially expressed mRNAs were involved in several different biological pathways where immunological networks were most enriched. Importantly, we discovered that HIV induces expression reversal of more than 150 lncRNAs between its active and latent infection. Also, hundreds of unique lncRNAs were identified in both infection conditions. The pathology specific "gene-expression reversal" and "on-and-off" switching of lncRNAs and associated mRNAs may lead to establish the relationship between active and HIV infection.
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Affiliation(s)
- Madhavan Nair
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Institute of Neuro-Immune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Center for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
| | - Vidya Sagar
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Institute of Neuro-Immune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Center for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
| | - Sudheesh Pilakka-Kanthikeel
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Institute of Neuro-Immune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
- Center for Personalized Nanomedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL-33199, USA
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Xie D, Han L, Luo Y, Liu Y, He S, Bai H, Wang S, Bo X. Exploring the associations of host genes for viral infection revealed by genome-wide RNAi and virus–host protein interactions. MOLECULAR BIOSYSTEMS 2015; 11:2511-9. [DOI: 10.1039/c5mb00309a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome-wide RNA interference screens have greatly facilitated the identification of essential host factors (EHFs) for viral infections, whose knockdown effects significantly influence virus replication but not host cell viability.
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Affiliation(s)
- Dafei Xie
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
| | - Lu Han
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
| | - Yifu Luo
- National University of Defense Technology
- Changsha
- China
| | - Yang Liu
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
| | - Song He
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
| | - Hui Bai
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
- No. 451 Hospital of Chinese People's Liberation Army
| | - Shengqi Wang
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
| | - Xiaochen Bo
- Department of Biotechnology
- Beijing Institute of Radiation Medicine
- Beijing
- China
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