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Wang Z, Liu C, Liu W, Lv X, Hu T, Yang F, Yang W, He L, Huang X. Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines. BMC Genomics 2024; 25:198. [PMID: 38378450 PMCID: PMC10877919 DOI: 10.1186/s12864-024-10101-y] [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: 06/16/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Cervical cancer (CC) causes more than 311,000 deaths annually worldwide. The integration of human papillomavirus (HPV) is a crucial genetic event that contributes to cervical carcinogenesis. Despite HPV DNA integration is known to disrupt the genomic architecture of both the host and viral genomes in CC, the complexity of this process remains largely unexplored. RESULTS In this study, we conducted whole-genome sequencing (WGS) at 55-65X coverage utilizing the PacBio long-read sequencing platform in SiHa and HeLa cells, followed by comprehensive analyses of the sequence data to elucidate the complexity of HPV integration. Firstly, our results demonstrated that PacBio long-read sequencing effectively identifies HPV integration breakpoints with comparable accuracy to targeted-capture Next-generation sequencing (NGS) methods. Secondly, we constructed detailed models of complex integrated genome structures that included both the HPV genome and nearby regions of the human genome by utilizing PacBio long-read WGS. Thirdly, our sequencing results revealed the occurrence of a wide variety of genome-wide structural variations (SVs) in SiHa and HeLa cells. Additionally, our analysis further revealed a potential correlation between changes in gene expression levels and SVs on chromosome 13 in the genome of SiHa cells. CONCLUSIONS Using PacBio long-read sequencing, we have successfully constructed complex models illustrating HPV integrated genome structures in SiHa and HeLa cells. This accomplishment serves as a compelling demonstration of the valuable capabilities of long-read sequencing in detecting and characterizing HPV genomic integration structures within human cells. Furthermore, these findings offer critical insights into the complex process of HPV16 and HPV18 integration and their potential contribution to the development of cervical cancer.
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Affiliation(s)
- Zhijie Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Wanxin Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xinyi Lv
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Ting Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Fan Yang
- Wuhan Kandwise Biotechnology, Inc. Wuhan, Hubei, China
| | - Wenhui Yang
- Wuhan Kandwise Biotechnology, Inc. Wuhan, Hubei, China
| | - Liang He
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Xiaoyuan Huang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
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2
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Schwartz S, Wu C, Kajitani N. RNA elements that control human papillomavirus mRNA splicing-targets for therapy? J Med Virol 2024; 96:e29473. [PMID: 38362929 DOI: 10.1002/jmv.29473] [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: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Human papillomaviruses (HPVs) cause more than 4.5% of all cancer in the world and more than half of these cases are attributed to human papillomavirus type 16 (HPV16). Prophylactic vaccines are available but antiviral drugs are not. Novel targets for therapy are urgently needed. Alternative RNA splicing is extensively used by HPVs to express all their genes and HPV16 is no exception. This process must function to perfection since mis-splicing could perturb the HPV gene expression program by altering mRNA levels or by generating dysfunctional mRNAs. Cis-acting RNA elements on the viral mRNAs and their cognate cellular trans-acting factors control papillomavirus RNA splicing. The precise but delicate nature of the splicing process renders splicing sensitive to interference. As such, papillomavirus RNA splicing is a potential target for therapy. Here we summarize our current understanding of cis-acting HPV16 RNA elements that control HPV16 mRNA splicing via cellular proteins and discuss how they may be exploited as targets for therapy to papillomavirus infections and cancer.
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Affiliation(s)
- Stefan Schwartz
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Chengjun Wu
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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3
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Jönsson J, Wang L, Kajitani N, Schwartz S. A novel HPV16 splicing enhancer critical for viral oncogene expression and cell immortalization. Nucleic Acids Res 2024; 52:316-336. [PMID: 37994701 PMCID: PMC10783526 DOI: 10.1093/nar/gkad1099] [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: 03/24/2023] [Revised: 10/18/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
High-risk carcinogenic human papillomaviruses (HPVs), e.g. HPV16, express the E6 and E7 oncogenes from two mRNAs that are generated in a mutually exclusive manner by splicing. The HPV16 E7 mRNA, also known as the E6*I/E7 mRNA, is produced by splicing between splice sites SD226 and SA409, while E6 mRNAs retain the intron between these splice sites. We show that splicing between HPV16 splice sites SD226 and SA409 is controlled by a splicing enhancer consisting of a perfect repeat of an adenosine-rich, 11 nucleotide sequence: AAAAGCAAAGA. Two nucleotide substitutions in both 11 nucleotide sequences specifically inhibited production of the spliced E6*I/E7 mRNA. As a result, production of E7 protein was reduced and the ability of HPV16 to immortalize human primary keratinocytes was abolished. The splicing-enhancing effect was mediated by the cellular TRAP150/THRAP3 protein that also enhanced splicing of other high-risk HPV E6*I/E7 mRNAs, but had no effect on low-risk HPV mRNAs. In summary, we have identified a novel splicing enhancer in the E6 coding region that is specific for high-risk HPVs and that is critically linked to HPV16 carcinogenic properties.
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Affiliation(s)
- Johanna Jönsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Lianqing Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
- Center of Translational Medicine, Zibo Central Hospital, 255036 Zibo, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Stefan Schwartz
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
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4
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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5
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Kajitani N, Schwartz S. The role of RNA-binding proteins in the processing of mRNAs produced by carcinogenic papillomaviruses. Semin Cancer Biol 2022; 86:482-496. [PMID: 35181475 DOI: 10.1016/j.semcancer.2022.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
Abstract
Human papillomaviruses (HPV) are epitheliotropic DNA tumor viruses that are prevalent in the human population. A subset of the HPVs termed high-risk HPVs (HR-HPVs) are causative agents of anogenital cancers and head-and-neck cancers. Cancer is the result of persistent high-risk HPV infections that have not been cleared by the immune system of the host. These infections are characterized by dysregulated HPV gene expression, in particular constitutive high expression of the HPV E6 and E7 oncogenes and absence of the highly immunogenic viral L1 and L2 capsid proteins. HPVs make extensive use of alternative mRNA splicing to express its genes and are therefore highly dependent on cellular RNA-binding proteins for proper gene expression. Levels of RNA-binding proteins are altered in HPV-containing premalignant cervical lesions and in cervical cancer. Here we review our current knowledge of RNA-binding proteins that control HPV gene expression. We focus on RNA-binding proteins that control expression of the E6 and E7 oncogenes since they initiate and drive development of cancer and on the immunogenic L1 and L2 proteins as there silencing may contribute to immune evasion during carcinogenesis. Furthermore, cellular RNA-binding proteins are essential for HPV gene expression and as such may be targets for therapy to HPV infections and HPV-driven cancers.
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Affiliation(s)
- Naoko Kajitani
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23, Uppsala, Sweden; Department of Laboratory Medicine, Lund University, BMC-B13, 221 84, Lund, Sweden
| | - Stefan Schwartz
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23, Uppsala, Sweden; Department of Laboratory Medicine, Lund University, BMC-B13, 221 84, Lund, Sweden.
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6
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Song L, Mao R, Ding L, Tian Z, Zhang M, Wang J, Wang M, Lyu Y, Liu C, Feng M, Jia H, Wang J. hnRNP E1 Regulates HPV16 Oncogene Expression and Inhibits Cervical Cancerization. Front Oncol 2022; 12:905900. [PMID: 35800060 PMCID: PMC9253288 DOI: 10.3389/fonc.2022.905900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/24/2022] [Indexed: 11/15/2022] Open
Abstract
hnRNP E1 (heterogeneous nuclear ribonucleoprotein E1) is an important RNA-binding protein (RBPs) that plays a vital role in tumor development. Human papillomavirus 16 (HPV16) contains numerous sites that can bind to RNA/DNA and may be modified by multiple RBPs, which contribute to HPV gene expression and HPV-associated cancer development. However, the effects of hnRNP E1 on HPV16 oncogenes in the development of cervical lesions remain unclear. A total of 816 participants with different grades of cervical lesions were enrolled in a community-based cohort established in Shanxi Province, China. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to analyze the association between hnRNP E1 mRNA expression and cervical lesions. Cells with up_ and down_regulated hnRNP E1 were established. hnRNP E1 functions were evaluated using cell counting kit-8, flow cytometry analyses, and chromatin immunoprecipitation sequencing. Our results showed that hnRNP E1 expression was linearly dependent on the severity of the cervical lesions. Low expression of HPV16 E2, high expression of E6, and a low ratio of E2 to E6 could increase the risk of cervical lesions. hnRNP E1 expression was correlated with HPV16 oncogene expression. hnRNP E1-relevant genes were involved in the dopaminergic synapses, Wnt signaling pathway, gnRH secretion, and mTOR signaling pathway. hnRNP E1 significantly inhibited cell proliferation, induced apoptosis, arrested the cell cycle at the G0/G1 stage, and decreased HPV16 E6 expression. Our results indicate that hnRNP E1 could downregulate HPV16 E6 oncogene expression and inhibit cervical cancerization, which sheds new light on preventing the carcinogenicity of HPV across a range of diseases by regulating RNA-binding proteins.
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Affiliation(s)
- Li Song
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Rui Mao
- Questrom School of Business, Boston University, Boston, MA, United States
| | - Ling Ding
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Zhiqiang Tian
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingxuan Zhang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Jiahao Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ming Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yuanjing Lyu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Chunliang Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Meijuan Feng
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Haixia Jia
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Jintao Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- *Correspondence: Jintao Wang,
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7
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Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [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: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
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8
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Hao C, Zheng Y, Jönsson J, Cui X, Yu H, Wu C, Kajitani N, Schwartz S. hnRNP G/RBMX enhances HPV16 E2 mRNA splicing through a novel splicing enhancer and inhibits production of spliced E7 oncogene mRNAs. Nucleic Acids Res 2022; 50:3867-3891. [PMID: 35357488 PMCID: PMC9023273 DOI: 10.1093/nar/gkac213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) E2 is an essential HPV16 protein. We have investigated how HPV16 E2 expression is regulated and have identifed a splicing enhancer that is required for production of HPV16 E2 mRNAs. This uridine-less splicing enhancer sequence (ACGAGGACGAGGACAAGGA) contains 84% adenosine and guanosine and 16% cytosine and consists of three ‘AC(A/G)AGG’-repeats. Mutational inactivation of the splicing enhancer reduced splicing to E2-mRNA specific splice site SA2709 and resulted in increased levels of unspliced E1-encoding mRNAs. The splicing enhancer sequence interacted with cellular RNA binding protein hnRNP G that promoted splicing to SA2709 and enhanced E2 mRNA production. The splicing-enhancing function of hnRNP G mapped to amino acids 236–286 of hnRNP G that were also shown to interact with splicing factor U2AF65. The interactions between hnRNP G and HPV16 E2 mRNAs and U2AF65 increased in response to keratinocyte differentiation as well as by the induction of the DNA damage response (DDR). The DDR reduced sumoylation of hnRNP G and pharmacological inhibition of sumoylation enhanced HPV16 E2 mRNA splicing and interactions between hnRNP G and E2 mRNAs and U2AF65. Intriguingly, hnRNP G also promoted intron retention of the HPV16 E6 coding region thereby inhibiting production of spliced E7 oncogene mRNAs.
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Affiliation(s)
- Chengyu Hao
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Yunji Zheng
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,School of Pharmacy, Binzhou Medical University, 264003 Yantai, China
| | - Johanna Jönsson
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Xiaoxu Cui
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Haoran Yu
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Liaoning IC Technology Key Lab, 116024 Dalian, China
| | - Naoko Kajitani
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Stefan Schwartz
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden.,Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
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9
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Cui X, Hao C, Gong L, Kajitani N, Schwartz S. HnRNP D activates production of HPV16 E1 and E6 mRNAs by promoting intron retention. Nucleic Acids Res 2022; 50:2782-2806. [PMID: 35234917 PMCID: PMC8934624 DOI: 10.1093/nar/gkac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) E1 and E6 proteins are produced from mRNAs with retained introns, but it has been unclear how these mRNAs are generated. Here, we report that hnRNP D act as a splicing inhibitor of HPV16 E1/E2- and E6/E7-mRNAs thereby generating intron-containing E1- and E6-mRNAs, respectively. N- and C-termini of hnRNP D contributed to HPV16 mRNA splicing control differently. HnRNP D interacted with the components of splicing machinery and with HPV16 RNA to exert its inhibitory function. As a result, the cytoplasmic levels of intron-retained HPV16 mRNAs were increased in the presence of hnRNP D. Association of hnRNP D with HPV16 mRNAs in the cytoplasm was observed, and this may correlate with unexpected inhibition of HPV16 E1- and E6-mRNA translation. Notably, hnRNP D40 interacted with HPV16 mRNAs in an HPV16-driven tonsillar cancer cell line and in HPV16-immortalized human keratinocytes. Furthermore, knockdown of hnRNP D in HPV16-driven cervical cancer cells enhanced production of the HPV16 E7 oncoprotein. Our results suggest that hnRNP D plays significant roles in the regulation of HPV gene expression and HPV-associated cancer development.
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Affiliation(s)
- Xiaoxu Cui
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Chengyu Hao
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Lijing Gong
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,China Institute of Sport and Health Sciences, Beijing Sport University, Haidian District, Beijing 100084, China
| | - Naoko Kajitani
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
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10
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Overexpression of m6A-factors METTL3, ALKBH5, and YTHDC1 alters HPV16 mRNA splicing. Virus Genes 2022; 58:98-112. [PMID: 35190939 PMCID: PMC8948141 DOI: 10.1007/s11262-022-01889-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/12/2022] [Indexed: 11/24/2022]
Abstract
We report that overexpression of the m6A-demethylase alkB homolog 5 RNA demethylase (ALKBH5) promoted production of intron retention on the human papillomavirus type 16 (HPV16) E6 mRNAs thereby promoting E6 mRNA production. ALKBH5 also altered alternative splicing of the late L1 mRNA by an exon skipping mechanism. Knock-down of ALKBH5 had the opposite effect on splicing of these HPV16 mRNAs. Overexpression of the m6A-methylase methyltransferase-like protein 3 (METLL3) induced production of intron-containing HPV16 E1 mRNAs over spliced E2 mRNAs and altered HPV16 L1 mRNA splicing in a manner opposite to ALKBH5. Overexpression of the nuclear m6A-“reader” YTH domain-containing protein 1 (YTHDC1), enhanced retention of the E6-encoding intron and promoted E6 mRNA production. We also show that HPV16 mRNAs are bound to YTHDC1 in human cells and that YTHDC1 affected splicing of HPV16 E6/E7 mRNAs produced from the episomal form of the HPV16 genome. Finally, we show that HPV16 mRNAs are m6A-methylated in tonsillar cancer cells. In summary, HPV16 mRNAs are methylated in HPV16-infected tonsillar cancer cells and overexpression of m6A-“writer” METTL3, m6A-“eraser” ALKBH5 and the m6A-“reader” YTHDC1 affected HPV16 mRNA splicing, suggesting that m6A plays an important role in the HPV16 gene expression program, at least in cancer cells.
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11
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Identification of heterogenous nuclear ribonucleoproteins (hnRNPs) and serine- and arginine-rich (SR) proteins that induce human papillomavirus type 16 late gene expression and alter L1 mRNA splicing. Arch Virol 2021; 167:563-570. [PMID: 34860285 PMCID: PMC8843915 DOI: 10.1007/s00705-021-05317-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/19/2021] [Indexed: 11/03/2022]
Abstract
We have determined the effect of seven serine- and arginine-rich (SR) proteins and 15 heterogenous nuclear ribonucleoproteins (hnRNPs) on human papillomavirus type 16 (HPV16) late gene expression. Of the seven SR proteins analyzed here, SRSF1, SRSF3, and SRSF9 induced HPV16 late gene expression, and five of the SR proteins affected HPV16 L1 mRNA splicing. Of the 15 hnRNP proteins analyzed here, hnRNP A2, hnRNP F, and hnRNP H efficiently induced HPV16 late gene expression, and all of the hnRNPs affected HPV16 L1 mRNA levels or mRNA splicing. Thus, the majority of SR proteins and hnRNPs have the potential to regulate HPV16 L1 mRNA splicing. Strict control of the expression of the immunogenic L1 and L2 capsid proteins may contribute to the ability of HPV16 to cause persistence.
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12
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Bernacchi S. Special Issue "Function and Structure of Viral Ribonucleoproteins Complexes". Viruses 2020; 12:v12121355. [PMID: 33256140 PMCID: PMC7760632 DOI: 10.3390/v12121355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN-CNRS UPR 9002, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
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