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Maueia C, Carulei O, Murahwa AT, Taku O, Manjate A, Mussá T, Williamson AL. Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology. Viruses 2024; 16:1314. [PMID: 39205288 PMCID: PMC11360388 DOI: 10.3390/v16081314] [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: 07/04/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Human papillomavirus 16 (HPV16) is an oncogenic virus responsible for the majority of invasive cervical cancer cases worldwide. Due to genetic modifications, some variants are more oncogenic than others. We analysed the HPV16 phylogeny in HPV16-positive cervical Desoxyribonucleic Acid (DNA) samples collected from South African and Mozambican women to detect the circulating lineages. METHODS Polymerase chain reaction (PCR) amplification of the long control region (LCR) and 300 nucleotides of the E6 region was performed using HPV16-specific primers on HPV16-positive cervical samples collected in women from South Africa and Mozambique. HPV16 sequences were obtained through Next Generation Sequencing (NGS) methods. Geneious prime and MEGA 11 software were used to align the sequences to 16 HPV16 reference sequences, gathering the A, B, C, and D lineages and generating the phylogenetic tree. Single nucleotide polymorphisms (SNPs) in the LCR and E6 regions were analysed and the phylogenetic tree was generated using Geneious Prime software. RESULTS Fifty-eight sequences were analysed. Of these sequences, 79% (46/58) were from women who had abnormal cervical cytology. Fifteen SNPs in the LCR and eight in the E6 region were found to be the most common in all sequences. The phylogenetic analysis determined that 45% of the isolates belonged to the A1 sublineage (European variant), 34% belonged to the C1 sublineage (African 1 variant), 16% belonged to the B1 and B2 sublineage (African 2 variant), two isolates belonged to the D1-3 sublineages (Asian-American variant), and one to the North American variant. CONCLUSIONS The African and European HPV16 variants were the most common circulating lineages in South African and Mozambican women. A high-grade squamous intraepithelial lesion (HSIL) was the most common cervical abnormality observed and linked to European and African lineages. These findings may contribute to understanding molecular HPV16 epidemiology in South Africa and Mozambique.
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Affiliation(s)
- Cremildo Maueia
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (O.C.); (A.T.M.); (O.T.); (A.-L.W.)
- Departamento de Microbiologia, Faculdade de Medicina, Universidade Eduardo Mondlane, Maputo P.O.Box 257, Mozambique; (A.M.); (T.M.)
- Instituto Nacional de Saúde, Maputo 3943, Mozambique
| | - Olivia Carulei
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (O.C.); (A.T.M.); (O.T.); (A.-L.W.)
| | - Alltalents T. Murahwa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (O.C.); (A.T.M.); (O.T.); (A.-L.W.)
| | - Ongeziwe Taku
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (O.C.); (A.T.M.); (O.T.); (A.-L.W.)
| | - Alice Manjate
- Departamento de Microbiologia, Faculdade de Medicina, Universidade Eduardo Mondlane, Maputo P.O.Box 257, Mozambique; (A.M.); (T.M.)
| | - Tufária Mussá
- Departamento de Microbiologia, Faculdade de Medicina, Universidade Eduardo Mondlane, Maputo P.O.Box 257, Mozambique; (A.M.); (T.M.)
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (O.C.); (A.T.M.); (O.T.); (A.-L.W.)
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
- SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Zhao Q, Yang S, Hao S, Chen Z, Tang L, Wu Z, Wu J, Xu M, Ma Z, Zhou L, Xu J, Qin Q. Identification of transcriptionally-active human papillomavirus integrants through nanopore sequencing reveals viable targets for gene therapy against cervical cancer. J Med Virol 2024; 96:e29769. [PMID: 38932482 DOI: 10.1002/jmv.29769] [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: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.
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Affiliation(s)
- Qianqian Zhao
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Shuaibing Yang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Shijia Hao
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zejia Chen
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lihua Tang
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhaoting Wu
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jiaxin Wu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Mingqian Xu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zebiao Ma
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jianzhen Xu
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Qingsong Qin
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
- International Science and Technology Collaboration Center for Emerging Infectious Diseases, Shantou University Medical College, Shantou, China
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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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Cui X, Li Y, Zhang C, Qi Y, Sun Y, Li W. Multiple HPV integration mode in the cell lines based on long-reads sequencing. Front Microbiol 2023; 14:1294146. [PMID: 38169727 PMCID: PMC10758443 DOI: 10.3389/fmicb.2023.1294146] [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: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Background The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome. Methods In this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines. Results We found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines. Conclusion Elucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.
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Affiliation(s)
- Xiaofang Cui
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | | | - Chuanpeng Zhang
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Yanwei Qi
- School of Control and Computer Engineering, North China Electric Power University, Beijing, China
| | | | - Weiyang Li
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
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Gauthier MA, Kadam A, Leveque G, Golabi N, Zeitouni A, Richardson K, Mascarella M, Sadeghi N, Loganathan SK. Long-read sequencing of oropharyngeal squamous cell carcinoma tumors reveal diverse patterns of high-risk Human Papillomavirus integration. Front Oncol 2023; 13:1264646. [PMID: 37916168 PMCID: PMC10616875 DOI: 10.3389/fonc.2023.1264646] [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: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction In North America and in most European countries, Human Papillomavirus (HPV) is responsible for over 70% of oropharyngeal squamous cell carcinomas. The burden of OPSCC, in high-income countries, has been steadily increasing over the past 20 years. As a result, in the USA and in the UK, the burden of HPV-related oropharyngeal squamous cell carcinoma in men has now surpassed that of cervical cancer in women. However, the oncogenic impact of high-risk HPV integration in oropharyngeal squamous cell carcinomas hasn't been extensively studied. The present study aimed to explore the patterns of HPV integration in oropharyngeal squamous cell carcinomas and to assess the feasibility and reliability of long-read sequencing technology in detecting viral integration events in oropharyngeal head and neck cancers. Methods A cohort of eight HPV-positive OPSCC pre-treatment patient tumors (four males and four females), were selected. All patients received a p16INK4A positive OPSCC diagnosis and were treated at the McGill University Health Centre, a quaternary center in Montreal. A minimum of 20mg of tumor tissue was used for DNA extraction. Extracted DNA was subjected to Nanopore long-read sequencing to detect and analyze for the presence of high-risk HPV sequences. PCR and Sanger sequencing experiments were performed to confirm Nanopore long-read sequencing readings. Results Nanopore long-read sequencing showed that seven out of eight patient samples displayed either integrated or episomal high-risk HPV sequences. Out of these seven samples, four displayed verifiable integration events upon bioinformatic analysis. Integration confirmation experiments were designed for all four samples using PCR-based methods. Sanger sequencing was also performed. Four distinct HPV integration patterns were identified: concatemer chromosomal integration in a single chromosome, bi-chromosomal concatemer integration, single chromosome complete integration and bi-chromosomal complete integration. HPV concatemer integration also proved more common than full HPV integration events. Conclusion and relevance Long-read sequencing technologies can be effectively used to assess HPV integration patterns in OPSCC tumors. Clinically, more research should be conducted on the prognostication value of high-risk HPV integration in OPSCC tumors using long-read sequencing technology.
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Affiliation(s)
- Marc-Andre Gauthier
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Adway Kadam
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Gary Leveque
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Nahid Golabi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anthony Zeitouni
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Keith Richardson
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Marco Mascarella
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nader Sadeghi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Oncology, McGill University, Montreal, QC, Canada
| | - Sampath Kumar Loganathan
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Experimental Medicine, Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada
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Zhao J, Zheng W, Wang L, Jiang H, Wang X, Hou J, Xu A, Cong J. Human papillomavirus (HPV) integration signature in cervical lesions: identification of MACROD2 gene as HPV hot spot integration site. Arch Gynecol Obstet 2023; 307:1115-1123. [PMID: 36008642 DOI: 10.1007/s00404-022-06748-1] [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: 06/24/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND High-risk HPV is clearly associated with cervical cancer. Integration of HPV DNA into the host genome is considered a key event in driving cervical carcinogenesis. However, the mechanism on how HR-HPV integration influences the host genome structure has remained enigmatic. METHODS In our study, 25 DNA samples including 11 from fresh-frozen cervical carcinomas and 14 from fresh-frozen high-grade squamous intraepithelial lesion (HSILs) were detected using the method of HPV capture combined with next generation sequencing. RESULTS We calculated the frequency in each viral gene or region and found that breakpoints were prone to occur in L1 and L2 instead of E2 in the cervical cancer (P = 0.0004 and P = 5.15 × 10-40) and HSIL group (P = 2.1 × 10-32 and P = 7.06 × 10-13). The results revealed that HPV16 showed a strong tendency toward intronic region (P = 5.02 × 10-64) but a subtle tendency toward intergenic region (P = 0.04). The most frequent integration site was in the MACROD2 gene (introns 2, 4, 5, 6, 8 and 9), which in MACROD2 functional domain. CONCLUSION Our results revealed that MACROD2 is HPV hot spot integration site in cervical lesions, and its deficiency alter DNA repair and sensitivity to DNA damage thought impaired PARP1 activity resulting in chromosome instability.
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Affiliation(s)
- Junwei Zhao
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Wei Zheng
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Liqian Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Haiyang Jiang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Xiuli Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Jianqing Hou
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Anli Xu
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
| | - Jianglin Cong
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
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