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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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Bi Y, Hu J, Zeng L, Chen G, Cai H, Cao H, Ma Q, Wu X. Characteristics of HPV integration in cervical adenocarcinoma and squamous carcinoma. J Cancer Res Clin Oncol 2023; 149:17973-17986. [PMID: 37966613 PMCID: PMC10725361 DOI: 10.1007/s00432-023-05494-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
Abstract
PURPOSE HPV integration usually occurs in HPV-related cancer, and is the main cause of cancer. But the carcinogenic mechanism of HPV integration is unclear. The study aims to provide a theoretical basis for understanding the pathogenesis of cervical adenocarcinoma (AC) and cervical squamous carcinoma (SCC). METHODS We used HPV capture sequencing to obtain HPV integration sites in AC and SCC, and analyzed cytobands, distribution of genetic and genomic elements, identified integration hotspot genes, clinicopathological parameters, breakpoints of HPV16 and performed pathway analysis. Then we conducted immunohistochemical (IHC) assay to preliminarily verify the expression of most frequently integrated genes in AC, STARD3 and ERBB2. RESULTS The results revealed that the most frequently observed integrated cytoband was 17q12 in AC and 21p11.2 in SCC, respectively. The breakpoints in both AC and SCC were more tended to occur within gene regions, compared to intergenetic regions. Compared to SCC samples, AC samples had a higher prevalence of genomic elements. In AC, HPV integration has no significantly difference with clinicopathological parameters, but in SCC integration correlated with differentiation (P < 0.05). Breakpoints of HPV in SCC located in LCR more frequently compared to AC, which destroyed the activation of promoter p97. Hotspot genes of HPV integration were STARD3 and ERBB2 in AC, and RNA45S rDNA and MIR3648-1 in SCC, respectively. Meanwhile, we preliminarily proved that the expression of STARD3 and ERBB2, the most frequently integrated genes, would increase after integration. CONCLUSION These results suggested that HPV may utilize the powerful hosts' promoters to express viral oncogenes and overexpression of viral oncogenes plays a significant role in the carcinogenesis of SCC. In AC, HPV integration may affect hosts' oncogenes, and the dysregulation of oncogenes may primarily contribute to progression of AC.
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Affiliation(s)
- Yuxin Bi
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Junbo Hu
- Department of Pathology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Ling Zeng
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongning Cai
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Huang Cao
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Quanfu Ma
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Xufeng Wu
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China.
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Li X, Wei X, Liu X, Wang N, Xu F, Liu X, Li Y, Zhou Y, Tang H, Bian M, Hou Y, Zhang L, Wang W, Liu Q. The analysis of HPV integration sites based on nanopore sequencing and the profiling changes along the course of photodynamic therapy. BMC Cancer 2023; 23:1052. [PMID: 37914994 PMCID: PMC10621124 DOI: 10.1186/s12885-023-11538-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
OBJECTIVE To detect the HPV genotype and integration sites in patients with high-risk HPV infection at different stages of photodynamic therapy using nanopore technology and to evaluate the treatment effect. METHODS Four patients with HPV infection were selected and subjected to photodynamic therapy, and cervical exfoliated cell was sampled at before treatment, after three courses of treatment and six courses of treatment, their viral abundance and insertion sites were analyzed by nanopore technology, and pathological examinations were performed before and after treatment. In this study, we developed a novel assay that combined viral sequence enrichment and Nanopore sequencing for identification of HPV genotype and integration sites at once. The assay has obvious advantages over qPCR or NGS-based methods, as it has better sensitivity after viral sequences enrichment and can generate long-reads (kb to Mb) for better detection rate of structure variations, moreover, fast turn-around time for real-time viral sequencing and analysis. RESULTS The pathological grade was reduced in all four patients after photodynamic therapy. Virus has been cleared in two cases after treatment, the virus amount reduced after treatment but not completely cleared in one case, and two type viruses were cleared and one type virus persisted after treatment in the last patient with multiple infection. Viral abundance and the number of integration sites were positively correlated. Gene enrichment analysis showed complete viral clearance in 1 patient and 3 patients required follow-up. CONCLUSION Nanopore sequencing can effectively monitor the abundance of HPV viruses and integration sites to show the presence status of viruses, and combined with the results of gene enrichment analysis, the treatment effect can be dynamically assessed.
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Affiliation(s)
- Xiulan Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xiaoke Wei
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Xin Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Nan Wang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Fuqiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xingyu Liu
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China
| | - Yanmei Li
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yuxiang Zhou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Huadong Tang
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Meina Bian
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Ying Hou
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lili Zhang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Weiwei Wang
- Geneis, Bldg A, 5 Guangshun North Street, Beijing, 100102, China.
| | - Qing Liu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
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Garza-Rodríguez ML, Oyervides-Muñoz MA, Pérez-Maya AA, Sánchez-Domínguez CN, Berlanga-Garza A, Antonio-Macedo M, Valdés-Chapa LD, Vidal-Torres D, Vidal-Gutiérrez O, Pérez-Ibave DC, Treviño V. Analysis of HPV Integrations in Mexican Pre-Tumoral Cervical Lesions Reveal Centromere-Enriched Breakpoints and Abundant Unspecific HPV Regions. Int J Mol Sci 2021; 22:ijms22063242. [PMID: 33810183 PMCID: PMC8005155 DOI: 10.3390/ijms22063242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023] Open
Abstract
Human papillomavirus (HPV) DNA integration is a crucial event in cervical carcinogenesis. However, scarce studies have focused on studying HPV integration (HPVint) in early-stage cervical lesions. Using HPV capture followed by sequencing, we investigated HPVint in pre-tumor cervical lesions. Employing a novel pipeline, we analyzed reads containing direct evidence of the integration breakpoint. We observed multiple HPV infections in most of the samples (92%) with a median integration rate of 0.06% relative to HPV mapped reads corresponding to two or more sequence breakages. Unlike cancer studies, most integrations events were unique (supported by one read), consistent with the lack of clonal selection. Congruent to other studies, we found that breakpoints could occur, practically, in any part of the viral genome. We noted that L1 had a higher frequency of rupture integration (25%). Based on host genome integration frequencies, we found previously reported integration sites in cancer for genes like FHIT, CSMD1, and LRP1B and putatively many new ones such as those exemplified in CSMD3, ROBO2, and SETD3. Similar host integrations regions and genes were observed in diverse HPV types within many genes and even equivalent integration positions in different samples and HPV types. Interestingly, we noted an enrichment of integrations in most centromeres, suggesting a possible mechanism where HPV exploits this structural machinery to facilitate integration. Supported by previous findings, overall, our analysis provides novel information and insights about HPVint.
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Affiliation(s)
- María Lourdes Garza-Rodríguez
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Mariel Araceli Oyervides-Muñoz
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico;
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Antonio Alí Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Celia Nohemí Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Anais Berlanga-Garza
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Mauro Antonio-Macedo
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Lezmes Dionicio Valdés-Chapa
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Diego Vidal-Torres
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Oscar Vidal-Gutiérrez
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Diana Cristina Pérez-Ibave
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Víctor Treviño
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Colonia Los Doctores, Nuevo León 64710, Mexico
- Correspondence:
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5
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Zeng X, Zhao L, Shen C, Zhou Y, Li G, Sung WK. HIVID2: an accurate tool to detect virus integrations in the host genome. Bioinformatics 2021; 37:1821-1827. [PMID: 33453108 DOI: 10.1093/bioinformatics/btab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/27/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes. RESULTS Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real data sets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration. AVAILABILITY HIVID2 can be accessed at https://github.com/zengxi-hada/HIVID2/. CONTACT Xi Zeng (zengxi@mail.hzau.edu.cn), Linghao Zhao (michael_yifan@126.com). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Linghao Zhao
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Chenhang Shen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
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6
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Van Arsdale A, Patterson NE, Maggi EC, Agoni L, Van Doorslaer K, Harmon B, Nevadunsky N, Kuo DY, Einstein MH, Lenz J, Montagna C. Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV-negative cervical cancer. Genes Chromosomes Cancer 2020; 59:84-95. [PMID: 31407403 PMCID: PMC6916423 DOI: 10.1002/gcc.22799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cervical carcinogenesis, the second leading cause of cancer death in women worldwide, is caused by multiple types of human papillomaviruses (HPVs). To investigate a possible role for HPV in a cervical carcinoma that was HPV-negative by PCR testing, we performed HPV DNA hybridization capture plus massively parallel sequencing. This detected a subgenomic, URR-E6-E7-E1 segment of HPV70 DNA, a type not generally associated with cervical cancer, inserted in an intron of the B-cell lymphoma/leukemia 11B (BCL11B) gene in the human genome. Long range DNA sequencing confirmed the virus and flanking BCL11B DNA structures including both insertion junctions. Global transcriptomic analysis detected multiple, alternatively spliced, HPV70-BCL11B, fusion transcripts with fused open reading frames. The insertion and fusion transcripts were present in an intraepithelial precursor phase of tumorigenesis. These results suggest oncogenicity of HPV70, identify novel BCL11B variants with potential oncogenic implications, and underscore the advantages of thorough genomic analyses to elucidate insights into HPV-associated tumorigenesis.
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Affiliation(s)
- Anne Van Arsdale
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Nicole E. Patterson
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Elaine C. Maggi
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Lorenzo Agoni
- Department of Women's and Children's HealthObstetrics & Gynecology Unit, Fondazione Poliambulanza Istituto OspedalieroBresciaItaly
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical SciencesCollege of Agriculture and Life Sciences BIO5 Institute University of ArizonaTusconArizonaUSA
| | - Bryan Harmon
- Department of PathologyAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Nicole Nevadunsky
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Dennis Y.S. Kuo
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Mark H. Einstein
- Department of Obstetrics, Gynecology, and Women's HealthRutgers New Jersey Medical SchoolNewarkNew Jersey
| | - Jack Lenz
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Cristina Montagna
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
- Department of PathologyAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
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7
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Kiseleva VI, Mkrtchyan LS, Ivanov SA, Lyubina LV, Bezyaeva GP, Panarina LV, Krikunova LI, Zamulaeva IA. The Presence of Human Papillomavirus DNA Integration is Associated with Poor Clinical Results in Patients with Third-Stage Cervical Cancer. Bull Exp Biol Med 2019; 168:87-91. [PMID: 31768781 DOI: 10.1007/s10517-019-04654-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Indexed: 11/26/2022]
Abstract
The presence of virus DNA integration into the cell genome was studied for 47 primary HPV16-positive patients with morphologically verified stage III cervical cancer. By using ROC analysis, the patients were divided into two groups: with and without HPV DNA integration into the host cell genome. The differences between the groups by the histological type, degree of tumor differentiation, and primary response to therapy were statistically insignificant. Virus DNA integration more than 7-fold reduced 5-year relapse-free survival and 1.7-fold reduced overall survival rate in comparison with patients without HPV DNA integration (p=0.0002 and p=0.05, respectively). The relative risk of adverse outcome of the disease in patients with the presence of HPV16 DNA integration increases by 4 times over a period of less than 3 years (р=0.0006) at high AUC level. The probability of earlier progression of the disease in patients with of HPV DNA integration calculated according to the Cox proportional hazards model was 85.5% (hazard ratio 5.96; p=0.002). Thus, the results suggest that the presence of HPV16 DNA integration into the cell genome is an independent factor in predicting clinical outcome of advanced cervical cancer and can serve as an effective criterion for the individual choice of treatment tactics for the patients.
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Affiliation(s)
- V I Kiseleva
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia.
| | - L S Mkrtchyan
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - S A Ivanov
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - L V Lyubina
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - G P Bezyaeva
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - L V Panarina
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - L I Krikunova
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
| | - I A Zamulaeva
- A. F. Tsyb Medical Radiological Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninsk, Russia
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8
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Lagström S, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Sci Rep 2019; 9:524. [PMID: 30679491 PMCID: PMC6345795 DOI: 10.1038/s41598-018-36669-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Maija Lepistö
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Roger Meisal
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital and Institute of Clinical Medicine, University of, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway.
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9
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Hu Z, Ma D. The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications. Cancer Med 2018; 7:5217-5236. [PMID: 30589505 PMCID: PMC6198240 DOI: 10.1002/cam4.1501] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/14/2018] [Accepted: 03/21/2018] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer is the third most common cancer in women worldwide, with concepts and knowledge about its prevention and treatment evolving rapidly. Human papillomavirus (HPV) has been identified as a major factor that leads to cervical cancer, although HPV infection alone cannot cause the disease. In fact, HPV-driven cancer is a small probability event because most infections are transient and could be cleared spontaneously by host immune system. With persistent HPV infection, decades are required for progression to cervical cancer. Therefore, this long time window provides golden opportunity for clinical intervention, and the fundament here is to elucidate the carcinogenic pattern and applicable targets during HPV-host interaction. In this review, we discuss the key factors that contribute to the persistence of HPV and cervical carcinogenesis, emerging new concepts and technologies for cancer interventions, and more urgently, how these concepts and technologies might lead to clinical precision medicine which could provide prediction, prevention, and early treatment for patients.
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Affiliation(s)
- Zheng Hu
- Department of Gynecological oncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityZhongshan 2nd RoadYuexiu, GuangzhouGuangdongChina
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
| | - Ding Ma
- Department of Obstetrics and GynecologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan, Hubei430030China
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10
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Abstract
Human papillomaviruses (HPVs) are a necessary cause of anogenital squamous cell carcinomas (SCC) and a subgroup of head and neck SCC, i.e., those originating in the oropharynx. The key events in high-risk HPV (HRHPV)-associated neoplastic progression include persistent infection, deregulated expression of virus early genes in basal epithelial cells, local immune suppression and the accumulation of chromosomal alterations. Evidence for these events particularly comes from studies of uterine cervical carcinogenesis; primary premalignant HRHPV-positive lesions of the head and neck mucosa are seldomly detected. Integration of virus DNA into host chromosomes is considered an important driver of carcinogenesis and observed in 40 up to 90 % of uterine cervical SCC (UCSCC) and oropharyngeal SCC (OPSCC), dependent on the integration detection method used and HRHPV type. In OPSCC, > 90 % HPV-positive tumors are infected with HPV16. Ten up to 60 % of HPV-positive tumors thus contain extrachromosomal (episomal) virus. In this chapter, causes and consequences of HPV integration are summarized from the literature, with special focus on the site of HPV integration in the cellular genome, and its effect on expression of viral oncogenes (particularly E6 and E7), on human (tumor) gene expression and on deregulation of cell proliferation, apoptosis and cell signaling pathways. Also data on DNA methylation, viral load and clinical outcome in relation to HPV integration are provided.
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Affiliation(s)
- Ernst Jan M Speel
- Unit Molecular Oncopathology & Diagnostics, Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ, Maastricht, The Netherlands.
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11
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Hong D, Liu J, Hu Y, Lu X, Li B, Li Y, Hu D, Lu W, Xie X, Cheng X. Viral E6 is overexpressed via high viral load in invasive cervical cancer with episomal HPV16. BMC Cancer 2017; 17:136. [PMID: 28202002 PMCID: PMC5311840 DOI: 10.1186/s12885-017-3124-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/08/2017] [Indexed: 11/18/2022] Open
Abstract
Background The integration of HR-HPV genome into host DNA is regarded as a key step for the development of cervical cancer. However, HR-HPV genome indeed exists as episome except for integrant. It may be alternative mechanisms in episome-associated carcinogenesis, although, by which HPV 16 episome induces cervical carcinogenesis is unclear now. Methods Ninety-three invasive cervical cancer tissues with HPV16 positive were collected. Viral physical status was calculated from comparing E2 to E6-copies and detection of viral load was made with realtime-PCR using copy numbers of E6. HPV16 E6 mRNA transcript levels were measured by realtime-PCR. The methylation frequency of HPV16 promoter was detected by PCR and pyrosequencing. Results In 93 samples, 21.5% (20/93) presented purely integrated viral genome, 53.8% (50/93) mixed viral genome, and 24.7% (23/93) purely episomal viral genome. Mean E6 expression in samples with purely episomal viral genomes was 7.13-fold higher than that with purely integrated viral genomes. Meanwhile, viral load in samples with purely episomal viral genomes was 4.53-fold higher than that with purely integrated viral genomes. E6 mRNA expression increased with the viral load in purely episomal cases. There were no differences of mean methylation frequency between purely episomal and integrated virus and among five CpG positions of HPV16 promoter for all samples. And there also was no correlation between E6 mRNA expression and methylation of HPV16 promoter among all samples with purely HPV16 episomal virus. Conclusions HPV16 with the purely episomal viral genomes exists in a definite proportion of invasive cervical cancer, and episomal HPV16 also overexpresses E6 mRNA, probably through a high level of viral load.
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Affiliation(s)
- Die Hong
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Jia Liu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Ying Hu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Xiaonan Lu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Baohua Li
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Yang Li
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Dongxiao Hu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Weiguo Lu
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Xing Xie
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China
| | - Xiaodong Cheng
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Women's Reproductive Health Laboratory of Zhejiang Province, Zhejiang University, Xueshi Rd 1#, Hangzhou, 310006, China.
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12
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Abstract
Persistent infection with high-risk human papillomavirus (HPV) genotypes is the leading cause of cervical cancer development. To this end several studies have focused on designing molecular assays for HPV genotyping, which are considered as the gold standard for the early diagnosis of HPV infection. Moreover, the tendency of HPV DNA to be integrated into the host chromosome is a determining event for cervical oncogenesis. Thus, the establishment of molecular techniques was promoted in order to investigate the physical status of the HPV DNA and the locus of viral insertion into the host chromosome. The molecular approaches that have been developed recently facilitate the collection of a wide spectrum of valuable information specific to each individual patient and therefore can significantly contribute to the establishment of a personalised prognosis, diagnosis and treatment of HPV-positive patients. The present review focuses on state of the art molecular assays for HPV detection and genotyping for intra-lesion analyses, it examines molecular approaches for the determination of HPV-DNA physical status and it discusses the criteria for selecting the most appropriate regions of viral DNA to be incorporated in HPV genotyping and in the determination of HPV-DNA physical status.
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13
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Genome-wide profiling of the human papillomavirus DNA integration in cervical intraepithelial neoplasia and normal cervical epithelium by HPV capture technology. Sci Rep 2016; 6:35427. [PMID: 27759101 PMCID: PMC5069689 DOI: 10.1038/srep35427] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/29/2016] [Indexed: 01/23/2023] Open
Abstract
HPV integration plays an important role in cervical carcinogenesis. HPV genotypes and the exact integration sites were investigated using HPV capture technology combined with next generation sequencing in 166 women. Three, one and six integration sites were verified in 7 HPV-positive ‘normal cervical epithelium’, 6 HPV-positive CIN2 and 15 HPV-positive CIN 3 samples, respectively. Of the 10 integrations, one and nine were involved with HPV33 and HPV16, respectively. Our study accurately evaluated HPV integration level in CINs and normal cervical tissues using high-throughput viral integration detection method providing basic evidence for HPV integration-driven cervical carcinogenesis.
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14
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Bodelon C, Untereiner ME, Machiela MJ, Vinokurova S, Wentzensen N. Genomic characterization of viral integration sites in HPV-related cancers. Int J Cancer 2016; 139:2001-11. [PMID: 27343048 DOI: 10.1002/ijc.30243] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/20/2016] [Accepted: 06/09/2016] [Indexed: 01/14/2023]
Abstract
Persistent infection with carcinogenic human papillomaviruses (HPV) causes the majority of anogenital cancers and a subset of head and neck cancers. The HPV genome is frequently found integrated into the host genome of invasive cancers. The mechanisms of how it may promote disease progression are not well understood. Thoroughly characterizing integration events can provide insights into HPV carcinogenesis. Individual studies have reported limited number of integration sites in cell lines and human samples. We performed a systematic review of published integration sites in HPV-related cancers and conducted a pooled analysis to formally test for integration hotspots and genomic features enriched in integration events using data from the Encyclopedia of DNA Elements (ENCODE). Over 1,500 integration sites were reported in the literature, of which 90.8% (N = 1,407) were in human tissues. We found 10 cytobands enriched for integration events, three previously reported ones (3q28, 8q24.21 and 13q22.1) and seven additional ones (2q22.3, 3p14.2, 8q24.22, 14q24.1, 17p11.1, 17q23.1 and 17q23.2). Cervical infections with HPV18 were more likely to have breakpoints in 8q24.21 (p = 7.68 × 10(-4) ) than those with HPV16. Overall, integration sites were more likely to be in gene regions than expected by chance (p = 6.93 × 10(-9) ). They were also significantly closer to CpG regions, fragile sites, transcriptionally active regions and enhancers. Few integration events occurred within 50 Kb of known cervical cancer driver genes. This suggests that HPV integrates in accessible regions of the genome, preferentially genes and enhancers, which may affect the expression of target genes.
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Affiliation(s)
- Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Michael E Untereiner
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Svetlana Vinokurova
- Laboratory of Molecular Biology of Viruses, NN Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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15
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Hang D, Zhou W, Jia M, Wang L, Zhou J, Yin Y, Ma H, Hu Z, Li N, Shen H. Genetic variants within microRNA-binding site of RAD51B are associated with risk of cervical cancer in Chinese women. Cancer Med 2016; 5:2596-601. [PMID: 27334422 PMCID: PMC5055154 DOI: 10.1002/cam4.797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/30/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022] Open
Abstract
RAD51B plays a central role in homologous recombinational repair (HRR) of DNA double-strand breaks (DSBs), which is important to prevent genomic instability, a hallmark of cancer. Recent studies suggested that common genetic variants of RAD51B may contribute to cancer susceptibility. In this study, we aimed to investigate whether potentially functional variants within miRNA-binding sites of RAD51B are associated with risk of cervical cancer. A total of 1486 cervical cancer patients and 1536 cancer-free controls were enrolled, and two genetic variants, rs963917 (A > G) and rs963918 (T > C), were genotyped in all participants. Using multivariate logistic regression analyses, we found that G allele of rs963917 conferred lower risk of cervical cancer compared to A allele (adjusted OR = 0.89, 95% CI = 0.80-0.99, P = 0.039). Similarly, rs963918 allele C was associated with a decreased risk for cervical cancer compared with allele T (adjusted OR = 0.84, 95% CI = 0.74-0.94, P = 0.004). Haplotype analyses showed that haplotype GC was also correlated with lower risk (OR = 0.83, 95% CI = 0.73-0.95, P = 0.005) compared with the most common haplotype AT. In summary, our study suggested that miRNA-binding site genetic variants of RAD51B may modify the susceptibility to cervical cancer, which is important to identify individuals with differential risk for this malignancy and to improve the effectiveness of preventive intervention.
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Affiliation(s)
- Dong Hang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meiqun Jia
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lihua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jing Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yin Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ni Li
- National Office for Cancer Prevention and Control, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing, China.
| | - Hongbin Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
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16
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E1 detection as prognosticator in human papillomavirus-positive head and neck cancers. Int J Biol Markers 2016; 31:0. [PMID: 27040135 DOI: 10.5301/jbm.5000193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
PURPOSE HPV-related locally advanced head and neck cancers (LA-HNCs) show a good prognosis. This study aimed to investigate the HPV prevalence in LA-HNCs and compare the prognostic value of E1, E6 and L1 genomic viral fragments and p16, individually and in combination, in order to find the best prognosticator in terms of overall survival (OS) and progression-free survival (PFS). PATIENTS AND METHODS HPV16 was searched in 255 LA-HNC formalin-fixed paraffin-embedded tumor tissues, 89 oropharyngeal cancers (OPCs), and 166 non-OPCs by DNA-PCR with 3 primer pairs. p16 was analyzed by immunohistochemistry in 235 patients. RESULTS The prevalence of positive samples decreased constantly from E6 to L1 and E1 in both OPCs and non-OPCs. Each LA-HNC patient highlighted variable positivity for each fragment. OPCs showed a higher prevalence of positive samples compared to non-OPCs.Positive coexistence of all the fragments was more common in OPCs (31.5%) than non-OPCs (4.2%), and E1 detection was always associated with E6 and L1. E1-positive OPCs showed improved OS (p = 0.012) and PFS (p = 0.036), while L1- or E6-positive ones did not. p16-positive patients were more prevalent in the OPC (29.8%) than the non-OPC group (7.3%) (p<0.0001) and its prognostic value was not superior to that of E1. However, the multivariate Cox analysis which included E1, L1, E6 status and p16 expression did not show a significant p value. CONCLUSIONS Though HPV16 positivity measured by DNA-PCR was higher for L1 and E6, they performed weakly as prognosticators; E1 might become a strong prognostic marker for OS and PFS in OPCs.
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17
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Tsakogiannis D, Bletsa M, Kyriakopoulou Z, Dimitriou TG, Kotsovassilis C, Panotopoulou E, Markoulatos P. Identification of rearranged sequences of HPV16 DNA in precancerous and cervical cancer cases. Mol Cell Probes 2015; 30:6-12. [PMID: 26627739 DOI: 10.1016/j.mcp.2015.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/06/2015] [Accepted: 11/20/2015] [Indexed: 12/18/2022]
Abstract
Integration of HPV16 DNA into the host chromosome is considered to be a crucial step towards genomic instability and cervical cancer development. Aim of the present study was to investigate the presence of HPV16 rearranged intra-viral sequences in HPV16-positive normal, precancerous and cervical cancer samples using the method of Restriction Site-PCR (RS-PCR). Sequence analysis of HPV16 integrants revealed for the first time in clinical samples two distinct rearranged intra-viral sequences, concerning the conjunction of E2 and L1 genes and the conjunction of E1 and L1 genes with inverted orientation. Furthermore mapping analysis of the E1 and E2 genes in cervical samples with rearranged intra-viral sequences of HPV16 genome was conducted in order to determine the integrity of viral genes. The identification of intra-viral rearrangements provides valuable information regarding the HPV16 DNA integration, and may be a significant biomarker for the presence of chromosomal instability and DNA damages in clinical samples.
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Affiliation(s)
- D Tsakogiannis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - M Bletsa
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - Z Kyriakopoulou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - T G Dimitriou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece
| | - C Kotsovassilis
- General Hospital of Athens, Clinical Biochemistry Dpt, Athens, Greece
| | - E Panotopoulou
- Research Centre of Oncology and Experimental Surgery, Anticancer Oncology Hospital of Athens "St Savvas", Athens, Greece
| | - P Markoulatos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Larissa, Greece.
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18
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Scheel A, Lin GC, McHugh JB, Komarck CM, Walline HM, Prince ME, Zacharek MA, Carey TE. Human papillomavirus infection and biomarkers in sinonasal inverted papillomas: clinical significance and molecular mechanisms. Int Forum Allergy Rhinol 2015; 5:701-7. [PMID: 26077310 PMCID: PMC4526407 DOI: 10.1002/alr.21524] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 12/27/2022]
Abstract
BACKGROUND The role of human papillomavirus (HPV) in sinonasal inverted papillomas (IPs) is controversial. Determining the prevalence of HPV infection and its impact on the molecular biology of these tumors is critical to characterizing its role in the pathogenesis of IPs. METHODS A total of 112 paraffin-embedded IPs from 90 patients were studied. A tissue microarray was constructed and stained for p16, p53, epidermal growth factor receptor (EGFR), and cyclin D1. HPV presence and types were determined using PGMY 09/11 primers and integration using HPV 11 detection of integrated papillomavirus sequences by ligation-mediated polymerase chain reaction (DIPS-PCR). RESULTS HPV was detected in 11 of 90 (12%) patients. HPV 11 was found in 9 samples. HPV 6 and HPV 27 were found in 1 sample each. EGFR staining proportion was higher in HPV-positive IPs vs HPV-negative specimens (56.2% vs 23.6%; p = 0.009). Differences in p16, p53, and cyclin D1 staining were not significant. HPV-positive lesions tend to progress to malignancy (p = 0.064). Three samples were analyzed for integration. Viral integration was found in both malignant tumors but not in the precursor IP. CONCLUSION Degradation of p53 and p16/cyclin D1 dysregulation are not important mechanisms in low-risk HPV-related IP. The low prevalence of HPV in this series indicates it is not a main etiological factor for IPs; however, when present, low-risk HPV may contribute to the biology of IPs through an increase of EGFR expression and a predisposition for malignant progression by integration into the cellular genome.
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Affiliation(s)
- Adam Scheel
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Giant C. Lin
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Jonathan B. McHugh
- Department of Pathology, University of Michigan Health Systems, Ann Arbor, MI
| | - Christine M. Komarck
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Heather M. Walline
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Mark E. Prince
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Mark A. Zacharek
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
| | - Thomas E. Carey
- Department of Otolaryngology, University of Michigan Health Systems, Ann Arbor, MI
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19
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Tsakogiannis D, Gortsilas P, Kyriakopoulou Z, Ruether IGA, Dimitriou TG, Orfanoudakis G, Markoulatos P. Sites of disruption within E1 and E2 genes of HPV16 and association with cervical dysplasia. J Med Virol 2015; 87:1973-80. [PMID: 25959607 DOI: 10.1002/jmv.24256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 04/28/2015] [Indexed: 12/25/2022]
Abstract
Integration of HPV16 DNA into the host chromosome usually disrupts the E1 and/or E2 genes. The present study investigated the disruption of E1, E2 genes in a total of eighty four HPV16-positive precancerous and cervical cancer specimens derived from Greek women (seventeen paraffin-embedded cervical biopsies and sixty seven Thin Prep samples). Complete E2 and E1 genes were amplified using three and nine overlapping primer sets respectively, in order to define the sites of disruption. Extensive mapping analysis revealed that disruption/deletion events within E2 gene occurred in high grade and cervical cancer samples (x(2) test, P < 0.01), while no evidence of E2 gene disruption was documented among low grade cervical intraepithelial neoplasias. In addition, disruptions within the E1 gene occur both in high and low grade cervical intraepithelial neoplasia. This leads to the assumption that in low grade cervical intraepithelial neoplasias only E1 gene disruption was involved (Fisher's exact test, P < 0.05), while in high grade malignancies and cervical cancer cases deletions in both E1 and E2 genes occurred. Furthermore, the most prevalent site of disruption of E1 gene was located between nucleotides 1059 and 1323, while the most prevalent deleted region of the E2 gene was located between nucleotides 3172 and 3649 (E2 hinge region). Therefore, it is proposed that each population has its own profile of frequencies and sites of disruptions and extensive mapping analysis of E1 and E2 genes is mandatory in order to determine suitable markers for HPV16 DNA integration analysis in distinct populations.
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Affiliation(s)
- D Tsakogiannis
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - P Gortsilas
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Z Kyriakopoulou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - I G A Ruether
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - T G Dimitriou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - G Orfanoudakis
- University of Strasbourg, Ecole Superieure de Biotechnologie de Strasbourg, CNRS FRE 3211-Oncoprotein Group, Illkirch, France
| | - P Markoulatos
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
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20
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Christiansen IK, Sandve GK, Schmitz M, Dürst M, Hovig E. Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis. PLoS One 2015; 10:e0119566. [PMID: 25793388 PMCID: PMC4368827 DOI: 10.1371/journal.pone.0119566] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/15/2015] [Indexed: 01/23/2023] Open
Abstract
Integration of human papillomavirus (HPV) into the host genome is regarded as a determining event in cervical carcinogenesis. However, the exact mechanism for integration, and the role of integration in stimulating cancer progression, is not fully characterized. Although integration sites are reported to appear randomly distributed over all chromosomes, fragile sites, translocation break points and transcriptionally active regions have all been suggested as being preferred sites for integration. In addition, more recent studies have reported integration events occurring within or surrounding essential cancer-related genes, raising the question whether these may reflect key events in the molecular genesis of HPV induced carcinomas. In a search for possible common denominators of the integration sites, we utilized the chromosomal coordinates of 121 viral-cellular fusion transcripts, and examined for statistical overrepresentation of integration sites with various features of ENCODE chromatin information data, using the Genomic HyperBrowser. We find that integration sites coincide with DNA that is transcriptionally active in mucosal epithelium, as judged by the relationship of integration sites to DNase hypersensitivity and H3K4me3 methylation data. Finding an association between integration and transcription is highly informative with regard to the spatio-temporal characteristics of the integration process. These results suggest that integration is an early event in carcinogenesis, more than a late product of chromosomal instability. If the viral integrations were more likely to occur in destabilized regions of the DNA, a completely random distribution of the integration sites would be expected. As a by-product of integration in actively transcribing DNA, a tendency of integration in or close to genes is likely to be observed. This increases the possibility of viral signals to modulate the expression of these genes, potentially contributing to the progression towards cancer.
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Affiliation(s)
- Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | | | - Martina Schmitz
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Matthias Dürst
- Department of Gynaecology, Jena University Hospital, Jena, Germany
| | - Eivind Hovig
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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21
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Kahla S, Kochbati L, Maalej M, Oueslati R. Situation of HPV16 E2 gene status during radiotherapy treatment of cervical carcinoma. Asian Pac J Cancer Prev 2015; 15:2869-73. [PMID: 24761916 DOI: 10.7314/apjcp.2014.15.6.2869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration within the E2 gene has been proposed as a critical event in cervical carcinogenesis. This study concerned whether HPV16 status and E2 gene intactness are predictive of radiation response in patients with cervical cancer. MATERIALS AND METHODS Biopsies of 44 patients with cervical cancer were collected before or after radiotherapy. The presence of HPV16 was assessed by polymerase chain reaction (PCR) using specific primers for the L1 region. E2 disruption was detected by amplifying the entire E2 gene. RESULTS HPV16 DNA was found in 54.5% of the clinical samples. Overall, 62.5% of the HPV16 positive tumors had integrated viral genome and 37.5% had episomal genome. There was a tendency of increase of HPV16 E2 negative tumors compared with HPV16 L1 ones in advanced stages (75% versus 20% in stage III respectively). Detection of E2 gene appeared influenced by the radiotherapy treatment, as the percentage of samples containing an intact HPV16 E2 was more frequent in pretreated patients compared to radiotherapy treated patients (66.6% versus 20%). The radiation therapy caused an eight-fold [OR= 8; CI=1.22-52.25; p=0.03] increase in the risk of HPV16 genome disruption. The integration status is influenced by the irradiation modalities, interestingly E2 disruption being found widely after radiotherapy treatment (75%) with a total fractioned dose of 50 Gy. CONCLUSIONS This study reveals that the status of the viral DNA may be used as a marker to optimize the radiation treatment.
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Affiliation(s)
- Saloua Kahla
- Unit of Immunology Microbiology Environmental and Carcinogenesis (IMEC), Science Faculty of Bizerte, University of Carthage, Jarzouna, Bizerte, Tunisia E-mail :
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22
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Tsakogiannis D, Kyriakopoulou Z, Ruether IGA, Amoutzias GD, Dimitriou TG, Diamantidou V, Kotsovassilis C, Markoulatos P. Determination of human papillomavirus 16 physical status through E1/E6 and E2/E6 ratio analysis. J Med Microbiol 2014; 63:1716-1723. [DOI: 10.1099/jmm.0.076810-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human papillomavirus (HPV) 16 genome integration into the host chromosome is a crucial event during the life cycle of the virus and a major step towards carcinogenesis. The integration of HPV16 DNA promotes a constitutive high expression level of E6 and E7 oncoproteins, resulting in the extensive proliferation of the infected epithelial cells. In the present report the physical status of the HPV16 genome was studied, through determination of E1/E6 and E2/E6 DNA copy number ratios in 61 cervical samples of low- and high-grade malignancy and 8 cervical cancer samples, all of them associated with HPV16 infection. The selection of E1, E2 and E6 amplification target regions was performed according to the most prevalent deleted/disrupted sites of E1 and E2 genes. For this target selection we also considered the most conserved regions of E1, E2 and E6 genes among the same HPV16 isolates that were recently reported by our group. The analysis of HPV16 DNA form revealed a significant association among the mixed DNA forms in low-grade and high-grade malignancies, (χ2, P<0.01). The comparative analysis of E1/E6 and E2/E6 in the same cervical samples provides an accurate picture of HPV16 DNA form and may reveal whether different HPV16 DNA integrants coexist in the same cervical sample or not. This study proposes that E1/E6 and E2/E6 ratios determine with accuracy the HPV16 DNA integration pattern and may predict multiple integration events in the examined sample, thus providing significant information about the progression of cervical dysplasia.
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Affiliation(s)
- Dimitris Tsakogiannis
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Zaharoula Kyriakopoulou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Irina Georgia Anna Ruether
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Grigoris D. Amoutzias
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Tilemachos G. Dimitriou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Valentina Diamantidou
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | | | - Panayotis Markoulatos
- Microbiology–Virology Laboratory, Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
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Gichuhi S, Ohnuma SI, Sagoo MS, Burton MJ. Pathophysiology of ocular surface squamous neoplasia. Exp Eye Res 2014; 129:172-82. [PMID: 25447808 PMCID: PMC4726664 DOI: 10.1016/j.exer.2014.10.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/17/2014] [Indexed: 12/22/2022]
Abstract
The incidence of ocular surface squamous neoplasia (OSSN) is strongly associated with solar ultraviolet (UV) radiation, HIV and human papilloma virus (HPV). Africa has the highest incidence rates in the world. Most lesions occur at the limbus within the interpalpebral fissure particularly the nasal sector. The nasal limbus receives the highest intensity of sunlight. Limbal epithelial crypts are concentrated nasally and contain niches of limbal epithelial stem cells in the basal layer. It is possible that these are the progenitor cells in OSSN. OSSN arises in the basal epithelial cells spreading towards the surface which resembles the movement of corneo-limbal stem cell progeny before it later invades through the basement membrane below. UV radiation damages DNA producing pyrimidine dimers in the DNA chain. Specific CC → TT base pair dimer transformations of the p53 tumour-suppressor gene occur in OSSN allowing cells with damaged DNA past the G1-S cell cycle checkpoint. UV radiation also causes local and systemic photoimmunosuppression and reactivates latent viruses such as HPV. The E7 proteins of HPV promote proliferation of infected epithelial cells via the retinoblastoma gene while E6 proteins prevent the p53 tumour suppressor gene from effecting cell-cycle arrest of DNA-damaged and infected cells. Immunosuppression from UV radiation, HIV and vitamin A deficiency impairs tumour immune surveillance allowing survival of aberrant cells. Tumour growth and metastases are enhanced by; telomerase reactivation which increases the number of cell divisions a cell can undergo; vascular endothelial growth factor for angiogenesis and matrix metalloproteinases (MMPs) that destroy the intercellular matrix between cells. Despite these potential triggers, the disease is usually unilateral. It is unclear how HPV reaches the conjunctiva.
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Affiliation(s)
- Stephen Gichuhi
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Department of Ophthalmology, University of Nairobi, P.O Box 19676-00202, Nairobi, Kenya.
| | - Shin-ichi Ohnuma
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK.
| | - Mandeep S Sagoo
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK; St. Bartholomew's Hospital, W Smithfield, London EC1A 7BE, UK.
| | - Matthew J Burton
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK.
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24
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Olthof NC, Huebbers CU, Kolligs J, Henfling M, Ramaekers FCS, Cornet I, van Lent-Albrechts JA, Stegmann APA, Silling S, Wieland U, Carey TE, Walline HM, Gollin SM, Hoffmann TK, de Winter J, Kremer B, Klussmann JP, Speel EJM. Viral load, gene expression and mapping of viral integration sites in HPV16-associated HNSCC cell lines. Int J Cancer 2014; 136:E207-18. [PMID: 25082736 DOI: 10.1002/ijc.29112] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 07/03/2014] [Indexed: 01/05/2023]
Abstract
HPV-related HNSCC generally have a better prognosis than HPV-negative HNSCC. However, a subgroup of HPV-positive tumors with poor prognosis has been recognized, particularly related to smoking, EGFR overexpression and chromosomal instability. Viral integration into the host genome might contribute to carcinogenesis, as is shown for cervical carcinomas. Therefore, all HPV16-positive HNSCC cell lines currently available have been carefully analyzed for viral and host genome parameters. The viral integration status, viral load, viral gene expression and the presence of aneusomies was evaluated in the cell lines UD-SCC-2, UM-SCC-047, UM-SCC-104, UPCI:SCC090, UPCI:SCC152, UPCI:SCC154 and 93VU147T. HPV integration was examined using FISH, APOT-PCR and DIPS-PCR. Viral load and the expression of the viral genes E2, E6 and E7 were determined via quantitative PCR. All cell lines showed integration-specific staining patterns and signals indicating transcriptional activity using FISH. APOT- and DIPS-PCR identified integration-derived fusion products in six cell lines and only episomal products for UM-SCC-104. Despite the observed differences in viral load and the number of viral integration sites, this did not relate to the identified viral oncogene expression. Furthermore, cell lines exhibited EGFR expression and aneusomy (except UPCI:SCC154). In conclusion, all HPV16-positive HNSCC cell lines showed integrated and/or episomal viral DNA that is transcriptionally active, although viral oncogene expression was independent of viral copy number and the number of viral integration sites. Because these cell lines also contain EGFR expression and aneusomy, which are parameters of poor prognosis, they should be considered suitable model systems for the development of new antiviral therapies.
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Affiliation(s)
- Nadine C Olthof
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands; Department of Molecular Cell Biology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, The Netherlands
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25
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Raybould R, Fiander A, Wilkinson GWG, Hibbitts S. HPV integration detection in CaSki and SiHa using detection of integrated papillomavirus sequences and restriction-site PCR. J Virol Methods 2014; 206:51-4. [PMID: 24880069 DOI: 10.1016/j.jviromet.2014.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/17/2014] [Accepted: 05/20/2014] [Indexed: 01/10/2023]
Abstract
Human Papillomavirus (HPV) infection is the primary cause of cervical neoplasia. HPV DNA is integrated into the human genome in the majority of cervical cancers. The nature of integration may differ with integration incorporating a single copy of HPV or occurring in concatenated form. Our understanding of HPV tumorigenesis is largely based on studies using characterised cell lines with defined integration sites; these cell lines provide an invaluable standard for validation of diagnostic assays. Cell lines also further understanding of integration mechanisms in clinical samples. The objective of this study was to explore integration assays and to investigate integration events in cell lines where HPV is integrated in concatenated form. Restriction site PCR and detection of integrated papillomavirus sequences were performed on DNA from SiHa and CaSki. A novel integration site on Xq27.3 and HPV genome rearrangements were detected in CaSki DNA. However, where integration was previously detected by FISH in CaSki, and reported to be integrated in concatenated form, integration was not detected by DIPS or RS-PCR. The data presented illustrate that HPV copy number can hinder integration detection; this needs consideration when interpreting results from tests applied to clinical samples.
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Affiliation(s)
- Rachel Raybould
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom.
| | - Alison Fiander
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Gavin W G Wilkinson
- Institute of Infection and Immunity, Section of Medical Microbiology, Tenovus Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Sam Hibbitts
- Institute of Cancer Research and Genetics, Section of Obstetrics and Gynecology, Main Building, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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26
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Jang MK, Shen K, McBride AA. Papillomavirus genomes associate with BRD4 to replicate at fragile sites in the host genome. PLoS Pathog 2014; 10:e1004117. [PMID: 24832099 PMCID: PMC4022725 DOI: 10.1371/journal.ppat.1004117] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
It has long been recognized that oncogenic viruses often integrate close to common fragile sites. The papillomavirus E2 protein, in complex with BRD4, tethers the viral genome to host chromatin to ensure persistent replication. Here, we map these targets to a number of large regions of the human genome and name them Persistent E2 and BRD4-Broad Localized Enrichments of Chromatin or PEB-BLOCs. PEB-BLOCs frequently contain deletions, have increased rates of asynchronous DNA replication, and are associated with many known common fragile sites. Cell specific fragile sites were mapped in human C-33 cervical cells by FANCD2 ChIP-chip, confirming the association with PEB-BLOCs. HPV-infected cells amplify viral DNA in nuclear replication foci and we show that these form adjacent to PEB-BLOCs. We propose that HPV replication, which hijacks host DNA damage responses, occurs adjacent to highly susceptible fragile sites, greatly increasing the chances of integration here, as is found in HPV-associated cancers. Papillomavirus cause persistent, but mostly self-limiting, infections of the host epithelium. However, a subset of oncogenic papillomaviruses is the causative agent of certain human cancers. In persistent infection the viral genomes are tethered to host chromosomes to maintain and partition the extrachromosomal viral genomes to daughter cells. However, in cancers viral DNA is often found integrated close to common fragile sites, regions prone to breakage, amplification and deletion. We show that the viral E2 and cellular BRD4 proteins are associated with fragile regions of the human genome and nucleate viral replication foci at these sites. This is a resourceful strategy for a virus that uses the host DNA damage response to amplify viral DNA. However, the outcome may be increased accidental integration of viral DNA, which in the case of the oncogenic viruses can promote carcinogenesis.
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Affiliation(s)
- Moon Kyoo Jang
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kui Shen
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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27
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Olthof NC, Speel EJM, Kolligs J, Haesevoets A, Henfling M, Ramaekers FCS, Preuss SF, Drebber U, Wieland U, Silling S, Lam WL, Vucic EA, Kremer B, Klussmann JP, Huebbers CU. Comprehensive analysis of HPV16 integration in OSCC reveals no significant impact of physical status on viral oncogene and virally disrupted human gene expression. PLoS One 2014; 9:e88718. [PMID: 24586376 PMCID: PMC3933331 DOI: 10.1371/journal.pone.0088718] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/10/2014] [Indexed: 12/21/2022] Open
Abstract
Infection with high-risk human papillomavirus (HPV) type 16 is an independent risk factor for the development of oropharyngeal squamous cell carcinomas (OSCC). However, it is unclear whether viral integration is an essential hallmark in the carcinogenic process of OSCC and whether HPV integration correlates with the level of viral gene transcription and influences the expression of disrupted host genes. We analyzed 75 patients with OSCC. HPV16-positivity was proven by p16INK4A immunohistochemistry, PCR and FISH. Viral integration was examined using DIPS- as well as APOT-PCR. Viral E2, E6 and E7 gene expression levels were quantified by quantitative reverse transcriptase (RT-q)PCR. Expression levels of 7 human genes disrupted by the virus were extracted from mRNA expression profiling data of 32 OSCCs. Viral copy numbers were assessed by qPCR in 73 tumors. We identified 37 HPV16-human fusion products indicating viral integration in 29 (39%) OSCC. In the remaining tumors (61%) only episome-derived PCR products were detected. When comparing OSCC with or without an integration-derived fusion product, we did not find significant differences in the mean RNA expression of viral genes E2, E6 and E7 or the viral copy numbers per cell, nor did the RNA expression of the HPV-disrupted genes differ from either group of OSCC. In conclusion, our data do not support the hypothesis that integration affects the levels of viral and/or HPV-disrupted human gene transcripts. Thus constitutive, rather than a high level, of expression of oncogene transcripts appears to be required in HPV-related OSCC.
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Affiliation(s)
- Nadine C. Olthof
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Ernst-Jan M. Speel
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jutta Kolligs
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
| | - Annick Haesevoets
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Mieke Henfling
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Frans C. S. Ramaekers
- Department of Molecular Cell Biology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Simon F. Preuss
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Cologne, Cologne, Germany
| | - Uta Drebber
- Institute for Pathology, University Hospital of Cologne, Cologne, Germany
| | - Ulrike Wieland
- Institute of Virology, National Reference Centre for Papilloma- and Polyomaviruses, University Hospital of Cologne, Cologne, Germany
| | - Steffi Silling
- Institute of Virology, National Reference Centre for Papilloma- and Polyomaviruses, University Hospital of Cologne, Cologne, Germany
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Emily A. Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Bernd Kremer
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Jens-P. Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital of Giessen, Giessen, Germany
| | - Christian U. Huebbers
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
- * e-mail:
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28
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Wang L, Dai SZ, Chu HJ, Cui HF, Xu XY. Integration sites and genotype distributions of human papillomavirus in cervical intraepithelial neoplasia. Asian Pac J Cancer Prev 2014; 14:3837-41. [PMID: 23886192 DOI: 10.7314/apjcp.2013.14.6.3837] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES To analyse HPV integration prevalence and genotype distributions in cervical intraepithelial neoplasia (CIN) in east part of China, furthermore to assess preferential sites for common HPV integrations and provide baseline information for cervical abnormality screening and prevention. METHODS Integration of HPV in 113 paraffin-embedded cervical intraepithelial neoplasia samples was assessed using Gencap technology in Key Laboratory of Biotechnologies in BGI-Shenzhen. RESULTS 64 samples were HPV-integrated and as the cervical lesions increased, the integration rate became higher significantly (P=0.002). Fifteen different HPV genotypes were detected, 14 high-risk (16, 18, 31, 33, 51, 52, 56, 58, 66, 68) and 1 low-risk (11). The most common genotypes were HPV-16, 58, 33, 52, 66, and 56. Thirteen patients had co-integration involving mainly HPV-16 and 58. The frequency of HPV gene disruption was higher in L1 and E1 genes than in other regions of the viral genomes. CONCLUSION Some 56.6% of CIN lesions in Qingdao had HPV integrations, and 67.2% of HPV-integrated patients were HPV-16 and 58, more prone to be integrated in younger patients below 45 years old. There exist preferential sites for HPV-16 and HPV-58 integration, and they are more likely to be disrupted in the L1 and E1 loci.
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Affiliation(s)
- Li Wang
- Qingdao University Medical College, Qingdao, China.
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