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Cao C, Xu Q, Zhu Z, Xu M, Wei Y, Lin S, Cheng S, Zhi W, Hong P, Huang X, Lin D, Cao G, Meng Y, Wu P, Peng T, Wei J, Ding W, Huang X, Sung W, Chen G, Ma D, Li G, Wu P. Three-dimensional chromatin analysis reveals Sp1 as a mediator to program and reprogram HPV-host epigenetic architecture in cervical cancer. Cancer Lett 2024; 588:216809. [PMID: 38471646 DOI: 10.1016/j.canlet.2024.216809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
Human papillomavirus (HPV) is predominantly associated with HPV-related cancers, however, the precise mechanisms underlying the HPV-host epigenetic architectures in HPV carcinogenesis remain elusive. Here, we employed high-throughput chromosome conformation capture (Hi-C) to comprehensively map HPV16/18-host chromatin interactions. Our study identified the transcription factor Sp1 as a pivotal mediator in programming HPV-host interactions. By targeting Sp1, the active histone modifications (H3K27ac, H3K4me1, and H3K4me3) and the HPV-host chromatin interactions are reprogrammed, which leads to the downregulation of oncogenes located near the integration sites in both HPV (E6/E7) and the host genome (KLF5/MYC). Additionally, Sp1 inhibition led to the upregulation of immune checkpoint genes by reprogramming histone modifications in host cells. Notably, humanized patient-derived xenograft (PDX-HuHSC-NSG) models demonstrated that Sp1 inhibition promoted anti-PD-1 immunotherapy via remodeling the tumor immune microenvironment in cervical cancer. Moreover, single-cell transcriptomic analysis validated the enrichment of transcription factor Sp1 in epithelial cells of cervical cancer. In summary, our findings elucidate Sp1 as a key mediator involved in the programming and reprogramming of HPV-host epigenetic architecture. Inhibiting Sp1 with plicamycin may represent a promising therapeutic option for HPV-related carcinoma.
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Affiliation(s)
- Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Zhixian Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ye Wei
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Wenhua Zhi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xingyu Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Da Lin
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yifan Meng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juncheng Wei
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyuan Huang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - WingKin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China; School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore
| | - Gang Chen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 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, China; National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Sastre-Garau X, Estrada-Virrueta L, Radvanyi F. HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas. Cancers (Basel) 2024; 16:1584. [PMID: 38672666 PMCID: PMC11048798 DOI: 10.3390/cancers16081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
In HPV-associated carcinomas, some examples of cancer-related genes altered by viral insertion and corresponding to potential therapeutic targets have been described, but no quantitative assessment of these events, including poorly recurrent targets, has been reported to date. To document these occurrences, we built and analyzed a database comprised of 1455 cases, including HPV genotypes and tumor localizations. Host DNA sequences targeted by viral integration were classified as "non-recurrent" (one single reported case; 838 loci), "weakly recurrent" (two reported cases; 82 loci), and highly recurrent (≥3 cases; 43 loci). Whereas the overall rate of cancer-related target genes was 3.3% in the Gencode database, this rate increased to 6.5% in "non-recurrent", 11.4% in "weakly recurrent", and 40.1% in "highly recurrent" genes targeted by integration (p = 4.9 × 10-4). This rate was also significantly higher in tumors associated with high-risk HPV16/18/45 than other genotypes. Among the genes targeted by HPV insertion, 30.2% corresponded to direct or indirect druggable targets, a rate rising to 50% in "highly recurrent" targets. Using data from the literature and the DepMap 23Q4 release database, we found that genes targeted by viral insertion could be new candidates potentially involved in HPV-associated oncogenesis. A more systematic characterization of HPV/host fusion DNA sequences in HPV-associated cancers should provide a better knowledge of HPV-driven carcinogenesis and favor the development of personalize patient treatments.
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Affiliation(s)
- Xavier Sastre-Garau
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, 94010 Créteil, France
| | - Lilia Estrada-Virrueta
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
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Guo T, Zamuner F, Ting S, Chen L, Rooper L, Tamayo P, Fakhry C, Gaykalova D, Mehra R. Clinical and genomic characterization of chemoradiation-resistant HPV-positive oropharyngeal squamous cell carcinoma. Front Oncol 2024; 14:1336577. [PMID: 38505587 PMCID: PMC10949886 DOI: 10.3389/fonc.2024.1336577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/25/2024] [Indexed: 03/21/2024] Open
Abstract
Introduction Most patients with HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) have an excellent response to chemoradiation, and trials are now investigating de-escalated treatment. However, up to 25% of patients with HPV-positive OPSCC will experience recurrence, and up to 5% will even progress through primary treatment. Currently, there are no molecular markers to identify patients with poor prognosis who would be harmed by de-escalation. Herein we report the clinical and genomic characteristics of persistent HPV-positive OPSCC after definitive platinum-based chemoradiation therapy. Methods Patients with HPV-positive OPSCC treated with curative intent platinum-based chemoradiation between 2007 and 2017 at two institutions and with a persistent locoregional disease were included. We evaluated clinical characteristics, including smoking status, age, stage, treatment, and overall survival. A subset of five patients had tissue available for targeted exome DNA sequencing and RNA sequencing. Genomic analysis was compared to a previously published cohort of 47 treatment-responsive HPV+ OPSCC tumors after batch correction. Mutational landscape, pathway activation, and OncoGPS tumor states were employed to characterize these tumors. Results Ten patients met the inclusion criteria. The tumor and nodal stages ranged from T1 to T4 and N1 to N2 by AJCC 8th edition staging. All patients were p16-positive by immunohistochemistry, and eight with available in situ hybridization were confirmed to be HPV-positive. The 1-year overall survival from the time of diagnosis was 57%, and the 2-year overall survival was 17%. TP53 mutations were present in three of five (60%) persistent tumors compared to 2% (one of 47) of treatment-responsive HPV-positive tumors (p = 0.008). Other genes with recurrent mutations in persistent HPV-positive OPSCC tumors were NF1, KMT2D, PIK3C2B, and TFGBR2. Compared to treatment-responsive HPV-positive tumors, persistent tumors demonstrated activation of DNA Repair and p53, EMT, MYC, SRC, and TGF-beta signaling pathways, with post-treatment samples demonstrating significant activation of the PI3K-EMT-Stem pathways compared to pretreatment samples. Conclusion Chemoradiation-resistant HPV-positive OPSCC occurs infrequently but portends a poor prognosis. These tumors demonstrate higher rates of p53 mutation and activation of MYC, SRC, and TGF-beta pathways. A comparison of tumors before and after treatment demonstrates PI3K-EMT-Stem pathways post-treatment in HPV-positive tumors with persistent disease after platinum-based chemoradiation.
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Affiliation(s)
- Theresa Guo
- Department of Otolaryngology, Moores Cancer Center, University of California, San Diego, San Diego, CA, United States
| | - Fernando Zamuner
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Stephanie Ting
- Department of Medicine, Division of Hematology-Oncology, University of California, San Diego, San Diego, CA, United States
| | - Liam Chen
- Division of Neuropathology, Department of Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Lisa Rooper
- Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, United States
| | - Pablo Tamayo
- Department of Medicine, Division of Hematology-Oncology, University of California, San Diego, San Diego, CA, United States
| | - Carole Fakhry
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Daria Gaykalova
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, United States
| | - Ranee Mehra
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Chihu-Amparan L, Pedroza-Saavedra A, Gutierrez-Xicotencatl L. The Immune Response Generated against HPV Infection in Men and Its Implications in the Diagnosis of Cancer. Microorganisms 2023; 11:1609. [PMID: 37375112 DOI: 10.3390/microorganisms11061609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Human papillomavirus (HPV) infection is associated with precancerous lesions and cancer of the genital tract both in women and men. The high incidence of cervical cancer worldwide focused the research on this infection mainly in women and to a lesser extent in men. In this review, we summarized epidemiological, immunological, and diagnostic data associated with HPV and cancer in men. We presented an overview of the main characteristics of HPV and infection in men that are associated with different types of cancer but also associated with male infertility. Men are considered important vectors of HPV transmission to women; therefore, identifying the sexual and social behavioral risk factors associated with HPV infection in men is critical to understand the etiology of the disease. It is also essential to describe how the immune response develops in men during HPV infection or when vaccinated, since this knowledge could help to control the viral transmission to women, decreasing the incidence of cervical cancer, but also could reduce other HPV-associated cancers among men who have sex with men (MSM). Finally, we summarized the methods used over time to detect and genotype HPV genomes, as well as some diagnostic tests that use cellular and viral biomarkers that were identified in HPV-related cancers.
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Affiliation(s)
- Lilia Chihu-Amparan
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
| | - Adolfo Pedroza-Saavedra
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
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Kusakabe M, Taguchi A, Tanikawa M, Hoshi D, Tsuchimochi S, Qian X, Toyohara Y, Kawata A, Wagatsuma R, Yamaguchi K, Yamamoto Y, Ikemura M, Sone K, Mori-Uchino M, Matsunaga H, Tsuruga T, Nagamatsu T, Kukimoto I, Wada-Hiraike O, Kawazu M, Ushiku T, Takeyama H, Oda K, Kawana K, Hippo Y, Osuga Y. Application of organoid culture from HPV18-positive small cell carcinoma of the uterine cervix for precision medicine. Cancer Med 2023; 12:8476-8489. [PMID: 36691316 PMCID: PMC10134306 DOI: 10.1002/cam4.5588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/27/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Small cell carcinoma of the uterine cervix (SCCC) is a rare and highly malignant human papillomavirus (HPV)-associated cancer in which human genes related to the integration site can serve as a target for precision medicine. The aim of our study was to establish a workflow for precision medicine of HPV-associated cancer using patient-derived organoid. METHODS Organoid was established from the biopsy of a patient diagnosed with HPV18-positive SCCC. Therapeutic targets were identified by whole exome sequencing (WES) and RNA-seq analysis. Drug sensitivity testing was performed using organoids and organoid-derived mouse xenograft model. RESULTS WES revealed that both the original tumor and organoid had 19 somatic variants in common, including the KRAS p.G12D pathogenic variant. Meanwhile, RNA-seq revealed that HPV18 was integrated into chromosome 8 at 8q24.21 with increased expression of the proto-oncogene MYC. Drug sensitivity testing revealed that a KRAS pathway inhibitor exerted strong anti-cancer effects on the SCCC organoid compared to a MYC inhibitor, which were also confirmed in the xenograft model. CONCLUSION In this study, we confirmed two strategies for identifying therapeutic targets of HPV-derived SCCC, WES for identifying pathogenic variants and RNA sequencing for identifying HPV integration sites. Organoid culture is an effective tool for unveiling the oncogenic process of rare tumors and can be a breakthrough for the development of precision medicine for patients with HPV-positive SCCC.
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Affiliation(s)
- Misako Kusakabe
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ayumi Taguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Hoshi
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Saki Tsuchimochi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Xi Qian
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Toyohara
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Kawata
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,CBBD-OIL, AIST-Waseda University, Tokyo, Japan
| | - Kohei Yamaguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mayuyo Mori-Uchino
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Tetsushi Tsuruga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,CBBD-OIL, AIST-Waseda University, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Katsutoshi Oda
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Nihon University School of Medicine, Tokyo, Japan
| | - Yoshitaka Hippo
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Wang C, Bai R, Liu Y, Wang K, Wang Y, Yang J, Cai H, Yang P. Multi-region sequencing depicts intratumor heterogeneity and clonal evolution in cervical cancer. Med Oncol 2023; 40:78. [PMID: 36635412 DOI: 10.1007/s12032-022-01942-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/24/2022] [Indexed: 01/13/2023]
Abstract
Cervical cancer is a heterogeneous malignancy mainly caused by human papillomavirus (HPV). While a few studies have revealed heterogeneity of cervical cancer in chromosome levels, the correlation between genetic heterogeneity and HPV integration in cervical cancer remains unknown. Here, we applied multi-region whole-exome sequencing and HPV integration analysis to explore intratumor heterogeneity in cervical cancer. We sequenced 20 tumor regions and 5 adjacent normal tissues from 5 cervical cancer patients, analysis based on somatic mutations and somatic copy number alterations (SCNAs) levels were performed. Variable heterogeneity was observed between the five patients with different tumor stages and HPV infection statuses. We found HPV integration has a positive effect on somatic mutation burden, but the relation to SCNAs remains unclear. Frequently mutated genes in cervical cancer were identified as trunk events, such as FBXW7, PIK3CA, FAT1 in somatic mutations and TP63, MECOM, PIK3CA, TBL1XR1 in SCNAs. New potential driver genes in cervical cancer were summarized including POU2F2, TCF7 and UBE2A. The SCNAs level has potential relation with tumor stage, and Signature 3 related to homologous recombination deficiency may be the appropriate biomarker in advanced cervical cancer. Mutation signature analysis also revealed a potential pattern that APOBEC-associated signature occurs in early stage and signatures associated with DNA damage repair arise at the later stage of cervical cancer evolution. In a conclusion, our study provides insights into the potential relationship between HPV infection and tumor heterogeneity. Those results enhanced our understanding of tumorigenesis and progression in cervical cancer.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Rui Bai
- Department of Obstetrics and Gynecology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, 832008, China
| | - Yu Liu
- Department of Obstetrics and Gynecology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, 832008, China
| | - Kun Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yu Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jian Yang
- Key Laboratory of Bio-Resources and Eco-Environment, Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Haoyang Cai
- Key Laboratory of Bio-Resources and Eco-Environment, Center of Growth, Metabolism, and Aging, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
| | - Ping Yang
- Department of Obstetrics and Gynecology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, 832008, China.
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8
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Prakasam G, Iqbal MA, Srivastava A, Bamezai RNK, Singh RK. HPV18 oncoproteins driven expression of PKM2 reprograms HeLa cell metabolism to maintain aerobic glycolysis and viability. Virusdisease 2022; 33:223-235. [PMID: 36277414 PMCID: PMC9481809 DOI: 10.1007/s13337-022-00776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Abstract
The molecular basis of human papillomavirus (HPV)-mediated cellular immortalization and malignant transformation has illustrated an indispensable role of viral E6/E7-oncoproteins. However, the impact of viral-oncoproteins on the metabolic phenotype of cancer cells remains ambiguous. We showed silencing of HPV18-encoded E6/E7-oncoprotein significantly reduced glucose consumption, lactate production, ATP level and viability. Silencing of HPV18-encoded E6/E7 in HeLa cells significantly down-regulated expression and activity of HK1, HK2, LDHA, and LDHB. Interestingly, there was an increased pyruvate kinase activity due to switch in expression from PKM2 isoform to PKM1. The switch in favor of alternatively spliced isoform PKM1, was regulated by viral-E6/E7-oncoprotein by inhibiting the c-Myc/hnRNP-axis. Further, the near absence of the PKM1 protein despite an adequate amount of PKM1 mRNA in HeLa cells was due to its proteasomal degradation. Our results suggests HPV18-encoded E6/E7 driven preferential expression of PKM2 is essential to support aerobic glycolysis and cell proliferation. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-022-00776-w.
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Affiliation(s)
- Gopinath Prakasam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Mohammad Askandar Iqbal
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, 110025 India
| | - Anusha Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Rameshwar N. K. Bamezai
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
- Delhi School of Public Health, University of Delhi, New Delhi, 110007 India
| | - Rajnish Kumar Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
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9
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Läsche M, Gallwas J, Gründker C. Like Brothers in Arms: How Hormonal Stimuli and Changes in the Metabolism Signaling Cooperate, Leading HPV Infection to Drive the Onset of Cervical Cancer. Int J Mol Sci 2022; 23:ijms23095050. [PMID: 35563441 PMCID: PMC9103757 DOI: 10.3390/ijms23095050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/06/2023] Open
Abstract
Despite all precautionary actions and the possibility of using vaccinations to counteract infections caused by human papillomaviruses (HPVs), HPV-related cancers still account for approximately 5% of all carcinomas. Worldwide, many women are still excluded from adequate health care due to their social position and origin. Therefore, immense efforts in research and therapy are still required to counteract the challenges that this disease entails. The special thing about an HPV infection is that it is not only able to trick the immune system in a sophisticated way, but also, through genetic integration into the host genome, to use all the resources available to the host cells to complete the replication cycle of the virus without activating the alarm mechanisms of immune recognition and elimination. The mechanisms utilized by the virus are the metabolic, immune, and hormonal signaling pathways that it manipulates. Since the virus is dependent on replication enzymes of the host cells, it also intervenes in the cell cycle of the differentiating keratinocytes and shifts their terminal differentiation to the uppermost layers of the squamocolumnar transformation zone (TZ) of the cervix. The individual signaling pathways are closely related and equally important not only for the successful replication of the virus but also for the onset of cervical cancer. We will therefore analyze the effects of HPV infection on metabolic signaling, as well as changes in hormonal and immune signaling in the tumor and its microenvironment to understand how each level of signaling interacts to promote tumorigenesis of cervical cancer.
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10
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Haręża DA, Wilczyński JR, Paradowska E. Human Papillomaviruses as Infectious Agents in Gynecological Cancers―Oncogenic Properties of Viral Proteins. Int J Mol Sci 2022; 23:ijms23031818. [PMID: 35163748 PMCID: PMC8836588 DOI: 10.3390/ijms23031818] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 01/25/2023] Open
Abstract
Human papillomaviruses (HPVs), which belong to the Papillomaviridae family, constitute a group of small nonenveloped double-stranded DNA viruses. HPV has a small genome that only encodes a few proteins, and it is also responsible for 5% of all human cancers, including cervical, vaginal, vulvar, penile, anal, and oropharyngeal cancers. HPV types may be classified as high- and low-risk genotypes (HR-HPVs and LR-HPVs, respectively) according to their oncogenic potential. HR-HPV 16 and 18 are the most common types worldwide and are the primary types that are responsible for most HPV-related cancers. The activity of the viral E6 and E7 oncoproteins, which interfere with critical cell cycle points such as suppressive tumor protein p53 (p53) and retinoblastoma protein (pRB), is the major contributor to HPV-induced neoplastic initiation and progression of carcinogenesis. In addition, the E5 protein might also play a significant role in tumorigenesis. The role of HPV in the pathogenesis of gynecological cancers is still not fully understood, which indicates a wide spectrum of potential research areas. This review focuses on HPV biology, the distribution of HPVs in gynecological cancers, the properties of viral oncoproteins, and the molecular mechanisms of carcinogenesis.
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Affiliation(s)
- Daria A. Haręża
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 93-232 Lodz, Poland;
- BioMedChem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, 90-237 Lodz, Poland
| | - Jacek R. Wilczyński
- Department of Surgical and Oncological Gynecology, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 93-232 Lodz, Poland;
- Correspondence: ; Tel.: +48-42-272-3629; Fax: +48-42-272-3630
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11
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Gameiro SF, Evans AM, Mymryk JS. The tumor immune microenvironments of HPV + and HPV - head and neck cancers. WIREs Mech Dis 2022; 14:e1539. [PMID: 35030304 DOI: 10.1002/wsbm.1539] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Human papillomaviruses (HPVs) are the etiological agent of a significant, and increasing, fraction of head and neck squamous cell carcinomas (HNSCC)-a heterogenous group of malignancies in the head and neck region. HPV infection accounts for approximately 25% of all cases, with the remainder typically caused by smoking and excessive alcohol consumption. These distinct etiologies lead to profound clinical and immunological differences between HPV-positive (HPV+ ) and HPV-negative (HPV- ) HNSCC, likely related to the expression of exogenous viral antigens in the HPV+ subtype. Specifically, HPV+ HNSCC patients generally exhibit better treatment response compared to those with HPV- disease, leading to a more favorable prognosis, with lower recurrence rate, and longer overall survival time. Importantly, a plethora of studies have illustrated that the tumor immune microenvironment (TIME) of HPV+ HNSCC has a strikingly distinct immune composition to that of its HPV- counterpart. The HPV+ TIME is characterized as being immunologically "hot," with more immune infiltration, higher levels of T-cell activation, and higher levels of immunoregulation compared to the more immunologically "cold" HPV- TIME. In general, cancers with an immune "hot" TIME exhibit better treatment response and superior clinical outcomes in comparison to their immune "cold" counterparts. Indeed, this phenomenon has also been observed in HPV+ HNSCC patients, highlighting the critical role of the TIME in influencing prognosis, and further validating the use of cancer therapies that capitalize on the mobilization and/or modulation of the TIME. This article is categorized under: Cancer > Molecular and Cellular Physiology Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Steven F Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Andris M Evans
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada.,Department of Otolaryngology, The University of Western Ontario, London, Ontario, Canada.,Department of Oncology, The University of Western Ontario, London, Ontario, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, Ontario, Canada
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12
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Ribera-Cortada I, Guerrero-Pineda J, Trias I, Veloza L, Garcia A, Marimon L, Diaz-Mercedes S, Alamo JR, Rodrigo-Calvo MT, Vega N, López Del Campo R, Parra-Medina R, Ajami T, Martínez A, Reig O, Ribal MJ, Corral-Molina JM, Jares P, Ordi J, Rakislova N. Pathogenesis of Penile Squamous Cell Carcinoma: Molecular Update and Systematic Review. Int J Mol Sci 2021; 23:251. [PMID: 35008677 DOI: 10.3390/ijms23010251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022] Open
Abstract
Penile squamous cell carcinoma (PSCC) is a rare but aggressive neoplasm with dual pathogenesis (human papillomavirus (HPV)-associated and HPV-independent). The development of targeted treatment is hindered by poor knowledge of the molecular landscape of PSCC. We performed a thorough review of genetic alterations of PSCC focused on somatic mutations and/or copy number alterations. A total of seven articles have been identified which, overall, include 268 PSCC. However, the series are heterogeneous regarding methodologies employed for DNA sequencing and HPV detection together with HPV prevalence, and include, in general, a limited number of cases, which results in markedly different findings. Reported top-ranked mutations involve TP53, CDKN2A, FAT1, NOTCH-1 and PIK3CA. Numerical alterations involve gains in MYC and EGFR, as well as amplifications in HPV integration loci. A few genes including TP53, CDKN2A, PIK3CA and CCND1 harbor both somatic mutations and copy number alterations. Notch, RTK-RAS and Hippo pathways are frequently deregulated. Nevertheless, the relevance of the identified alterations, their role in signaling pathways or their association with HPV status remain elusive. Combined targeting of different pathways might represent a valid therapeutic approach in PSCC. This work calls for large-scale sequencing studies with robust HPV testing to improve the genomic understanding of PSCC.
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13
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Symer DE, Akagi K, Geiger HM, Song Y, Li G, Emde AK, Xiao W, Jiang B, Corvelo A, Toussaint NC, Li J, Agrawal A, Ozer E, El-Naggar AK, Du Z, Shewale JB, Stache-Crain B, Zucker M, Robine N, Coombes KR, Gillison ML. Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers. Genome Res 2021; 32:55-70. [PMID: 34903527 PMCID: PMC8744672 DOI: 10.1101/gr.275911.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022]
Abstract
Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes. The HPV oncoproteins E6 and E7 are necessary but insufficient for cancer formation, indicating that additional secondary genetic events are required. Here, we investigate potential oncogenic impacts of virus integration. Analysis of 105 HPV-positive oropharyngeal cancers by whole-genome sequencing detects virus integration in 77%, revealing five statistically significant sites of recurrent integration near genes that regulate epithelial stem cell maintenance (i.e., SOX2, TP63, FGFR, MYC) and immune evasion (i.e., CD274). Genomic copy number hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with their local density. The frequency of genes expressed at extreme outlier levels is increased 86-fold within ±150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute to carcinogenesis in a large majority of HPV-positive oropharyngeal cancers by inducing extensive disruption of host genome structure and gene expression.
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Affiliation(s)
- David E Symer
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Keiko Akagi
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Yang Song
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gaiyun Li
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Weihong Xiao
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Bo Jiang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - André Corvelo
- New York Genome Center, New York, New York 10013, USA
| | | | - Jingfeng Li
- Division of Medical Oncology, Department of Internal Medicine, Ohio State University, Columbus, Ohio 43210, USA
| | - Amit Agrawal
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Enver Ozer
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Adel K El-Naggar
- Division of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zoe Du
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jitesh B Shewale
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Mark Zucker
- Department of Biomedical Informatics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | | | - Kevin R Coombes
- Department of Biomedical Informatics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Maura L Gillison
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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14
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Spiotto MT, Taniguchi CM, Klopp AH, Colbert LE, Lin SH, Wang L, Frederick MJ, Osman AA, Pickering CR, Frank SJ. Biology of the Radio- and Chemo-Responsiveness in HPV Malignancies. Semin Radiat Oncol 2021; 31:274-285. [PMID: 34455983 DOI: 10.1016/j.semradonc.2021.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In multiple anatomic sites, patients with cancers associated with the Human Papillomavirus (HPV) experience better locoregional control and overall survival after radiotherapy and/or chemoradiotherapy than patients with HPV-negative cancers. These improved outcomes suggest that relatively unique biological features in HPV-positive cancers may increase sensitivity to DNA damaging agents as well as an impaired DNA damage response. This review will address potential biological mechanisms driving this increased sensitivity of HPV-positive cancer to radiation and/or chemotherapy. This review will discuss the clinical and preclinical observations that support the intrinsic radiosensitivity and/or chemosensitivity of HPV-positive cancers. Furthermore, this review will highlight the molecular mechanisms for increased radiation sensitivity using the classical "4 Rs" of radiobiology: repair, reassortment, repopulation, and reoxygenation. First, HPV-positive cancers have increased DNA damage due to increased oxidative stress and impaired DNA damage repair due to the altered activity TP53, p16, TIP60, and other repair proteins. Second, irradiated HPV-positive cancer cells display increased G2/M arrest leading to reassortment of cancer cells in more radiosensitive phases of the cell cycle. In addition, HPV-positive cancers have less radioresistant cancer stem cell subpopulations that may limit their repopulation during radiotherapy. Finally, HPV-positive cancers may also have less hypoxic tumor microenvironments that make these cancers more sensitive to radiation than HPV-negative cells. We will also discuss extrinsic immune and microenvironmental factors enriched in HPV-positive cancers that facilities responses to radiation. Therefore, these potential biological mechanisms may underpin the improved clinical outcomes often observed in these virally induced cancers.
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Affiliation(s)
- Michael T Spiotto
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX.
| | - Cullen M Taniguchi
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Li Wang
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | | | - Abdullah A Osman
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - Steven J Frank
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX
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15
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McEllin B, Searle BC, DePledge L, Sun G, Cobbs C, Karimi M. Detection of Human Papillomavirus Integration in Brain Metastases from Oropharyngeal Tumors by Targeted Sequencing. Viruses 2021; 13:1536. [PMID: 34452401 DOI: 10.3390/v13081536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus (HPV) positive and negative head and neck squamous cell carcinoma (HNSCC) are known to have differential phenotypes, including the incidence and location of metastases. HPV positive (HPV+) HNSCC are more likely to metastasize to distant sites, such as the lung, brain, and skin. Among these locations, metastasis to the brain is a rare event, and little is known about specific risk factors for this phenotype. In this report, we describe two patients who developed brain metastases from HNSCC. Both patient tumors had p16INK4a overexpression, suggesting these tumors were HPV+. This was confirmed after PCR, in situ hybridization, and mass spectrometry detected the presence of HPV type 16 (HPV16) DNA, RNA and protein. To further characterize the presence of HPV16, we used a target enrichment strategy on tumor DNA and RNA to isolate the viral sequences from the brain metastases. Analysis by targeted next generation sequencing revealed that both tumors had the HPV genome integrated into the host genome at known hotspots, 8q24.21 and 14q24.1. Applying a similar target enrichment strategy to a larger cohort of HPV+ HNSCC brain metastases could help to identify biomarkers that can predict metastasis and/or identify novel therapeutic options.
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16
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Groves IJ, Drane ELA, Michalski M, Monahan JM, Scarpini CG, Smith SP, Bussotti G, Várnai C, Schoenfelder S, Fraser P, Enright AJ, Coleman N. Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis. PLoS Pathog 2021; 17:e1009875. [PMID: 34432858 PMCID: PMC8439666 DOI: 10.1371/journal.ppat.1009875] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/14/2021] [Accepted: 08/07/2021] [Indexed: 12/26/2022] Open
Abstract
Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art 'HPV integrated site capture' (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a 'looping' mechanism by which flanking host regions become amplified. Furthermore, using our 'HPV16-specific Region Capture Hi-C' technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a 'cancer-causing gene' is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.
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Affiliation(s)
- Ian J. Groves
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Emma L. A. Drane
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marco Michalski
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jack M. Monahan
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Cinzia G. Scarpini
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen P. Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Giovanni Bussotti
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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17
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Weeramange CE, Liu Z, Hartel G, Li Y, Vasani S, Langton-Lockton J, Kenny L, Morris L, Frazer I, Tang KD, Punyadeera C. Salivary High-Risk Human Papillomavirus DNA as a Biomarker for Human Papillomavirus-Driven Head and Neck Cancers. J Mol Diagn 2021; 23:1334-1342. [PMID: 34325059 DOI: 10.1016/j.jmoldx.2021.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022] Open
Abstract
High-risk human papillomavirus (HR-HPV) infection is a major risk factor of head and neck cancers (HNCs). Despite the rising prevalence of HPV-driven HNC (HPV-HNC), biomarkers for detection, prognostication, and disease monitoring are lacking. To evaluate the capacity of salivary HR-HPV DNA as a biomarker of HPV-HNC, the salivary HR-HPV statuses of 491 and 10 patients with primary and recurrent HNC, respectively, were determined at diagnosis, using quantitative real-time PCR, with tumor cyclin-dependent kinase inhibitor 2A (p16) expression determined by IHC analysis. Patients with oropharyngeal cancer (OPC) (n = 215) were followed up for ≤5 years. Survival characteristics were evaluated in terms of event-free and cause-specific survival. Of the primary-HNC cohort, 43.2% were positive for salivary HR-HPV DNA, with most having OPC. Salivary HR-HPV DNA was detected in 81.4% of tumor p16-positive OPC patients at diagnosis. Prognosis in salivary HR-HPV-positive OPC patients was favorable compared with that in salivary HR-HPV-negative patients (event-free survival, hazard ratio = 0.42 [95% CI, 0.21-0.81, P = 0.010]; cause-specific survival, hazard ratio = 0.39 [95% CI, 0.18-0.86, P = 0.019]). In the recurrent-HNC cohort, salivary HR-HPV DNA was detected in 83.3% of those who previously had tumor p16-positive HNC. These findings indicate that this liquid biopsy-based, noninvasive biomarker could be essential in the detection and management of HPV-HNC.
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Affiliation(s)
- Chameera E Weeramange
- Saliva & Liquid Biopsy Translational Laboratory, Faculty of Health, School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia; Translational Research Institute, Brisbane, Queensland, Australia; Department of Medical Laboratory Sciences, Faculty of Health Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Zhen Liu
- Department of Otolaryngology, The University of Queensland, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Gunter Hartel
- Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yinan Li
- Saliva & Liquid Biopsy Translational Laboratory, Faculty of Health, School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia; Translational Research Institute, Brisbane, Queensland, Australia
| | - Sarju Vasani
- Department of Otolaryngology, The University of Queensland, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Julian Langton-Lockton
- Metro-North Sexual Health and HIV Service, Metro North Health, Brisbane, Queensland, Australia
| | - Lizbeth Kenny
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; Central Integrated Regional Cancer Service, Queensland Health, Brisbane, Queensland, Australia
| | - Luc Morris
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ian Frazer
- Translational Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Kai D Tang
- Saliva & Liquid Biopsy Translational Laboratory, Faculty of Health, School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia; Translational Research Institute, Brisbane, Queensland, Australia.
| | - Chamindie Punyadeera
- Saliva & Liquid Biopsy Translational Laboratory, Faculty of Health, School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia; Translational Research Institute, Brisbane, Queensland, Australia.
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18
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Aldersley J, Lorenz DR, Mouw KW, D'Andrea AD, Gabuzda D. Genomic Landscape of Primary and Recurrent Anal Squamous Cell Carcinomas in Relation to HPV Integration, Copy-Number Variation, and DNA Damage Response Genes. Mol Cancer Res 2021; 19:1308-1321. [PMID: 33883185 DOI: 10.1158/1541-7786.mcr-20-0884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/02/2021] [Accepted: 04/16/2021] [Indexed: 12/26/2022]
Abstract
The incidence of anal squamous cell carcinoma (ASCC) has been increasing, particularly in populations with HIV. Human papillomavirus (HPV) is the causal factor in 85% to 90% of ASCCs, but few studies evaluated HPV genotypes and integrations in relation to genomic alterations in ASCC. Using whole-exome sequence data for primary (n = 56) and recurrent (n = 31) ASCC from 72 patients, we detected HPV DNA in 87.5% of ASCC, of which HPV-16, HPV-18, and HPV-6 were detected in 56%, 22%, and 33% of HIV-positive (n = 9) compared with 83%, 3.2%, and 1.6% of HIV-negative cases (n = 63), respectively. Recurrent copy-number variations (CNV) involving genes with documented roles in cancer included amplification of PI3KCA and deletion of APC in primary and recurrent tumors; amplifications of CCND1, MYC, and NOTCH1 and deletions of BRCA2 and RB1 in primary tumors; and deletions of ATR, FANCD2, and FHIT in recurrent tumors. DNA damage response genes were enriched among recurrently deleted genes in recurrent ASCCs (P = 0.001). HPV integrations were detected in 29 of 76 (38%) ASCCs and were more frequent in stage III-IV versus stage I-II tumors. HPV integrations were detected near MYC and CCND1 amplifications and recurrent targets included NFI and MUC genes. These results suggest HPV genotypes in ASCC differ by HIV status, HPV integration is associated with ASCC progression, and DNA damage response genes are commonly disrupted in recurrent ASCCs. IMPLICATIONS: These data provide the largest whole-exome sequencing study of the ASCC genomic landscape to date and identify HPV genotypes, integrations, and recurrent CNVs in primary or recurrent ASCCs.
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Affiliation(s)
- Jordan Aldersley
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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19
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Sastre-Garau X, Harlé A. Pathology of HPV-Associated Head and Neck Carcinomas: Recent Data and Perspectives for the Development of Specific Tumor Markers. Front Oncol 2020; 10:528957. [PMID: 33312940 PMCID: PMC7701329 DOI: 10.3389/fonc.2020.528957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022] Open
Abstract
A significant subset of carcinomas developed in the head and neck (H&NCs) are associated with specific human papillomaviruses (HPV) genotypes. In particular, 40–60% of oropharyngeal carcinoma cases are linked to HPV. Epidemiological studies have demonstrated that HPV oral infections are predominantly sexually transmitted and are more frequent among men (10–18%) than women (3.6–8.8%). Although there is a large diversity of HPV genotypes associated with H&NCs, HPV16 lineage represents 83% of the reported cases. The prognostic value of HPV as a biological parameter is well recognized. However, the use of HPV DNA as a diagnostic and/or predictive marker is not fully developed. Recent data reporting the physical state of the HPV genome in tumors have shown that HPV DNA integration into the tumor cell genome could lead to the alteration of cellular genes implicated in oncogenesis. Most importantly, HPV DNA corresponds to a tumor marker that can be detected in the blood of patients. Profile of the HPV DNA molecular patterns in tumor cells using New Genome Sequencing-based technologies, allows the identification of highly specific tumor markers valuable for the development of innovative diagnostic and therapeutic approaches. This review will summarize recent epidemiological data concerning HPV-associated H&NCs, the genomic characterization of these tumors, including the presence of HPV DNA in tumor cells, and will propose perspectives for developing improved care of patients with HPV-associated H&NCs, based on the use of viral sequences as personalized tumor markers and, over the longer term, as a therapeutic target.
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Affiliation(s)
- Xavier Sastre-Garau
- Service de Pathologie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR7039 CRAN, service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
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20
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Zheng Y, Dubois W, Benham C, Batchelor E, Levens D. FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells. Commun Biol 2020; 3:545. [PMID: 33005010 PMCID: PMC7530719 DOI: 10.1038/s42003-020-01264-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/01/2020] [Indexed: 11/24/2022] Open
Abstract
Physiologically, MYC levels must be precisely set to faithfully amplify the transcriptome, but in cancer MYC is quantitatively misregulated. Here, we study the variation of MYC amongst single primary cells (B-cells and murine embryonic fibroblasts, MEFs) for the repercussions of variable cellular MYC-levels and setpoints. Because FUBPs have been proposed to be molecular “cruise controls” that constrain MYC expression, their role in determining basal or activated MYC-levels was also examined. Growing cells remember low and high-MYC setpoints through multiple cell divisions and are limited by the same expression ceiling even after modest MYC-activation. High MYC MEFs are enriched for mRNAs regulating inflammation and immunity. After strong stimulation, many cells break through the ceiling and intensify MYC expression. Lacking FUBPs, unstimulated MEFs express levels otherwise attained only with stimulation and sponsor MYC chromatin changes, revealed by chromatin marks. Thus, the FUBPs enforce epigenetic setpoints that restrict MYC expression. Ying Zheng et al. characterize MYC gene and protein expression in single mammalian cells in response to various external signals. They find that individual cells show either high or low basal MYC expression setpoints, and that adherence to these setpoints as well as the magnitude of the response of MYC to stimulation, is controlled by FUBP1 and FUBP2.
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Affiliation(s)
- Ying Zheng
- Lab of Pathology, National Cancer Institutes, Bethesda, MD, USA
| | - Wendy Dubois
- Lab of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institutes, Bethesda, MD, USA
| | - Craig Benham
- Biomedical Engineering, University of California, Davis, CA, USA
| | - Eric Batchelor
- Masonic Cancer Center and Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - David Levens
- Lab of Pathology, National Cancer Institutes, Bethesda, MD, USA.
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21
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Cao C, Hong P, Huang X, Lin D, Cao G, Wang L, Feng B, Wu P, Shen H, Xu Q, Ren C, Meng Y, Zhi W, Yu R, Wei J, Ding W, Tian X, Zhang Q, Li W, Gao Q, Chen G, Li K, Sung WK, Hu Z, Wang H, Li G, Wu P. HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. J Genet Genomics 2020; 47:437-450. [PMID: 33023834 DOI: 10.1016/j.jgg.2020.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Integration of human papillomavirus (HPV) DNA into the human genome is a reputed key driver of cervical cancer. However, the effects of HPV integration on chromatin structural organization and gene expression are largely unknown. We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19. We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome, RNA, chromatin immunoprecipitation and high-throughput chromosome conformation capture (Hi-C) sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis. Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities, with correlation found between three-dimensional (3D) structural change and gene expression. Importantly, HPV integration divided one topologically associated domain (TAD) into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106, with a decrease in PEG3 expression and an increase in CCDC106 expression. This expression dysregulation was further confirmed using 10 samples from our cohort, which exhibited the same HPV-CCDC106 integration. In summary, we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling. Thus, this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.
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Affiliation(s)
- Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; 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
| | - Xingyu Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; 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
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liming Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Bei Feng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Hui Shen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; 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
| | - Ci Ren
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Yifan Meng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Wenhua Zhi
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Ruidi Yu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Juncheng Wei
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Wei Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Qinglei Gao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Gang Chen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China
| | - Kezhen Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, 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 Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Zheng Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Gynecological Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; 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.
| | - Peng Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, 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, China.
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22
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James CD, Morgan IM, Bristol ML. The Relationship between Estrogen-Related Signaling and Human Papillomavirus Positive Cancers. Pathogens 2020; 9:pathogens9050403. [PMID: 32455952 PMCID: PMC7281727 DOI: 10.3390/pathogens9050403] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
High risk-human papillomaviruses (HPVs) are known carcinogens. Numerous reports have linked the steroid hormone estrogen, and the expression of estrogen receptors (ERs), to HPV-related cancers, although the exact nature of the interactions remains to be fully elucidated. Here we will focus on estrogen signaling and describe both pro and potentially anti-cancer effects of this hormone in HPV-positive cancers. This review will summarize: (1) cell culture-related evidence, (2) animal model evidence, and (3) clinical evidence demonstrating an interaction between estrogen and HPV-positive cancers. This comprehensive review provides insights into the potential relationship between estrogen and HPV. We suggest that estrogen may provide a potential therapeutic for HPV-related cancers, however additional studies are necessary.
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Affiliation(s)
- Claire D. James
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
| | - Iain M. Morgan
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
- VCU Massey Cancer Center, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA
- Correspondence: (I.M.M.); (M.L.B.); Tel.: +1-804-628-3356 (M.L.B.)
| | - Molly L. Bristol
- School of Dentistry, Philips Institute for Oral Health Research, Virginia Commonwealth University (VCU), Richmond, VA 23298, USA;
- Correspondence: (I.M.M.); (M.L.B.); Tel.: +1-804-628-3356 (M.L.B.)
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23
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Macedo J, Silva E, Nogueira L, Coelho R, da Silva J, Dos Santos A, Teixeira-Júnior AA, Belfort M, Silva G, Khayat A, de Oliveira E, Dos Santos AP, Cavalli LR, Pereira SR. Genomic profiling reveals the pivotal role of hrHPV driving copy number and gene expression alterations, including mRNA downregulation of TP53 and RB1 in penile cancer. Mol Carcinog 2020; 59:604-617. [PMID: 32212199 DOI: 10.1002/mc.23185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
The incidence of penile cancer (PeCa) is increasing worldwide, however, the highest rates are reported in underdeveloped countries. The molecular mechanisms that underly the onset and progression of these tumors are still unclear. Therefore, our goal was to determine the genome-wide copy number alterations and the involvement of human papiloma virus (HPV) (TP53 and RB1), inflammatory (COX2 and EGFR), and PI3K/AKT pathway (AKT1, AKT2, EGFR, ERBB3, ERBB4, PIK3CA, and PTEN) associated genes in patients with PeCa from a high incidence region in Brazil (Maranhão). HPV genotyping was performed by nest-PCR and genome sequencing, copy number alterations (CNAs) by array comparative genomic hybridization and gene copy number status, gene, and protein expression by quantitative polymerase chain reaction, reverse transcriptase-quantitative polymerase chain reaction, and immunohistochemistry, respectively. HPV genotyping revealed one of the highest frequencies of HPV reported in PeCa, affecting 96.4% of the cases. The most common CNAs observed were located at the HPV integration sites, such as 2p12-p11.2 and 14q32.33, where ADAM 6, KIAA0125, LINC00226, LINC00221, and miR7641-2, are mapped. Increased copy number of ERBB3 and EGFR genes were observed in association with COX2 and EGFR overexpression, reinforcing the role of the inflammatory pathway in PeCa, and suggesting anti-EGFR and anti-COX2 inhibitors as promising therapies for PeCa. Additionally, TP53 and RB1 messenger RNA downregulation was observed, suggesting the occurrence of other mechanisms for repression of these oncoproteins, in addition to the canonical HPV/TP53/RB1 signaling pathway. Our data reinforce the role of epigenetic events in abnormal gene expression in HPV-associated carcinomas and suggest the pivotal role of HPV driving CNAs and controlling gene expression in PeCa.
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Affiliation(s)
- Juliana Macedo
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Elis Silva
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | | | - Ronald Coelho
- Aldenora Bello Cancer Hospital, São Luís, Maranhão, Brazil
| | - Jenilson da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Maranhão, Brazil.,Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Alcione Dos Santos
- Public Health Department, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | | | - Marta Belfort
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Gyl Silva
- Biology Undergraduate Course, Department of Pathology, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - André Khayat
- Oncology Research Center, Federal University of Pará, Belém, Pará, Brazil
| | - Edivaldo de Oliveira
- Tissue Culture and Cytogenetics Laboratory, Institute of Evandro Chagas, Belém, Pará, Brazil
| | - Ana Paula Dos Santos
- Department of Physiological Sciences, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Luciane R Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil.,Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia, United States
| | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Maranhão, Brazil
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24
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Gu Y, Lin X, Kapoor A, Chow MJ, Jiang Y, Zhao K, Tang D. The Oncogenic Potential of the Centromeric Border Protein FAM84B of the 8q24.21 Gene Desert. Genes (Basel) 2020; 11:genes11030312. [PMID: 32183428 PMCID: PMC7140883 DOI: 10.3390/genes11030312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
FAM84B is a risk gene in breast and prostate cancers. Its upregulation is associated with poor prognosis of prostate cancer, breast cancer, and esophageal squamous cell carcinoma. FAM84B facilitates cancer cell proliferation and invasion in vitro, and xenograft growth in vivo. The FAM84B and Myc genes border a 1.2 Mb gene desert at 8q24.21. Co-amplification of both occurs in 20 cancer types. Mice deficient of a 430 Kb fragment within the 1.2 Mb gene desert have downregulated FAM84B and Myc expressions concurrent with reduced breast cancer growth. Intriguingly, Myc works in partnership with other oncogenes, including Ras. FAM84B shares similarities with the H-Ras-like suppressor (HRASLS) family over their typical LRAT (lecithin:retinal acyltransferase) domain. This domain contains a catalytic triad, H23, H35, and C113, which constitutes the phospholipase A1/2 and O-acyltransferase activities of HRASLS1-5. These enzymatic activities underlie their suppression of Ras. FAM84B conserves H23 and H35 but not C113 with both histidine residues residing within a highly conserved motif that FAM84B shares with HRASLS1-5. Deletion of this motif abolishes FAM84B oncogenic activities. These properties suggest a collaboration of FAM84B with Myc, consistent with the role of the gene desert in strengthening Myc functions. Here, we will discuss recent research on FAM84B-derived oncogenic potential.
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Affiliation(s)
- Yan Gu
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mathilda Jing Chow
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yanzhi Jiang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Kuncheng Zhao
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- Correspondence: ; Tel.: +(905)-522-1155 (ext. 35168)
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Ferreira AR, Ramalho AC, Marques M, Ribeiro D. The Interplay between Antiviral Signalling and Carcinogenesis in Human Papillomavirus Infections. Cancers (Basel) 2020; 12:cancers12030646. [PMID: 32164347 PMCID: PMC7139948 DOI: 10.3390/cancers12030646] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Human papillomaviruses (HPV) are the causative agents of the most common sexually transmitted infection worldwide. While infection is generally asymptomatic and can be cleared by the host immune system, when persistence occurs, HPV can become a risk factor for malignant transformation. Progression to cancer is actually an unintended consequence of the complex HPV life cycle. Different antiviral defence mechanisms recognize HPV early in infection, leading to the activation of the innate immune response. However, the virus has evolved several specific strategies to efficiently evade the antiviral immune signalling. Here, we review and discuss the interplay between HPV and the host cell innate immunity. We further highlight the evasion strategies developed by different HPV to escape this cellular response and focus on the correlation with HPV-induced persistence and tumorigenesis.
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Affiliation(s)
| | | | | | - Daniela Ribeiro
- Correspondence: ; Tel.: +351-234-247 014; Fax: +351-234-372-587
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26
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Abstract
Myc is a crucial player in cellular proliferation and a known regulator of cancer pathobiology. Modulation of Myc expression targeting the Myc Protein-Protein Interactors (PPIs) like Myc-Max has till now been the most explored approach. However, this approach threatens the normal cells where Myc expression is required for proliferation. This demands the need for a new strategy to indirectly modulate Myc expression. Indirect modulation can be achieved by regulating Myc turnover. FBXW7 mediates the ubiquitination and subsequent degradation of Myc which is reversed by USP28. In this study, the interaction of USP28 with FBXW7 as well as with its substrate, Ubiquitin (Ub) were used as targets. Computation based high-throughput screening of bioactive small chemicals using molecular docking method was implemented to predict USP28 inhibitors. For the two regions, docking study with AutoDock Vina gave top 10 best scoring drugs which were identified and tabulated. The two regions defined in the study as FBXW7 binding and Ub binding also encompass the areas in which USP28 differed from USP25, a homologue with a different role. Out of these the best scoring drugs were explored for their role in cancer, if any. This study was performed keeping in mind re-purposing of these known drugs for possible alternative anti-Myc cancer therapy.
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Affiliation(s)
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India.
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, India.
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27
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Abstract
Human papillomavirus (HPV)-induced cervical cancer is a major health issue among women from the poorly/under-developed sectors of the world. It accounts for a high-mortality rate because of its late diagnosis and poor prognosis. Initial establishment and subsequent progression of this form of cancer are completely dependent on two major oncogenes E6 and E7, which are expressed constitutively leading to tumorigenesis. Thus, manipulation of these genes represents the most successful form of cervical cancer therapy. In the present article, information on structural, functional, and clinical dimensions of E6 and E7 activity has been reviewed. The genome organization and protein structure of E6 and E7 have been discussed followed by their mechanism to establish the six major cancer hallmarks in cervical tissues for tumor propagation. The later section of this review article deals with the different modes of therapeutics, which functions by deregulating E6 and E7 activity. Since E6 and E7 are the biomarkers of a cervical cancer cell and are the ones driving the cancer progression, therapeutic approaches targeting E6 and E7 have been proved to be highly efficient in terms of focused removal of abnormally propagating malignant cells. Therapeutics including different forms of vaccines to advanced genome editing techniques, which suppress E6 and E7 activity, have been found to successfully bring down the population of cervical cancer cells infected with HPV. T-cell mediated immunotherapy is another upcoming successful form of treatment to eradicate HPV-infected tumorigenic cells. Additionally, therapeutics using natural compounds from plants or other natural repositories, i.e., phytotherapeutic approaches have also been reviewed here, which prove their anticancer potential through E6 and E7 inhibitory effects. Thus, E6 and E7 repression through any of these methods is a significant approach toward cervical cancer therapy, described in details in this review along with an insight into the signaling pathways and molecular mechanistic of E6 and E7 action.
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Affiliation(s)
| | - Rita Kundu
- Cell Biology Laboratory, Department of Botany, Centre of Advanced Studies, University of Calcutta, Kolkata, India
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28
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Pérot P, Biton A, Marchetta J, Pourcelot AG, Nazac A, Marret H, Hébert T, Chrétien D, Demazoin MC, Falguières M, Arowas L, Laude H, Heard I, Eloit M. Broad-Range Papillomavirus Transcriptome as a Biomarker of Papillomavirus-Associated Cervical High-Grade Cytology. J Mol Diagn 2019; 21:768-781. [PMID: 31416693 DOI: 10.1016/j.jmoldx.2019.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/07/2019] [Accepted: 04/02/2019] [Indexed: 10/26/2022] Open
Abstract
Human papillomaviruses (HPVs) are responsible for >99% of cervical cancers. Molecular diagnostic tests based on the detection of viral DNA or RNA have low positive predictive values for the identification of cancer or precancerous lesions. Triage with the Papanicolaou test lacks sensitivity; and even when combined with molecular detection of high-risk HPV, this results in a significant number of unnecessary colposcopies. We have developed a broad-range detection test of HPV transcripts to take a snapshot of the transcriptome of 16 high-risk or putative high-risk HPVs in cervical lesions (HPVs 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68, 73, and 82). The purpose of this novel molecular assay, named HPV RNA-Seq, is to detect and type HPV-positive samples and to determine a combination of HPV reads at certain specific viral spliced junctions that can better correlate with high-grade cytology, reflecting the presence of precancerous cells. In a proof-of-concept study conducted on 55 patients, starting from cervical smears, we have shown that HPV RNA-Seq can detect papillomaviruses with performances comparable to a widely used HPV reference molecular diagnostic kit; and a combination of the number of sequencing reads at specific early versus late HPV transcripts can be used as a marker of high-grade cytology, with encouraging diagnostic performances as a triage test.
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Affiliation(s)
- Philippe Pérot
- Pathogen Discovery Laboratory, Biology of Infection Unit, Institut Pasteur, Paris, France
| | - Anne Biton
- Bioinformatics and Biostatistics Hub (C3BI), Institut Pasteur, Paris, France
| | | | | | - André Nazac
- Hôpital Le Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Henri Marret
- Centre Olympe de Gouges, Centre Hospitalier Universitaire Bretonneau, Tours, France
| | - Thomas Hébert
- Centre Olympe de Gouges, Centre Hospitalier Universitaire Bretonneau, Tours, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Biology of Infection Unit, Institut Pasteur, Paris, France
| | - Marie-Christine Demazoin
- French Human Papillomavirus Reference Laboratory (Centre National de Référence des Papillomavirus Humains), Institut Pasteur, Paris, France
| | - Michaël Falguières
- French Human Papillomavirus Reference Laboratory (Centre National de Référence des Papillomavirus Humains), Institut Pasteur, Paris, France
| | - Laurence Arowas
- French Human Papillomavirus Reference Laboratory (Centre National de Référence des Papillomavirus Humains), Institut Pasteur, Paris, France
| | - Hélène Laude
- French Human Papillomavirus Reference Laboratory (Centre National de Référence des Papillomavirus Humains), Institut Pasteur, Paris, France
| | - Isabelle Heard
- French Human Papillomavirus Reference Laboratory (Centre National de Référence des Papillomavirus Humains), Institut Pasteur, Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Biology of Infection Unit, Institut Pasteur, Paris, France; National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, France.
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Adashek JJ, Necchi A, Spiess PE. Updates in the molecular epidemiology and systemic approaches to penile cancer. Urol Oncol 2019; 37:403-8. [DOI: 10.1016/j.urolonc.2019.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/10/2019] [Accepted: 04/14/2019] [Indexed: 01/01/2023]
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30
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Chen X, Kost J, Sulovari A, Wong N, Liang WS, Cao J, Li D. A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Res 2019; 29:819-830. [PMID: 30872350 PMCID: PMC6499315 DOI: 10.1101/gr.242529.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/11/2019] [Indexed: 12/31/2022]
Abstract
Oncoviral infection is responsible for 12%–15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early-stage clonal viral integrations. To implement this strategy, we developed VIcaller, a novel platform for identifying viral integrations that are derived from any characterized viruses and shared by a large proportion of tumor cells using whole-genome sequencing (WGS) data. The sensitivity and precision were confirmed with simulated and benchmark cancer data sets. By applying this platform to cancer WGS data sets with proven or speculated viral etiology, we newly identified or confirmed clonal integrations of hepatitis B virus (HBV), human papillomavirus (HPV), Epstein-Barr virus (EBV), and BK Virus (BKV), suggesting the involvement of these viruses in early stages of tumorigenesis in affected tumors, such as HBV in TERT and KMT2B (also known as MLL4) gene loci in liver cancer, HPV and BKV in bladder cancer, and EBV in non-Hodgkin's lymphoma. We also showed the capacity of VIcaller to identify integrations from some uncharacterized viruses. This is the first study to systematically investigate the strategy and method of virome-wide screening of clonal integrations to identify oncoviruses. Searching clonal viral integrations with our platform has the capacity to identify virus-caused cancers and discover cancer viral etiologies.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nathalie Wong
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong 999077, P.R. China
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jian Cao
- Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA
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31
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Cheng TH, Lam W, Teoh JY. Molecular Basics on Genitourinary Malignancies. Urol Oncol 2019. [DOI: 10.1007/978-3-319-42623-5_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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Jeannot E, Harlé A, Holmes A, Sastre-Garau X. Nuclear factor I X is a recurrent target for HPV16 insertions in anal carcinomas. Genes Chromosomes Cancer 2018; 57:638-644. [PMID: 30264502 DOI: 10.1002/gcc.22675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Anal carcinomas (AC) are associated with human papillomavirus (HPV) DNA sequences, but little is known about the physical state of the viral genome in carcinoma cells. To define the integration status and gene(s) targeted by viral insertions in AC, tumor DNAs extracted from 35 tumor specimen samples in patients with HPV16-associated invasive carcinoma were analyzed using the detection of integrated papillomavirus sequences-PCR approach. The genomic status at integration sites was assessed using comparative genomic hybridization-array assay and gene expression using reverse transcription quantitative PCR (RT-qPCR). HPV16 DNA was found integrated in 25/35 (71%) cases and the integration locus could be determined at the molecular level in 19 cases (29 total integration loci). HPV DNA was inserted on different chromosomes, but 5 cases harbored viral sequences at 19p13.2, within the nuclear factor I X (NFIX) locus. Viral DNA mapped between the most distal and the two proximal alternatively expressed exons of this gene in three cases (CA21, CA04, and CA35) and upstream of this gene (663 kb and 2.3 Mb) in the others. CGH arrays showed genomic gains/amplifications at the NFIX region, associated with HPV within the gene and RT-qPCR, revealed NFIX mRNA overexpression. Other genes targeted by integration were IL20RB, RPS6KA2, MSRA1, PIP5K1B, SLX4IP, CECR1, BCAR3, ATF6, CSNK1G1, APBA2, AGK, ILF3, PVT1, TRMT1, RAD51B, FASN, CCDC57, DSG3, and ZNF563. We identified recurrent targeting of NFIX by HPV16 insertion in anal carcinomas, supporting a role for this gene in oncogenesis, as reported for non-HPV tumors.
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Affiliation(s)
- Emmanuelle Jeannot
- Department of Theranostic and Diagnostic Medicine, Institut Curie, PSL Research University, Paris, Saint-Cloud, France
| | - Alexandre Harlé
- Université de Lorraine, Nancy, France.,CNRS UMR 7039 CRAN, Vandoeuvre-Lès-Nancy, France.,Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
| | - Allyson Holmes
- Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Institut Curie, PSL Research University, Paris, France
| | - Xavier Sastre-Garau
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
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34
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Schütze DM, Krijgsman O, Snijders PJ, Ylstra B, Weischenfeldt J, Mardin BR, Stütz AM, Korbel JO, de Winter JP, Meijer CJ, Quint WG, Bosch L, Wilting SM, Steenbergen RD. Immortalization capacity of HPV types is inversely related to chromosomal instability. Oncotarget 2016; 7:37608-21. [PMID: 26993771 DOI: 10.18632/oncotarget.8058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/28/2016] [Indexed: 01/17/2023] Open
Abstract
High-risk human papillomavirus (hrHPV) types induce immortalization of primary human epithelial cells. Previously we demonstrated that immortalization of human foreskin keratinocytes (HFKs) is HPV type dependent, as reflected by the presence or absence of a crisis period before reaching immortality. This study determined how the immortalization capacity of ten hrHPV types relates to DNA damage induction and overall genomic instability in HFKs. Twenty five cell cultures obtained by transduction of ten hrHPV types (i.e. HPV16/18/31/33/35/45/51/59/66/70 E6E7) in two or three HFK donors each were studied. All hrHPV-transduced HFKs showed an increased number of double strand DNA breaks compared to controls, without exhibiting significant differences between types. However, immortal descendants of HPV-transduced HFKs that underwent a prior crisis period (HPV45/51/59/66/70-transduced HFKs) showed significantly more chromosomal aberrations compared to those without crisis (HPV16/18/31/33/35-transduced HFKs). Notably, the hTERT locus at 5p was exclusively gained in cells with a history of crisis and coincided with increased expression. Chromothripsis was detected in one cell line in which multiple rearrangements within chromosome 8 resulted in a gain of MYC. Together we demonstrated that upon HPV-induced immortalization, the number of chromosomal aberrations is inversely related to the viral immortalization capacity. We propose that hrHPV types with reduced immortalization capacity in vitro, reflected by a crisis period, require more genetic host cell aberrations to facilitate immortalization than types that can immortalize without crisis. This may in part explain the observed differences in HPV-type prevalence in cervical cancers and emphasizes that changes in the host cell genome contribute to HPV-induced carcinogenesis.
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35
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Cheng THT, Lam W, Teoh JYC. Molecular Basics on Genitourinary Malignancies. Urol Oncol 2018. [DOI: 10.1007/978-3-319-42603-7_45-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Chipollini J, Chaing S, Azizi M, Kidd LC, Kim P, Spiess PE. Advances in Understanding of Penile Carcinogenesis: The Search for Actionable Targets. Int J Mol Sci 2017; 18:E1777. [PMID: 28813024 DOI: 10.3390/ijms18081777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 08/13/2017] [Accepted: 08/14/2017] [Indexed: 12/13/2022] Open
Abstract
Penile cancer (PeCa) is a rare malignancy with potentially devastating effects. Squamous cell carcinoma is the most common variant with distinct precancerous lesions before development into invasive disease. Involvement of the inguinal lymph nodes is the most important prognostic factor in PeCa, and once disease is present outside the groin, prognosis is poor. Metastatic PeCa is challenging to treat and often requires multidisciplinary approaches in management. Due to its rarity, molecular understanding of the disease continues to be limited with most studies based on small, single center series. Thus far, it appears PeCa has diverse mechanisms of carcinogenesis affecting similar molecular pathways. In this review, we evaluate the current landscape of the molecular carcinogenesis of PeCa and explore ongoing research on potential actionable targets of therapy. The emergence of anti-epidermal growth factor receptor (EGFR) and other immunotherapeutic strategies may improve outcomes for PeCa patients.
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37
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Chuerduangphui J, Pientong C, Patarapadungkit N, Chotiyano A, Vatanasapt P, Kongyingyoes B, Promthet S, Swangphon P, Bumrungthai S, Pimson C, Ekalaksananan T. Amplification of EGFR and cyclin D1 genes associated with human papillomavirus infection in oral squamous cell carcinoma. Med Oncol 2017; 34:148. [DOI: 10.1007/s12032-017-1010-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/20/2017] [Indexed: 12/28/2022]
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38
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Shen C, Liu Y, Shi S, Zhang R, Zhang T, Xu Q, Zhu P, Chen X, Lu F. Long-distance interaction of the integrated HPV fragment with MYC gene and 8q24.22 region upregulating the allele-specific MYC expression in HeLa cells. Int J Cancer 2017; 141:540-548. [PMID: 28470669 PMCID: PMC5518216 DOI: 10.1002/ijc.30763] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 12/17/2022]
Abstract
Human papillomavirus (HPV) infection is the most important risk factor for cervical cancer development. In HeLa cell line, the HPV viral genome is integrated at 8q24 in one allele of chromosome 8. It has been reported that the HPV fragment integrated in HeLa genome can cis‐activate the expression of proto‐oncogene MYC, which is located at 500 kb downstream of the integrated site. However, the underlying molecular mechanism of this regulation is unknown. A recent study reported that MYC was highly expressed exclusively from the HPV‐integrated haplotype, and a long‐range chromatin interaction between the integrated HPV fragment and MYC gene has been hypothesized. In this study, we provided the experimental evidences supporting this long‐range chromatin interaction in HeLa cells by using Chromosome Conformation Capture (3C) method. We found that the integrated HPV fragment, MYC and 8q24.22 was close to each other and might form a trimer in spatial location. When knocking out the integrated HPV fragment or 8q24.22 region from chromosome 8 by CRISPR/Cas9 system, the expression of MYC reduced dramatically in HeLa cells. Interestingly, decreased expression was only observed in three from eight cell clones, when only one 8q24.22 allele was knocked out. Functionally, HPV knockout caused senescence‐associated acidic β‐gal activity in HeLa cells. These data indicate a long‐distance interaction of the integrated HPV fragment with MYC gene and 8q24.22 region, providing an alternative mechanism relevant to the carcinogenicity of HPV integration. What's new? Infection with human papillomavirus (HPV) is a well‐established risk factor for cervical cancer. The mechanism by which HPV integration into the host genome influences cervical oncogenesis, however, is not fully understood. Using chromosome conformation capture, the authors of this study provide evidence for carcinogenic involvement of a long‐range chromatin interaction between integrated HPV fragments, the proto‐oncogene MYC, and the 8q24.22 chromosomal region in HeLa cells. Knock‐out of either the integrated HPV fragment or the 8q24.22 region in HeLa cells significantly reduced MYC expression. The findings offer an alternative explanation for the carcinogenic mechanism of HPV viral genome integration.
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Affiliation(s)
- Congle Shen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yongzhen Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shu Shi
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ruiyang Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Qiang Xu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengfei Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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39
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Yuan H, Krawczyk E, Blancato J, Albanese C, Zhou D, Wang N, Paul S, Alkhilaiwi F, Palechor-Ceron N, Dakic A, Fang S, Choudhary S, Hou TW, Zheng YL, Haddad BR, Usuda Y, Hartmann D, Symer D, Gillison M, Agarwal S, Wangsa D, Ried T, Liu X, Schlegel R. HPV positive neuroendocrine cervical cancer cells are dependent on Myc but not E6/E7 viral oncogenes. Sci Rep 2017; 7:45617. [PMID: 28378747 PMCID: PMC5381214 DOI: 10.1038/srep45617] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 03/02/2017] [Indexed: 12/23/2022] Open
Abstract
Using conditional cell reprogramming, we generated a stable cell culture of an extremely rare and aggressive neuroendocrine cervical cancer. The cultured cells contained HPV-16, formed colonies in soft agar and rapidly produced tumors in immunodeficient mice. The HPV-16 genome was integrated adjacent to the Myc gene, both of which were amplified 40-fold. Analysis of RNA transcripts detected fusion of the HPV/Myc genes, arising from apparent microhomologous recombination. Spectral karyotyping (SKY) and fluorescent-in-situ hybridization (FISH) demonstrated coordinate localization and translocation of the amplified Myc and HPV genes on chromosomes 8 and 21. Similar to the primary tumor, tumor cell cultures expressed very high levels of the Myc protein and, in contrast to all other HPV-positive cervical cancer cell lines, they harbored a gain-of-function mutation in p53 (R273C). Unexpectedly, viral oncogene knockdown had no effect on the growth of the cells, but it did inhibit the proliferation of a conventional HPV-16 positive cervical cancer cell line. Knockdown of Myc, but not the mutant p53, significantly inhibited tumor cell proliferation. On the basis of these data, we propose that the primary driver of transformation in this aggressive cervical cancer is not HPV oncogene expression but rather the overexpression of Myc.
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Affiliation(s)
- Hang Yuan
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Ewa Krawczyk
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Jan Blancato
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Christopher Albanese
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA.,Department of Oncology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Dan Zhou
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Naidong Wang
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Siddartha Paul
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Faris Alkhilaiwi
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA.,College of Pharmacy, King Abulaziz University, Jeddah, Saudi Arabia
| | - Nancy Palechor-Ceron
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Aleksandra Dakic
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Shuang Fang
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Sujata Choudhary
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Tung-Wei Hou
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Yun-Ling Zheng
- Department of Oncology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Bassem R Haddad
- Department of Oncology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Yukari Usuda
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Dan Hartmann
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - David Symer
- Human Cancer Genetics Program and Dept. of Molecular Virology, Immunology and Medical Genetics, Ohio State University Comprehensive Cancer Center, USA
| | - Maura Gillison
- Dept. of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Seema Agarwal
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Danny Wangsa
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas Ried
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Xuefeng Liu
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
| | - Richard Schlegel
- Department of Pathology, Georgetown University Medical School, Washington DC, 20057, USA
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40
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Zhao JW, Fang F, Guo Y, Zhu TL, Yu YY, Kong FF, Han LF, Chen DS, Li F. HPV16 integration probably contributes to cervical oncogenesis through interrupting tumor suppressor genes and inducing chromosome instability. J Exp Clin Cancer Res 2016; 35:180. [PMID: 27884161 PMCID: PMC5123399 DOI: 10.1186/s13046-016-0454-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022]
Abstract
Background The integration of human papilloma virus (HPV) into host genome is one of the critical steps that lead to the progression of precancerous lesion into cancer. However, the mechanisms and consequences of such integration events are poorly understood. This study aims to explore those questions by studying high risk HPV16 integration in women with cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (SCC). Methods Specifically, HPV integration status of 13 HPV16-infected patients were investigated by ligation-mediated PCR (DIPS-PCR) followed by DNA sequencing. Results In total, 8 HPV16 integration sites were identified inside or around genes associated with cancer development. In particular, the well-studied tumor suppressor genes SCAI was found to be integrated by HPV16, which would likely disrupt its expression and therefore facilitate the migration of tumor. On top of that, we observed several cases of chromosome translocation events coincide with HPV integration, which suggests the existence of chromosome instability. Additionally, short overlapping sequences were observed between viral derived and host derived fragments in viral-cellular junctions, indicating that integration was mediated by micro homology-mediated DNA repair pathway. Conclusions Overall, our study suggests a model in which HPV16 might contribute to oncogenesis not only by disrupting tumor suppressor genes, but also by inducing chromosome instability. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0454-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Wei Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Fang Fang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Yi Guo
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Tai-Lin Zhu
- Abbey College Cambridge, Homerton Gardens, Cambridge, CB2 8EB, UK
| | - Yun-Yun Yu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Fan-Fei Kong
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Ling-Fei Han
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Dong-Sheng Chen
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK. .,Fitzwilliam College, University of Cambridge, Storey's Way, Cambridge, CB3 0DG, UK.
| | - Fang Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China.
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41
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Hayashida M, Daibata M, Tagami E, Taguchi T, Maekawa F, Takeoka K, Fukutsuka K, Shimomura D, Hayashi T, Iwatani Y, Ohno H. Establishment and characterization of a novel Hodgkin lymphoma cell line, AM-HLH, carrying the Epstein-Barr virus genome integrated into the host chromosome. Hematol Oncol 2016; 35:567-575. [PMID: 27813134 DOI: 10.1002/hon.2369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 01/12/2023]
Abstract
We describe the establishment and characterization of a cell line, AM-HLH, obtained from a patient with Epstein-Barr virus-positive (EBV+ ) nodular sclerosis-type Hodgkin lymphoma (HL). The cells were positive for CD2 and CD30 and negative for CD15. The immunoglobulin heavy- and κ light-chain genes were rearranged. The karyotype was of the triploid range. Southern blotting using the EBV terminal repeat probe detected 3 hybridizing bands that were identical to those of the parental HL material. The cells expressed EBV-encoded RNAs as well as latent genes (EBNA1, EBNA2, LMP1, and LMP2A) and lytic genes (BZLF1 and BALF2). Fluorescence in situ hybridization (FISH) with the cosmid pJB8 clone containing a fragment of EBV DNA as a probe revealed multiple hybridization signals at a marker chromosome. Additional FISH using whole chromosome painting and centromere probes in combination with multicolor FISH determined that multiple EBV copies were clustered within the chromosome 20 materials of the marker chromosome. Culture supernatants of AM-HLH contained IL-10 as measured by the bead-based immunoassay. It is possible that an integrated EBV genome and cellular genes on chromosome 20 were coamplified, leading to the enhanced expression of genes involved in cell growth control. The AM-HLH cell line will be useful to clarify the role of cytokines in the development of EBV+ HL.
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Affiliation(s)
- Masahiko Hayashida
- Tenri Institute of Medical Research, Tenri, Japan.,Department of Biomedical Informatics, Division of Health Science, Osaka University School of Medicine, Suita, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Erika Tagami
- Department of Molecular and Cellular Biology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Takahiro Taguchi
- Division of Human Health and Medical Science, Graduate School of Kuroshio Science, Kochi University, Nankoku, Japan
| | | | - Kayo Takeoka
- Tenri Institute of Medical Research, Tenri, Japan
| | | | | | - Takamasa Hayashi
- Department of Hematology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Yoshinori Iwatani
- Department of Biomedical Informatics, Division of Health Science, Osaka University School of Medicine, Suita, Japan
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Tenri, Japan.,Department of Hematology, Tenri Hospital, Tenri, Japan
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42
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Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R 3rd, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, Chen F, Ding L. Divergent viral presentation among human tumors and adjacent normal tissues. Sci Rep 2016; 6:28294. [PMID: 27339696 DOI: 10.1038/srep28294] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022] Open
Abstract
We applied a newly developed bioinformatics system called VirusScan to investigate the viral basis of 6,813 human tumors and 559 adjacent normal samples across 23 cancer types and identified 505 virus positive samples with distinctive, organ system- and cancer type-specific distributions. We found that herpes viruses (e.g., subtypes HHV4, HHV5, and HHV6) that are highly prevalent across cancers of the digestive tract showed significantly higher abundances in tumor versus adjacent normal samples, supporting their association with these cancers. We also found three HPV16-positive samples in brain lower grade glioma (LGG). Further, recurrent HBV integration at the KMT2B locus is present in three liver tumors, but absent in their matched adjacent normal samples, indicating that viral integration induced host driver genetic alterations are required on top of viral oncogene expression for initiation and progression of liver hepatocellular carcinoma. Notably, viral integrations were found in many genes, including novel recurrent HPV integrations at PTPN13 in cervical cancer. Finally, we observed a set of HHV4 and HBV variants strongly associated with ethnic groups, likely due to viral sequence evolution under environmental influences. These findings provide important new insights into viral roles of tumor initiation and progression and potential new therapeutic targets.
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43
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Flippot R, Malouf GG, Su X, Khayat D, Spano JP. Oncogenic viruses: Lessons learned using next-generation sequencing technologies. Eur J Cancer 2016; 61:61-8. [PMID: 27156225 DOI: 10.1016/j.ejca.2016.03.086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/25/2016] [Accepted: 03/30/2016] [Indexed: 01/04/2023]
Abstract
Fifteen percent of cancers are driven by oncogenic human viruses. Four of those viruses, hepatitis B virus, human papillomavirus, Merkel cell polyomavirus, and human T-cell lymphotropic virus, integrate the host genome. Viral oncogenesis is the result of epigenetic and genetic alterations that happen during viral integration. So far, little data have been available regarding integration mechanisms and modifications in the host genome. However, the emergence of high-throughput sequencing and bioinformatic tools enables researchers to establish the landscape of genomic alterations and predict the events that follow viral integration. Cooperative working groups are currently investigating these factors in large data sets. Herein, we provide novel insights into the initiating events of cancer onset during infection with integrative viruses. Although much remains to be discovered, many improvements are expected from the clinical point of view, from better prognosis classifications to better therapeutic strategies.
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Affiliation(s)
- Ronan Flippot
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
| | - Gabriel G Malouf
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France.
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, U.S.A
| | - David Khayat
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
| | - Jean-Philippe Spano
- University Hospital Pitié Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie, Paris, France
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44
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Holmes A, Lameiras S, Jeannot E, Marie Y, Castera L, Sastre-Garau X, Nicolas A. Mechanistic signatures of HPV insertions in cervical carcinomas. NPJ Genom Med 2016; 1:16004. [PMID: 29263809 PMCID: PMC5685317 DOI: 10.1038/npjgenmed.2016.4] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 01/12/2016] [Accepted: 01/27/2016] [Indexed: 12/18/2022] Open
Abstract
To identify new personal biomarkers for the improved diagnosis, prognosis and biological follow-up of human papillomavirus (HPV)-associated carcinomas, we developed a generic and comprehensive Capture-HPV method followed by Next Generation Sequencing (NGS). Starting from biopsies or circulating DNA samples, this Capture-NGS approach rapidly identifies the HPV genotype, HPV status (integrated, episomal or absence), the viral-host DNA junctions and the associated genome rearrangements. This analysis of 72 cervical carcinomas identified five HPV signatures. The first two signatures contain two hybrid chromosomal-HPV junctions whose orientations are co-linear (2J-COL) or non-linear (2J-NL), revealing two modes of viral integration associated with chromosomal deletion or amplification events, respectively. The third and fourth signatures exhibit 3-12 hybrid junctions, either clustered in one locus (MJ-CL) or scattered at distinct loci (MJ-SC) while the fifth signature consists of episomal HPV genomes (EPI). Cross analyses between the HPV signatures and the clinical and virological data reveal unexpected biased representation with respect to the HPV genotype, patient age and disease outcome, suggesting functional relevance(s) of this new classification. Overall, our findings establish a facile and comprehensive rational approach for the molecular detection of any HPV-associated carcinoma and definitive personalised sequence information to develop sensitive and specific biomarkers for each patient.
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Affiliation(s)
- Allyson Holmes
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Paris
, France
| | - Sonia Lameiras
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Paris
, France
| | - Emmanuelle Jeannot
- Department of Biopathology, Institut Curie, PSL Research University, Paris
, France
| | - Yannick Marie
- Institut du Cerveau et de la Moelle épinière (ICM), Genotyping and Sequencing Platform, Pitié-Salpêtrière Hôpital, Paris, France
| | - Laurent Castera
- Department of Genetics, Centre François Baclesse, Caen, France
| | - Xavier Sastre-Garau
- Department of Biopathology, Institut Curie, PSL Research University, Paris
, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Paris
, France
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45
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Abstract
Penile cancer is a rare malignancy, which can be a source of devastating psychosexual distress because of its implication on sexual function and self-image. Current penile staging relies on invasive techniques and is often inaccurate. The authors review the promising biomarkers currently under investigation and their application to the staging and prognosis of penile cancer. Further development of such biomarkers provides the potential of improved clinical management of this disease.
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Affiliation(s)
- Camille Vuichoud
- Division of Urology, Brigham and Women's Hospital, Harvard Medical School, 45 Francis Street, Boston, MA 02115, USA
| | - Julia Klap
- Division of Urology, Brigham and Women's Hospital, Harvard Medical School, 45 Francis Street, Boston, MA 02115, USA
| | - Kevin R Loughlin
- Division of Urology, Brigham and Women's Hospital, Harvard Medical School, 45 Francis Street, Boston, MA 02115, USA.
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46
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Abstract
Enabled by high-throughput sequencing approaches, epithelial cancers across a range of tissue types are seen to harbor gene fusions as integral to their landscape of somatic aberrations. Although many gene fusions are found at high frequency in several rare solid cancers, apart from fusions involving the ETS family of transcription factors which have been seen in approximately 50 % of prostate cancers, several other common solid cancers have been shown to harbor recurrent gene fusions at low frequencies. On the other hand, many gene fusions involving oncogenes, such as those encoding ALK, RAF or FGFR kinase families, have been detected across multiple different epithelial carcinomas. Tumor-specific gene fusions can serve as diagnostic biomarkers or help define molecular subtypes of tumors; for example, gene fusions involving oncogenes such as ERG, ETV1, TFE3, NUT, POU5F1, NFIB, PLAG1, and PAX8 are diagnostically useful. Tumors with fusions involving therapeutically targetable genes such as ALK, RET, BRAF, RAF1, FGFR1–4, and NOTCH1–3 have immediate implications for precision medicine across tissue types. Thus, ongoing cancer genomic and transcriptomic analyses for clinical sequencing need to delineate the landscape of gene fusions. Prioritization of potential oncogenic “drivers” from “passenger” fusions, and functional characterization of potentially actionable gene fusions across diverse tissue types, will help translate these findings into clinical applications. Here, we review recent advances in gene fusion discovery and the prospects for medicine.
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47
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Sastre-Garau X. Human papillomavirus (HPV) insertional mutation as a dynamic & specific tumour biomarker in HPV-associated carcinoma. Indian J Med Res 2015; 142:507-8. [PMID: 26658581 PMCID: PMC4743333 DOI: 10.4103/0971-5916.171266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Xavier Sastre-Garau
- Chef du Département de BioPathologie, Institut Curie, 26 rue d'Ulm, 75248 PARIS Cedex 05, France
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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Doolittle-Hall JM, Cunningham Glasspoole DL, Seaman WT, Webster-Cyriaque J. Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics. Cancers (Basel) 2015; 7:2217-35. [PMID: 26569308 DOI: 10.3390/cancers7040887] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV), hepatitis B virus (HBV) or Merkel cell polyomavirus (MCPyV). These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats) and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures.
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Álvarez-Argüelles ME, Oña-Navarro MD, Rojo-Alba S, Torrens-Muns M, Junquera-Llaneza ML, Antonio-Boga J, Pérez-Castro S, Melón-García S. Quantification of human papilloma virus (HPV) DNA using the Cobas 4800 system in women with and without pathological alterations attributable to the virus. J Virol Methods 2015; 222:95-102. [DOI: 10.1016/j.jviromet.2015.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/22/2015] [Accepted: 05/31/2015] [Indexed: 12/25/2022]
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