Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses

de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90.

Article  PubMed  Google Scholar 

McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head Neck. 1998;20:250–65.

Article  CAS  PubMed  Google Scholar 

Schache AG, Powell NG, Cuschieri KS, Robinson M, Leary S, Mehanna H, et al. HPV-related oropharynx cancer in the United Kingdom: an evolution in the understanding of disease etiology. Cancer Res. 2016;76:6598–606.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Muzaffar J, Bari S, Kirtane K, Chung CH. Recent advances and future directions in clinical management of head and neck squamous cell carcinoma. Cancers. 2021;13:338.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brisson M, Kim JJ, Canfell K, Drolet M, Gingras G, Burger EA, et al. Impact of HPV vaccination and cervical screening on cervical cancer elimination: a comparative modelling analysis in 78 low-income and lower-middle-income countries. Lancet Lond Engl. 2020;395:575–90.

Article  Google Scholar 

Muñoz N, Bosch FX, de Sanjosé S, Herrero R, Castellsagué X, Shah KV, et al. Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med. 2003;348:518–27.

Article  PubMed  Google Scholar 

Basukala O, Banks L. The not-so-good, the bad and the ugly: HPV E5, E6 and E7 oncoproteins in the orchestration of carcinogenesis. Viruses. 2021;13:1892.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roden RBS, Stern PL. Opportunities and challenges for human papillomavirus vaccination in cancer. Nat Rev Cancer. 2018;18:240–54.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Della Fera AN, Warburton A, Coursey TL, Khurana S, McBride AA. Persistent human papillomavirus infection. Viruses. 2021;13:321.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fan J, Fu Y, Peng W, Li X, Shen Y, Guo E, et al. Multi-omics characterization of silent and productive HPV integration in cervical cancer. Cell Genomics. 2023;3: 100211.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, et al. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020;39:6327–39.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Massimi P, Pim D, Bertoli C, Bouvard V, Banks L. Interaction between the HPV-16 E2 transcriptional activator and p53. Oncogene. 1999;18:7748–54.

Article  CAS  PubMed  Google Scholar 

Muller M, Jacob Y, Jones L, Weiss A, Brino L, Chantier T, et al. Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for E2 molecular functions. PLOS Pathog. 2012;8: e1002761.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Scarth JA, Patterson MR, Morgan EL, Macdonald A. The human papillomavirus oncoproteins: a review of the host pathways targeted on the road to transformation. J Gen Virol. 2021;2021(102): 001540.

Google Scholar 

Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 2015;43:W566–70.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2:401–4.

Article  PubMed  Google Scholar 

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6:11.

Article  Google Scholar 

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14:128.

Article  PubMed  PubMed Central  Google Scholar 

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44:W90-97.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, et al. Gene set knowledge discovery with Enrichr. Curr Protoc. 2021;1: e90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37:773–82.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18:248–62.

Article  CAS  PubMed  Google Scholar 

Bosch FX, Manos MM, Muñoz N, Sherman M, Jansen AM, Peto J, et al. Prevalence of human papillomavirus in cervical cancer: a worldwide perspective. J Natl Cancer Inst. 1995;87:796–802.

Article  CAS  PubMed  Google Scholar 

Bruni D, Angell HK, Galon J. The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy. Nat Rev Cancer. 2020;20:662–80.

Article  CAS  PubMed  Google Scholar 

Campos-Parra AD, Pérez-Quintanilla M, Martínez-Gutierrez AD, Pérez-Montiel D, Coronel-Martínez J, Millan-Catalan O, et al. Molecular differences between squamous cell carcinoma and adenocarcinoma cervical cancer subtypes: potential prognostic biomarkers. Curr Oncol. 2022;29:4689–702.

Article  PubMed  PubMed Central  Google Scholar 

Chakravarthy A, Reddin I, Henderson S, Dong C, Kirkwood N, Jeyakumar M, et al. Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance. Nat Commun. 2022;13:5818.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sunthamala N, Thierry F, Teissier S, Pientong C, Kongyingyoes B, Tangsiriwatthana T, et al. E2 proteins of high risk human papillomaviruses down-modulate STING and IFN-κ transcription in keratinocytes. PLoS ONE. 2014;9: e91473.

Article  PubMed  PubMed Central  Google Scholar 

Evans MR, James CD, Bristol ML, Nulton TJ, Wang X, Kaur N, et al. Human papillomavirus 16 E2 regulates keratinocyte gene expression relevant to cancer and the viral life cycle. J Virol. 2019;93:e01941-e2018.

CAS  PubMed  PubMed Central  Google Scholar 

Raikhy G, Woodby BL, Scott ML, Shin G, Myers JE, Scott RS, et al. Suppression of stromal interferon signaling by human papillomavirus 16. J Virol. 2019;93:e00458-e519.

Article  CAS  PubMed  PubMed Central  Google Scholar 

French D, Belleudi F, Mauro MV, Mazzetta F, Raffa S, Fabiano V, et al. Expression of HPV16 E5 down-modulates the TGFbeta signaling pathway. Mol Cancer. 2013;12:38.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Scott ML, Woodby BL, Ulicny J, Raikhy G, Orr AW, Songock WK, et al. Human papillomavirus 16 E5 inhibits interferon signaling and supports episomal viral maintenance. J Virol. 2020;94:e01582-e1619.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qin T, Li S, Henry LE, Liu S, Sartor MA. Molecular tumor subtypes of HPV-positive head and neck cancers: biological characteristics and implications for clinical outcomes. Cancers. 2021;13:2721.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pyeon D, Newton MA, Lambert PF, den Boon JA, Sengupta S, Marsit CJ, et al. Fundamental differences in cell cycle deregulation in human papillomavirus–positive and human papillomavirus–negative head/neck and cervical cancers. Cancer Res. 2007;67:4605–19.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keck MK, Zuo Z, Khattri A, Stricker TP, Brown CD, Imanguli M, et al. Integrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypes. Clin Cancer Res. 2015;21:870–81.

Article  CAS  PubMed  Google Scholar 

Zhang Y, Koneva LA, Virani S, Arthur AE, Virani A, Hall PB, et al. Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number alterations, PIK3CA mutation, and pathway signatures. Clin Cancer Res. 2016;22:4735–45.

留言 (0)

沒有登入
gif