BACKGROUND: Human papillomaviruses (HPVs) induce a subset of head and neck squamous cell carcinomas (HNSCC) and anogenital cancers, particularly cervical cancer (CC). The major viral proteins that contribute to tumorigenesis are the E6 and E7 oncoproteins, whose expression is usually enhanced after the integration of viral DNA into the host genome. Recently, an alternative tumorigenesis pathway has been suggested in approximately half of HNSCC and CC cases associated with HPV infection. This pathway is characterized by extrachromosomal HPV persistence and increased expression of the viral E2, E4, and E5 genes. The E6, E7, E5, and E2 proteins have been shown to modify the expression of numerous cellular immune-related genes. The antitumor immune response is a critical factor in the prognosis of HPV-driven cancers, and its characterization may contribute to the prediction and personalization of the increasingly used cancer immunotherapy. METHODS: We analyzed the immune characteristics of HPV-dependent tumors and their association with carcinogenesis types. Transcriptomic HNSCC and CC datasets from The Cancer Genome Atlas were used for this analysis. RESULTS: Clustering with immune-related genes resulted in two clusters of HPV16-positive squamous cell carcinomas in both tumor types: cluster 1 had higher activation of immune responses, including stimulation of the antigen processing and presentation pathway, which was associated with higher immune cell infiltration and better overall survival, and cluster 2 was characterized by keratinization. In CC, the distribution of tumor samples into clusters 1 and 2 did not depend on the level of E2/E5 expression, but in HNSCC, most E2/E5-high tumors were localized in cluster 1 and E2/E5-low tumors in cluster 2. Further analysis did not reveal any association between the E2/E5 levels and the expression of immune-related genes. CONCLUSIONS: Our results suggest that while the detection of immune responses associated with preserved expression of genes encoding components of antigen processing and presentation machinery in HPV-driven tumors may be markers of better prognosis and an important factor in therapy selection, the type of carcinogenesis does not seem to play a decisive role in the induction of antitumor immunity.

Department of Genetics and Microbiology Faculty of Science Charles University BIOCEV 252 50 Vestec Czech Republic

Zobrazit více v PubMed

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–e190. doi: 10.1016/S2214-109X(19)30488-7. PubMed DOI

McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head Neck. 1998;20:250–265. doi: 10.1002/(SICI)1097-0347(199805)20:3<250::AID-HED11>3.0.CO;2-O. PubMed DOI

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;76:6598–6606. doi: 10.1158/0008-5472.CAN-16-0633. PubMed DOI PMC

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. doi: 10.3390/cancers13020338. PubMed DOI PMC

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;395:575–590. doi: 10.1016/S0140-6736(20)30068-4. PubMed DOI PMC

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;348:518–527. doi: 10.1056/NEJMoa021641. PubMed DOI

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. doi: 10.3390/v13101892. PubMed DOI PMC

Roden RBS, Stern PL. Opportunities and challenges for human papillomavirus vaccination in cancer. Nat Rev Cancer. 2018;18:240–254. doi: 10.1038/nrc.2018.13. PubMed DOI PMC

Della Fera AN, Warburton A, Coursey TL, Khurana S, McBride AA. Persistent human papillomavirus infection. Viruses. 2021;13:321. doi: 10.3390/v13020321. PubMed DOI PMC

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. doi: 10.1016/j.xgen.2022.100211. PubMed DOI PMC

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;39:6327–6339. doi: 10.1038/s41388-020-01431-8. PubMed DOI PMC

Massimi P, Pim D, Bertoli C, Bouvard V, Banks L. Interaction between the HPV-16 E2 transcriptional activator and p53. Oncogene. 1999;18:7748–7754. doi: 10.1038/sj.onc.1203208. PubMed DOI

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. doi: 10.1371/journal.ppat.1002761. PubMed DOI PMC

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. PubMed PMC

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–W570. doi: 10.1093/nar/gkv468. PubMed DOI PMC

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;2:401–404. doi: 10.1158/2159-8290.CD-12-0095. PubMed DOI PMC

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. doi: 10.1126/scisignal.2004088. PubMed DOI PMC

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. doi: 10.1186/1471-2105-14-128. PubMed DOI PMC

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. doi: 10.1093/nar/gkw377. PubMed DOI PMC

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. doi: 10.1002/cpz1.90. PubMed DOI PMC

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;37:773–782. doi: 10.1038/s41587-019-0114-2. PubMed DOI PMC

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;18:248–262. doi: 10.1016/j.celrep.2016.12.019. PubMed DOI

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. doi: 10.1093/jnci/87.11.796. PubMed DOI

Bruni D, Angell HK, Galon J. The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy. Nat Rev Cancer. 2020;20:662–680. doi: 10.1038/s41568-020-0285-7. PubMed DOI

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;29:4689–4702. doi: 10.3390/curroncol29070372. PubMed DOI PMC

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. doi: 10.1038/s41467-022-33544-x. PubMed DOI PMC

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. doi: 10.1371/journal.pone.0091473. PubMed DOI PMC

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. PubMed PMC

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. doi: 10.1128/JVI.00458-19. PubMed DOI PMC

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. doi: 10.1186/1476-4598-12-38. PubMed DOI PMC

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. doi: 10.1128/JVI.01582-19. PubMed DOI PMC

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. doi: 10.3390/cancers13112721. PubMed DOI PMC

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;67:4605–4619. doi: 10.1158/0008-5472.CAN-06-3619. PubMed DOI PMC

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;21:870–881. doi: 10.1158/1078-0432.CCR-14-2481. PubMed DOI

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;22:4735–4745. doi: 10.1158/1078-0432.CCR-16-0323. PubMed DOI PMC

Lu X, Jiang L, Zhang L, Zhu Y, Hu W, Wang J, et al. Immune signature-based subtypes of cervical squamous cell carcinoma tightly associated with human papillomavirus type 16 expression, molecular features, and clinical outcome. Neoplasia. 2019;21:591–601. doi: 10.1016/j.neo.2019.04.003. PubMed DOI PMC

Locati LD, Serafini MS, Iannò MF, Carenzo A, Orlandi E, Resteghini C, et al. Mining of self-organizing map gene-expression portraits reveals prognostic stratification of HPV-positive head and neck squamous cell carcinoma. Cancers. 2019;11:1057. doi: 10.3390/cancers11081057. PubMed DOI PMC

Wang J, Li Z, Gao A, Wen Q, Sun Y. The prognostic landscape of tumor-infiltrating immune cells in cervical cancer. Biomed Pharmacother. 2019;120:109444. doi: 10.1016/j.biopha.2019.109444. PubMed DOI

He M, Wang Y, Zhang G, Cao K, Yang M, Liu H. The prognostic significance of tumor-infiltrating lymphocytes in cervical cancer. J Gynecol Oncol. 2021;32:e32. doi: 10.3802/jgo.2021.32.e32. PubMed DOI PMC

Yu S, Li X, Zhang J, Wu S. Development of a novel immune infiltration-based gene signature to predict prognosis and immunotherapy response of patients with cervical cancer. Front Immunol. 2021;12:709493. doi: 10.3389/fimmu.2021.709493. PubMed DOI PMC

Zuo Z, Xiong J, Zeng C, Jiang Y, Xiong K, Tao H, et al. Exploration of a robust and prognostic immune related gene signature for cervical squamous cell carcinoma. Front Mol Biosci. 2021;8:625470. doi: 10.3389/fmolb.2021.625470. PubMed DOI PMC

Li X, Cheng Y, Cheng Y, Shi H. Transcriptome analysis reveals the immune infiltration profiles in cervical cancer and identifies KRT23 as an immunotherapeutic target. Front Oncol. 2022;12:779356. doi: 10.3389/fonc.2022.779356. PubMed DOI PMC

Wang N, Nanding A, Jia X, Wang Y, Yang C, Fan J, et al. Mining of immunological and prognostic-related biomarker for cervical cancer based on immune cell signatures. Front Immunol. 2022;13:993118. doi: 10.3389/fimmu.2022.993118. PubMed DOI PMC

Evans AM, Salnikov M, Gameiro SF, Maleki Vareki S, Mymryk JS. HPV-positive and -negative cervical cancers are immunologically distinct. J Clin Med. 2022;11:4825. doi: 10.3390/jcm11164825. PubMed DOI PMC

Evans AM, Salnikov M, Tessier TM, Mymryk JS. Reduced MHC class I and II expression in HPV-negative vs HPV-positive cervical cancers. Cells. 2022;11:3911. doi: 10.3390/cells11233911. PubMed DOI PMC

Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer immune evasion through loss of MHC class I antigen presentation. Front Immunol. 2021;12:636568. doi: 10.3389/fimmu.2021.636568. PubMed DOI PMC

Cornel AM, Mimpen IL, Nierkens S. MHC class I downregulation in cancer: underlying mechanisms and potential targets for cancer immunotherapy. Cancers. 2020;12:1760. doi: 10.3390/cancers12071760. PubMed DOI PMC

Shklovskaya E, Rizos H. MHCclass I deficiency in solid tumors and therapeutic strategies to overcome it. Int J Mol Sci. 2021;22:6741. doi: 10.3390/ijms22136741. PubMed DOI PMC

de Vries NL, van de Haar J, Veninga V, Chalabi M, Ijsselsteijn ME, van der Ploeg M, et al. γδ T cells are effectors of immunotherapy in cancers with HLA class I defects. Nature. 2023;613:743–750. doi: 10.1038/s41586-022-05593-1. PubMed DOI PMC

Abdallah F, Coindre S, Gardet M, Meurisse F, Naji A, Suganuma N, et al. Leukocyte immunoglobulin-like receptors in regulating the immune response in infectious diseases: a window of opportunity to pathogen persistence and a sound target in therapeutics. Front Immunol. 2021;12:717998. doi: 10.3389/fimmu.2021.717998. PubMed DOI PMC

Barkal AA, Weiskopf K, Kao KS, Gordon SR, Rosental B, Yiu YY, et al. Engagement of MHC class I by the inhibitory receptor LILRB1 suppresses macrophages and is a target of cancer immunotherapy. Nat Immunol. 2018;19:76–84. doi: 10.1038/s41590-017-0004-z. PubMed DOI PMC

Gyöngyösi E, Szalmás A, Ferenczi A, Póliska S, Kónya J, Veress G. Transcriptional regulation of genes involved in keratinocyte differentiation by human papillomavirus 16 oncoproteins. Arch Virol. 2015;160:389–398. doi: 10.1007/s00705-014-2305-y. PubMed DOI

Dust K, Carpenter M, Chen JC, Grant C, McCorrister S, Westmacott GR, et al. Human papillomavirus 16 E6 and E7 oncoproteins alter the abundance of proteins associated with DNA damage response, immune signaling and epidermal differentiation. Viruses. 2022;14:1764. doi: 10.3390/v14081764. PubMed DOI PMC

Zeng P-H, Yin W-J. The cGAS/STING signaling pathway: a cross-talk of infection, senescence and tumors. Cell Cycle. 2023;22:38–56. doi: 10.1080/15384101.2022.2109899. PubMed DOI PMC

Lau L, Gray EE, Brunette RL, Stetson DB. DNA tumor virus oncogenes antagonize the cGAS-STING DNA-sensing pathway. Science. 2015;350:568–571. doi: 10.1126/science.aab3291. PubMed DOI

Lou M, Huang D, Zhou Z, Shi X, Wu M, Rui Y, et al. DNA virus oncoprotein HPV18 E7 selectively antagonizes cGAS-STING-triggered innate immune activation. J Med Virol. 2023;95:e28310. doi: 10.1002/jmv.28310. PubMed DOI PMC

Luo X, Donnelly CR, Gong W, Heath BR, Hao Y, Donnelly LA, et al. HPV16 drives cancer immune escape via NLRX1-mediated degradation of STING. J Clin Invest. 2020;130:1635–1652. doi: 10.1172/JCI129497. PubMed DOI PMC

Lo Cigno I, Calati F, Borgogna C, Zevini A, Albertini S, Martuscelli L, et al. Human papillomavirus E7 oncoprotein subverts host innate immunity via SUV39H1-mediated epigenetic silencing of immune sensor genes. J Virol. 2020;94:e01812–e1819. doi: 10.1128/JVI.01812-19. PubMed DOI PMC

Miyauchi S, Kim SS, Jones RN, Zhang L, Guram K, Sharma S, et al. Human papillomavirus E5 suppresses immunity via inhibition of the immunoproteasome and STING pathway. Cell Rep. 2023;42:112508. doi: 10.1016/j.celrep.2023.112508. PubMed DOI PMC

Ronco LV, Karpova AY, Vidal M, Howley PM. Human papillomavirus 16 E6 oncoprotein binds to interferon regulatory factor-3 and inhibits its transcriptional activity. Genes Dev. 1998;12:2061–2072. doi: 10.1101/gad.12.13.2061. PubMed DOI PMC

Shaikh MH, Bortnik V, McMillan NAJ, Idris A. cGAS-STING responses are dampened in high-risk HPV type 16 positive head and neck squamous cell carcinoma cells. Microb Pathog. 2019;132:162–5. doi: 10.1016/j.micpath.2019.05.004. PubMed DOI

Bortnik V, Wu M, Julcher B, Salinas A, Nikolic I, Simpson KJ, et al. Loss of HPV type 16 E7 restores cGAS-STING responses in human papilloma virus-positive oropharyngeal squamous cell carcinomas cells. J Microbiol Immunol Infect. 2021;54:733–739. doi: 10.1016/j.jmii.2020.07.010. PubMed DOI

Gardella B, Gritti A, Soleymaninejadian E, Pasquali MF, Riemma G, La Verde M, et al. New perspectives in therapeutic vaccines for HPV: a critical review. Medicina. 2022;58:860. doi: 10.3390/medicina58070860. PubMed DOI PMC

Bhatt KH, Neller MA, Srihari S, Crooks P, Lekieffre L, Aftab BT, et al. Profiling HPV-16–specific T cell responses reveals broad antigen reactivities in oropharyngeal cancer patients. J Exp Med. 2020;217:e20200389. doi: 10.1084/jem.20200389. PubMed DOI PMC

Eberhardt CS, Kissick HT, Patel MR, Cardenas MA, Prokhnevska N, Obeng RC, et al. Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer. Nature. 2021;597:279–284. doi: 10.1038/s41586-021-03862-z. PubMed DOI PMC

McInnis C, Bhatia S, Vijaykumar B, Tian Q, Sun Y, Leistritz-Edwards D, et al. Identification of HPV16 E1 and E2-specific T cells in the oropharyngeal cancer tumor microenvironment. J Immunother Cancer. 2023;11:e006721. doi: 10.1136/jitc-2023-006721. PubMed DOI PMC

Dillon S, Sasagawa T, Crawford A, Prestidge J, Inder MK, Jerram J, et al. Resolution of cervical dysplasia is associated with T-cell proliferative responses to human papillomavirus type 16 E2. J Gen Virol. 2007;88:803–813. doi: 10.1099/vir.0.82678-0. PubMed DOI

Paaso A, Koskimaa H-M, Welters MJ, Grénman S, Syrjänen K, van der Burg SH, et al. Cell mediated immunity against HPV16 E2, E6 and E7 peptides in women with incident CIN and in constantly HPV-negative women followed-up for 10-years. J Transl Med. 2015;13:163. doi: 10.1186/s12967-015-0498-9. PubMed DOI PMC

Yan F, Cowell LG, Tomkies A, Day AT. Therapeutic vaccination for HPV-mediated cancers. Curr Otorhinolaryngol Rep. 2023;11:44–61. doi: 10.1007/s40136-023-00443-8. PubMed DOI PMC