Top

BMC Cancer

Published in:

Open Access 01-12-2021 | Human Papillomavirus | Research article

Coordinated action of human papillomavirus type 16 E6 and E7 oncoproteins on competitive endogenous RNA (ceRNA) network members in primary human keratinocytes

Authors: Brigitta László, László Antal, Eszter Gyöngyösi, Anita Szalmás, Szilárd Póliska, György Veress, József Kónya

Published in: BMC Cancer | Issue 1/2021

Abstract

Background

miRNAs and lncRNAs can regulate cellular biological processes both under physiological and pathological conditions including tumour initiation and progression. Interactions between differentially expressed diverse RNA species, as a part of a complex intracellular regulatory network (ceRNA network), may contribute also to the pathogenesis of HPV-associated cancer. The purpose of this study was to investigate the global expression changes of miRNAs, lncRNAs and mRNAs driven by the E6 and E7 oncoproteins of HPV16, and construct a corresponding ceRNA regulatory network of coding and non-coding genes to suggest a regulatory network associated with high-risk HPV16 infections. Furthermore, additional GO and KEGG analyses were performed to understand the consequences of mRNA expression alterations on biological processes.

Methods

Small and large RNA deep sequencing were performed to detect expression changes of miRNAs, lncRNAs and mRNAs in primary human keratinocytes expressing HPV16 E6, E7 or both oncoproteins. The relationships between lncRNAs, miRNAs and mRNAs were predicted by using StarBase v2.0, DianaTools-LncBase v.2 and miRTarBase. The lncRNA-miRNA-mRNA regulatory network was visualized with Cytoscape v3.4.0. GO and KEEG pathway enrichment analysis was performed using DAVID v6.8.

Results

We revealed that 85 miRNAs in 21 genomic clusters and 41 lncRNAs were abnormally expressed in HPV E6/E7 expressing cells compared with controls. We constructed a ceRNA network with members of 15 lncRNAs – 43 miRNAs – 358 mRNAs with significantly altered expressions. GO and KEGG functional enrichment analyses identified numerous cancer related genes, furthermore we recognized common miRNAs as key regulatory elements in biological pathways associated with tumorigenesis driven by HPV16.

Conclusions

The multiple molecular changes driven by E6 and E7 oncoproteins resulting in the malignant transformation of HPV16 host cells occur, at least in part, due to the abnormal alteration in expression and function of non-coding RNA molecules through their intracellular competing network.

Available only for authorised users

Faridi R, Zahra A, Khan K, Idrees M. Oncogenic potential of human papillomavirus (HPV) and its relation with cervical cancer. Virol J. 2011;8(1):269. https://doi.org/10.1186/1743-422X-8-269.CrossRefPubMedPubMedCentral

zur Hausen H. Papillomaviruses and cancer: from basic studies to clinical application. Nat Rev Cancer 2002;2(5):342–350, DOI: https://doi.org/10.1038/nrc798.

de Freitas AC, Coimbra EC, Leitao MC. Molecular targets of HPV oncoproteins: potential biomarkers for cervical carcinogenesis. Biochim Biophys Acta. 2014;1845(2):91–103. https://doi.org/10.1016/j.bbcan.2013.12.004.CrossRefPubMed

Korzeniewski N, Spardy N, Duensing A, Duensing S. Genomic instability and cancer: lessons learned from human papillomaviruses. Cancer Lett. 2011;305(2):113–22. https://doi.org/10.1016/j.canlet.2010.10.013.CrossRefPubMed

Moody CA, Laimins LA. Human papillomavirus oncoproteins: pathways to transformation. Nat Rev Cancer. 2010;10(8):550–60. https://doi.org/10.1038/nrc2886.CrossRefPubMed

Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet. 2009;5(4):e1000459. https://doi.org/10.1371/journal.pgen.1000459.CrossRefPubMedPubMedCentral

Ponting CP, Belgard TG. Transcribed dark matter: meaning or myth? Hum Mol Genet. 2010;19(R2):R162–8. https://doi.org/10.1093/hmg/ddq362.CrossRefPubMedPubMedCentral

Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15–20. https://doi.org/10.1016/j.cell.2004.12.035.CrossRefPubMed

Liz J, Esteller M. lncRNAs and microRNAs with a role in cancer development. Biochim Biophys Acta. 2016;1859(1):169–76. https://doi.org/10.1016/j.bbagrm.2015.06.015.CrossRefPubMed

10.

Melo SA, Esteller M. Dysregulation of microRNAs in cancer: playing with fire. FEBS Lett. 2011;585(13):2087–99. https://doi.org/10.1016/j.febslet.2010.08.009.CrossRefPubMed

11.

Ribeiro J, Sousa H. MicroRNAs as biomarkers of cervical cancer development: a literature review on miR-125b and miR-34a. Mol Biol Rep. 2014;41(3):1525–31. https://doi.org/10.1007/s11033-013-2998-0.CrossRefPubMed

12.

Romero-Cordoba SL, Salido-Guadarrama I, Rodriguez-Dorantes M, Hidalgo-Miranda A. miRNA biogenesis: biological impact in the development of cancer. Cancer biology & therapy. 2014;15(11):1444–55. https://doi.org/10.4161/15384047.2014.955442.CrossRef

13.

Hosseini ES, Meryet-Figuiere M, Sabzalipoor H, Kashani HH, Nikzad H, Asemi Z. Dysregulated expression of long noncoding RNAs in gynecologic cancers. Mol Cancer. 2017;16(1):107. https://doi.org/10.1186/s12943-017-0671-2.CrossRefPubMedPubMedCentral

14.

Hu W, Alvarez-Dominguez JR, Lodish HF. Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO Rep. 2012;13(11):971–83. https://doi.org/10.1038/embor.2012.145.CrossRefPubMedPubMedCentral

15.

Peng L, Yuan X, Jiang B, Tang Z, Li GC. LncRNAs: key players and novel insights into cervical cancer. Tumour Biol. 2016;37(3):2779–88. https://doi.org/10.1007/s13277-015-4663-9.CrossRefPubMed

16.

Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81(1):145–66. https://doi.org/10.1146/annurev-biochem-051410-092902.CrossRefPubMed

17.

Fu Y, Biglia N, Wang Z, Shen Y, Risch HA, Lu L, et al. Long non-coding RNAs, ASAP1-IT1, FAM215A, and LINC00472, in epithelial ovarian cancer. Gynecol Oncol. 2016;143(3):642–9. https://doi.org/10.1016/j.ygyno.2016.09.021.CrossRefPubMedPubMedCentral

18.

Jones M, Lal A. MicroRNAs, wild-type and mutant p53: more questions than answers. RNA Biol. 2012;9(6):781–91. https://doi.org/10.4161/rna.20146.CrossRefPubMedPubMedCentral

19.

Kitagawa M, Kitagawa K, Kotake Y, Niida H, Ohhata T. Cell cycle regulation by long non-coding RNAs. Cell Mol Life Sci. 2013;70(24):4785–94. https://doi.org/10.1007/s00018-013-1423-0.CrossRefPubMedPubMedCentral

20.

Li DS, Ainiwaer JL, Sheyhiding I, Zhang Z, Zhang LW. Identification of key long non-coding RNAs as competing endogenous RNAs for miRNA-mRNA in lung adenocarcinoma. Eur Rev Med Pharmacol Sci. 2016;20(11):2285–95.PubMed

21.

Qin R, Chen Z, Ding Y, Hao J, Hu J, Guo F. Long non-coding RNA MEG3 inhibits the proliferation of cervical carcinoma cells through the induction of cell cycle arrest and apoptosis. Neoplasma. 2013;60(5):486–92. https://doi.org/10.4149/neo_2013_063.CrossRefPubMed

22.

Wilting SM, Verlaat W, Jaspers A, Makazaji NA, Agami R, Meijer CJ, et al. Methylation-mediated transcriptional repression of microRNAs during cervical carcinogenesis. Epigenetics. 2013;8(2):220–8. https://doi.org/10.4161/epi.23605.CrossRefPubMedPubMedCentral

23.

Yan X, Hu Z, Feng Y, Hu X, Yuan J, Zhao SD, et al. Comprehensive genomic characterization of long non-coding RNAs across human cancers. Cancer Cell. 2015;28(4):529–40. https://doi.org/10.1016/j.ccell.2015.09.006.CrossRefPubMedPubMedCentral

24.

Zhang J, Fan D, Jian Z, Chen GG, Lai PB. Cancer specific long noncoding RNAs show differential expression patterns and competing endogenous RNA potential in hepatocellular carcinoma. PLoS One. 2015;10(10):e0141042. https://doi.org/10.1371/journal.pone.0141042.CrossRefPubMedPubMedCentral

25.

Vojtechova Z, Tachezy R. The Role of miRNAs in Virus-Mediated Oncogenesis. International Journal of Molecular Sciences 2018;19:1217. https://doi.org/10.3390/ijms19041217.

26.

Kolenda T, Kopczynska M, Guglas K, Teresiak A, Blizniak R, Lasinska I, et al. EGOT lncRNA in head and neck squamous cell carcinomas. Polish J Pathol. 2018;69(4):356–65. https://doi.org/10.5114/pjp.2018.81695.CrossRef

27.

Sailer V, Charpentier A, Dietrich J, Vogt TJ, Franzen A, Bootz F, et al. Intragenic DNA methylation of PITX1 and the adjacent long non-coding RNA C5orf66-AS1 are prognostic biomarkers in patients with head and neck squamous cell carcinomas. 2018;13(2):e0192742.

28.

Harden ME, Munger K. Human papillomavirus molecular biology. Mutation Res Rev Mutation Res. 2017;772:3–12. https://doi.org/10.1016/j.mrrev.2016.07.002.CrossRef

29.

Harden ME, Prasad N, Griffiths A, Munger K. Modulation of microRNA-mRNA Target Pairs by Human Papillomavirus 16 Oncoproteins. mBio. 2017;8(1):e02170-16. https://doi.org/10.1128/mBio.02170-16.

30.

Sharma S, Hussain S, Soni K, Singhal P, Tripathi R, Ramachandran VG, et al. Novel MicroRNA signatures in HPV-mediated cervical carcinogenesis in Indian women. Tumour Biol. 2016;37(4):4585–95. https://doi.org/10.1007/s13277-015-4248-7.CrossRefPubMed

31.

Wang X, Wang HK, Li Y, Hafner M, Banerjee NS, Tang S, et al. microRNAs are biomarkers of oncogenic human papillomavirus infections. Proc Natl Acad Sci U S A. 2014;111(11):4262–7. https://doi.org/10.1073/pnas.1401430111.CrossRefPubMedPubMedCentral

32.

Wilting SM, Snijders PJ, Verlaat W, Jaspers A, van de Wiel MA, van Wieringen WN, et al. Altered microRNA expression associated with chromosomal changes contributes to cervical carcinogenesis. Oncogene. 2013;32(1):106–16. https://doi.org/10.1038/onc.2012.20.CrossRefPubMed

33.

Yablonska S, Hoskins EE, Wells SI, Khan SA. Identification of miRNAs dysregulated in human foreskin keratinocytes (HFKs) expressing the human papillomavirus (HPV) Type 16 E6 and E7 oncoproteins. MicroRNA (Shariqah, United Arab Emirates). 2013;2(1):2–13.

34.

Zheng ZM, Wang X. Regulation of cellular miRNA expression by human papillomaviruses. Biochim Biophys Acta. 2011;1809(11–12):668–77. https://doi.org/10.1016/j.bbagrm.2011.05.005.CrossRefPubMedPubMedCentral

35.

Deftereos G, Corrie SR, Feng Q, Morihara J, Stern J, Hawes SE, et al. Expression of mir−21 and mir-143 in cervical specimens ranging from histologically normal through to invasive cervical cancer. PLoS One. 2011;6(12):e28423. https://doi.org/10.1371/journal.pone.0028423.CrossRefPubMedPubMedCentral

36.

Fang J, Zhang H, Jin S. Epigenetics and cervical cancer: from pathogenesis to therapy. Tumour Biol. 2014;35(6):5083–93. https://doi.org/10.1007/s13277-014-1737-z.CrossRefPubMed

37.

Peta E, Sinigaglia A, Masi G, Di Camillo B, Grassi A, Trevisan M, et al. HPV16 E6 and E7 upregulate the histone lysine demethylase KDM2B through the c-MYC/miR-146a-5p axys. 2018;37(12):1654–1668.

38.

Zamani S, Sohrabi A, Hosseini SM, Rahnamaye-Farzami M, Akbari A. Deregulation of miR−21 and miR-29a in Cervical Cancer Related to HPV Infection. MicroRNA (Shariqah, United Arab Emirates). 2019;8(2):110–5.

39.

Yang L, Yi K, Wang H, Zhao Y, Xi M. Comprehensive analysis of lncRNAs microarray profile and mRNA-lncRNA co-expression in oncogenic HPV-positive cervical cancer cell lines. Oncotarget. 2016;7(31):49917–29. https://doi.org/10.18632/oncotarget.10232.CrossRefPubMedPubMedCentral

40.

Zhao M, Qiu Y, Yang B, Sun L, Hei K, Du X, et al. Long non-coding RNAs involved in gynecological cancer. Int J Gynecol Cancer. 2014;24(7):1140–5. https://doi.org/10.1097/IGC.0000000000000212.CrossRefPubMed

41.

Barr JA, Hayes KE, Brownmiller T, Harold AD, Jagannathan R, Lockman PR, et al. Long non-coding RNA FAM83H-AS1 is regulated by human papillomavirus 16 E6 independently of p53 in cervical cancer cells. Sci Rep. 2019;9(1):3662. https://doi.org/10.1038/s41598-019-40094-8.CrossRefPubMedPubMedCentral

42.

Sharma S, Munger K. Expression of the cervical carcinoma expressed PCNA regulatory (CCEPR) long noncoding RNA is driven by the human papillomavirus E6 protein and modulates cell proliferation independent of PCNA. Virology. 2018;518:8–13. https://doi.org/10.1016/j.virol.2018.01.031.CrossRefPubMed

43.

Iancu IV, Anton G, Botezatu A, Huica I, Nastase A, Socolov DG, et al. LINC01101 and LINC00277 expression levels as novel factors in HPV-induced cervical neoplasia. 2017;21(12):3787–3794.

44.

Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell. 2011;146(3):353–8. https://doi.org/10.1016/j.cell.2011.07.014.CrossRefPubMedPubMedCentral

45.

Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, et al. microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene. 2011;30(47):4750–6. https://doi.org/10.1038/onc.2011.193.CrossRefPubMedPubMedCentral

46.

Liang WC, Fu WM, Wong CW, Wang Y, Wang WM, Hu GX, et al. The lncRNA H19 promotes epithelial to mesenchymal transition by functioning as miRNA sponges in colorectal cancer. Oncotarget. 2015;6(26):22513–25. https://doi.org/10.18632/oncotarget.4154.CrossRefPubMedPubMedCentral

47.

Liu S, Song L, Zeng S, Zhang L. MALAT1-miR-124-RBG2 axis is involved in growth and invasion of HR-HPV-positive cervical cancer cells. Tumour Biol. 2016;37(1):633–40. https://doi.org/10.1007/s13277-015-3732-4.CrossRefPubMed

48.

Zhang J, Yao T, Wang Y, Yu J, Liu Y, Lin Z. Long noncoding RNA MEG3 is downregulated in cervical cancer and affects cell proliferation and apoptosis by regulating miR-21. Cancer biology & therapy. 2016;17(1):104–13. https://doi.org/10.1080/15384047.2015.1108496.CrossRef

49.

Zhou X, Ji G, Ke X, Gu H, Jin W, Zhang G. MiR−141 inhibits gastric Cancer proliferation by interacting with long noncoding RNA MEG3 and Down-regulating E2F3 expression. Dig Dis Sci. 2015;60(11):3271–82. https://doi.org/10.1007/s10620-015-3782-x.CrossRefPubMed

50.

Gyongyosi E, Szalmas A, Ferenczi A, Konya J, Gergely L, Veress G. Effects of human papillomavirus (HPV) type 16 oncoproteins on the expression of involucrin in human keratinocytes. Virol J. 2012;9(1):36. https://doi.org/10.1186/1743-422X-9-36.CrossRefPubMedPubMedCentral

51.

Gyongyosi E, Szalmas A, Ferenczi A, Poliska S, Konya J, Veress G. Transcriptional regulation of genes involved in keratinocyte differentiation by human papillomavirus 16 oncoproteins. Arch Virol. 2015;160(2):389–98. https://doi.org/10.1007/s00705-014-2305-y.CrossRefPubMed

52.

Borbély AA, Murvai M, Kónya J, Beck Z, Gergely L, Li F, et al. Effects of human papillomavirus type 16 oncoproteins on survivin gene expression. J Gen Virol. 2006;87(Pt 2):287–94. https://doi.org/10.1099/vir.0.81067-0.CrossRefPubMed

53.

Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(Database issue):D92–7. https://doi.org/10.1093/nar/gkt1248.CrossRefPubMed

54.

Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, et al. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016;44(D1):D231–8. https://doi.org/10.1093/nar/gkv1270.CrossRefPubMed

55.

Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016;44(D1):D239–47. https://doi.org/10.1093/nar/gkv1258.CrossRefPubMed

56.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504. https://doi.org/10.1101/gr.1239303.CrossRefPubMedPubMedCentral

57.

Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.CrossRefPubMed

58.

Szalmas A, Gyongyosi E, Ferenczi A, Laszlo B, Karosi T, Csomor P, et al. Activation of Src, Fyn and yes non-receptor tyrosine kinases in keratinocytes expressing human papillomavirus (HPV) type 16 E7 oncoprotein. Virol J. 2013;10(1):79. https://doi.org/10.1186/1743-422X-10-79.CrossRefPubMedPubMedCentral

59.

Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res. 2019;47(D1):D155–d62. https://doi.org/10.1093/nar/gky1141.CrossRefPubMed

60.

McLaughlin-Drubin ME, Munger K. Oncogenic activities of human papillomaviruses. Virus Res. 2009;143(2):195–208. https://doi.org/10.1016/j.virusres.2009.06.008.CrossRefPubMedPubMedCentral

61.

Ou L, Wang D, Zhang H, Yu Q, Hua F. Decreased expression of miR−138-5p by lncRNA H19 in cervical Cancer promotes tumor proliferation. Oncol Res. 2018;26(3):401–10. https://doi.org/10.3727/096504017X15017209042610.CrossRefPubMedPubMedCentral

62.

Graham SV, Faizo AAA. Control of human papillomavirus gene expression by alternative splicing. Virus Res. 2017;231:83–95. https://doi.org/10.1016/j.virusres.2016.11.016.CrossRefPubMedPubMedCentral

63.

Li Y, Cai Q, Lin L, Xu C. MiR-875 and miR-3144 switch the human papillomavirus 16 E6/E6* mRNA ratio through the EGFR pathway and a direct targeting effect. Gene. 2018;679:389–97. https://doi.org/10.1016/j.gene.2018.09.015.CrossRefPubMed

64.

Vande Pol SB, Klingelhutz AJ. Papillomavirus E6 oncoproteins. Virology. 2013;445(1–2):115–37. https://doi.org/10.1016/j.virol.2013.04.026.CrossRefPubMed

65.

Benetatos L, Vartholomatos G, Hatzimichael E. MEG3 imprinted gene contribution in tumorigenesis. Int J Cancer. 2011;129(4):773–9. https://doi.org/10.1002/ijc.26052.CrossRefPubMed

66.

Baldassarre A, Masotti A. Long non-coding RNAs and p53 regulation. Int J Mol Sci. 2012;13(12):16708–17. https://doi.org/10.3390/ijms131216708.CrossRefPubMedPubMedCentral

Title: Coordinated action of human papillomavirus type 16 E6 and E7 oncoproteins on competitive endogenous RNA (ceRNA) network members in primary human keratinocytes
Authors: Brigitta László
László Antal
Eszter Gyöngyösi
Anita Szalmás
Szilárd Póliska
György Veress
József Kónya
Publication date: 01-12-2021
Publisher: BioMed Central
Keyword: Human Papillomavirus
Published in: BMC Cancer / Issue 1/2021
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/s12885-021-08361-y

2024 ASCO Annual Meeting Coverage

Highlights of the Day: Breast cancer – metastatic

Breast Cancer Video

In this session, Dr. Wolff provides his key takeaways from the data presented in the metastatic breast cancer oral abstract session at ASCO 2024.

Watch now

Highlights of the Day: Gynecologic cancer

Gynecologic Cancer Video

Highlights of the Day: Breast Cancer – local/regional/adjuvant

Breast Cancer Video

Neoadjuvant dual immunotherapy improves melanoma outcomes

04-06-2024 Melanoma News

» View more highlights on the ASCO 2024 congress hub page

Webinar | 19-02-2024 | 17:30 (CET)

Keynote webinar | Spotlight on antibody–drug conjugates in cancer

Watch now

Antibody–drug conjugates (ADCs) are novel agents that have shown promise across multiple tumor types. Explore the current landscape of ADCs in breast and lung cancer with our experts, and gain insights into the mechanism of action, key clinical trials data, existing challenges, and future directions.

Dr. Véronique Diéras

Prof. Fabrice Barlesi

Developed by: Springer Medicine

Image Credits

ASCO 2024 | Highlights of the Day: Breast cancer – metastatic/© 2024 American Society of Clinical Oncology, all rights reserved., ASCO 2024 | Highlights of the Day: Gynecologic Cancer/© 2024 American Society of Clinical Oncology, all rights reserved., ASCO 2024 | Highlights of the Day: Breast Cancer – local/regional/adjuvant/© 2024 American Society of Clinical Oncology, all rights reserved., Melanoma/© selvanegra / Getty Images / iStock, Antibody drug conjugated with cytotoxic payload/© Love Employee / Getty images / iStock

2024 ASCO Annual Meeting

Springer Medicine

Abstract

Background

Methods

Results

Conclusions

Please log in to get access to this content

Other articles of this Issue 1/2021

Factors to improve distress and fatigue in Cancer survivorship; further understanding through text analysis of interviews by machine learning

Comparing the characteristics and predicting the survival of patients with head and neck melanoma versus body melanoma: a population-based study

Impact of relative dose intensity of oxaliplatin in adjuvant therapy among stage III colon cancer patients on early recurrence: a retrospective cohort study

Correction to: Mitochondrial DNA abnormalities provide mechanistic insight and predict reactive oxygen species-stimulating drug efficacy

Bioinformatics analysis of the transcriptional expression of minichromosome maintenance proteins as potential indicators of survival in patients with cervical cancer