Skip to content
1887

Journal of Medical Microbiology logo Journal of Medical Microbiology

Volume 71, Issue 1

Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis No Access

Abstract

Infection with high-risk human papillomavirus (HPV) types, specifically HPV type 16 (HPV16), is considered to be the most important risk factor in the development of cervical intraepithelial neoplasia and cancer. The long control region (LCR) is a noncoding region that comprises approximately 10 % of the HPV genome and contains regulatory elements for viral transcription and replication. Sequence variations in LCR may impact on the replication efficiency and oncogenic potential of the virus.

Studies documenting variations in LCR of HPV16 isolates pertaining to cervical neoplastic status in India are limited.

The present study was designed to characterize variations in the LCR of Indian isolates of HPV16 and study their association with cervical disease grades.

The LCR was amplified and sequenced from HPV16 positive cervical samples belonging to different cervical disease grades. Sequences were aligned to identify variations and potential transcription factor binding sites (TFbs) were predicted using the JASPAR database in addition to phylogenetic studies.

Among the 163 HPV16 isolates analysed, 47 different nucleotide variations were detected in the LCR, of which 25 are reported for first time in Indian isolates. Point mutations were detected in 35/54 (64.8 %) samples with normal cervical status, 44/50 (88 %) samples with low-grade cervical disease and 53/59 (89.8 %) samples with high-grade cervical disease. Variations T6586C, G6657A and T6850G were significantly associated with high-grade cervical status. Thirteen LCR variations were detected in the binding sites for CEBPB, ETS1, JUN, MYB, NFIL3, PHOX2A and SOX9 transcription factors.

The present study helped to identify unique variations in the LCRs of HPV16 Indian isolates. The variations in the A4 sub-lineage were significantly associated with high-grade disease status. The isolates belonging to the A4 and D3 sub-lineages harboured mutations in putative TFbs, implying a potential impact on viral replication and progression to cervical cancer.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cervical cancer , human papillomavirus 16 , long control region , phylogeny , transcription factors and virus bioinformatics
Funding
This study was supported by the:
  • Department of Science and Technology, Government of India
    • Principle Award Recipient: UrmilaKulkarni-Kale
  • Department of Science and Technology, Government of India
    • Principle Award Recipient: AratiMane
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001475
2022-01-18
2025-04-21
Loading full text...

Full text loading...

References

  1. Bruni L, Albero G, Serrano B, Mena M, Collado JJ, et al India: Human Papillomavirus and Related Diseases, Summary Report 2019. Barcelona: ICO/IARC Information Centre on HPV and Cancer (HPV Information Centre); 2019 https://hpvcentre.net/statistics/reports/IND.pdf
  2. Stanley MA, Pett MR, Coleman N. HPV: from infection to cancer. Biochem Soc Trans 2007; 35:1456–1460 [View Article]
     [Google Scholar]
  3. Burk RD, Chen Z, Van Doorslaer K. Human papillomaviruses: genetic basis of carcinogenicity. Public Health Genomics 2009; 12:281–290 [View Article] [PubMed]
     [Google Scholar]
  4. Dai S, Li C, Yan Z, Zhou Z, Wang X et al. Association of human papillomavirus type 16 long control region variations with cervical cancer in a Han Chinese population. Int J Med Sci 2020; 17:931–938 [View Article] [PubMed]
     [Google Scholar]
  5. Connor MO, Chan SY, Bernard HU. Transcription factor binding sites in the long control region of genital hpvs. Human papillomaviruses. 1995. Compendium (G Myers, Ed), III-A 199521–40
     [Google Scholar]
  6. Ribeiro AL, Caodaglio AS, Sichero L. Regulation of HPV transcription. Clinics (Sao Paulo) 2018; 73:e486s [View Article] [PubMed]
     [Google Scholar]
  7. Kämmer C, Warthorst U, Torrez-Martinez N, Wheeler CM, Pfister H. Sequence analysis of the long control region of human papillomavirus type 16 variants and functional consequences for P97 promoter activity. J Gen Virol 2000; 81:1975–1981 [View Article]
     [Google Scholar]
  8. Lace MJ, Isacson C, Anson JR, Lörincz AT, Wilczynski SP et al. Upstream regulatory region alterations found in human papillomavirus type 16 (HPV-16) isolates from cervical carcinomas increase transcription, ori function, and HPV immortalization capacity in culture. J Virol 2009; 83:7457–7466 [View Article] [PubMed]
     [Google Scholar]
  9. Pientong C, Wongwarissara P, Ekalaksananan T, Swangphon P, Kleebkaow P et al. Association of human papillomavirus type 16 long control region mutation and cervical cancer. Virol J 2013; 10:10 [View Article] [PubMed]
     [Google Scholar]
  10. Hubert WG. Variant upstream regulatory region sequences differentially regulate human papillomavirus type 16 DNA replication throughout the viral life cycle. J Virol 2005; 79:5914–5922 [View Article] [PubMed]
     [Google Scholar]
  11. Cullen M, Boland JF, Schiffman M, Zhang X, Wentzensen N et al. Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection. Papillomavirus Res 2015; 1:3–11 [View Article] [PubMed]
     [Google Scholar]
  12. Mirabello L, Yeager M, Cullen M, Boland JF, Chen Z et al. HPV16 sublineage associations with histology-specific cancer risk using HPV whole-genome sequences in 3200 women. J Natl Cancer Inst 2016; 108:djw100 [View Article] [PubMed]
     [Google Scholar]
  13. Clifford GM, Tenet V, Georges D, Alemany L, Pavón MA et al. Human papillomavirus 16 sub-lineage dispersal and cervical cancer risk worldwide: Whole viral genome sequences from 7116 HPV16-positive women. Papillomavirus Res 2019767–74 [View Article] [PubMed]
     [Google Scholar]
  14. Cornet I, Gheit T, Iannacone MR, Vignat J, Sylla BS et al. HPV16 genetic variation and the development of cervical cancer worldwide. Br J Cancer 2013; 108:240–244 [View Article] [PubMed]
     [Google Scholar]
  15. Nicolás-Párraga S, Alemany L, de Sanjosé S, Bosch FX, Bravo IG et al. Differential HPV16 variant distribution in squamous cell carcinoma, adenocarcinoma and adenosquamous cell carcinoma. Int J Cancer 2017; 140:2092–2100 [View Article]
     [Google Scholar]
  16. Fang L, Lin X, Yang Y, Song Z, Ding X et al. Genetic variability, phylogeny and functional implication of the long control region in human papillomavirus type 16, 18 and 58 in Chengdu, China. Virol J 2020; 17:106 [View Article] [PubMed]
     [Google Scholar]
  17. Mane A, Patil L, Limaye S, Nirmalkar A, Kulkarni‐Kale U. Characterization of major capsid protein (L1) variants of Human papillomavirus type 16 by cervical neoplastic status in Indian women: Phylogenetic and functional analysis. J Med Virol 2020; 92:1303–1308 [View Article]
     [Google Scholar]
  18. Solomon D, Davey D, Kurman R, Moriarty A, O’Connor D et al. The 2001 Bethesda System: terminology for reporting results of cervical cytology. JAMA 2002; 287:2114–2119 [View Article]
     [Google Scholar]
  19. Richart RM. A modified terminology for cervical intraepithelial neoplasia. Obstet Gynecol 1990; Jan;75(1):131–133
     [Google Scholar]
  20. Pande S, Jain N, Prusty BK, Bhambhani S, Gupta S et al. Human papillomavirus type 16 variant analysis of E6, E7, and L1 genes and long control region in biopsy samples from cervical cancer patients in north India. J Clin Microbiol 2008; 46:1060–1066 [View Article] [PubMed]
     [Google Scholar]
  21. Vetrovský T, Baldrian P, Morais D. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics 2018; 34:2292–2294 [View Article] [PubMed]
     [Google Scholar]
  22. Parton A. Nucleotide sequence of the HPV16 L1 open reading frame. Nucl Acids Res 1990; 18:3631 [View Article]
     [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  24. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–W235 [View Article]
     [Google Scholar]
  25. Kolekar P, Kale M, Kulkarni-Kale U. Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping. Molecular Phylogenet Evol 2012; 65:510–522 [View Article]
     [Google Scholar]
  26. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article]
     [Google Scholar]
  27. Martin DP, Murrell B, Khoosal A, Muhire B. Detecting and Analyzing Genetic Recombination Using RDP4. Methods Mol Biol 2017; 1525:433–460 [View Article] [PubMed]
     [Google Scholar]
  28. Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004; 32:D91–4 [View Article] [PubMed]
     [Google Scholar]
  29. Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res 2020; 48:D87–D92 [View Article] [PubMed]
     [Google Scholar]
  30. Mosmann JP, Monetti MS, Frutos MC, Kiguen AX, Venezuela RF et al. Mutation detection of E6 and LCR genes from HPV 16 associated with carcinogenesis. Asian Pac J Cancer Prev 2015; 16:1151–1157 [View Article] [PubMed]
     [Google Scholar]
  31. Xi J, Chen J, Xu M, Yang H, Luo J et al. Genetic variability and functional implication of the long control region in HPV-16 variants in Southwest China. PLoS ONE 2017; 12:e0182388 [View Article]
     [Google Scholar]
  32. Zhe X, Xin H, Pan Z, Jin F, Zheng W et al. Genetic variations in E6, E7 and the long control region of human papillomavirus type 16 among patients with cervical lesions in Xinjiang, China. Cancer Cell Int 2019; 19:65 [View Article] [PubMed]
     [Google Scholar]
  33. Zhao J, Zhu J, Guo J, Zhu T, Zhong J et al. Genetic variability and functional implication of HPV16 from cervical intraepithelial neoplasia in Shanghai women. J Med Virol 2019; 92:372–381 [View Article]
     [Google Scholar]
  34. Sichero L, Sobrinho JS, Villa LL. Identification of novel cellular transcription factors that regulate early promoters of human papillomavirus types 18 and 16. J Infect Dis 2012; 206:867–874 [View Article]
     [Google Scholar]
  35. Wang HY, Lian P, Zheng PS. SOX9, a potential tumor suppressor in cervical cancer, transactivates p21WAF1/CIP1 and suppresses cervical tumor growth. Oncotarget 2015; 6:20711–20722 [View Article] [PubMed]
     [Google Scholar]
  36. Mitra P. Transcription regulation of MYB: a potential and novel therapeutic target in cancer. Ann Transl Med 2018; 6:443 [View Article] [PubMed]
     [Google Scholar]
  37. Dittmer J. The role of the transcription factor Ets1 in carcinoma. Seminars in Cancer Biology 2015; 35:20–38 [View Article]
     [Google Scholar]
  38. Wang F, Gao Y, Tang L, Ning K, Geng N et al. A novel PAK4-CEBPB-CLDN4 axis involving in breast cancer cell migration and invasion. Biochemical and Biophysical Research Communications 2019; 511:404–408 [View Article]
     [Google Scholar]
  39. Vishnoi K, Viswakarma N, Rana A, Rana B. Transcription Factors in Cancer Development and Therapy. Cancers (Basel) 2020; 12:E2296 [View Article] [PubMed]
     [Google Scholar]
  40. Wang R, Chen X, Xu T, Xia R, Han L et al. MiR-326 regulates cell proliferation and migration in lung cancer by targeting phox2a and is regulated by hotair. Am J Cancer Res 2016; Jan 15;6(2):173–186
     [Google Scholar]
  41. Veress G, Szarka K, Dong XP, Gergely L, Pfister H. Functional significance of sequence variation in the E2 gene and the long control region of human papillomavirus type 16. J Gen Virol 1999; 80:1035–1043 [View Article]
     [Google Scholar]
  42. Dong XP, Stubenrauch F, Beyer-Finkler E, Pfister H. Prevalence of deletions of YY1-binding sites in episomal HPV 16 DNA from cervical cancers. Int J Cancer 1994; 58:803–808 [View Article]
     [Google Scholar]
  43. Kämmer C, Tommasino M, Syrjänen S, Delius H, Hebling U et al. Variants of the long control region and the E6 oncogene in European human papillomavirus type 16 isolates: implications for cervical disease. Br J Cancer 2002; 86:269–273 [View Article] [PubMed]
     [Google Scholar]
  44. Frati ER, Bianchi S, Amendola A, Colzani D, Petrelli F et al. Genetic characterization of variants of HPV‑16, HPV‑18 and HPV‑52 circulating in Italy among general and high‑risk populations. Mol Med Report 2019; Feb;21(2:894–902 [View Article]
     [Google Scholar]
/content/journal/jmm/10.1099/jmm.0.001475
Loading
Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis
J. Med. Microbiol. 71, 001475 (2022); https://doi.org/10.1099/jmm.0.001475
/content/journal/jmm/10.1099/jmm.0.001475
/content/journal/jmm/10.1099/jmm.0.001475
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error