Comprehensive bioinformatic analysis reveals oncogenic role of H2A.Z isoforms in cervical cancer progression

Document Type : Original Article

Authors

1 Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México

2 Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, 39090, Gro, México

3 Division of Infectious Diseases, Stanford University School of Medicine, United States

4 Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, México. Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico

Abstract

Objective(s): Cervical cancer ranks as the fourth most common neoplasia in women worldwide in which epigenetic alterations play an important role. Several studies have reported pro-oncogenic role of the histone variant H2A.Z in different types of cancer; however, the role of H2A.Z in cervical cancer remains poorly studied. This study aimed to determine the potential role of H2A.Z in cervical cancer through a bioinformatic approach.
Materials and Methods: H2A.Z expression was analyzed in The Human Protein Atlas, The Cancer Genome Atlas, and Gene Expression Omnibus datasets. The promoter regions of H2AZ1 and H2AZ2 genes were downloaded from Expasy, and the prediction of transcription factor binding motifs was performed using CONSITE, Alibaba, and ALGGEN. ChIP-seq and RNA-seq data from HeLa-S3 cells were downloaded from ENCODE. The discovery motif was investigated using MEME-ChIP. The functional annotation was examined in Enrich.
Results: The expression of H2A.Z is elevated in cervical cancer. Interestingly, DNA methylation, copy number, and transcription factors AP2α and ELK1 are involved in H2A.Z overexpression. Additionally, H2A.Z is enriched on promoter and enhancer regions of genes involved in pathways associated with cancer development. In these regions, H2A.Z enables the recruitment of transcription factors such as NRF1, NFYA, and RNA Pol II. Finally, H2A.Z allows the expression of genes associated with proliferation in patients with cervical cancer.
Conclusion: Our findings suggest that H2A.Z overexpression and its presence in promoters and enhancers could be regulating the transcription of genes involved in cervical carcinogenesis.

Keywords

References

1. Arbyn M, Weiderpass E, Bruni L, de Sanjose S, Saraiya M, Ferlay J, et al. Estimates of incidence and mortality of cervical cancer in 2018: a worldwide analysis. Lancet Glob Health 2020; 8:e191-e203.
2. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2018; 68:394-424.
3. Benard VB, Watson M, Saraiya M, Harewood R, Townsend JS, Stroup AM, et al. Cervical cancer survival in the United States by race and stage (2001-2009): Findings from the CONCORD-2 study. Cancer 2017; 123 Suppl 24:5119-5137.
4. Munoz N, Castellsague X, de Gonzalez AB, Gissmann L. Chapter 1: HPV in the etiology of human cancer. Vaccine 2006; 24 Suppl 3:S3/1-10.
5. Fang J, Zhang H, Jin S. Epigenetics and cervical cancer: from pathogenesis to therapy. Tumor Biology 2014; 35:5083-5093.
6. Darwiche N. Epigenetic mechanisms and the hallmarks of cancer: An intimate affair. Am J Cancer Res 2020; 10:1954-1978.
7. Fang J, Zhang H, Jin S. Epigenetics and cervical cancer: from pathogenesis to therapy. Tumour Biol 2014; 35:5083-5093.
8. Vardabasso C, Hasson D, Ratnakumar K, Chung CY, Duarte LF, Bernstein E. Histone variants: emerging players in cancer biology. Cell Mol Life Sci 2014; 71:379-404.
9. Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics & Chromatin 2019; 12:1-22.
10. Vardabasso C, Gaspar-Maia A, Hasson D, Punzeler S, Valle-Garcia D, Straub T, et al. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Mol Cell 2015; 59:75-88.
11. Svotelis A, Gevry N, Grondin G, Gaudreau L. H2A.Z overexpression promotes cellular proliferation of breast cancer cells. Cell Cycle 2010; 9:364-370.
12. Valdés-Mora F, Gould CM, Colino-Sanguino Y, Qu W, Song JZ, Taylor KM, et al. Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer. Nat Commun 2017; 8:1346.
13. Yang B, Tong R, Liu H, Wu J, Chen D, Xue Z, et al. H2A.Z regulates tumorigenesis, metastasis and sensitivity to cisplatin in intrahepatic cholangiocarcinoma. Int J Oncol 2018; 52:1235-1245.
14. Kim K, Punj V, Choi J, Heo K, Kim J-M, Laird PW, et al. Gene dysregulation by histone variant H2A.Z in bladder cancer. Epigenetics Chromatin 2013; 6:34.
15. Avila-Lopez PA, Guerrero G, Nunez-Martinez HN, Peralta-Alvarez CA, Hernandez-Montes G, Alvarez-Hilario LG, et al. H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma. Oncogene 2021; 40:2065-2080.
16. Zlatanova J, Thakar A. H2A.Z: view from the top. Structure 2008; 16:166-179.
17. Matsuda R, Hori T, Kitamura H, Takeuchi K, Fukagawa T, Harata M. Identification and characterization of the two isoforms of the vertebrate H2A.Z histone variant. Nucleic Acids Res 2010; 38:4263-4273.
18. Henikoff S, Smith MM. Histone variants and epigenetics. Cold Spring Harb Perspect Biol 2015; 7:a019364.
19. Dryhurst D, Ishibashi T, Rose KL, Eirín-López JM, McDonald D, Silva-Moreno B, et al. Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates. BMC Biol 2009; 7:86.
20. Colwill K, Graslund S. A roadmap to generate renewable protein binders to the human proteome. Nat Methods 2011; 8:551-558.
21. Tang Z, Li C, Kang B, Gao G, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res 2017; 45:W98-W102.
22. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res 2013; 41:D991-995.
23. Scotto L, Narayan G, Nandula SV, Arias-Pulido H, Subramaniyam S, Schneider A, et al. Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression. Genes Chromosomes Cancer 2008; 47:755-765.
24. Zhai Y, Kuick R, Nan B, Ota I, Weiss SJ, Trimble CL, et al. Gene expression analysis of preinvasive and invasive cervical squamous cell carcinomas identifies HOXC10 as a key mediator of invasion. Cancer Res 2007; 67:10163-10172.
25. Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi B, et al. UALCAN: A portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia 2017; 19:649-658.
26. 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.
27. 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:pl1.
28. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res 2012; 40:W597-603.
29. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol 2011; 29:24-26.
30. Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 2002; 18:1427-1431.
31. Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, et al. DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. Nucleic Acids Res 2017; 45:D888-D895.
32. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489:57-74.
33.Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, et al. The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 2018; 46:D794-D801.
34. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 2018; 46:W537-W544.
35. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25.
36. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-2079.
37. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137.
38. Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 2016; 44:W160-165.
39. Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015; 31:2382-2383.
40. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods 2015; 12:357-360.
41. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30:923-930.
42. Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 2013; 45:1113-1120.
43. Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 2016; 44:e71.
44. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15:550-570.
45. Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 2010; 26:2438-2444.
46. 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.
47. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009; 37:W202-208.
48. Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011; 27:1653-1659.
49. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: Protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research 2018; 47:D607-D613.
50. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 2015; 16:22-34.
51. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 2010; 28:495-501.
52. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005; 102:15545-15550.
53. Wickham H. ggplot2-Elegant Graphics for Data Analysis. Springer International Publishing. Cham, Switzerland 2016.
54. Thakar A, Gupta P, Ishibashi T, Finn R, Silva-Moreno B, Uchiyama S, et al. H2A.Z and H3.3 histone variants affect nucleosome structure: biochemical and biophysical studies. Biochemistry 2009; 48:10852-10857.
55. Ni Z, Olsen JB, Guo X, Zhong G, Ruan ED, Marcon E, et al. Control of the RNA polymerase II phosphorylation state in promoter regions by CTD interaction domain-containing proteins RPRD1A and RPRD1B. Transcription 2011; 2:237-242.
56. Subramanian V, Fields PA, Boyer LA. H2A.Z: A molecular rheostat for transcriptional control. F1000Prime Rep 2015; 7:01.
57. Peng Y, Zhang Y. Enhancer and super-enhancer: Positive regulators in gene transcription. Animal Model Exp Med 2018; 1:169-179.
58. Yu S, Wang G, Shi Y, Xu H, Zheng Y, Chen Y. MCMs in Cancer: Prognostic Potential and Mechanisms. Anal Cell Pathol 2020; 2020:3750294.
59. Boyer AS, Walter D, Sorensen CS. DNA replication and cancer: From dysfunctional replication origin activities to therapeutic opportunities. Semin Cancer Biol 2016; 37-38:16-25.
60. Nebert DW. Transcription factors and cancer: an overview. Toxicology 2002; 181-182:131-141.
61. Kanwal R, Gupta K, Gupta S. Cancer epigenetics: an introduction. Methods Mol Biol 2015; 1238:3-25.
62. Stabach PR, Thiyagarajan MM, Woodfield GW, Weigel RJ. AP2α alters the transcriptional activity and stability of p53. Oncogene 2006; 25:2148-2159.
63. Kawahara T, Shareef HK, Aljarah AK, Ide H, Li Y, Kashiwagi E, et al. ELK1 is up-regulated by androgen in bladder cancer cells and promotes tumor progression. Oncotarget 2015; 6:29860-29876.
64. Wang X, Luo X, Chen C, Tang Y, Li L, Mo B, et al. The Ap-2alpha/Elk-1 axis regulates Sirpalpha-dependent tumor phagocytosis by tumor-associated macrophages in colorectal cancer. Signal Transduct Target Ther 2020; 5:35.
65. Yang HJ. Aberrant DNA methylation in cervical carcinogenesis. Chin J Cancer 2013; 32:42-48.
66. Feng C, Dong J, Chang W, Cui M, Xu T. The progress of methylation regulation in gene expression of cervical cancer. Int J Genomics 2018; 2018:8260652.
67. Shao X, Lv N, Liao J, Long J, Xue R, Ai N, et al. Copy number variation is highly correlated with differential gene expression: A pan-cancer study. BMC Med Genet 2019; 20:175.
68. Yang WT, Zhao ZX, Li B, Zheng PS. NF-YA transcriptionally activates the expression of SOX2 in cervical cancer stem cells. PLoS One 2019; 14:e0215494.
69. Fischer M, Quaas M, Wintsche A, Müller GA, Engeland K. Polo-like kinase 4 transcription is activated via CRE and NRF1 elements, repressed by DREAM through CDE/CHR sites and deregulated by HPV E7 protein. Nucleic Acids Research 2013; 42:163-180.
70. Johannsen E, Lambert PF. Epigenetics of human papillomaviruses. Virology 2013; 445:205-212.
71. Serra E, Zemzoumi K, di Silvio A, Mantovani R, Lardans V, Dissous C. Conservation and divergence of NF-Y transcriptional activation function. Nucleic Acids Res 1998; 26:3800-3805.
72. Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques PE, Gevry N. The histone variant H2A.Z is an important regulator of enhancer activity. Nucleic Acids Res 2015; 43:9742-9756.
Iranian Journal of Basic Medical Sciences
Volume 24, Issue 11
November 2021
Pages 1470-1481

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