Identification of differentially‑expressed genes by DNA methylation in cervical cancer

Lee,Heun‑Sik; Yun,Jun  Ho; Jung,Junghee; Yang,Young; Kim,Bong‑Jo; Lee,Sung‑Jong; Yoon,Joo  Hee; Moon,Yong; Kim,Jeong‑Min; Kwon,Yong‑Il

doi:10.3892/ol.2015.2917

Identification of differentially‑expressed genes by DNA methylation in cervical cancer

Authors:
- Heun‑Sik Lee
- Jun Ho Yun
- Junghee Jung
- Young Yang
- Bong‑Jo Kim
- Sung‑Jong Lee
- Joo Hee Yoon
- Yong Moon
- Jeong‑Min Kim
- Yong‑Il Kwon
View Affiliations

Affiliations: Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Chungcheongbuk‑do 363‑951, Republic of Korea, Macrogen Inc., Seoul 153‑023, Republic of Korea, Center for Women's Disease, Department of Biological Science, Sookmyung Women's University, Seoul 140‑742, Republic of Korea, Department of Obstetrics and Gynecology, Saint Vincent's Hospital, the Catholic University, Suwon, Gyeonggi-do 442‑723, Republic of Korea, Department of Public Health Administration, Namseoul University, Cheonan, Chungcheongnam-do 331‑707, Republic of Korea, Department of Obstetrics and Gynecology, Kangdong Sacred Heart Hospital, Hallym University Medical Center, Seoul 134‑701, Republic of Korea
Published online on: January 29, 2015 https://doi.org/10.3892/ol.2015.2917
Pages: 1691-1698

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

To identify novel cervical cancer‑related genes that are regulated by DNA methylation, integrated analyses of genome‑wide DNA methylation and RNA expression profiles were performed using the normal and tumor regions of tissues from four patients; two with cervical cancer and two with pre‑invasive cancer. The present study identified 19 novel cervical cancer‑related genes showing differential RNA expression by DNA methylation. A number of the identified genes were novel cervical cancer‑related genes and their differential expression was confirmed in a publicly available database. Among the candidate genes, the epigenetic regulation and expression of three genes, CAMK2N1, ALDH1A3 and PPP1R3C, was validated in HeLa cells treated with a demethylating reagent using methylation‑specific polymerase chain reaction (PCR) and quantitative PCR, respectively. From these results, the expression of the CAMK2N1, ALDH1A3 and PPP1R3C genes are were shown to be suppressed in cervical cancers by DNA methylation. These genes may be involved in the progression or initiation of cervical cancer.

View Figures

View References

1	Forouzanfar MH, Foreman KJ, Delossantos AM, et al: Breast and cervical cancer in 187 countries between 1980 and 2010: a systematic analysis. Lancet. 378:1461–1484. 2011. View Article : Google Scholar : PubMed/NCBI
2	Woodman CB, Collins SI and Young LS: The natural history of cervical HPV infection: unresolved issues. Nat Rev Cancer. 7:11–22. 2007. View Article : Google Scholar
3	Jensen KE, Schmiedel S, Frederiksen K, et al: Risk for cervical intraepithelial neoplasia grade 3 or worse in relation to smoking among women with persistent human papillomavirus infection. Cancer Epidemiol Biomarkers Prev. 21:1949–1955. 2012. View Article : Google Scholar : PubMed/NCBI
4	Werness BA, Levine AJ and Howley PM: Association of human papillomavirus types 16 and 18 E6 proteins with p53. Science. 248:76–79. 1990. View Article : Google Scholar : PubMed/NCBI
5	Dyson N, Howley PM, Münger K and Harlow E: The human papilloma virus-16 E7 oncoprotein is able to bind to the retinoblastoma gene product. Science. 243:934–937. 1989. View Article : Google Scholar : PubMed/NCBI
6	Whiteside MA, Siegel EM and Unger ER: Human papillomavirus and molecular considerations for cancer risk. Cancer. 113(10 Suppl): 2981–2994. 2008. View Article : Google Scholar : PubMed/NCBI
7	Esteller M: Epigenetics in cancer. N Engl J Med. 358:1148–1159. 2008. View Article : Google Scholar : PubMed/NCBI
8	Feinberg AP and Vogelstein B: Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature. 301:89–92. 1983. View Article : Google Scholar : PubMed/NCBI
9	Herman JG, Merlo A, Mao L, et al: Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res. 55:4525–4530. 1995.PubMed/NCBI
10	Silva TD, Vidigal VM, Felipe AV, et al: DNA methylation as an epigenetic biomarker in colorectal cancer. Oncol Lett. 6:1687–1692. 2013.PubMed/NCBI
11	Jeong DH, Youm MY, Kim YN, et al: Promoter methylation of p16, DAPK, CDH1, and TIMP-3 genes in cervical cancer: correlation with clinicopathologic characteristics. Int J Gynecol Cancer. 16:1234–1240. 2006. View Article : Google Scholar : PubMed/NCBI
12	Neyaz MK, Kumar RS, Hussain S, et al: Effect of aberrant promoter methylation of FHIT and RASSF1A genes on susceptibility to cervical cancer in a North Indian population. Biomarkers. 13:597–606. 2008. View Article : Google Scholar : PubMed/NCBI
13	Lendvai A, Johannes F, Grimm C, et al: Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. Epigenetics. 7:1268–1278. 2012. View Article : Google Scholar : PubMed/NCBI
14	Sun Z, Asmann YW, Kalari KR, et al: Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One. 6:e174902011. View Article : Google Scholar : PubMed/NCBI
15	Li M, Balch C, Montgomery JS, et al: Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer. BMC Med Genomics. 2:342009. View Article : Google Scholar : PubMed/NCBI
16	Irizarry RA, Ladd-Acosta C, Carvalho B, et al: Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18:780–790. 2008. View Article : Google Scholar : PubMed/NCBI
17	Agarwal SM, Raghav D, Singh H and Raghava GP: CCDB: a curated database of genes involved in cervix cancer. Nucleic Acids Res. 39:D975–979. 2011. View Article : Google Scholar :
18	Shin G, Kang TW, Yang S, et al: GENT: gene expression database of normal and tumor tissues. Cancer Inform. 10:149–157. 2011.PubMed/NCBI
19	Eisen MB, Spellman PT, Brown PO and Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 95:14863–14868. 1998. View Article : Google Scholar : PubMed/NCBI
20	Huang da W, Sherman BT, Tan Q, et al: The DAVID Gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R1832007. View Article : Google Scholar : PubMed/NCBI
21	Kim JM, Sohn HY, Yoon SY, et al: Identification of gastric cancer-related genes using a cDNA microarray containing novel expressed sequence tags expressed in gastric cancer cells. Clin Cancer Res. 11:473–482. 2005.PubMed/NCBI
22	Li LC and Dahiya R: MethPrimer: designing primers for methylation PCRs. Bioinformatics. 18:1427–1431. 2002. View Article : Google Scholar : PubMed/NCBI
23	Chao A, Wang TH, Lee YS, et al: Molecular characterization of adenocarcinoma and squamous carcinoma of the uterine cervix using microarray analysis of gene expression. Int J Cancer. 119:91–98. 2006. View Article : Google Scholar : PubMed/NCBI
24	Song JY, Lee JK, Lee NW, et al: Microarray analysis of normal cervix, carcinoma in situ, and invasive cervical cancer: identification of candidate genes in pathogenesis of invasion in cervical cancer. Int J Gynecol Cancer. 18:1051–1059. 2008. View Article : Google Scholar : PubMed/NCBI
25	Kavanagh E, Tsapara A, Matter K and Balda MS: Tight junctions and the regulation of epithelial cell proliferation and gene expression. Tight Junctions. Springer; pp. 101–115. 2006, View Article : Google Scholar
26	Togami S, Nomoto M, Higashi M, et al: Expression of mucin antigens (MUC1 and MUC16) as a prognostic factor for mucinous adenocarcinoma of the uterine cervix. J Obstet Gynaecol Res. 36:588–597. 2010. View Article : Google Scholar : PubMed/NCBI
27	Munro EG, Jain M, Oliva E, et al: Upregulation of MUC4 in cervical squamous cell carcinoma: pathologic significance. Int J Gynecol Pathol. 28:127–133. 2009. View Article : Google Scholar : PubMed/NCBI
28	Shames DS, Girard L, Gao B, et al: A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med. 3:e4862006. View Article : Google Scholar : PubMed/NCBI
29	Zhang W, Yan W, You G, et al: Genome-wide DNA methylation profiling identifies ALDH1A3 promoter methylation as a prognostic predictor in G-CIMP-primary glioblastoma. Cancer Lett. 328:120–125. 2013. View Article : Google Scholar
30	Wong YF, Cheung TH, Tsao GS, et al: Genome-wide gene expression profiling of cervical cancer in Hong Kong women by oligonucleotide microarray. Int J Cancer. 118:2461–2469. 2006. View Article : Google Scholar
31	Bonazzi VF, Irwin D and Hayward NK: Identification of candidate tumor suppressor genes inactivated by promoter methylation in melanoma. Genes Chromosomes Cancer. 48:10–21. 2009. View Article : Google Scholar
32	Kim JH, Dhanasekaran SM, Prensner JR, et al: Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 21:1028–1041. 2011. View Article : Google Scholar : PubMed/NCBI
33	Wang C, Li N, Liu X, Zheng Y and Cao X: A novel endogenous human CaMKII inhibitory protein suppresses tumor growth by inducing cell cycle arrest via p27 stabilization. J Biol Chem. 283:11565–11574. 2008. View Article : Google Scholar : PubMed/NCBI