Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome

Du,Jiang; Zhang,Lin

doi:10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome

Authors:
- Jiang Du
- Lin Zhang
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Affiliations: Department of Thoracic Surgery, Chinese Medical University Affiliated No. 1 Hospital, Shenyang, Liaoning 110001, P.R. China
Published online on: May 29, 2015 https://doi.org/10.3892/or.2015.4023
Pages: 585-594
Copyright: © Du et al. This is an open access article distributed under the terms of Creative Commons Attribution License [CC BY_NC 3.0].

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Abstract

Lung adenocarcinoma, as a common type of non-small cell lung cancer (40%), poses a significant threat to public health worldwide. The present study aimed to determine the transcriptional regulatory mechanisms in lung adenocarcinoma. Illumina sequence data GSE 37764 including expression profiling, methylation profiling and non-coding RNA profiling of 6 never-smoker Korean female patients with non-small cell lung adenocarcinoma were obtained from the Gene Expression Omnibus (GEO) database. Differentially methylated genes, differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) between normal and tumor tissues of the same patients were screened with tools in R. Functional enrichment analysis of a variety of differential genes was performed. DEG-specific methylation and transcription factors (TFs) were analyzed with ENCODE ChIP-seq. The integrated regulatory network of DEGs, TFs and miRNAs was constructed. Several overlapping DEGs, such as v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) were screened. DEGs were centrally modified by histones of tri-methylation of lysine 27 on histone H3 (H3K27me3) and di-acetylation of lysine 12 or 20 on histone H2 (H2BK12/20AC). Upstream TFs of DEGs were enriched in different ChIP-seq clusters, such as glucocorticoid receptors (GRs). Two miRNAs (miR-126-3p and miR-30c-2-3p) and three TFs including homeobox A5 (HOXA5), Meis homeobox 1 (MEIS1) and T-box 5 (TBX5), played important roles in the integrated regulatory network conjointly. These DEGs, and DEG-related histone modifications, TFs and miRNAs may be important in the pathogenesis of lung adenocarcinoma. The present results may indicate directions for the next step in the study of the further elucidation and targeted prevention of lung adenocarcinoma.

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1	Toh CK, Gao F, Lim WT, Leong SS, Fong KW, Yap SP, Hsu AA, Eng P, Koong HN, Thirugnanam A, et al: Never-smokers with lung cancer: Epidemiologic evidence of a distinct disease entity. J Clin Oncol. 24:2245–2251. 2006. View Article : Google Scholar : PubMed/NCBI
2	Subramanian J and Govindan R: Lung cancer in never smokers: A review. J Clin Oncol. 25:561–570. 2007. View Article : Google Scholar : PubMed/NCBI
3	Yano T, Haro A, Shikada Y, Maruyama R and Maehara Y: Non-small cell lung cancer in never smokers as a representative ‘non-smoking-associated lung cancer̓: Epidemiology and clinical features. Int J Clin Oncol. 16:287–293. 2011. View Article : Google Scholar : PubMed/NCBI
4	Molina JR, Yang P, Cassivi SD, Schild SE and Adjei AA: Non-small cell lung cancer: Epidemiology, risk factors, treatment, and survivorship. Mayo Clin Proc. 83:584–594. 2008. View Article : Google Scholar : PubMed/NCBI
5	Su JL, Shih JY, Yen ML, Jeng YM, Chang CC, Hsieh CY, Wei LH, Yang PC and Kuo ML: Cyclooxygenase-2 induces EP1-and HER-2/Neu-dependent vascular endothelial growth factor-C up-regulation: A novel mechanism of lymphangiogenesis in lung adenocarcinoma. Cancer Res. 64:554–564. 2004. View Article : Google Scholar : PubMed/NCBI
6	Skobe M, Hawighorst T, Jackson DG, Prevo R, Janes L, Velasco P, Riccardi L, Alitalo K, Claffey K and Detmar M: Induction of tumor lymphangiogenesis by vEGF-C promotes breast cancer metastasis. Nat Med. 7:192–198. 2001. View Article : Google Scholar : PubMed/NCBI
7	Heaney AP, Singson R, McCabe CJ, Nelson V, Nakashima M and Melmed S: Expression of pituitary-tumour transforming gene in colorectal tumours. Lancet. 355:716–719. 2000. View Article : Google Scholar : PubMed/NCBI
8	Bevilacqua G, Sobel ME, Liotta LA and Steeg PS: Association of low nm23 RNA levels in human primary infiltrating ductal breast carcinomas with lymph node involvement and other histopathological indicators of high metastatic potential. Cancer Res. 49:5185–5190. 1989.PubMed/NCBI
9	Billah S, Stewart J, Staerkel G, Chen S, Gong Y and Guo M: EGFR and KRAS mutations in lung carcinoma: Molecular testing by using cytology specimens. Cancer Cytopathol. 119:111–117. 2011. View Article : Google Scholar : PubMed/NCBI
10	Ju YS, Lee WC, Shin JY, Lee S, Bleazard T, Won JK, Kim YT, Kim JI, Kang JH and Seo JS: A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res. 22:436–445. 2012. View Article : Google Scholar :
11	Togashi Y, Soda M, Sakata S, Sugawara E, Hatano S, Asaka R, Nakajima T, Mano H and Takeuchi K: KLC1-ALK: A novel fusion in lung cancer identified using a formalin-fixed paraffin-embedded tissue only. PLoS One. 7:e313232012. View Article : Google Scholar : PubMed/NCBI
12	Kim SC, Jung Y, Park J, Cho S, Seo C, Kim J, Kim P, Park J, Seo J, Kim J, et al: A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers. PLoS One. 8:e555962013. View Article : Google Scholar : PubMed/NCBI
13	Bolger AM, Lohse M and Usadel B: Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 30:2114–2120. 2014. View Article : Google Scholar : PubMed/NCBI
14	Langmead B and Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357–359. 2012. View Article : Google Scholar : PubMed/NCBI
15	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G and Durbin R: 1000 Genome Project Data Processing Subgroup: The sequence alignment/map format and SAMtools. Bioinformatics. 25:2078–2079. 2009. View Article : Google Scholar : PubMed/NCBI
16	Lienhard M, Grimm C, Morkel M, Herwig R and Chavez L: MEDIPS: Genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics. 30:284–286. 2014. View Article : Google Scholar :
17	Quinlan AR and Hall IM: BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 26:841–842. 2010. View Article : Google Scholar : PubMed/NCBI
18	Trapnell C, Pachter L and Salzberg SL: TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics. 25:1105–1111. 2009. View Article : Google Scholar : PubMed/NCBI
19	Anders S, Reyes A and Huber W: Detecting differential usage of exons from RNA-seq data. Genome Res. 22:2008–2017. 2012. View Article : Google Scholar : PubMed/NCBI
20	Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ and Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28:511–515. 2010. View Article : Google Scholar : PubMed/NCBI
21	Wang WC, Lin FM, Chang WC, Lin KY, Huang HD and Lin NS: miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics. 10:3282009. View Article : Google Scholar : PubMed/NCBI
22	Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W and Robinson MD: Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 8:1765–1786. 2013. View Article : Google Scholar : PubMed/NCBI
23	Lewis BP, Burge CB and Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 120:15–20. 2005. View Article : Google Scholar : PubMed/NCBI
24	Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, et al: DAvID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35(Web Server issue): W169–W175. 2007. View Article : Google Scholar : PubMed/NCBI
25	Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T and Hatzigeorgiou AG: TarBase 6.0: Capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 40:D222–D229. 2012. View Article : Google Scholar :
26	Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, Paraskevopoulou MD, Prionidis K, Dalamagas T and Hatzigeorgiou AG: DIANA miRPath v.2.0: Investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res. 40:W498–W504. 2012. View Article : Google Scholar : PubMed/NCBI
27	Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR and Ma’ayan A: ChEA: Transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics. 26:2438–2444. 2010. View Article : Google Scholar : PubMed/NCBI
28	Consortium EP: ENCODE Project Consortium: The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 306:636–640. 2004. View Article : Google Scholar
29	Huang GT, Athanassiou C and Benos PV: mirConnX: Condition-specific mRNA-microRNA network integrator. Nucleic Acids Res. 39(suppl): W416–W423. 2011. View Article : Google Scholar : PubMed/NCBI
30	Zhang WC, Shyh-Chang N, Yang H, Rai A, Umashankar S, Ma S, Soh BS, Sun LL, Tai BC, Nga ME, et al: Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis. Cell. 148:259–272. 2012. View Article : Google Scholar : PubMed/NCBI
31	Joshi M, Liu X and Belani CP: Taxanes, past, present, and future impact on non-small cell lung cancer. Anticancer Drugs. 25:571–583. 2014. View Article : Google Scholar : PubMed/NCBI
32	Joseph P, Bowman B, Galban S and Rehemtulla A: A Kras driven murine model elucidates oncogenic role of FADD in lung cancer. Department of Radiation Oncology, University of Michigan; Ann Arbor, MI: 2013, Honor’s Bachelor’s Thesis. http://deepblue.lib.umich.edu/bitstream/handle/2027.42/98916/parijo.pdf?sequence=1.
33	Rauch TA, Wang Z, Wu X, Kernstine KH, Riggs AD and Pfeifer GP: DNA methylation biomarkers for lung cancer. Tumour Biol. 33:287–296. 2012. View Article : Google Scholar
34	Reddy ES, Rao VN and Papas TS: The erg gene: A human gene related to the ets oncogene. Proc Natl Acad Sci USA. 84:6131–6135. 1987. View Article : Google Scholar : PubMed/NCBI
35	Thoms JA, Birger Y, Foster S, Knezevic K, Kirschenbaum Y, Chandrakanthan V, Jonquieres G, Spensberger D, Wong JW, Oram SH, et al: ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer. Blood. 117:7079–7089. 2011. View Article : Google Scholar : PubMed/NCBI
36	Leyten GH, Hessels D, Jannink SA, Smit FP, de Jong H, Cornel EB, de Reijke TM, Vergunst H, Kil P, Knipscheer BC, et al: Prospective multicentre evaluation of PCA3 and TMPRSS2-ERG gene fusions as diagnostic and prognostic urinary biomarkers for prostate cancer. Eur Urol. 65:534–542. 2012. View Article : Google Scholar : PubMed/NCBI
37	Durkin ME, Ullmannova V, Guan M and Popescu NC: Deleted in liver cancer 3 (DLC-3), a novel Rho GTPase-activating protein, is downregulated in cancer and inhibits tumor cell growth. Oncogene. 26:4580–4589. 2007. View Article : Google Scholar : PubMed/NCBI
38	Mokarram P, Kumar K, Brim H, Naghibalhossaini F, Saberi-firoozi M, Nouraie M, Green R, Lee E, Smoot DT and Ashktorab H: Distinct high-profile methylated genes in colorectal cancer. PLoS One. 4:e70122009. View Article : Google Scholar : PubMed/NCBI
39	Bornstein P: Thrombospondins function as regulators of angiogenesis. J Cell Commun Signal. 3:189–200. 2009. View Article : Google Scholar : PubMed/NCBI
40	Brezillon S, Zeltz C, Schneider L, Terryn C, Vuillermoz B, Ramont L, Perrau C, Pluot M, Diebold MD, Radwanska A, et al: Lumican inhibits B16F1 melanoma cell lung metastasis. J Physiol Pharmacol. 60(Suppl 4): 15–22. 2009.
41	Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I and Zhao K: High-resolution profiling of histone methylations in the human genome. Cell. 129:823–837. 2007. View Article : Google Scholar : PubMed/NCBI
42	Hussain M, Rao M, Humphries AE, Hong JA, Liu F, Yang M, Caragacianu D and Schrump DS: Tobacco smoke induces polycomb-mediated repression of Dickkopf-1 in lung cancer cells. Cancer Res. 69:3570–3578. 2009. View Article : Google Scholar : PubMed/NCBI
43	Chen X, Song N, Matsumoto K, Nanashima A, Nagayasu T, Hayashi T, Ying M, Endo D, Wu Z and Koji T: High expression of trimethylated histone H3 at lysine 27 predicts better prognosis in non-small cell lung cancer. Int J Oncol. 43:1467–1480. 2013.PubMed/NCBI
44	Bogush TA, Dudko EA, Beme AA, Bogush EA, Kim AI, Polotsky BE, Tjuljandin SA and Davydov MI: Estrogen receptors, antiestrogens, and non-small cell lung cancer. Biochemistry (Mosc). 75:1421–1427. 2010. View Article : Google Scholar
45	Mak P, Chang C, Pursell B and Mercurio AM: Estrogen receptor β sustains epithelial differentiation by regulating prolyl hydroxylase 2 transcription. Proc Natl Acad Sci USA. 110:4708–4713. 2013. View Article : Google Scholar
46	Zhao G, Nie Y, Lv M, He L, Wang T and Hou Y: ERβ-mediated estradiol enhances epithelial mesenchymal transition of lung adenocarcinoma through increasing transcription of midkine. Mol Endocrinol. 26:1304–1315. 2012. View Article : Google Scholar : PubMed/NCBI
47	Schlossmacher G, Stevens A and White A: Glucocorticoid receptor-mediated apoptosis: Mechanisms of resistance in cancer cells. J Endocrinol. 211:17–25. 2011. View Article : Google Scholar : PubMed/NCBI
48	Koutsimpelas D, Pongsapich W, Heinrich U, Mann S, Mann WJ and Brieger J: Promoter methylation of MGMT, MLH1 and RASSF1A tumor suppressor genes in head and neck squamous cell carcinoma: Pharmacological genome demethylation reduces proliferation of head and neck squamous carcinoma cells. Oncol Rep. 27:1135–1141. 2012.PubMed/NCBI
49	Abe M, Hamada J, Takahashi O, Takahashi Y, Tada M, Miyamoto M, Morikawa T, Kondo S and Moriuchi T: Disordered expression of HOX genes in human non-small cell lung cancer. Oncol Rep. 15:797–802. 2006.PubMed/NCBI
50	Svingen T and Tonissen KF: Altered HOX gene expression in human skin and breast cancer cells. Cancer Biol Ther. 2:518–523. 2003. View Article : Google Scholar : PubMed/NCBI
51	Argiropoulos B, Yung E and Humphries RK: Unraveling the crucial roles of Meis1 in leukemogenesis and normal hematopoiesis. Genes Dev. 21:2845–2849. 2007. View Article : Google Scholar : PubMed/NCBI
52	Hatcher CJ, Kim M-S, Mah CS, Goldstein MM, Wong B, Mikawa T and Basson CT: TBX5 transcription factor regulates cell proliferation during cardiogenesis. Dev Biol. 230:177–188. 2001. View Article : Google Scholar : PubMed/NCBI
53	Aherne NJ, Rangaswamy G and Thirion P: Prostate cancer in a male with Holt-Oram syndrome: First clinical association of the TBX5 mutation. Case Rep Urol. 2013:4053432013.PubMed/NCBI
54	Miko E, Margitai Z, Czimmerer Z, Várkonyi I, Dezso B, Lányi A, Bacsó Z and Scholtz B: miR-126 inhibits proliferation of small cell lung cancer cells by targeting SLC7A5. FEBS Lett. 585:1191–1196. 2011. View Article : Google Scholar : PubMed/NCBI
55	Zhou H, Xu X, Xun Q, Yu D, Ling J, Guo F, Yan Y, Shi J and Hu Y: microRNA-30c negatively regulates endometrial cancer cells by targeting metastasis-associated gene-1. Oncol Rep. 27:807–812. 2012.