Genome-wide profiling of long non-coding RNA expression patterns in the EGFR-TKI resistance of lung adenocarcinoma by microarray

Wu,Ying; Yu,Dan-Dan; Hu,Yong; Yan,Dali; Chen,Xiu; Cao,Hai‑Xia; Yu,Shao-Rong; Wang,Zhuo; Feng,Ji-Feng

doi:10.3892/or.2016.4758

Genome-wide profiling of long non-coding RNA expression patterns in the EGFR-TKI resistance of lung adenocarcinoma by microarray

Authors:
- Ying Wu
- Dan-Dan Yu
- Yong Hu
- Dali Yan
- Xiu Chen
- Hai‑Xia Cao
- Shao-Rong Yu
- Zhuo Wang
- Ji-Feng Feng
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Affiliations: The First Clinical School of Nanjing Medical University, Nanjing, Jiangsu 210009, P.R. China, Department of Chemotherapy, Nanjing Medical University Affiliated Cancer Hospital Cancer Institute of Jiangsu Province, Nanjing, Jiangsu 210009, P.R. China, The Fourth Clinical School of Nanjing Medical University, Nanjing, Jiangsu 210009, P.R. China
Published online on: April 20, 2016 https://doi.org/10.3892/or.2016.4758
Pages: 3371-3386

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Abstract

Mutations in the epidermal growth factor receptor (EGFR) make lung adenocarcinoma cells sensitive to EGFR tyrosine kinase inhibitors (TKIs). Long-term cancer therapy may cause the occurrence of acquired resistance to EGFR TKIs. Long non-coding RNAs (lncRNAs) play important roles in tumor formation, tumor metastasis and the development of EGFR-TKI resistance in lung cancer. To gain insight into the molecular mechanisms of EGFR-TKI resistance, we generated an EGFR-TKI-resistant HCC827-8-1 cell line and analyzed expression patterns by lncRNA microarray and compared it with its parental HCC827 cell line. A total of 1,476 lncRNA transcripts and 1,026 mRNA transcripts were dysregulated in the HCC827‑8-1 cells. The expression levels of 7 chosen lncRNAs were validated by real-time quantitative PCR. As indicated by functional analysis, several groups of lncRNAs may be involved in the bio-pathways associated with EGFR-TKI resistance through their cis- and/or trans‑regulation of protein-coding genes. Thus, lncRNAs may be used as novel candidate biomarkers and potential targets in EGFR-TKI therapy in the future.

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1	Jackman DM, Miller VA, Cioffredi LA, Yeap BY, Jänne PA, Riely GJ, Ruiz MG, Giaccone G, Sequist LV and Johnson BE: Impact of epidermal growth factor receptor and KRAS mutations on clinical outcomes in previously untreated non-small cell lung cancer patients: Results of an online tumor registry of clinical trials. Clin Cancer Res. 15:5267–5273. 2009. View Article : Google Scholar : PubMed/NCBI
2	Godin-Heymann N, Bryant I, Rivera MN, Ulkus L, Bell DW, Riese DJ II, Settleman J and Haber DA: Oncogenic activity of epidermal growth factor receptor kinase mutant alleles is enhanced by the T790M drug resistance mutation. Cancer Res. 67:7319–7326. 2007. View Article : Google Scholar : PubMed/NCBI
3	McDermott U, Pusapati RV, Christensen JG, Gray NS and Settleman J: Acquired resistance of non-small cell lung cancer cells to MET kinase inhibition is mediated by a switch to epidermal growth factor receptor dependency. Cancer Res. 70:1625–1634. 2010. View Article : Google Scholar : PubMed/NCBI
4	Yamamoto C, Basaki Y, Kawahara A, Nakashima K, Kage M, Izumi H, Kohno K, Uramoto H, Yasumoto K, Kuwano M, et al: Loss of PTEN expression by blocking nuclear translocation of EGR1 in gefitinib-resistant lung cancer cells harboring epidermal growth factor receptor-activating mutations. Cancer Res. 70:8715–8725. 2010. View Article : Google Scholar : PubMed/NCBI
5	Lee JT: Epigenetic regulation by long noncoding RNAs. Science. 338:1435–1439. 2012. View Article : Google Scholar : PubMed/NCBI
6	Qiu M, Xu Y, Yang X, Wang J, Hu J, Xu L and Yin R: CCAT2 is a lung adenocarcinoma-specific long non-coding RNA and promotes invasion of non-small cell lung cancer. Tumour Biol. 35:5375–5380. 2014. View Article : Google Scholar : PubMed/NCBI
7	Gutschner T, Hämmerle M, Eissmann M, Hsu J, Kim Y, Hung G, Revenko A, Arun G, Stentrup M, Gross M, et al: The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res. 73:1180–1189. 2013. View Article : Google Scholar :
8	Liu XH, Liu ZL, Sun M, Liu J, Wang ZX and De W: The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer. BMC Cancer. 13:4642013. View Article : Google Scholar : PubMed/NCBI
9	Liu Z1, Sun M, Lu K, Liu J, Zhang M, Wu W, De W, Wang Z and Wang R: The long noncoding RNA HOTAIR contributes to cisplatin resistance of human lung adenocarcinoma cells via downregualtion of p21^WAF1/CIP1 expression. PLoS One. 8:e772932013. View Article : Google Scholar
10	Dong S, Qu X, Li W, Zhong X, Li P, Yang S, Chen X, Shao M and Zhang L: The long non-coding RNA, GAS5, enhances gefitinib-induced cell death in innate EGFR tyrosine kinase inhibitor-resistant lung adenocarcinoma cells with wide-type EGFR via downregulation of the IGF-1R expression. J Hematol Oncol. 8:432015. View Article : Google Scholar : PubMed/NCBI
11	Wu Y, Yu DD, Hu Y, Cao HX, Yu SR, Liu SW and Feng JF: LXR ligands sensitize EGFR-TKI-resistant human lung cancer cells in vitro by inhibiting Akt activation. Biochem Biophys Res Commun. 467:900–905. 2015. View Article : Google Scholar : PubMed/NCBI
12	Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2^−ΔΔ^CT method. Methods. 25:402–408. 2001. View Article : Google Scholar
13	Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458:223–227. 2009. View Article : Google Scholar : PubMed/NCBI
14	Efron B and Tibshirani R: Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol. 23:70–86. 2002. View Article : Google Scholar : PubMed/NCBI
15	Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, et al: lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 477:295–300. 2011. View Article : Google Scholar : PubMed/NCBI
16	Remon J, Morán T, Majem M, Reguart N, Dalmau E, Márquez-Medina D and Lianes P: Acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors in EGFR-mutant non-small cell lung cancer: A new era begins. Cancer Treat Rev. 40:93–101. 2014. View Article : Google Scholar
17	Li LH, Wu P, Lee JY, Li PR, Hsieh WY, Ho CC, Ho CL, Chen WJ, Wang CC, Yen MY, et al: Hinokitiol induces DNA damage and autophagy followed by cell cycle arrest and senescence in gefitinib-resistant lung adenocarcinoma cells. PLoS One. 9:e1042032014. View Article : Google Scholar : PubMed/NCBI
18	Ju L and Zhou C: Association of integrin beta1 and c-MET in mediating EGFR TKI gefitinib resistance in non-small cell lung cancer. Cancer Cell Int. 13:152013. View Article : Google Scholar : PubMed/NCBI
19	Terai H, Soejima K, Yasuda H, Sato T, Naoki K, Ikemura S, Arai D, Ohgino K, Ishioka K, Hamamoto J, et al: Long-term exposure to gefitinib induces acquired resistance through DNA methylation changes in the EGFR-mutant PC9 lung cancer cell line. Int J Oncol. 46:430–436. 2015.
20	Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, et al: Long noncoding RNAs with enhancer-like function in human cells. Cell. 143:46–58. 2010. View Article : Google Scholar : PubMed/NCBI
21	Yang X, Zhang Y, Hosaka K, Andersson P, Wang J, Tholander F, Cao Z, Morikawa H, Tegnér J, Yang Y, et al: VEGF-B promotes cancer metastasis through a VEGF-A-independent mechanism and serves as a marker of poor prognosis for cancer patients. Proc Natl Acad Sci USA. 112:E2900–E2909. 2015. View Article : Google Scholar : PubMed/NCBI
22	Guttman M and Rinn JL: Modular regulatory principles of large non-coding RNAs. Nature. 482:339–346. 2012. View Article : Google Scholar : PubMed/NCBI
23	Vaishnav YNV, Vaishnav MY and Pant V: The molecular and functional characterization of E2F-5 transcription factor. Biochem Biophys Res Commun. 242:586–592. 1998. View Article : Google Scholar : PubMed/NCBI
24	Stewart ZA, Westfall MD and Pietenpol JA: Cell-cycle dysregulation and anticancer therapy. Trends Pharmacol Sci. 24:139–145. 2003. View Article : Google Scholar : PubMed/NCBI
25	Suenaga M, Yamaguchi A, Soda H, Orihara K, Tokito Y, Sakaki Y, Umehara M, Terashi K, Kawamata N, Oka M, et al: Antiproliferative effects of gefitinib are associated with suppression of E2F-1 expression and telomerase activity. Anticancer Res. 26:3387–3391. 2006.PubMed/NCBI
26	Okabe T, Okamoto I, Tsukioka S, Uchida J, Hatashita E, Yamada Y, Yoshida T, Nishio K, Fukuoka M, Jänne PA, et al: Addition of S-1 to the epidermal growth factor receptor inhibitor gefitinib overcomes gefitinib resistance in non-small cell lung cancer cell lines with MET amplification. Clin Cancer Res. 15:907–913. 2009. View Article : Google Scholar : PubMed/NCBI
27	Lindeman GJ, Gaubatz S, Livingston DM and Ginsberg D: The subcellular localization of E2F-4 is cell-cycle dependent. Proc Natl Acad Sci USA. 94:5095–5100. 1997. View Article : Google Scholar : PubMed/NCBI
28	Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 448:553–560. 2007. View Article : Google Scholar : PubMed/NCBI
29	Rakha EA, Pinder SE, Paish EC, Robertson JF and Ellis IO: Expression of E2F-4 in invasive breast carcinomas is associated with poor prognosis. J Pathol. 203:754–761. 2004. View Article : Google Scholar : PubMed/NCBI
30	Garneau H, Paquin MC, Carrier JC and Rivard N: E2F4 expression is required for cell cycle progression of normal intestinal crypt cells and colorectal cancer cells. J Cell Physiol. 221:350–358. 2009. View Article : Google Scholar : PubMed/NCBI
31	Molina-Privado I, Jiménez-P R, Montes-Moreno S, Chiodo Y, Rodríguez-Martínez M, Sánchez-Verde L, Iglesias T, Piris MA and Campanero MR: E2F4 plays a key role in Burkitt lymphoma tumorigenesis. Leukemia. 26:2277–2285. 2012. View Article : Google Scholar : PubMed/NCBI
32	Sirito M, Lin Q, Deng JM, Behringer RR and Sawadogo M: Overlapping roles and asymmetrical cross-regulation of the USF proteins in mice. Proc Natl Acad Sci USA. 95:3758–3763. 1998. View Article : Google Scholar : PubMed/NCBI
33	Nielsen FC, Pedersen K, Hansen TV, Rourke IJ and Rehfeld JF: Transcriptional regulation of the human cholecystokinin gene: Composite action of upstream stimulatory factor, Sp1, and members of the CREB/ATF-AP-1 family of transcription factors. DNA Cell Biol. 15:53–63. 1996. View Article : Google Scholar : PubMed/NCBI
34	Viney TJ, Schmidt TW, Gierasch W, Sattar AW, Yaggie RE, Kuburas A, Quinn JP, Coulson JM and Russo AF: Regulation of the cell-specific calcitonin/calcitonin gene-related peptide enhancer by USF and the Foxa2 forkhead protein. J Biol Chem. 279:49948–49955. 2004. View Article : Google Scholar : PubMed/NCBI
35	Paterson JM, Morrison CF, Mendelson SC, McAllister J and Quinn JP: An upstream stimulatory factor (USF) binding motif is critical for rat preprotachykinin-A promoter activity in PC12 cells. Biochem J. 310:401–406. 1995. View Article : Google Scholar : PubMed/NCBI
36	Hadsell DL, Bonnette S, George J, Torres D, Klimentidis Y, Gao S, Haney PM, Summy-Long J, Soloff MS, Parlow AF, et al: Diminished milk synthesis in upstream stimulatory factor 2 null mice is associated with decreased circulating oxytocin and decreased mammary gland expression of eukaryotic initiation factors 4E and 4G. Mol Endocrinol. 17:2251–2267. 2003. View Article : Google Scholar : PubMed/NCBI
37	Gao E, Wang Y, Alcorn JL and Mendelson CR: Transcription factor USF2 is developmentally regulated in fetal lung and acts together with USF1 to induce SP-A gene expression. Am J Physiol Lung Cell Mol Physiol. 284:L1027–L1036. 2003. View Article : Google Scholar : PubMed/NCBI
38	Coulson JM, Edgson JL, Marshall-Jones ZV, Mulgrew R, Quinn JP and Woll PJ: Upstream stimulatory factor activates the vasopressin promoter via multiple motifs, including a non-canonical E-box. Biochem J. 369:549–561. 2003. View Article : Google Scholar
39	McMurray HR and McCance DJ: Human papillomavirus type 16 E6 activates TERT gene transcription through induction of c-Myc and release of USF-mediated repression. J Virol. 77:9852–9861. 2003. View Article : Google Scholar : PubMed/NCBI
40	Goueli BS and Janknecht R: Regulation of telomerase reverse transcriptase gene activity by upstream stimulatory factor. Oncogene. 22:8042–8047. 2003. View Article : Google Scholar : PubMed/NCBI
41	Pawar SA, Szentirmay MN, Hermeking H and Sawadogo M: Evidence for a cancer-specific switch at the CDK4 promoter with loss of control by both USF and c-Myc. Oncogene. 23:6125–6135. 2004. View Article : Google Scholar : PubMed/NCBI
42	Coulson JM, Fiskerstrand CE, Woll PJ and Quinn JP: E-box motifs within the human vasopressin gene promoter contribute to a major enhancer in small-cell lung cancer. Biochem J. 344:961–970. 1999. View Article : Google Scholar : PubMed/NCBI
43	Grace CO, Fink G and Quinn JP: Characterization of potential regulatory elements within the rat arginine vasopressin proximal promoter. Neuropeptides. 33:81–90. 1999. View Article : Google Scholar
44	Khattar NH, Lele SM and Kaetzel CS: Down-regulation of the polymeric immunoglobulin receptor in non-small cell lung carcinoma: Correlation with dysregulated expression of the transcription factors USF and AP2. J Biomed Sci. 12:65–77. 2005. View Article : Google Scholar : PubMed/NCBI
45	Ocejo-Garcia M, Baokbah TA, Ashurst HL, Cowlishaw D, Soomro I, Coulson JM and Woll PJ: Roles for USF-2 in lung cancer proliferation and bronchial carcinogenesis. J Pathol. 206:151–159. 2005. View Article : Google Scholar : PubMed/NCBI
46	Chen B, Hsu R, Li Z, Kogut PC, Du Q, Rouser K, Camoretti-Mercado B and Solway J: Upstream stimulatory factor 1 activates GATA5 expression through an E-box motif. Biochem J. 446:89–98. 2012. View Article : Google Scholar : PubMed/NCBI
47	Kakita T, Hasegawa K, Morimoto T, Kaburagi S, Wada H and Sasayama S: p300 protein as a coactivator of GATA-5 in the transcription of cardiac-restricted atrial natriuretic factor gene. J Biol Chem. 274:34096–34102. 1999. View Article : Google Scholar : PubMed/NCBI
48	Singh MK, Li Y, Li S, Cobb RM, Zhou D, Lu MM, Epstein JA, Morrisey EE and Gruber PJ: Gata4 and Gata5 cooperatively regulate cardiac myocyte proliferation in mice. J Biol Chem. 285:1765–1772. 2010. View Article : Google Scholar :
49	Tummala R, Romano RA, Fuchs E and Sinha S: Molecular cloning and characterization of AP-2 epsilon, a fifth member of the AP-2 family. Gene. 321:93–102. 2003. View Article : Google Scholar : PubMed/NCBI
50	Hoffman TL, Javier AL, Campeau SA, Knight RD and Schilling TF: Tfap2 transcription factors in zebrafish neural crest development and ectodermal evolution. J Exp Zoolog B Mol Dev Evol. 308:679–691. 2007. View Article : Google Scholar
51	Kuckenberg P, Kubaczka C and Schorle H: The role of transcription factor Tcfap2c/TFAP2C in trophectoderm development. Reprod Biomed Online. 25:12–20. 2012. View Article : Google Scholar : PubMed/NCBI
52	Li W and Cornell RA: Redundant activities of Tfap2a and Tfap2c are required for neural crest induction and development of other non-neural ectoderm derivatives in zebrafish embryos. Dev Biol. 304:338–354. 2007. View Article : Google Scholar : PubMed/NCBI
53	Li X, Glubrecht DD and Godbout R: AP2 transcription factor induces apoptosis in retinoblastoma cells. Genes Chromosomes Cancer. 49:819–830. 2010.PubMed/NCBI
54	Van Otterloo E, Li W, Garnett A, Cattell M, Medeiros DM and Cornell RA: Novel Tfap2-mediated control of soxE expression facilitated the evolutionary emergence of the neural crest. Development. 139:720–730. 2012. View Article : Google Scholar : PubMed/NCBI
55	Rappoport JZ and Simon SM: Endocytic trafficking of activated EGFR is AP-2 dependent and occurs through preformed clathrin spots. J Cell Sci. 122:1301–1305. 2009. View Article : Google Scholar : PubMed/NCBI
56	Park JM, Wu T, Cyr AR, Woodfield GW, De Andrade JP, Spanheimer PM, Li T, Sugg SL, Lal G, Domann FE, et al: The role of Tcfap2c in tumorigenesis and cancer growth in an activated Neu model of mammary carcinogenesis. Oncogene. 34:6105–6104. 2015. View Article : Google Scholar : PubMed/NCBI
57	Perkins SM, Bales C, Vladislav T, Althouse S, Miller KD, Sandusky G, Badve S and Nakshatri H: TFAP2C expression in breast cancer: Correlation with overall survival beyond 10 years of initial diagnosis. Breast Cancer Res Treat. 152:519–531. 2015. View Article : Google Scholar : PubMed/NCBI
58	Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 22:1775–1789. 2012. View Article : Google Scholar : PubMed/NCBI
59	Rinn JL and Chang HY: Genome regulation by long noncoding RNAs. Annu Rev Biochem. 81:145–166. 2012. View Article : Google Scholar : PubMed/NCBI