The long non-coding RNA EPB41L4A-AS2 inhibits tumor proliferation and is associated with favorable prognoses in breast cancer and other solid tumors

Oncotarget

Volumn 7, Issue 15, 2016, Pages 20704-20717

  Xu, Shouping ^a   Wang, Peiyuan ^a   You, Zilong ^a   Meng, Hongxue ^a   Mu, Guannan ^a   Bai, Xianan ^a   Zhang, Guangwen ^a   Zhang, Jinfeng ^a   Pang, Da ^a,b  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b Biopharmaceutical Institute   (China)

Author keywords

Antisense lncRNA; Breast cancer; EPB41L4A AS2; Prognostic value; Proliferation

Indexed keywords

LONG UNTRANSLATED RNA; LONG UNTRANSLATED RNA EPB41L4A AS2; UNCLASSIFIED DRUG; TUMOR MARKER;

ADULT; ARTICLE; BREAST CANCER; BREAST CANCER CELL LINE; CANCER CELL; CANCER INHIBITION; CANCER PATIENT; CANCER PROGNOSIS; CANCER TISSUE; CELL PROLIFERATION; CLINICAL FEATURE; COHORT ANALYSIS; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; DISEASE COURSE; EXPRESSION VECTOR; GENE; GENE EXPRESSION; GENE FUNCTION; GENE ONTOLOGY; GENE OVEREXPRESSION; GENETIC ASSOCIATION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; KIDNEY CANCER; LUNG CANCER; LUNG CANCER CELL LINE; MAJOR CLINICAL STUDY; META ANALYSIS; NONHUMAN; PREDICTIVE VALUE; REFERENCE VALUE; RENAL CANCER CELL LINE; SOLID TUMOR; VALIDATION STUDY; APOPTOSIS; BREAST TUMOR; FEMALE; GENE EXPRESSION REGULATION; GENETICS; KIDNEY TUMOR; LUNG TUMOR; MIDDLE AGED; PATHOLOGY; PROGNOSIS; SURVIVAL RATE; TUMOR CELL CULTURE;

APOPTOSIS; BIOMARKERS, TUMOR; BREAST NEOPLASMS; CELL PROLIFERATION; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; KIDNEY NEOPLASMS; LUNG NEOPLASMS; MIDDLE AGED; PROGNOSIS; RNA, LONG NONCODING; SURVIVAL RATE; TUMOR CELLS, CULTURED;

EID: 84964727009     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.8007     Document Type: Article

References (70)

1. DeSantis C, Ma J, Bryan L, Jemal A. Breast cancer statistics, 2013. CA Cancer J Clin. 2014; 64:52-62.
2. Siegel R, Ma J, Zou Z, Jemal A. Cancer statistics, 2014. CA Cancer J Clin. 2014; 64:9-29.
3. Pagani O, Senkus E, Wood W, Colleoni M, Cufer T, Kyriakides S, Costa A, Winer EP, Cardoso F, Force E-MT. International guidelines for management of metastatic breast cancer: can metastatic breast cancer be cured? J Natl Cancer Inst. 2010; 102:456-463.
4. Stevens RG, Brainard GC, Blask DE, Lockley SW, Motta ME. Breast cancer and circadian disruption from electric lighting in the modern world. CA Cancer J Clin. 2014; 64:207-218.
5. Huang CC, Tu SH, Lien HH, Huang CS, Huang CJ, Lai LC, Tsai MH, Chuang EY. Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures. Breast Cancer Res Treat. 2014; 147:353-370.
6. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009; 136:629-641.
7. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009; 23:1494-1504.
8. Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nat Struct Mol Biol. 2014; 21:633-640.
9. Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014; 15:7-21.
10. Fukuoka H, Takahashi Y. The role of genetic and epigenetic changes in pituitary tumorigenesis. Neurol Med Chir (Tokyo). 2014; 54:943-957.
11. McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015; 521:232-236.
12. Yarmishyn AA, Kurochkin IV. Long noncoding RNAs: a potential novel class of cancer biomarkers. Front Genet. 2015; 6:145.
13. Okugawa Y, Grady WM, Goel A. Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers. Gastroenterology. 2015; 149:1204-1225 e1212.
14. Meseure D, Drak Alsibai K, Nicolas A, Bieche I, Morillon A. Long Noncoding RNAs as New Architects in Cancer Epigenetics, Prognostic Biomarkers, and Potential Therapeutic Targets. Biomed Res Int. 2015; 2015:320214.
15. Jin K, Luo G, Xiao Z, Liu Z, Liu C, Ji S, Xu J, Liu L, Long J, Ni Q, Yu X. Noncoding RNAs as potential biomarkers to predict the outcome in pancreatic cancer. Drug Des Devel Ther. 2015; 9:1247-1255.
16. Cui W, Qian Y, Zhou X, Lin Y, Jiang J, Chen J, Zhao Z, Shen B. Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. BMC genomics. 2015; 16:S3.
17. Wang J, Zhang KY, Liu SM, Sen S. Tumor-associated circulating microRNAs as biomarkers of cancer. Molecules. 2014; 19:1912-1938.
18. Veltri WR. Non-coding RNAs as biomarkers for metastatic prostate cancer. Lancet Oncol. 2014; 15:1412-1413.
19. Ronnau CG, Verhaegh GW, Luna-Velez MV, Schalken JA. Noncoding RNAs as novel biomarkers in prostate cancer. Biomed Res Int. 2014; 2014:591703.
20. Prensner JR, Zhao S, Erho N, Schipper M, Iyer MK, Dhanasekaran SM, Magi-Galluzzi C, Mehra R, Sahu A, Siddiqui J, Davicioni E, Den RB, Dicker AP, et al. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol. 2014; 15: 1469-1480.
21. Lee B, Mazar J, Aftab MN, Qi F, Shelley J, Li JL, Govindarajan S, Valerio F, Rivera I, Thurn T, Tran TA, Kameh D, Patel V, et al. Long noncoding RNAs as putative biomarkers for prostate cancer detection. J Mol Diagn. 2014; 16:615-626.
22. Bussemakers MJ, van Bokhoven A, Verhaegh GW, Smit FP, Karthaus HF, Schalken JA, Debruyne FM, Ru N, Isaacs WB. DD3: a new prostate-specific gene, highly overexpressed in prostate cancer. Cancer Res. 1999; 59:5975-5979.
23. Crawford ED, Rove KO, Trabulsi EJ, Qian J, Drewnowska KP, Kaminetsky JC, Huisman TK, Bilowus ML, Freedman SJ, Glover WL, Jr., Bostwick DG. Diagnostic performance of PCA3 to detect prostate cancer in men with increased prostate specific antigen: a prospective study of 1, 962 cases. J Urol. 2012; 188:1726-1731.
24. Wang XS, Zhang Z, Wang HC, Cai JL, Xu QW, Li MQ, Chen YC, Qian XP, Lu TJ, Yu LZ, Zhang Y, Xin DQ, Na YQ, et al. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin Cancer Res. 2006; 12:4851-4858.
25. Zhang XW, Bu P, Liu L, Zhang XZ, Li J. Overexpression of long non-coding RNA PVT1 in gastric cancer cells promotes the development of multidrug resistance. Biochem Biophys Res Commun. 2015; 462:227-232.
26. Wang Y, Zhang D, Wu K, Zhao Q, Nie Y, Fan D. Long noncoding RNA MRUL promotes ABCB1 expression in multidrug-resistant gastric cancer cell sublines. Mol Cell Biol. 2014; 34:3182-3193.
27. Takahashi K, Yan IK, Wood J, Haga H, Patel T. Involvement of extracellular vesicle long noncoding RNA (linc-VLDLR) in tumor cell responses to chemotherapy. Mol Cancer Res. 2014; 12:1377-1387.
28. Godinho MF, Wulfkuhle JD, Look MP, Sieuwerts AM, Sleijfer S, Foekens JA, Petricoin EF, 3rd, Dorssers LC, van Agthoven T. BCAR4 induces antioestrogen resistance but sensitises breast cancer to lapatinib. Br J Cancer. 2012; 107:947-955.
29. Li T, Xie J, Shen C, Cheng D, Shi Y, Wu Z, Deng X, Chen H, Shen B, Peng C, Li H, Zhan Q, Zhu Z. Upregulation of long noncoding RNA ZEB1-AS1 promotes tumor metastasis and predicts poor prognosis in hepatocellular carcinoma. Oncogene. 2015. Jun 15. doi: 10.1038/onc.2015.223. [Epub ahead of print].
30. Cheng Z, Guo J, Chen L, Luo N, Yang W, Qu X. A long noncoding RNA AB073614 promotes tumorigenesis and predicts poor prognosis in ovarian cancer. Oncotarget. 2015; 6:25381-25389. doi: 10.18632/oncotarget.4541.
31. Bo H, Gong Z, Zhang W, Li X, Zeng Y, Liao Q, Chen P, Shi L, Lian Y, Jing Y, Tang K, Li Z, Zhou Y, et al. Upregulated long non-coding RNA AFAP1-AS1 expression is associated with progression and poor prognosis of nasopharyngeal carcinoma. Oncotarget. 2015; 6:20404-20418. doi: 10.18632/oncotarget.4057.
32. Zhang EB, Kong R, Yin DD, You LH, Sun M, Han L, Xu TP, Xia R, Yang JS, De W, Chen J. Long noncoding RNA ANRIL indicates a poor prognosis of gastric cancer and promotes tumor growth by epigenetically silencing of miR-99a/miR-449a. Oncotarget. 2014; 5:2276-2292. doi: 10.18632/oncotarget.1902.
33. Quagliata L, Matter MS, Piscuoglio S, Arabi L, Ruiz C, Procino A, Kovac M, Moretti F, Makowska Z, Boldanova T, Andersen JB, Hammerle M, Tornillo L, et al. Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Hepatology. 2014; 59:911-923.
34. Hu Y, Wang J, Qian J, Kong X, Tang J, Wang Y, Chen H, Hong J, Zou W, Chen Y, Xu J, Fang JY. Long noncoding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer. Cancer Res. 2014; 74:6890-6902.
35. Hu Y, Chen HY, Yu CY, Xu J, Wang JL, Qian J, Zhang X, Fang JY. A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget. 2014; 5:2230-2242. doi: 10.18632/oncotarget.1895.
36. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S, Miyano S, Mori M. Long noncoding RNA HOTAIR regulates polycombdependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011; 71: 6320-6326.
37. Meng L, Ward AJ, Chun S, Bennett CF, Beaudet AL, Rigo F. Towards a therapy for Angelman syndrome by targeting a long non-coding RNA. Nature. 2015; 518:409-412.
38. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, et al. Complete sequencing and characterization of 21, 243 full-length human cDNAs. Nat Genet. 2004; 36:40-45.
39. Feigin ME, Xue B, Hammell MC, Muthuswamy SK. G-protein-coupled receptor GPR161 is overexpressed in breast cancer and is a promoter of cell proliferation and invasion. Proc Natl Acad Sci U S A. 2014; 111:4191-4196.
40. Huang Y, Vasilatos SN, Boric L, Shaw PG, Davidson NE. Inhibitors of histone demethylation and histone deacetylation cooperate in regulating gene expression and inhibiting growth in human breast cancer cells. Breast Cancer Res Treat. 2012; 131:777-789.
41. Jin ZT, Li K, Li M, Ren ZG, Wang FS, Zhu JY, Leng XS, Yu WD. G-protein coupled receptor 34 knockdown impairs the proliferation and migration of HGC-27 gastric cancer cells in vitro. Chin Med J (Engl). 2015; 128:545-549.
42. Klein DK, Hoffmann S, Ahlskog JK, O'Hanlon K, Quaas M, Larsen BD, Rolland B, Rosner HI, Walter D, Kousholt AN, Menzel T, Lees M, Johansen JV, et al. Cyclin F suppresses B-Myb activity to promote cell cycle checkpoint control. Nat Commun. 2015; 6:5800.
43. Li XY, Jiang LJ, Chen L, Ding ML, Guo HZ, Zhang W, Zhang HX, Ma XD, Liu XZ, Xi XD, Chen SJ, Chen Z, Zhu J. RIG-I modulates Src-mediated AKT activation to restrain leukemic stemness. Mol Cell. 2014; 53:407-419.
44. Piunti A, Rossi A, Cerutti A, Albert M, Jammula S, Scelfo A, Cedrone L, Fragola G, Olsson L, Koseki H, Testa G, Casola S, Helin K, et al. Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication. Nat Commun. 2014; 5:3649.
45. Shio S, Kodama Y, Ida H, Shiokawa M, Kitamura K, Hatano E, Uemoto S, Chiba T. Loss of RUNX3 expression by histone deacetylation is associated with biliary tract carcinogenesis. Cancer Sci. 2011; 102:776-783.
46. Szabo A, Fekete T, Koncz G, Kumar BV, Pazmandi K, Foldvari Z, Hegedus B, Garay T, Bacsi A, Rajnavolgyi E, Lanyi A. RIG-I inhibits the MAPK-dependent proliferation of BRAF mutant melanoma cells via MKP-1. Cell Signal. 2016.
47. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007; 316:1484-1488.
48. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, et al. The transcriptional landscape of the mammalian genome. Science. 2005; 309:1559-1563.
49. Lipovich L, Johnson R, Lin CY. MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochim Biophys Acta. 2010; 1799:597-615.
50. Chen LL, Carmichael GG. Long noncoding RNAs in mammalian cells: what, where, and why? Wiley Interdiscip Rev RNA. 2010; 1:2-21.
51. Wei Y, Niu B. Role of MALAT1 as a Prognostic Factor for Survival in Various Cancers: A Systematic Review of the Literature with Meta-Analysis. Dis Markers. 2015; 2015:164635.
52. Yang L, Bai HS, Deng Y, Fan L. High MALAT1 expression predicts a poor prognosis of cervical cancer and promotes cancer cell growth and invasion. Eur Rev Med Pharmacol Sci. 2015; 19:3187-3193.
53. Zhang J, Zhang B, Wang T, Wang H. LncRNA MALAT1 overexpression is an unfavorable prognostic factor in human cancer: evidence from a meta-analysis. Int J Clin Exp Med. 2015; 8:5499-5505.
54. Loewen G, Jayawickramarajah J, Zhuo Y, Shan B. Functions of lncRNA HOTAIR in lung cancer. J Hematol Oncol. 2014; 7:90.
55. Gokmen-Polar Y, Vladislav IT, Neelamraju Y, Janga SC, Badve S. Prognostic impact of HOTAIR expression is restricted to ER-negative breast cancers. Sci Rep. 2015; 5:8765.
56. Gu Y, Chen T, Li G, Yu X, Lu Y, Wang H, Teng L. LncRNAs: emerging biomarkers in gastric cancer. Future Oncol. 2015; 11:2427-2441.
57. Wang S, Wang Z. Prognostic value of long noncoding RNA HOTAIR in digestive system malignancies. J Gastroenterol Hepatol. 2015; 30:1123-1133.
58. Yu X, Li Z. Long non-coding RNA HOTAIR: A novel oncogene (Review). Mol Med Rep. 2015; 12:5611-5618.
59. Zhao W, Dong S, Duan B, Chen P, Shi L, Gao H, Qi H. HOTAIR is a predictive and prognostic biomarker for patients with advanced gastric adenocarcinoma receiving fluorouracil and platinum combination chemotherapy. Am J Transl Res. 2015; 7:1295-1302.
60. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25: 1915-1927.
61. Guo X, Gao L, Liao Q, Xiao H, Ma X, Yang X, Luo H, Zhao G, Bu D, Jiao F, Shao Q, Chen R, Zhao Y. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res. 2013; 41:e35.
62. Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, Zhao G, Luo H, Bu D, Zhao H, Skogerbo G, Wu Z, Zhao Y. Largescale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011; 39:3864-3878.
63. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, et al. Antisense transcription in the mammalian transcriptome. Science. 2005; 309:1564-1566.
64. Pang KC, Frith MC, Mattick JS. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 2006; 22:1-5.
65. Morris KV, Vogt PK. Long antisense non-coding RNAs and their role in transcription and oncogenesis. Cell cycle. 2010; 9:2544-2547.
66. Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature. 2008; 451:202-206.
67. Goldhirsch A, Winer EP, Coates AS, Gelber RD, Piccart-Gebhart M, Thurlimann B, Senn HJ, Panel M. Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2013. Ann Oncol. 2013; 24:2206-2223.
68. Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC bioinformatics. 2010; 11:221.
69. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4:44-57.
70. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005; 4:Article17.