A lincRNA connected to cell mortality and epigenetically-silenced in most common human cancers

Epigenetics

Volumn 10, Issue 11, 2015, Pages 1074-1083

  Vrba, Lukas ^a   Garbe, James C ^b   Stampfer, Martha R ^a,b   Futscher, Bernard W ^a,c  

^a UNIVERSITY OF ARIZONA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

Author keywords

Breast cancer; DNA methylation; Epigenetics; HMEC; Immortality; lincRNA; lncRNA; Mammary epithelia; MORT; ncRNA; ZNF667 AS1

Indexed keywords

LONG UNTRANSLATED RNA; MORT LONG NONCODING RNA, HUMAN;

ADULT; AGED; ARTICLE; BREAST EPITHELIUM CELL; CELL DEATH; CELL IMMORTALIZATION; CPG ISLAND; DISEASE ASSOCIATION; DNA METHYLATION; DOWN REGULATION; EPIGENETICS; FEMALE; GENE EXPRESSION; GENE ONTOLOGY; GENE SILENCING; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MICROARRAY ANALYSIS; NEOPLASM; PHENOTYPE; REAL TIME POLYMERASE CHAIN REACTION; VERY ELDERLY; YOUNG ADULT; CELL SURVIVAL; CYTOLOGY; DNA MICROARRAY; EPITHELIUM CELL; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; MAMMARY GLAND; MIDDLE AGED; PROCEDURES; TUMOR CELL LINE;

AGED, 80 AND OVER; CELL LINE, TUMOR; CELL SURVIVAL; DNA METHYLATION; EPIGENESIS, GENETIC; EPITHELIAL CELLS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MAMMARY GLANDS, HUMAN; MIDDLE AGED; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, LONG NONCODING; YOUNG ADULT;

EID: 84962022244     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.1080/15592294.2015.1106673     Document Type: Article

References (44)

1. Garbe JC, Vrba L, Sputova K, Fuchs L, Novak P, Brothman AR, Jackson M, Chin K, LaBarge MA, Watts G, et al. Immortalization of normal human mammary epithelial cells in two steps by direct targeting of senescence barriers does not require gross geno-mic alterations. Cell Cycle 2014; 13:3423-35; PMID:25485586; http://dx.doi.org/10.4161/15384101.2014.954456
2. Lee JK, Garbe JC, Vrba L, Miyano M, Futscher BW, Stampfer MR, LaBarge MA. Age and the means of bypassing stasis influence the intrinsic subtype of immortalized human mammary epithelial cells. Front Cell Dev Biol 2015; 3:13; PMID:25815289; http://dx.doi.org/10.3389/fcell.2015.00013
3. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 2015; 47:199-208; PMID:25599403; http://dx.doi.org/10.1038/ng.3192
4. Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013; 154:26-46; PMID:23827673; http://dx.doi.org/10.1016/j.cell.2013.06.020
5. Keniry A, Oxley D, Monnier P, Kyba M, Dandolo L, Smits G, Reik W. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat Cell Biol 2012; 14:659-65; PMID:22684254; http://dx.doi.org/10.1038/ncb2521
6. Cech TR, Steitz JA. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 2014; 157:77-94; PMID:24679528; http://dx.doi.org/10.1016/j.cell.2014.03.008
7. Brannan CI, Dees EC, Ingram RS, Tilghman SM. The product of the H19 gene may function as an RNA. Mol Cell Biol 1990; 10:28-36; PMID:1688465; http://dx.doi.org/10.1128/MCB.10.1.28
8. Rinn JL, Chang HY. Genome regulation by long non-coding RNAs. Annu Rev Biochem 2012; 81:145-66; PMID:22663078; http://dx.doi.org/10.1146/annurev-biochem-051410-092902
9. Penny GD, Kay GF, Sheardown SA, Rastan S, Brock-dorffN. Requirement for Xist in X chromosome in activation. Nature 1996; 379:131-7; PMID:8538762; http://dx.doi.org/10.1038/379131a0
10. Gendrel AV, Heard E. Noncoding RNAs and epige-netic mechanisms during X-chromosome inactivation. Annu Rev Cell Dev Biol 2014; 30:561-80; PMID:25000994; http://dx.doi.org/10.1146/annurev-cellbio-101512-122415
11. Heard E, Chaumeil J, Masui O, Okamoto I. Mammalian X-chromosome inactivation: an epigenetics paradigm. Cold Spring Harbor Symposia Quantitative Biol 2004; 69:89-102; PMID:16117637; http://dx.doi.org/10.1101/sqb.2004.69.89
12. Lee Jeannie T, Bartolomei Marisa S. X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease. Cell 2013; 152:1308-23; PMID:23498939; http://dx.doi.org/10.1016/j.cell.2013.02.016
13. Vincent-Salomon A, Ganem-Elbaz C, Manie E, Raynal V, Sastre-Garau X, Stoppa-Lyonnet D, Stern MH, Heard E. X inactive-specific transcript RNA coating and genetic instability of the X chromosome in BRCA1 breast tumors. Cancer Res 2007; 67:5134-40; PMID:17545591; http://dx.doi.org/10.1158/0008-5472.CAN-07-0465
14. Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Sci 2013; 341:1237973; PMID:23828888; http://dx.doi.org/10.1126/science.1237973
15. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by non-coding RNAs. Cell 2007; 129:1311-23; PMID:17604720; http://dx.doi.org/10.1016/j.cell.2007.05.022
16. Esteller M. Non-coding RNAs in human disease. Nat Rev Genet 2011; 12:861-74; PMID:22094949; http://dx.doi.org/10.1038/nrg3074
17. Ling H, Vincent K, Pichler M, Fodde R, Berindan-Neagoe I, Slack FJ, Calin GA. Junk DNA and the long non-coding RNA twist in cancer genetics. Oncogene 2015; 34(39):5003-11
18. Mitra SA, Mitra AP, Triche TJ. A central role for long non-coding RNA in cancer. Front Genet 2012; 3:17; PMID:22363342; http://dx.doi.org/10.3389/fgene.2012.00017
19. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chroma-tin state to promote cancer metastasis. Nature 2010; 464:1071-6; PMID:20393566; http://dx.doi.org/10.1038/nature08975
20. Ji P, Diederichs S, Wang W, Boing S, Metzger R, Schneider PM, Tidow N, Brandt B, Buerger H, Bulk E, et al. MALAT-1, a novel noncoding RNA, and thy-mosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003; 22:8031-41; PMID:12970751; http://dx.doi.org/10.1038/sj.onc.1206928
21. Pontier SM, Muller WJ. Integrins in mammary-stem-cell biology and breast-cancer progression—a role in cancer stem cells? J Cell Sci 2009; 122:207-14; PMID:19118213; http://dxdoi.org/10.1242/jcs.040394
22. Mizejewski GJ. Role of integrins in cancer: survey of expression patterns. Proc Soc Exp Biol Med 1999; 222:124-38; PMID:10564536; http://dx.doi.org/10.1046/j.1525-1373.1999.d01-122.x
23. Hynes RO. Integrins: Bidirectional, Allosteric Signaling Machines. Cell 2002; 110:673-87; PMID:12297042; http://dx.doi.org/10.1016/S0092-8674(02)00971-6
24. Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res 2013; 41:e74; PMID:23335781; http://dx.doi.org/10.1093/nar/gkt006
25. 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 2012; 22:177589; PMID:22955988; http://dx.doi.org/10.1101/gr.132159.111
26. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483:603-7; PMID:22460905; http://dx.doi.org/10.1038/nature11003
27. American_Cancer_Society. Cancer Facts and Figures 2015. In: Society AC, ed. Atlanta: American Cancer Society, 2015
28. Li Y, Pan J, Li JL, Lee JH, Tunkey C, Saraf K, Garbe JC, Whitley MZ, Jelinsky SA, Stampfer MR, et al. Transcriptional changes associated with breast cancer occur as normal human mammary epithelial cells overcome senescence barriers and become immortalized. Mol Cancer 2007; 6:7; PMID:17233903; http://dx.doi.org/10.1186/1476-4598-6-7
29. Stampfer MR, LaBarge MA, Garbe JC. An Integrated Human Mammary Epithelial Cell Culture System for Studying Carcinogenesis and Aging. In: Schatten H, ed. Cell and Molecular Biology of Breast Cancer. New York: Springer Science eBusiness Media, 2013:323-61
30. Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I. Principles of long noncoding RNA evolution derived from direct comparison of tran-scriptomes in 17 species. Cell Rep 2015; 11:1110-22; PMID:25959816; http://dx.doi.org/10.1016/j.celrep.2015.04.023
31. Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 2013; 9:e1003470; PMID:23637635
32. Garbe JC, Bhattacharya S, Merchant B, Bassett E, Swisshelm K, Feiler HS, Wyrobek AJ, Stampfer MR. Molecular distinctions between stasis and telomere attrition senescence barriers shown by long-term culture of normal human mammary epithelial cells. Cancer Res 2009; 69:7557-68; PMID:19773443; http://dx.doi.org/10.1158/0008-5472.CAN-09-0270
33. Oshiro MM, Watts GS, Wozniak RJ, Junk DJ, Munoz-Rodriguez JL, Domann FE, Futscher BW. Mutant p53 and aberrant cytosine methylation cooperate to silence gene expression. Oncogene 2003;22:3624-34; PMID:12789271; http://dx.doi.org/10.1038/sj.onc.1206545
34. Rice JC, Massey-Brown KS, Futscher BW. Aberrant methylation of the BRCA1 CpG island promoter is associated with decreased BRCA1 mRNA in sporadic breast cancer cells. Oncogene 1998; 17:1807-12; PMID:9778046; http://dx.doi.org/10.1038/sj.onc.1202086
35. R_Development_Core_Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2015
36. Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 2007; 8:485-99; PMID:17189563; http://dx.doi.org/10.1093/biostatistics/kxl042
37. Smyth GK. Limma: linear models for microarray data. In: Gentleman RCV, Huber W, Irizarry R, Dudoit S, ed. Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer, 2005:397-420
38. Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007; 23:25-78; PMID:17098774; http://dx.doi.org/10.1093/bioinformatics/btl567
39. Dinger ME, Pang KC, Mercer TR, Mattick JS. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 2008; 4:e1000176; PMID:19043537; http://dx.doi.org/10.1371/journal.pcbi.1000176
40. Novak P, Jensen TJ, Garbe JC, Stampfer MR, Futscher BW. Stepwise DNA methylation changes are linked to escape from defined proliferation barriers and mammary epithelial cell immortalization. Cancer Res 2009;69:5251-8; PMID:19509227; http://dx.doi.org/10.1158/0008-5472.CAN-08-4977
41. Vrba L, Junk DJ, Novak P, Futscher BW. p53 induces distinct epigenetic states at its direct target promoters. BMC Genomics 2008; 9:486; PMID:18922183; http://dx.doi.org/10.1186/1471-2164-9-486
42. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-11; PMID:19289445; http://dx.doi.org/10.1093/bioinformatics/btp120
43. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAM tools. Bio-informatics 2009; 25:2078-9; PMID:19505943; http://dx.doi.org/10.1093/bioinformatics/btp352
44. Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014; 15:R29; PMID:24485249; http://dx.doi.org/10.1186/gb-2014-15-2-r29