Increased MicroRNA activity in human cancers

PLoS ONE

Volumn 4, Issue 6, 2009, Pages

  Israel, Ariel ^a   Sharan, Roded ^b   Ruppin, Eytan ^b   Galun, Eithan ^a  

^a HADASSAH HEBREW UNIVERSITY MEDICAL CENTER   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; BREAST CANCER; CARCINOGENICITY; CONTROLLED STUDY; DOWN REGULATION; GENE CONTROL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE TARGETING; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; QUANTITATIVE STUDY; SIGNAL TRANSDUCTION; THYROID PAPILLARY CARCINOMA; BIOLOGY; BREAST TUMOR; CARCINOMA; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA MICROARRAY; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; METABOLISM; METHODOLOGY; NEOPLASM; STATISTICAL MODEL; THYROID TUMOR;

BREAST NEOPLASMS; CARCINOMA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; MODELS, STATISTICAL; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; THYROID NEOPLASMS;

EID: 67649488086     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006045     Document Type: Article

References (43)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
3. Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, et al. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435: 974-978.
4. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435: 839-843.
5. Hornstein E, Shomron N (2006) Canalization of development by microRNAs. Nat Genet 38 Suppl 1: S20-24.
6. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, et al. (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310: 1817-1821.
7. Esquela-Kerscher A, Slack FJ (2006) Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6: 259-269.
8. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
9. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103: 2257-2261.
10. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, et al. (2006) microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci U S A 103: 9136-9141.
11. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
12. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123: 1133-1146.
13. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103: 2746-2751.
14. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
15. Segal E, Friedman N, Kaminski N, Regev A, Koller D (2005) From signatures to models: understanding cancer using microarrays. Nat Genet 37 Suppl: S38-45.
16. Arora A, Simpson DA (2008) Individual mRNA expression profiles reveal the effects of specific microRNAs. Genome Biol 9: R82.
17. Cheng C, Li LM (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE 3: e1989.
18. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
19. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
20. Beaudoing E, Gautheret D (2001) Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res 11: 1520-1526.
21. Zhang H, Lee JY, Tian B (2005) Biased alternative polyadenylation in human tissues. Genome Biol 6: R100.
22. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31: 51-54.
23. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, et al. (2005) NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 33: D562-566.
24. Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, et al. (2007) ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35: D747-750.
25. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
26. Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 13: 773-780.
27. Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, et al. (2007) Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS ONE 2: e807.
28. Wang X, Wang X (2006) Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res 34: 1646-1652.
29. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438: 685-689.
30. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 102: 19075-19080.
31. Richardson AL, Wang ZC, De Nicolo A, Lu X, Brown M, et al. (2006) X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell 9: 121-132.
32. Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-524.
33. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
34. Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J, et al. (2007) Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. Rna 13: 1894-1910.
35. Novak P, Jensen T, Oshiro MM, Wozniak RJ, Nouzova M, et al. (2006) Epigenetic inactivation of the HOXA gene cluster in breast cancer. Cancer Res 66: 10664-10670.
36. Shalgi R, Lieber D, Oren M, Pilpel Y (2007) Global and Local Architecture of the Mammalian microRNA-Transcription Factor Regulatory Network. PLoS Comput Biol 3: e131.
37. Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, et al. (2007) Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem.
38. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
39. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64-71.
40. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
41. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65: 7065-7070.
42. Pallante P, Visone R, Ferracin M, Ferraro A, Berlingieri MT, et al. (2006) MicroRNA deregulation in human thyroid papillary carcinomas. Endocr Relat Cancer 13: 497-508.
43. Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T (2007) Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet 39: 673-677.