Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement

Cell

Volumn 161, Issue 4, 2015, Pages 790-802

  Goodarzi, Hani ^a   Liu, Xuhang ^a   Nguyen, Hoang C B ^a   Zhang, Steven ^a   Fish, Lisa ^a   Tavazoie, Sohail F ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID TRANSFER RNA; GLUTAMIC ACID TRANSFER RNA; GLYCINE TRANSFER RNA; LOCKED NUCLEIC ACID; LUCIFERASE; RIBOSOME RNA; RNA FRAGMENT; TRANSFER RNA; TYROSINE TRANSFER RNA; UNCLASSIFIED DRUG; Y BOX BINDING PROTEIN 1; OLIGONUCLEOTIDE; SMALL UNTRANSLATED RNA; YBX1 PROTEIN, HUMAN;

3' UNTRANSLATED REGION; AMINO ACID SEQUENCE; ANGIOGENESIS; ANIMAL CELL; ARTICLE; BINDING SITE; BREAST CANCER; BREAST CANCER CELL LINE; CANCER GROWTH; CANCER INHIBITION; CARCINOGENESIS; CELL FUNCTION; CELL HYPOXIA; CELL INVASION; CELL PROLIFERATION; CONTROLLED STUDY; CROSS LINKING; DOWN REGULATION; EMBRYO; ENZYME ACTIVATION; ENZYME ACTIVITY; GENE EXPRESSION; GENE SILENCING; GENETIC STABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; IN VITRO STUDY; INTRACELLULAR SIGNALING; METASTASIS; MOLECULAR RECOGNITION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEPLETION; PROTEIN RNA BINDING; PROTEIN SYNTHESIS; RNA SEQUENCE; RNA STABILITY; RNA TRANSCRIPTION; RNA TRANSLATION; TRANSIENT TRANSFECTION; TRANSLATION INITIATION; TUMOR INVASION; UPREGULATION; ANTAGONISTS AND INHIBITORS; BREAST TUMOR; GENETICS; HEK293 CELL LINE; METABOLISM; PATHOLOGY; SEQUENCE ANALYSIS;

BREAST NEOPLASMS; HEK293 CELLS; HUMANS; NEOPLASM METASTASIS; OLIGONUCLEOTIDES; RNA, SMALL UNTRANSLATED; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; Y-BOX-BINDING PROTEIN 1;

EID: 84928975328     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.02.053     Document Type: Article

References (36)

1. E. Borek, B.S. Baliga, C.W. Gehrke, C.W. Kuo, S. Belman, W. Troll, and T.P. Waalkes High turnover rate of transfer RNA in tumor tissue Cancer Res. 37 1977 3362 3366
2. R.G. Bristow, and R.P. Hill Hypoxia and metabolism. Hypoxia, DNA repair and genetic instability Nat. Rev. Cancer 8 2008 180 192
3. C. Cole, A. Sobala, C. Lu, S.R. Thatcher, A. Bowman, J.W.S. Brown, P.J. Green, G.J. Barton, and G. Hutvagner Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs RNA 15 2009 2147 2160
4. O. Elemento, N. Slonim, and S. Tavazoie A universal framework for regulatory element discovery across all genomes and data types Mol. Cell 28 2007 337 350
5. M.M. Emara, P. Ivanov, T. Hickman, N. Dawra, S. Tisdale, N. Kedersha, G.F. Hu, and P. Anderson Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly J. Biol. Chem. 285 2010 10959 10968
6. H. Fu, J. Feng, Q. Liu, F. Sun, Y. Tie, J. Zhu, R. Xing, Z. Sun, and X. Zheng Stress induces tRNA cleavage by angiogenin in mammalian cells FEBS Lett. 583 2009 437 442
7. J. Gebetsberger, and N. Polacek Slicing tRNAs to boost functional ncRNA diversity RNA Biol. 10 2013 1798 1806
8. B. Gyorffy, A. Lánczky, and Z. Szállási Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients Endocr. Relat. Cancer 19 2012 197 208
9. P. Ivanov, M.M. Emara, J. Villen, S.P. Gygi, and P. Anderson Angiogenin-induced tRNA fragments inhibit translation initiation Mol. Cell 43 2011 613 623
10. K. Jürchott, R.J. Kuban, T. Krech, N. Blüthgen, U. Stein, W. Walther, C. Friese, S.M. Kiełbasa, U. Ungethüm, and P. Lund Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells PLoS Genet. 6 2010 e1001231
11. E. Karaca, S. Weitzer, D. Pehlivan, H. Shiraishi, T. Gogakos, T. Hanada, S.N. Jhangiani, W. Wiszniewski, M. Withers, I.M. Campbell Baylor Hopkins Center for Mendelian Genomics Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function Cell 157 2014 636 650
12. J. Krol, I. Loedige, and W. Filipowicz The widespread regulation of microRNA biogenesis, function and decay Nat. Rev. Genet. 11 2010 597 610
13. A. Lasham, W. Samuel, H. Cao, R. Patel, R. Mehta, J.L. Stern, G. Reid, A.G. Woolley, L.D. Miller, and M.A. Black YB-1, the E2F pathway, and regulation of tumor cell growth J. Natl. Cancer Inst. 104 2012 133 146
14. Y.S. Lee, Y. Shibata, A. Malhotra, and A. Dutta A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes & Development 23 2009 2639 2649
15. A. Lujambio, and S.W. Lowe The microcosmos of cancer Nature 482 2012 347 355
16. K. Matsumoto, and B.H. Bay Significance of the Y-box proteins in human cancers J. Mol. Genet. Med. 1 2005 11 17
17. A.J. Minn, G.P. Gupta, P.M. Siegel, P.D. Bos, W. Shu, D.D. Giri, A. Viale, A.B. Olshen, W.L. Gerald, and J. Massagué Genes that mediate breast cancer metastasis to lung Nature 436 2005 518 524
18. M.W. Moyer Targeting hypoxia brings breath of fresh air to cancer therapy Nat. Med. 18 2012 636 637
19. L. Salmena, L. Poliseno, Y. Tay, L. Kats, and P.P. Pandolfi A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146 2011 353 358
20. G.L. Semenza Regulation of mammalian O2 homeostasis by hypoxia-inducible factor 1 Annu. Rev. Cell Dev. Biol. 15 1999 551 578
21. C. Shen, and W.G. Kaelin Jr. The VHL/HIF axis in clear cell renal carcinoma Semin. Cancer Biol. 23 2013 18 25
22. J. Speer, C.W. Gehrke, K.C. Kuo, T.P. Waalkes, and E. Borek tRNA breakdown products as markers for cancer Cancer 44 1979 2120 2123
23. D.M. Thompson, and R. Parker Stressing out over tRNA cleavage Cell 138 2009 215 219
24. T. Uchiumi, A. Fotovati, T. Sasaguri, K. Shibahara, T. Shimada, T. Fukuda, T. Nakamura, H. Izumi, T. Tsuzuki, M. Kuwano, and K. Kohno YB-1 is important for an early stage embryonic development: neural tube formation and cell proliferation J. Biol. Chem. 281 2006 40440 40449
25. J. Ule, K. Jensen, A. Mele, and R.B. Darnell CLIP: a method for identifying protein-RNA interaction sites in living cells Methods 37 2005 376 386
26. W.R. Wilson, and M.P. Hay Targeting hypoxia in cancer therapy Nat. Rev. Cancer 11 2011 393 410
27. Y. Wu, S. Yamada, H. Izumi, Z. Li, S. Shimajiri, K.Y. Wang, Y.P. Liu, K. Kohno, and Y. Sasaguri Strong YB-1 expression is associated with liver metastasis progression and predicts shorter disease-free survival in advanced gastric cancer J. Surg. Oncol. 105 2012 724 730
28. C.L. Zhang, and R.B. Darnell Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data Nat. Biotechnol. 29 2011 607 614
29. C. Desmedt, F. Piette, S. Loi, Y. Wang, F. Lallemand, B. Haibe-Kains, G. Viale, M. Delorenzi, Y. Zhang, M.S. d'Assignies TRANSBIG Consortium Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series Clin. Cancer Res. 13 2007 3207 3214
30. H. Goodarzi, O. Elemento, and S. Tavazoie Revealing global regulatory perturbations across human cancers Mol. Cell 36 2009 900 911
31. B. Györffy, A. Lanczky, A.C. Eklund, C. Denkert, J. Budczies, Q. Li, and Z. Szallasi An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients Breast Cancer Res. Treat. 123 2010 725 731
32. B. Langmead, and S.L. Salzberg Fast gapped-read alignment with Bowtie 2 Nat. Methods 9 2012 357 359
33. D.D. Licatalosi, A. Mele, J.J. Fak, J. Ule, M. Kayikci, S.W. Chi, T.A. Clark, A.C. Schweitzer, J.E. Blume, and X.N. Wang HITS-CLIP yields genome-wide insights into brain alternative RNA processing Nature 456 2008 464 469
34. K.J. Png, N. Halberg, M. Yoshida, and S.F. Tavazoie A microRNA regulon that mediates endothelial recruitment and metastasis by cancer cells Nature 481 2012 190 194
35. D. Ray, H. Kazan, E.T. Chan, L. Peña Castillo, S. Chaudhry, S. Talukder, B.J. Blencowe, Q. Morris, and T.R. Hughes Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins Nat. Biotechnol. 27 2009 667 670
36. S.F. Tavazoie, C. Alarcón, T. Oskarsson, D. Padua, Q. Wang, P.D. Bos, W.L. Gerald, and J. Massagué Endogenous human microRNAs that suppress breast cancer metastasis Nature 451 2008 147 152