A comprehensive repertoire of tRNA-derived fragments in prostate cancer

Oncotarget

Volumn 7, Issue 17, 2016, Pages 24766-24777

  Olvedy, Michael ^a,d,e   Scaravilli, Mauro ^b,c   Hoogstrate, Youri ^a   Visakorpi, Tapio ^b,c   Jenster, Guido ^a   Martens Uzunova, Elena S ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^c TAMPERE UNIVERSITY HOSPITAL   (Finland)

^d DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^e UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Biomarker; Non coding RNA; Prostate cancer (PCa); RNA sequencing; tRNA derived fragments (tRFs)

Indexed keywords

SMALL UNTRANSLATED RNA; TRANSFER RNA; TRANSFER RNA DERIVED FRAGMENT; UNCLASSIFIED DRUG; RNA PRECURSOR;

ARTICLE; BIOINFORMATICS; CANCER GRADING; CANCER PROGNOSIS; CANCER RECURRENCE; CANCER STAGING; CANCER SURVIVAL; CARCINOGENESIS; COMPARATIVE STUDY; CONTROLLED STUDY; DISEASE ASSOCIATION; DOWN REGULATION; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE MAPPING; GENETIC CONSERVATION; GENETIC DATABASE; GLEASON SCORE; HUMAN; MALE; POLYMERASE CHAIN REACTION; PROGRESSION FREE SURVIVAL; PROSTATE CANCER; RNA SEQUENCE; SURVIVAL RATE; SURVIVAL TIME; UPREGULATION; VALIDATION PROCESS; GENETICS; PROSTATE TUMOR;

HUMANS; MALE; PROSTATIC NEOPLASMS; RNA PRECURSORS; RNA, SMALL UNTRANSLATED; RNA, TRANSFER;

EID: 84966562875     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.8293     Document Type: Article

References (40)

1. Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray F. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. International journal of cancer Journal international du cancer. 2015; 136:E359-386.
2. Nam RK, Cheung P, Herschorn S, Saskin R, Su J, Klotz LH, Chang M, Kulkarni GS, Lee Y, Kodama RT, Narod SA. Incidence of complications other than urinary incontinence or erectile dysfunction after radical prostatectomy or radiotherapy for prostate cancer: a population-based cohort study. The Lancet Oncology. 2014; 15:223-231.
3. Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y. Hidden layers of human small RNAs. BMC genomics. 2008; 9:157.
4. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicerdependent small RNAs derived from tRNAs. RNA. 2009; 15:2147-2160.
5. Lee YS, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev. 2009; 23:2639-2649.
6. Thompson DM, Parker R. Stressing out over tRNA cleavage. Cell. 2009; 138:215-219.
7. Martens-Uzunova ES, Olvedy M, Jenster G. Beyond microRNA--novel RNAs derived from small non-coding RNA and their implication in cancer. Cancer letters. 2013; 340:201-211.
8. Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC biology. 2014; 12:78.
9. Thompson DM, Parker R. The RNase Rny1p cleaves tRNAs and promotes cell death during oxidative stress in Saccharomyces cerevisiae. J Cell Biol. 2009; 185:43-50.
10. Yamasaki S, Ivanov P, Hu GF, Anderson P. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol. 2009; 185:35-42.
11. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA. Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA. 2010; 16:673-695.
12. Kumar P, Mudunuri SB, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res. 2015; 43:D141-145.
13. Thompson DM, Lu C, Green PJ, Parker R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA. 2008; 14:2095-2103.
14. Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH. Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PLoS One. 2010; 5:e10563.
15. Goodarzi H, Liu X, Nguyen HC, Zhang S, Fish L, Tavazoie SF. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell. 2015; 161:790-802.
16. Martens-Uzunova ES, Jalava SE, Dits NF, van Leenders GJ, Moller S, Trapman J, Bangma CH, Litman T, Visakorpi T, Jenster G. Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer. Oncogene. 2012; 31:978-991.
17. Nawrot B, Sochacka E, Duchler M. tRNA structural and functional changes induced by oxidative stress. Cellular and molecular life sciences: CMLS. 2011; 68:4023-4032.
18. Gebetsberger J, Zywicki M, Kunzi A, Polacek N. tRNAderived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea. 2012; 2012:260909.
19. Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell. 2011; 43:613-623.
20. Zhang S, Sun L, Kragler F. The phloem-delivered RNA pool contains small noncoding RNAs and interferes with translation. Plant Physiol. 2009; 150:378-387.
21. Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proceedings of the National Academy of Sciences of the United States of America. 2013; 110:1404-1409.
22. Telonis A, Loher, P., Honda, S., Jing, Y., Palazzo, J., Kirino, Y., & Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015. doi: 10.18632/oncotarget.4695.
23. Hoogstrate Y, Jenster G, Martens-Uzunova ES. FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data. Bioinformatics. 2014.
24. Martens-Uzunova ES, Hoogstrate Y, Kalsbeek A, Pigmans B, Vredenbregt-van den Berg M, Dits N, Nielsen SJ, Baker A, Visakorpi T, Bangma C, Jenster G. C/D-box snoRNAderived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. Oncotarget. 2015. doi: 10.18632/oncotarget.4172.
25. Couvillion MT, Sachidanandam R, Collins K. A growthessential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev. 2010; 24:2742-2747.
26. Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG. Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA. 2012; 18:915-929.
27. Couvillion MT, Bounova G, Purdom E, Speed TP, Collins K. A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Mol Cell. 2012; 48:509-520.
28. van der Heul-Nieuwenhuijsen L, Hendriksen PJ, van der Kwast TH, Jenster G. Gene expression profiling of the human prostate zones. BJU international. 2006; 98:886-897.
29. Trujillo KA, Heaphy CM, Mai M, Vargas KM, Jones AC, Vo P, Butler KS, Joste NE, Bisoffi M, Griffith JK. Markers of fibrosis and epithelial to mesenchymal transition demonstrate field cancerization in histologically normal tissue adjacent to breast tumors. International journal of cancer Journal international du cancer. 2011; 129:1310-1321.
30. Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P. Angiogenininduced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem. 2010; 285:10959-10968.
31. Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viralcellular double-stranded RNA hybrid. Nucleic Acids Res. 2009; 37:6575-6586.
32. Cai P, Piao X, Hao L, Liu S, Hou N, Wang H, Chen Q. A deep analysis of the small non-coding RNA population in Schistosoma japonicum eggs. PLoS One. 2013; 8:e64003.
33. Garcia-Silva MR, Frugier M, Tosar JP, Correa-Dominguez A, Ronalte-Alves L, Parodi-Talice A, Rovira C, Robello C, Goldenberg S, Cayota A. A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol Biochem Parasitol. 2010; 171:64-73.
34. Li Z, Ender C, Meister G, Moore PS, Chang Y, John B. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res. 2012; 40:6787-6799.
35. Thedieck K, Holzwarth B, Prentzell MT, Boehlke C, Klasener K, Ruf S, Sonntag AG, Maerz L, Grellscheid SN, Kremmer E, Nitschke R, Kuehn EW, Jonker JW, Groen AK, Reth M, Hall MN, et al. Inhibition of mTORC1 by astrin and stress granules prevents apoptosis in cancer cells. Cell. 2013; 154:859-874.
36. Sobala A, Hutvagner G. Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biol. 2013; 10.
37. Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008; 22:2773-2785.
38. Rudinger-Thirion J, Lescure A, Paulus C, Frugier M. Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element. Proceedings of the National Academy of Sciences of the United States of America. 2011; 108:E794-802.
39. Helm M. Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res. 2006; 34:721-733.
40. Hendriksen PJ, Dits NF, Kokame K, Veldhoven A, van Weerden WM, Bangma CH, Trapman J, Jenster G. Evolution of the androgen receptor pathway during