A comprehensive repertoire of tRNA-derived fragments in prostate cancer
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Michael Olvedy1,4,5,*, Mauro Scaravilli2,3,*, Youri Hoogstrate1, Tapio Visakorpi2,3,#, Guido Jenster1,#, Elena S. Martens-Uzunova1,#
1Department of Urology, Erasmus MC, Rotterdam, The Netherlands
2Institute of Biosciences and Medical Technology-BioMediTech, University of Tampere, Tampere, Finland
3Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
4Current address: VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
5Current address: Center for Human Genetics, KULeuven, Leuven, Belgium
*These authors contributed equally to this work
#Three last authors contributed equally to this work
Elena S. Martens-Uzunova, e-mail: firstname.lastname@example.org
Keywords: tRNA-derived fragments (tRFs), prostate cancer (PCa), RNA-sequencing, non-coding RNA, biomarker
Received: September 04, 2015 Accepted: March 02, 2016 Published: March 23, 2016
Prostate cancer (PCa) is the most common cancer among men in developed countries. Although its genetic background is thoroughly investigated, rather little is known about the role of small non-coding RNAs (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a new class of sncRNAs, which are present in a broad range of species and have been reported to play a role in several cellular processes. Here, we analyzed the expression of tRFs in fresh frozen patient samples derived from normal adjacent prostate and different stages of PCa by RNA-sequencing. We identified 598 unique tRFs, many of which are deregulated in cancer samples when compared to normal adjacent tissue. Most of the identified tRFs are derived from the 5’- and 3’-ends of mature cytosolic tRNAs, but we also found tRFs produced from other parts of tRNAs, including pre-tRNA trailers and leaders, as well as tRFs from mitochondrial tRNAs. The 5’-derived tRFs comprise the most abundant class of tRFs in general and represent the major class among upregulated tRFs. The 3’-derived tRFs types are dominant among downregulated tRFs in PCa. We validated the expression of three tRFs using qPCR. The ratio of tRFs derived from tRNALysCTT and tRNAPheGAA emerged as a good indicator of progression-free survival and a candidate prognostic marker. This study provides a systematic catalogue of tRFs and their dysregulation in PCa and can serve as the basis for further research on the biomarker potential and functional roles of tRFs in this disease.
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