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Expression profile of tRNA-derived fragments in pancreatic cancer.
Oncol Lett 2019; 18(3):3104-3114OL

Abstract

Pancreatic cancer is a deadly disease, the deadliest of all the solid tumors; the 5-year survival rate of patients with this disease is ~8%. Previously, high-throughput sequencing has led to the discovery of novel small non-coding RNAs, also known as transfer RNA-derived fragments (tRFs). Studies have suggested that tRFs may be novel biomarkers for certain diseases. However, the expression of tRFs in pancreatic cancer has yet to be characterized. In the present study, the expression levels of tRFs observed in clinical pancreatic cancer samples were analyzed, quantitative PCR (qPCR) was performed to validate the tRFs expression levels and bioinformatics predictions were analyzed. The results revealed that the pancreatic cancer samples screened out a total of 48 tRFs and transfer RNA halves (tiRNAs). There were four tRFs and tiRNAs selected for qPCR validation; the findings were consistent with the sequencing results. Bioinformatic predictions revealed that AS-tDR-000064 was predicted to have 2,450 target genes; AS-tDR-000069 was predicted 445 target genes; AS-tDR-000102 was predicted 746 target genes; and AS-tDR-001391 was predicted 216 target genes. Gene Ontology (GO) analyses demonstrated that the target genes of AS-tDR-000064 were mostly enriched in 'the regulation of cellular processes' (Biological Process), 'the synapses' (Cellular Component) and 'enzyme binding' (Molecular Function). The target genes of AS-tDR-000069 were mostly enriched in 'signaling' (Biological Process), 'the plasma membrane' (Cellular Component) and 'phosphatidylinositol 3-kinase (PI3K) binding'(Molecular Function), the target genes of AS-tDR-000102 were mostly enriched in 'axon development' (Biological Process), 'the synapse' (Cellular Component) and 'sequence-specific DNA binding' (Molecular Function) and the target genes of AS-tDR-001391 were mostly enriched in 'the neuromuscular processes' (Biological Process), the neurons' (Cellular Component) and 'PDZ domain binding' (Molecular Function). The Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the target genes of AS-tDR-000064 were mostly enriched in 'the Ras signaling pathway', the target genes of AS-tDR-000069 were mostly enriched in 'the cancer pathways', the target genes of AS-tDR-000102 were mostly enriched in 'axon guidance' and the target genes of AS-tDR-001391 were mostly enriched in 'the PI3K/protein kinase-B signaling pathway'.

Authors+Show Affiliations

Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu 213003, P.R. China. Department of General Surgery, Wujin Hospital Affiliated to Jiangsu University, Changzhou, Jiangsu 213002, P.R. China.Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu 213003, P.R. China.Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu 213003, P.R. China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31452788

Citation

Jin, Lei, et al. "Expression Profile of tRNA-derived Fragments in Pancreatic Cancer." Oncology Letters, vol. 18, no. 3, 2019, pp. 3104-3114.
Jin L, Zhu C, Qin X. Expression profile of tRNA-derived fragments in pancreatic cancer. Oncol Lett. 2019;18(3):3104-3114.
Jin, L., Zhu, C., & Qin, X. (2019). Expression profile of tRNA-derived fragments in pancreatic cancer. Oncology Letters, 18(3), pp. 3104-3114. doi:10.3892/ol.2019.10601.
Jin L, Zhu C, Qin X. Expression Profile of tRNA-derived Fragments in Pancreatic Cancer. Oncol Lett. 2019;18(3):3104-3114. PubMed PMID: 31452788.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Expression profile of tRNA-derived fragments in pancreatic cancer. AU - Jin,Lei, AU - Zhu,Chunfu, AU - Qin,Xihu, Y1 - 2019/07/11/ PY - 2018/09/04/received PY - 2019/05/24/accepted PY - 2019/8/28/entrez PY - 2019/8/28/pubmed PY - 2019/8/28/medline KW - Gene Ontology analysis KW - Kyoto Encyclopedia of Genes and Genomes pathway analysis KW - bioinformatics prediction KW - high-throughput sequencing KW - quantitative reverse-transcription PCR KW - transfer RNA halves KW - transfer RNA-derived fragments SP - 3104 EP - 3114 JF - Oncology letters JO - Oncol Lett VL - 18 IS - 3 N2 - Pancreatic cancer is a deadly disease, the deadliest of all the solid tumors; the 5-year survival rate of patients with this disease is ~8%. Previously, high-throughput sequencing has led to the discovery of novel small non-coding RNAs, also known as transfer RNA-derived fragments (tRFs). Studies have suggested that tRFs may be novel biomarkers for certain diseases. However, the expression of tRFs in pancreatic cancer has yet to be characterized. In the present study, the expression levels of tRFs observed in clinical pancreatic cancer samples were analyzed, quantitative PCR (qPCR) was performed to validate the tRFs expression levels and bioinformatics predictions were analyzed. The results revealed that the pancreatic cancer samples screened out a total of 48 tRFs and transfer RNA halves (tiRNAs). There were four tRFs and tiRNAs selected for qPCR validation; the findings were consistent with the sequencing results. Bioinformatic predictions revealed that AS-tDR-000064 was predicted to have 2,450 target genes; AS-tDR-000069 was predicted 445 target genes; AS-tDR-000102 was predicted 746 target genes; and AS-tDR-001391 was predicted 216 target genes. Gene Ontology (GO) analyses demonstrated that the target genes of AS-tDR-000064 were mostly enriched in 'the regulation of cellular processes' (Biological Process), 'the synapses' (Cellular Component) and 'enzyme binding' (Molecular Function). The target genes of AS-tDR-000069 were mostly enriched in 'signaling' (Biological Process), 'the plasma membrane' (Cellular Component) and 'phosphatidylinositol 3-kinase (PI3K) binding'(Molecular Function), the target genes of AS-tDR-000102 were mostly enriched in 'axon development' (Biological Process), 'the synapse' (Cellular Component) and 'sequence-specific DNA binding' (Molecular Function) and the target genes of AS-tDR-001391 were mostly enriched in 'the neuromuscular processes' (Biological Process), the neurons' (Cellular Component) and 'PDZ domain binding' (Molecular Function). The Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the target genes of AS-tDR-000064 were mostly enriched in 'the Ras signaling pathway', the target genes of AS-tDR-000069 were mostly enriched in 'the cancer pathways', the target genes of AS-tDR-000102 were mostly enriched in 'axon guidance' and the target genes of AS-tDR-001391 were mostly enriched in 'the PI3K/protein kinase-B signaling pathway'. SN - 1792-1074 UR - https://www.unboundmedicine.com/medline/citation/31452788/Expression_profile_of_tRNA_derived_fragments_in_pancreatic_cancer_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31452788/ DB - PRIME DP - Unbound Medicine ER -