Contribution of miRNAs, tRNAs and tRFs to Aberrant Signaling and Translation Deregulation in Lung Cancer.

Ilias Skeparnias,Panagiotis Alexopoulos,George Kyriakopoulos,Christos K Kontos,Dimitrios Dougenis,Andreas Scorilas,Katerina Grafanaki,Constantinos Stathopoulos,Dimitrios Anastasakis

doi:10.3390/cancers12103056

Abstract

Transcriptomics profiles of miRNAs, tRNAs or tRFs are used as biomarkers, after separate examination of several cancer cell lines, blood samples or biopsies. However, the possible contribution of all three profiles on oncogenic signaling and translation as a net regulatory effect, is under investigation. The present analysis of miRNAs and tRFs from lung cancer biopsies indicated putative targets, which belong to gene networks involved in cell proliferation, transcription and translation regulation. In addition, we observed differential expression of specific tRNAs along with several tRNA-related genes with possible involvement in carcinogenesis. Transfection of lung adenocarcinoma cells with two identified tRFs and subsequent NGS analysis indicated gene targets that mediate signaling and translation regulation. Broader analysis of all major signaling and translation factors in several biopsy specimens revealed a crosstalk between the PI3K/AKT and MAPK pathways and downstream activation of eIF4E and eEF2. Subsequent polysome profile analysis and 48S pre-initiation reconstitution experiments showed increased global translation rates and indicated that aberrant expression patterns of translation initiation factors could contribute to elevated protein synthesis. Overall, our results outline the modulatory effects that possibly correlate the expression of important regulatory non-coding RNAs with aberrant signaling and translation deregulation in lung cancer.

Highlights

In almost all cancers, miRNAs target and control the fate of several important mRNAs involved in carcinogenesis and tumor suppression [1]
Based on the transcriptomic profile of miRNAs, tRNA-derivedRNA fragments (tRFs) and tRNAs and the fact that statistically significant miRNAs and tRFs detected in the present study have common predicted gene targets that play role in signaling pathways and translation regulation, we examined the expression and activation patterns of key components from both processes, after comparison of tumor and normal tissue specimens
We provide a comprehensive outline of events that link the expression patterns of miRNAs, tRFs and tRNAs with aberrant signaling and deregulated translation initiation, in lung cancer biopsy specimens (Figure S6)

Summary

Introduction

MiRNAs target and control the fate of several important mRNAs involved in carcinogenesis and tumor suppression [1]. RNA fragments (tRFs), a heterogeneous group of small non-coding RNAs (14–40 nt) first detected in the urine of cancer patients, is a representative example which highlights the regulatory role of tRNAs, beyond translation [3,4]. The major types of tRFs are tRF-5, tRF-3, tRF-1, 50 tRNA half, 30 tRNA half and i-tRFs and they all derive either from premature or mature tRNAs after cleavage on specific sites by important ribonucleases [5]. Mammalian tRF-5 and tRF-3 types correspond to the 50 part or the 30 part of the tRNA, respectively. TRF-5 are divided into three subtypes (a, b, and c) which vary in size (14–16 nt, 22–24 nt and 28–30 nt respectively) and derive from different cleavage sites at the D-loop (tRF-5a) or the D-stem (tRF-5b and c). The generation of tRF-1 type is mediated by the excision of the 30 -UUU trailers of pre-mature tRNAs by RNase Z (encoded by ELAC) and further trimming

Objectives

Methods

Results

Discussion

Conclusion