TsRNA signatures in cancer

Veronica Balatti,Antonio Ciardi,Andrea Russo,Letizia Perracchio,Yuri Pekarsky,Luisa Tomasello,Carlo M Croce,Terri L Messier,Peter K Vogt,Jonathan R Hart,Dario Veneziano,Gary S Stein,Alexey Palamarchuk,Giovanni Nigita,Catherine Bell,Edoardo Pescarmona,Alessandra Drusco,Anna Antenucci,Curtis C Harris,Jane B Lian,Mariantonia Carosi,Nicholas H Farina,Maria Grazia Diodoro ,P Visca ,Chang Gong Liu

doi:10.1073/pnas.1706908114

Abstract

Small, noncoding RNAs are short untranslated RNA molecules, some of which have been associated with cancer development. Recently we showed that a class of small RNAs generated during the maturation process of tRNAs (tRNA-derived small RNAs, hereafter "tsRNAs") is dysregulated in cancer. Specifically, we uncovered tsRNA signatures in chronic lymphocytic leukemia and lung cancer and demonstrated that the ts-4521/3676 cluster (now called "ts-101" and "ts-53," respectively), ts-46, and ts-47 are down-regulated in these malignancies. Furthermore, we showed that tsRNAs are similar to Piwi-interacting RNAs (piRNAs) and demonstrated that ts-101 and ts-53 can associate with PiwiL2, a protein involved in the silencing of transposons. In this study, we extended our investigation on tsRNA signatures to samples collected from patients with colon, breast, or ovarian cancer and cell lines harboring specific oncogenic mutations and representing different stages of cancer progression. We detected tsRNA signatures in all patient samples and determined that tsRNA expression is altered upon oncogene activation and during cancer staging. In addition, we generated a knocked-out cell model for ts-101 and ts-46 in HEK-293 cells and found significant differences in gene-expression patterns, with activation of genes involved in cell survival and down-regulation of genes involved in apoptosis and chromatin structure. Finally, we overexpressed ts-46 and ts-47 in two lung cancer cell lines and performed a clonogenic assay to examine their role in cell proliferation. We observed a strong inhibition of colony formation in cells overexpressing these tsRNAs compared with untreated cells, confirming that tsRNAs affect cell growth and survival.

Highlights

Small, noncoding RNAs are short untranslated RNA molecules, some of which have been associated with cancer development
Our analysis revealed that five tRNA-derived small RNAs (tsRNAs) are down-regulated in both chronic lymphocytic leukemia (CLL) and lung cancer, whereas ts-4 is upregulated in these two malignancies
We found that ts-46 and ts-47 are downregulated in CLL and lung cancer and showed that tsRNAs can act like Piwi-interacting RNAs (piRNAs) by interacting with Piwi proteins

Summary

Introduction

Small, noncoding RNAs are short untranslated RNA molecules, some of which have been associated with cancer development. We observed a strong inhibition of colony formation in cells overexpressing these tsRNAs compared with untreated cells, confirming that tsRNAs affect cell growth and survival These molecules, which we defined as single-stranded small RNAs, 16–48 nt long, ending with a stretch of four Ts [4]. We previously showed that tsRNAs can interact with both Ago and Piwi proteins, potentially affecting the regulation of gene expression at a pretranscriptional level (by interacting with the epigenetic machinery while in the nucleus, similar to piRNAs) and at a posttranscriptional level (by 3′ UTR targeting after exportation to the cytoplasm, similar to miRNAs) [4, 12, 16]. We showed that ts-53 targets the 3′ UTR of TCL1, a key oncogene in the development of aggressive CLL, and that its down-regulation in leukemic cells is inversely correlated with TCL1 expression. Ts-46 and ts-47 affect cell growth in lung cancer cell lines, further confirming the involvement of tsRNAs in cancer pathogenesis

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