tsRNA signatures in cancer

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 knockedout 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.tsRNA | tRF | tDR | ncRNA | tRNA fragments

Identification of tRNA‐derived small RNA (tsRNA) responsive to the tumor suppressor, RUNX1, in breast cancer

“…To determine whether tsRNA expression may be regulated by RUNX1 in breast cancer, we interrogated global tsRNA levels using a validated custom microarray (Balatti et al, ) in RUNX1‐expressing normal‐like MCF10A mammary epithelial cells or RUNX1‐low MCF10CA1a malignant breast cancer cell lines. Both RUNX1 protein and mRNA were effectively silenced in MCF10A cells with two different shRNA (shR1‐C1 and shR1‐C4) and exogenously overexpressed in MCF10CA1a cells as previously shown (Hong, Fritz, Finstad et al, ; Hong et al, ).…”

“…Both RUNX1 protein and mRNA were effectively silenced in MCF10A cells with two different shRNA (shR1‐C1 and shR1‐C4) and exogenously overexpressed in MCF10CA1a cells as previously shown (Hong, Fritz, Finstad et al, ; Hong et al, ). After normalization and probeset summarization, relative log 2 expression levels for all 113 established tsRNA (Balatti et al, ) were subjected to PCA. The six MCF10A samples infected with RUNX1 shRNA cluster together (blue and yellow spheres, top left), disparate from the cluster of MCF10A nonsilencing control (red spheres) and MCF10CA1a cells with ectopic RUNX1 expression (green spheres; Figure a).…”

“…Our previous studies present compelling evidence that RUNX1 expression in mammary cells and inhibits tumorigenic potential supporting maintenance of an epithelial‐like phenotype; RUNX1 protein and mRNA expression are reduced in breast cancer cell lines (Hong, Fritz, Finstad et al, ; Hong et al, ). The expression of candidate RUNX1‐responsive tsRNA, ts‐19, ts‐29, ts‐46, and ts‐112, was curated from our initial microarray study (Balatti et al, ) and plotted to discover dynamic regulation in breast cancer cell models (Figure a–d). All four tsRNA exhibit significantly different expression (ANOVA p < .05) in the triple‐negative MDA‐MB‐231 breast cancer cell line compared with MCF10A cells.…”

“…Biological replicate mean ( n = 3) and SEM graphed; ANOVA significance. Microarray tsRNA expression data from (Balatti et al, ). (e) qPCR validation of ts‐112 expression normalized to U6 and average expression in MCF10A biological replicates ( n = 3).…”

tRNA-Derived Fragments as Novel Predictive Biomarkers for Trastuzumab-Resistant Breast Cancer

“…5'-tRHs, but not 3'-tRHs, play a role in inhibiting protein synthesis and promoting the assembly of stress granules [52,53]. tRFs have been identified to copurify with Argonaute and Piwi complexes, which suggests that such tRNA-derived fragments could function as miRNAs or piRNAs [54][55][56]. Recently 5'-tRF series were also found to inhibit translation independently of siRNA [57].…”