XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis

The functions and modifications of tRNA-derived small RNAs in cancer biology

Recent progress in noncoding RNA research has highlighted transfer RNA-derived small RNAs (tsRNAs) as key regulators of gene expression, linking them to numerous cellular functions. tsRNAs, which are produced by ribonucleases such as angiogenin and Dicer, are classified based on their size and cleavage positions. They play diverse regulatory roles at the transcriptional, post-transcriptional, and translational levels. Furthermore, tRNAs undergo various modifications that influence their biogenesis, stability, functionality, biochemical characteristics, and protein-binding affinity. tsRNAs, with their aberrant expression patterns and modifications, act as both oncogenes and tumor suppressors. This review explores the biogenetic pathways of tsRNAs and their complex roles in gene regulation. We then focus on the importance of RNA modifications in tsRNAs, evaluating their impact on the biogenesis and biological functions on tsRNAs. Furthermore, we summarize recent data indicating that tsRNAs exhibit varied expression profiles across different cancer types, highlighting their potential as innovative biomarkers and therapeutic targets. This discussion integrates both existing and new knowledge about tsRNAs, emphasizing their importance in cancer biology and clinical advancement.

A general framework to over-express tRNA-derived fragments from their parental tRNAs in mammalian cells

tRNA-derived fragments (tRFs), generated from the cleavage of mature or precursor tRNAs are a category of regulatory noncoding RNAs with diverse functions in physiological or pathophysiological conditions. Here we describe a framework for the over-expression of tRFs from their parental tRNAs in mammalian cells. The process involves bioinformatics analysis to identify specific tRNAs that produce the tRF, PCR amplification of corresponding tRNA genes, and insertion into expression vectors. Transfection is carried out in HEK293T cells and detection of tRFs is achieved through northern blotting and dual luciferase reporter assays. In the latter, a complementary sequence to the tRF of interest is inserted into the luciferase reporter. By observing the reduction in luciferase activity, we can validate the expression of tRFs. This method enables precise study of tRF functions and their roles in cellular processes.

Oncogene 5'-3' exoribonuclease 2 enhances epidermal growth factor receptor signaling pathway to promote epithelial-mesenchymal transition and metastasis in non-small-cell lung cancer

Objective

Epithelial-mesenchymal transition (EMT) and metastasis are the primary causes of mortality in non-small-cell lung cancer (NSCLC). 5'-3' exoribonuclease 2 (XRN2) plays an important role in the process of tumor EMT. Thus, this investigation mainly aimed to clarify the precise molecular pathways through which XRN2 contributes to EMT and metastasis in NSCLC.

Material and Methods

Western blot and quantitative real-time polymerase chain reaction were first used to assess XRN2 levels in NSCLC cells. Subsequently, short hairpin RNA-XRN2 (Sh-XRN2) and XRN2 overexpression (Ov-XRN2) plasmids were transfected to NSCLC cells. The effects of Sh-XRN2 and Ov-XRN2 on NSCLC cell migration and invasion were evaluated by Transwell assay. Western blot experiments were conducted to assess the effects of Sh-XRN2 and Ov-XRN2 on proteins related to EMT and the epidermal growth factor receptor (EGFR) signaling pathway in H460 cells. Then, Sh-XRN2 and EGFR overexpression (Ov-EGFR) plasmids were transfected to NSCLC cells. Changes in NSCLC cell migration and invasion were measured using a Transwell assay with Sh-XRN2 and Sh-XRN2+Ov-EGFR. Changes in the expression of proteins related to EMT in NSCLC cells were detected by Western blot assays with Sh-XRN2 and Sh-XRN2+Ov-EGFR. Furthermore, a subcutaneous tumor model for NSCLC was established. Immunohistochemical analysis was performed to assess the levels of Cluster of Differentiation 31 (CD31) in lung metastatic lesions. H460 cells transfected with Sh-XRN2, Ov-XRN2 or Sh-XRN2+Ov-EGFR were co-cultured with human umbilical vein endothelial cells (HUVECs) to assess the tube formation ability of the cells.

Results

Compared with those observed in human bronchial epithelial cells (BEAS-2B cells), XRN2 expression levels were significantly upregulated in NSCLC cell lines (H460 cells) (P < 0.001). XRN2 overexpression considerably promoted the NSCLC cell migration and invasion, EMT process, and tube formation ability of HUVECs (P < 0.001). On the contrary, XRN2 knockdown led to a reduction in these processes. In addition, XRN2 overexpression increased the expression levels of CD31 in lung metastatic lesions and activated the phosphorylation of EGFR signaling pathway (P < 0.001). Furthermore, Sh-XRN2+Ov-EGFR significantly promoted migration, invasion, and EMT processes in H460 cells (P < 0.001). In the meantime, compared with the co-H460+Sh-XRN2+Ov-NC group, co-H460+Sh-XRN2+Ov-EGFR significantly enhanced the tube formation ability of HUVECs (P < 0.001).

Conclusion

XRN2 promoted EMT and metastasis in NSCLC through improving the phosphorylation of the EGFR signaling pathway in NSCLC cells.

A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB

RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.