5’tiRNA-Pro-TGG,a novel tRNA halve,promotes oncogenesis in sessile serrated lesions and serrated pathway of colorectal cancer

BACKGROUND Transfer RNA(tRNA)-derived small RNAs(tsRNAs)are small fragments that form when tRNAs severe.tRNA halves(tiRNAs),a subcategory of tsRNA,are involved in the oncogenic processes of many tumors.However,their specific role in sessile serrated lesions(SSLs),a precancerous lesion often observed in the colon,has not yet been elucidated.AIM To identify SSL-related tiRNAs and their potential role in the development of SSLs and serrated pathway of colorectal cancer(CRC).METHODS Small-RNA sequencing was conducted in paired SSLs and their adjacent normal control(NC)tissues.The expression levels of five SSL-related tiRNAs were validated by q-polymerase chain reaction.Cell counting kit-8 and wound healing assays were performed to detect cell proliferation and migration.The target genes and sites of tiRNA-1:33-Pro-TGG-1(5′tiRNA-Pro-TGG)were predicted by TargetScan and miRanda algorithms.Metabolism-associated and immune-related pathways were analyzed by single-sample gene set enrichment analysis.Functional analyses were performed to establish the roles of 5′tiRNA-Pro-TGG based on the target genes.RESULTS In total,we found 52 upregulated tsRNAs and 28 downregulated tsRNAs in SSLs compared to NC.The expression levels of tiRNA-1:33-Gly-CCC-2,tiRNA-1:33-Pro-TGG-1,and tiRNA-1:34-Thr-TGT-4-M25′tiRNAs were higher in SSLs than those in NC,while that of 5′tiRNA-Pro-TGG was associated with the size of SSLs.It was demonstrated that 5′tiRNAPro-TGG promoted cell proliferation and migration of RKO cell in vitro.Then,heparanase 2(HPSE2)was identified as a potential target gene of 5′tiRNA-Pro-TGG.Its lower expression was associated with a worse prognosis in CRC.Further,lower expression of HPSE2 was observed in SSLs compared to normal controls or conventional adenomas and in BRAF-mutant CRC compared to BRAF-wild CRC.Bioinformatics analyses revealed that its low expression was associated with a low interferonγresponse and also with many metabolic pathways such as riboflavin,retinol,and cytochrome p450 drug metabolism pathways.CONCLUSION tiRNAs may profoundly impact the development of SSLs.5′tiRNA-Pro-TGG potentially promotes the progression of serrated pathway CRC through metabolic and immune pathways by interacting with HPSE2 and regulating its expression in SSLs and BRAF-mutant CRC.In the future,it may be possible to use tiRNAs as novel biomarkers for early diagnosis of SSLs and as potential therapeutic targets in serrated pathway of CRC.

Extensive profiling of the expressions of tRNAs and tRNA-derived fragments(tRFs)reveals the complexities of tRNA and tRF populations in plants

Evidence is emerging that t RNA-derived fragments(t RFs)are regulatory molecules.Studies of t RFs in plants have been based on conventional small RNA sequencing,and focused on profiling of t RF-5 and t RF-3 species.A more comprehensive and quantitative analysis of the entire t RF population is highly necessary.Here,we employ t RNA-seq and YAMAT-seq,and develop a bioinformatics tool to comprehensively profile the expressions of t RNAs and t RFs in plants.We show that in Arabidopsis,approximately half of t RNA genes are extremely weakly expressed,accounting for only 1%of total t RNA abundance,while~12%of t RNA genes contribute to~80%of t RNA abundance.Our t RNA sequencings in various plants reveal that t RNA expression profiles exhibit a cross-species conserved pattern.By characterizing the composition of a highly heterogeneous t RF population,we show that t RNA halves and previously unnoticed 10–16-nt tiny t RFs represent substantial portions.The highly accumulated 13-nt and 16-nt tiny t RFs in Arabidopsis indicate that tiny t RFs are not random t RNA degradation products.Finally,we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of t RNAs and t RFs in the model plants Arabidopsis and rice.

Plant transfer RNA-derived fragments:Biogenesis and functions

Processing of mature transfer RNAs(tRNAs)produces complex populations of tRNA-derived fragments(tRFs).Emerging evidence shows that tRFs have important functions in bacteria,animals,and plants.Here,we review recent advances in understanding plant tRFs,focusing on their biological and cellular functions,such as regulating stress responses,mediating plant-pathogen interactions,and modulating post-transcriptional gene silencing and translation.We also review sequencing strategies and bioinformatics resources for studying tRFs in plants.Finally,we discuss future directions for plant tRF research,which will expand our knowledge of plant non-coding RNAs.