Integrated analysis of tRNA-derived small RNAs in proliferative human aortic smooth muscle cells

Abstract

Background Abnormal proliferation of vascular smooth muscle cells (VSMCs) contributes to vascular remodeling diseases. Recently, it has been discovered that tRNA-derived small RNAs (tsRNAs), a new type of noncoding RNAs, are related to the proliferation and migration of VSMCs. tsRNAs regulate target gene expression through miRNA-like functions. This study aims to explore the potential of tsRNAs in human aortic smooth muscle cell (HASMC) proliferation. Methods High-throughput sequencing was performed to analyze the tsRNA expression profile of proliferative and quiescent HASMCs. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate the sequence results and subcellular distribution of AS-tDR-001370, AS-tDR-000067, AS-tDR-009512, and AS-tDR-000076. Based on the microRNA-like functions of tsRNAs, we predicted target promoters and mRNAs and constructed tsRNA–promoter and tsRNA–mRNA interaction networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to reveal the function of target genes. EdU incorporation assay, Western blot, and dual-luciferase reporter gene assay were utilized to detect the effects of tsRNAs on HASMC proliferation. Results Compared with quiescent HASMCs, there were 1838 differentially expressed tsRNAs in proliferative HASMCs, including 887 with increased expression (fold change > 2, p < 0.05) and 951 with decreased expression (fold change < ½, p < 0.05). AS-tDR-001370, AS-tDR-000067, AS-tDR-009512, and AS-tDR-000076 were increased in proliferative HASMCs and were mainly located in the nucleus. Bioinformatics analysis suggested that the four tsRNAs involved a variety of GO terms and pathways related to VSMC proliferation. AS-tDR-000067 promoted HASMC proliferation by suppressing p53 transcription in a promoter-targeted manner. AS-tDR-000076 accelerated HASMC proliferation by attenuating mitofusin 2 (MFN2) levels in a 3′-untranslated region (UTR)-targeted manner. Conclusions During HASMC proliferation, the expression levels of many tsRNAs are altered. AS-tDR-000067 and AS-tDR-000076 act as new factors promoting VSMC proliferation.

Transfer RNA-derived small RNA tRF-Glu-CTC attenuates neointimal formation via inhibition of fibromodulin

“…tsRNAs have been identified as biomarkers or potential therapeutic targets in many cardiovascular diseases, including rheumatic heart disease [ 40 ], cardiac hypertrophy [ 13 ], heart failure [ 16 ], atherosclerosis [ 41 ], and aortic dissection [ 42 ]. There is evidence that tsRNAs regulate the proliferation [ 43 ] and phenotypic switching [ 44 ] of VSMCs. In our previous work, we also found that tRF-Gln-CTG induced vascular intimal hyperplasia by inhibiting FAS cell surface death receptors [ 17 ].…”

Identification of Circulating tRNA-Derived Small RNAs As Potential Biomarkers for Sepsis-Induced Acute Respiratory Distress Syndrome

“…To date, with the application of high-throughput sequencing and advances in bioinformatics techniques, an increasing number of tsRNAs in EVs have been reported to be associated with different diseases 28 . The regulatory mechanisms of tsRNAs identi ed so far are diverse: (1) they regulate mRNA stability, similar to miRNAs; (2) they inhibit the initiation and extension of translation; (3) they regulate ribosome biogenesis; and (4) they function as a novel type of epigenetic factor that alter the spatial conformation of proteins and thus affect their functions, such as DNA methylation, histone modi cation, and chromatin remodeling 29 . In various diseases, different tsRNAs have been implicated in regulatory roles.…”

tRNA-Derived Small RNAs: A Novel Regulatory Small Noncoding RNA in Renal Diseases

“…These complexes are then transported to the nucleus, enhancing the interaction between EEF1A1 and the MDM2 proto-oncogene (MDM2), ultimately promoting GC progression [49]. Additionally, Zhao et al [50] found that the upregulated tRF-Tyr in laryngeal squamous cell carcinoma enhances tumor progression by binding with lactate dehydrogenase A (LDHA), affecting its phosphorylation and leading to increased lactic acid accumulation [50]. These studies highlight the diverse biological roles of tsRNAs, which involve direct binding to target proteins, formation of complexes for intracellular transport, and regulation of posttranslational modifications.…”