Differential Expression and Bioinformatics Analysis of tRF/tiRNA in Endometriosis Patients

Abstract

Background. Endometriosis (EMs) is a benign chronic condition that tends to recur in women of childbearing age, with an incidence of approximately 10%. It is a multifactorial disease for which the pathogenesis is currently unclear. This study is aimed at investigating the expression and clinical significance of tRNA-derived small RNA (tsRNA), a novel noncoding small RNA with potential regulatory functions, in endometriosis. Methods. The tRF/tiRNA expression profiles in endometrial tissues from three pairs of endometriosis patients and controls were detected by tRF&tiRNA PCR microarray technology and then verified by quantitative real-time polymerase chain reaction (qPCR). The target genes and target sites of TRF396, tiRNA-5030-GlnTTG-3, TRF308, and TRF320 were predicted by miRanda, and the network diagram of their interaction with miRNA was drawn. The impact of tRNA-derived fragments on the pathogenesis of endometriosis was analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results. Two upregulated and 19 downregulated tRNA-derived fragments were identified. The qRT-PCR results of 2 upregulated and 2 downregulated RNA-derived fragments were consistent with the RNA Seq data. The OR2B4 gene related to TRF396, the DGAT1 gene related to tiRNA-5030-GlnTTG-3, the KLF16 gene of TRF308, and the RNF213 gene of TRF320 had significant correlations. Gene Ontology and pathway analysis showed that the target genes of TRF396 and tiRNA-5030-GlnTTG-3 were mainly involved in the intrinsic components of the membrane and the overall composition of the membrane in cell components; molecular functions mainly involve olfactory conduction and G protein-coupled receptor activity. In the biological process, it was mainly involved in the detection of sensory stimuli. The target genes of TRF308 and TRF320 were mainly involved in the intracellular part; molecular functions are mainly related to DNA binding transcription factor activity and protein binding and mainly related to biological regulation of biological processes. Pathway analysis showed that the RAP1 signaling pathway and the AXON GUIDANCE signaling pathway may participate in the progression of endometriosis. Conclusion. The differential expression of tRF/tiRNA in endometriosis may be related to the pathogenesis of endometriosis. Furthermore, tRF/tiRNA may be a biomarker for the diagnosis and treatment of EMs in the future.

Scatter Irradiation of Rat Brain Triggers Sex- and Brain Region-Specific Changes in the Expression of Non-Coding RNA Fragments

“…Many tiRNAs and tRFs are differentially expressed in response to stress, with most data coming from the realm of cancer biology [ 60 ]. tiRNAs and tRFs are also found to be differentially expressed in other diseases/conditions, including diabetic retinopathy [ 61 ], endometriosis [ 25 ], spinal cord injury [ 62 ], and many more. Some are involved in multiple pathologies—5′tiRNA-His-GTG was shown to respond to tissue hypoxia and may be involved in malignancy [ 29 ].…”

“…In pathology, tRFs were found to be differentially expressed in various cancers [ 21 ] and amyotrophic lateral sclerosis [ 22 ]. Various tiRNAs were even proposed to be hallmarks of various diseases [ 23 , 24 , 25 ] and as therapy options; in the latter, specific tRFs derived from exosomes were shown to alleviate systemic lupus erythematosus [ 26 ].…”

Network pharmacological analysis and molecular docking of Huangqin-Baizhu herb pair in the treatment of threatened abortion

“…And in vitro and in vivo experiments have found that RAP1 acts on the AKT signaling pathway to promote the growth of trophoblast cells, [41] ensuring that the early embryo receives sufficient trophoblast. In addition, clinical and laboratory experiments [42,43] have found that the levels of RAP1 and EPAC1 are higher in ectopic endometrium than in normal endometrium and they are positively correlated. It is speculated that RAP1 and EPAC1 may play a synergistic role in promoting the formation of new microvessels in endometrium and the proliferation and adhesion of endometrial cells, which are beneficial to embryo implantation.…”

Systematic and integrated analysis of tRNA-derived small RNAs reveals novel potential pathogenesis targets of sarcoidosis

“…Although the mechanism of tsRNA action is yet to be elucidated, recent evidence suggests a miRNA-like mode of action, and bioinformatic prediction of tsRNA (whether tRF or tiRNA) will still use similar miRNAs for prediction in some studies [46][47][48][49][50] . miRNAs can recognise their mRNA targets using their seed sequence (positions 2-7nt at their 5 ends) and suppress global mRNA translational activities.…”