Microarray Analysis Reveals Changes in tRNA-Derived Small RNAs (tsRNAs) Expression in Mice with Septic Cardiomyopathy

Abstract

tRNA-derived small RNAs (tsRNAs) as a novel non-coding RNA have been studied in many cardiovascular diseases, but the relationship between tsRNAs and septic cardiomyopathy has not been investigated. We sought to analyze changes of the expression profile of tsRNAs in septic cardiomyopathy and reveal an important role for tsRNAs. Methods: We constructed a sepsis model by cecal ligation and puncture (CLP) in mice, and microarray analysis was used to find differentially expressed tsRNAs. Quantitative real-time PCR was used to verify the expression of tsRNAs and the interference effect of angiogenin (ANG), a key nuclease producing tsRNAs. Bioinformatics analysis was used to predict target genes and functions. CCK-8 and LDH release assays were used to detect cell viability and cell death. Results: A total of 158 tsRNAs were screened, of which 101 were up-regulated and 57 were down-regulated. A total of 8 tsRNAs were verified by qPCR, which was consistent with microarray results. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses suggest that these tsRNAs may be associated with the Wnt signaling pathway and participate in cellular process. The expression of tsRNAs decreased after the interference of the key nuclease ANG, while CCK-8 suggested a corresponding decrease in cell viability and an increase in the release of LDH (cell death), indicating that tsRNAs can protect cardiomyocytes during the development of septic cardiomyopathy, reduced cardiomyocyte death. Conclusions: A total of 158 tsRNAs changed significantly in septic cardiomyopathy, and these tsRNAs may play a protective role in the development of septic cardiomyopathy.

Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions

“…For this analysis, we chose lncRNAs that were highly upregulated with a raw signal intensity of more than 100 (corresponding to the highly expressed genes in microarrays). Only lncRNAs listed in GENCODE and Ensemble or characterized by Cabili et al ( Yuan et al, 2022 ) were chosen for annotation purposes. We obtained data on miRNA binding to particular lncRNAs using LncBase v.2, included in DIANA Tools ( Paraskevopoulou et al, 2016 ).…”

“…The 3-OH-ended RNA was then denatured by DMSO and enzymatically labeled with Cy3. This ligation of small RNAs with Cy3 dye directly at their 3′-OH ends, completely avoids RNA pretreatments to remove internal RNA modifications, abortive reverse transcription due to the modifications and RNA fold hindrance, and skewed PCR amplification steps ( Yuan et al, 2022 ). All these help to preserve the fidelity of native small RNA levels and achieve the unbiased high quantification accuracy.…”