Microarray Analysis of Differentially Expressed Profiles of Circular RNAs in a Mouse Model of Intestinal Ischemia/Reperfusion Injury with and Without Ischemic Postconditioning

Abstract

Background/Aims: Ischemic postconditioning (iPoC) represents a promising strategy to mitigate ischemia/reperfusion (I/R) injury of the intestine, yet the mechanisms of this treatment remain to be elucidated. Circular RNAs (circRNAs), a novel class of endogenous non-coding RNAs, have recently been recognized as important regulators of gene expression and pathological processes. Here, we aimed to investigate the expression patterns of circRNAs after intestinal I/R with and without iPoC and, furthermore, to explore the potential mechanisms of iPoC in relation to the differentially expressed circRNAs. Methods: The global circRNA and mRNA expression profiles in mouse intestinal mucosa were initially screened by microarray (n = 3 per group) and quantitative real-time PCR was used to validate the expression pattern of circRNAs and mRNAs. Bioinformatics analysis including Gene ontology, KEGG pathway analysis, microRNA binding sites identification and circRNA-miRNA-mRNA network construction were utilized for in-depth mechanism exploration. Results: There were 4 up- and 58 downregulated circRNAs as well as 322 up- and 199 downregulated mRNAs in the intestinal I/R group compared with the sham group, whereas compared with I/R, iPoC treatment significantly upregulated 12 circRNAs and 129 mRNAs and downregulated 21 circRNAs and 174 mRNAs. The expression levels of a randomly selected set of 6 circRNAs and 5 mRNAs were successfully validated by qRT-PCR. Through a systematic comparison of the direction of circRNA expression changes in all groups, we identified two circRNAs, circRNA_012412 and circRNA_016863, that may be closely associated with the protective mechanisms of iPoC. Finally, four possible circRNA_012412/circRNA_016863-miRNA-mRNA pathways were predicted, which may play important roles in endogenous protective signaling in iPoC. Conclusions: This study was the first to comprehensively delineate the expression profiles of circRNAs in a mouse model of intestinal I/R and iPoC and provides novel clues for understanding the mechanisms of iPoC against intestinal I/R injury.

Genome-Wide RNA-Sequencing Reveals Massive Circular RNA Expression Changes of the Neurotransmission Genes in the Rat Brain after Ischemia–Reperfusion

“…Specifically, profiling analysis of circRNAs and mRNAs in human temporal lobe epilepsy with hippocampal sclerosis has been conducted [ 44 ]. Furthermore, microarray and functional enrichment analysis of circRNAs and mRNAs in a mouse model of intestinal IR injury with and without ischemic post-conditioning was performed [ 58 ]. Here, our results may indicate the specificity of the formation and degradation of circRNAs and mRNAs during cerebral IR, as well as the specific mechanisms of functioning of various linear and circular RNAs, which appear to be related to the uniqueness of their structures.…”

Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies

“…In our literature search, 15 studies made use of transcriptomics technology to study intestinal IR injury versus sham surgery in animals [10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] (Table 1, part I). The aims of these studies ranged from exploring overall changes in gene expression in intestinal IR for a better understanding of the pathological process and/or to identify potential therapeutic targets [10,16,17,21], to specific testing of a therapeutic intervention [11,13,15,18,19], or both [12,14,23,24]. For these studies, mice were most commonly used to establish an intestinal IR model [11,13,[15][16][17][18][19]21], and two studies made use of rats [10,14].…”

“…The aims of these studies ranged from exploring overall changes in gene expression in intestinal IR for a better understanding of the pathological process and/or to identify potential therapeutic targets [10,16,17,21], to specific testing of a therapeutic intervention [11,13,15,18,19], or both [12,14,23,24]. For these studies, mice were most commonly used to establish an intestinal IR model [11,13,[15][16][17][18][19]21], and two studies made use of rats [10,14].…”

A genome-wide circular RNA transcriptome in rat

“…(reported identified exonuclease-treated transcripts >25 000) [ 3 , 4 ] and Salzman et al (identified circRNA from different human cell types) [ 5 ] showed the abundance of circRNAs and established it as emerging class of noncoding RNAs. Till now, circ are identified in a number of organisms including model organisms like humans [ 3 , 6–9 ], worms [ 10 ], Drosophila [ 10 , 11 ], mouse [ 12–14 ], chicken [ 15 , 16 ], and pig [ 17–19 ]. Circs are known to exist as cell-line specific and tissue-specific isoforms [ 20 , 21 ] and are also known to have conserved splice sites.…”