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Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions.

ABSTRACT: As a novel class of noncoding RNAs, circular RNAs (circRNAs) have been reported to play a role in various biological processes. Some circRNAs may serve as microRNA (miRNA) sponges, regulating transcription or splicing. Herein, we investigated the expression profiles and interactions of miRNAs/isomiRs and circRNAs in male patients with esophageal cancer. We found that some miRNA genes generated two deregulated miRNA products (miR-#-5p and miR-#-3p), and these products were consistently abnormally expressed. Some circRNAs were predicted to be miRNA sponges for specific miRNAs. Some of these typically showed opposing expression patterns in cancer tissues: one upregulated and the other downregulated. Although fewer miRNAs were predicted to interact with circRNAs, the number of predicted interactions would be substantially increased if detailed isomiRs were involved. High sequence similarity across multiple isomiRs suggested that they might interact with circRNAs, similar to the interaction of homologous miRNAs with circRNAs. At the isomiR level, due to the characteristics of the sequences and expression patterns involved, the cross-talk between different ncRNAs is complicated despite simplification of the isomiRs involved through clustering. We expect that our results may provide methods for further study of the cross-talk among ncRNAs and elucidate their biological roles in human diseases.

SUBMITTER: Guo L

PROVIDER: S-EPMC5845524 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions.

Guo Li L Zheng Liang L Zhao Yang Y Wang Qianyun Q

BioMed research international 20180225

As a novel class of noncoding RNAs, circular RNAs (circRNAs) have been reported to play a role in various biological processes. Some circRNAs may serve as microRNA (miRNA) sponges, regulating transcription or splicing. Herein, we investigated the expression profiles and interactions of miRNAs/isomiRs and circRNAs in male patients with esophageal cancer. We found that some miRNA genes generated two deregulated miRNA products (miR-#-5p and miR-#-3p), and these products were consistently abnormally ...[more]

PMID: 29682564

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Project description:BackgroundCircRNAs are noncoding RNA molecules that have recently been described and shown to regulate miRNA functionality. While recent studies have suggested such circRNAs to be associated with pain related diseases in humans, no comprehensive migraine-related circRNA profiles have been generated, and there is currently no clear understanding of whether they can serve as regulators of migraine pathology.MethodsWe initially conducted a circRNA microarray analysis of the plasma of migraine patients and healthy controls. Based upon these data, we then selected 8 differentially expressed circRNAs and confirmed their expression in more migraine patient plasma samples via real-time PCR. We then performed functional and pathway enrichment analyses. Lastly, using a robust rank aggregation approach, we constructed a ceRNA network according to predicted circRNA-miRNA and miRNA-mRNA pairs in these migraine patient samples.ResultsWe were able to detect 2039 circRNAs in our patient samples, with 794 of 1245 these circRNAs being up- and downregulated in migraine patients relative to controls, respectively (fold change ≥ 1.5, p < 0.01). A qRT-PCR analysis confirmed that the expression of hsa_circRNA_100236, hsa_circRNA_102413, and hsa_circRNA_000367 was significantly enhanced in migraine patients, whereas the expression of hsa_circRNA_103809, hsa_circRNA_103670, and hsa_circRNA_101833 was significantly reduced in these individuals relative to healthy controls. We found these differentially regulated circRNAs to be associated with numerous predicted biological processes, with enrichment analyses suggesting that they may modulate the PI3K-Akt signaling so as to promote inflammation to drive migraine development. However, further research will be needed to formally test these mechanistic possibilities and to validate these circRNAs as potential biomarkers of migraine patients.ConclusionsOur results offer new potential insights into the mechanistic basis of this condition and suggest that hsa_circRNA_000367 and hsa_circRNA_102413 may offer value as regulators of migraine pathology.

Dataset Information

Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions.

Publications

Profiling and Bioinformatic Analyses Indicate Differential circRNA and miRNA/isomiR Expression and Interactions.

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