Competitive endogenous RNA networks: integrated analysis of non-coding RNA and mRNA expression profiles in infantile hemangioma

Abstract

Infantile hemangioma (IH) is the most common vascular tumour in infants. The pathogenesis of IH is complex and poorly understood. Therefore, achieving a deeper understanding of IH pathogenesis is of great importance. Here, we used the Ribo-Zero RNA-Seq and HiSeq methods to examine the global expression profiles of protein-coding transcripts and non-coding RNAs, including miRNAs and lncRNAs, in IH and matched normal skin controls. Bioinformatics assessments including gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed. Of the 16370 identified coding transcripts, only 144 were differentially expressed (fold change ≥ 2, P ≤ 0.05), including 84 up-regulated and 60 down-regulated transcripts in the IH samples compared with the matched normal skin controls. Gene ontology analysis of these differentially expressed transcripts revealed 60 genes involved in immune system processes, 62 genes involved in extracellular region regulation, and 35 genes involved in carbohydrate derivative binding. In addition, 256 lncRNAs and 142 miRNAs were found to be differentially expressed. Of these, 177 lncRNAs and 42 miRNAs were up-regulated in IH, whereas 79 lncRNAs and 100 miRNAs were down-regulated. By analysing the Ribo-Zero RNA-Seq data in combination with the matched miRNA profiles, we identified 1256 sponge modulators that participate in 87 miRNA-mediated, 70 lncRNA-mediated and 58 mRNA-mediated interactions. In conclusion, our study uncovered a competitive endogenous RNA (ceRNA) network that could further the understanding of the mechanisms underlying IH development and supply new targets for investigation.

The Regulatory Roles of Non-coding RNAs in Angiogenesis and Neovascularization From an Epigenetic Perspective

“…They also found more than a thousand sponge modulators involved in miRNA-, lncRNA-, and mRNA-mediated interactions. These findings suggest the presence of an endogenous ncRNA regulatory network associated with the development of IH and other vascular diseases (121).…”

Long non-coding RNA ATB promotes human non-small cell lung cancer proliferation and metastasis by suppressing miR-141-3p

“…https://doi.org/10.1371/journal.pone.0229118.g004 processes through acting as ceRNAs to regulate microRNAs (miRNAs) [26][27][28]. we proposed that lncRNA-ATB might act as a ceRNA to regulate relevant cellular control.…”

Matrix Hyaluronan-CD44 Interaction Activates MicroRNA and LncRNA Signaling Associated With Chemoresistance, Invasion, and Tumor Progression

“…During the regulation of miRNA expression, lncRNA can compete the common response elements of miRNAs (161). LncRNAs can also bind DNAs, RNAs and proteins by acting as decoy, guide or scaffold (161).…”

“…During the regulation of miRNA expression, lncRNA can compete the common response elements of miRNAs (161). LncRNAs can also bind DNAs, RNAs and proteins by acting as decoy, guide or scaffold (161). LncRNA has been reported to bind to many different miRNAs including miR-145 in a variety of cancer cells resulting in carcinogenesis, tumor cell migration, invasion or drug resistance (152, 153, 162–167, 167–169).…”