Multiple transcriptome analysis of Piwil2-induced cancer stem cells, including piRNAs, mRNAs and miRNAs reveals the mechanism of tumorigenesis and development.

Abstract

Cancer stem cells play important roles in the process of tumorigenesis. Our research group obtained cancer stem cell-like cells named Piwil2-iCSCs by reprogramming human preputial fibroblasts (FBs) with the PIWIL2 gene, but the mechanism of Piwil2-iCSCs is still unclear. We sequenced the piRNAs, miRNAs and mRNAs of Piwil2-iCSCs and FBs, and analyzed the differences. Gene Ontology (GO) and, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and gene set enrichment analysis (GSEA) were performed on the differentially expressed (DE) mRNAs. In addition, we analyzed the variable shear events and fusion genes in the Piwil2-iCSCs. Target gene prediction and functional enrichment analysis were performed for the DE miRNAs. A total of 1119 DE mRNAs, 220 DE piRNAs, and 440 DE miRNAs were obtained between the Piwil2-iCSCs and FBs. Functional enrichment analysis showed that the genes with upregulated expression were mainly involved in DNA repair, mismatch repair, base excision repair, and nucleotide excision repair. Genes with downregulated expression were mainly involved in the TGF-β receptor signaling pathway, senescence and autophagy in cancer. More frequent shear events occurred in Piwil2-iCSCs and FBs, especially in intron retention (IR) events. We also identified three fusion genes MCM3AP-C21orf58, LRRFIP2-CAV3 and TMEM184B-DMC1. Enrichment analysis of DE miRNAs showed that they were associated with apoptosis, the TGF-β signaling pathway, and the stem cell regulatory signaling pathway. In particular, target gene prediction of the top three miRNAs with upregulated expression showed that they targeted SMAD, GREM1 and other genes to participate in the regulation of TGF-β and other pathways. PIWIL2-induced cancer stem cells have significantly altered levels of miRNAs, piRNAs and mRNAs.TGF-β, autophagy, apoptosis and other pathways may play an important role in stem cell development. The occurrence of alternative splicing and fusion genes may be related to the occurrence of cancer stem cells.