PAX6 is frequently expressed in ependymal tumours and associated with prognostic relevant subgroups

Role of PAX6, TRPA1, BCL11B, MCOLN2, CUX1, EMX1 in colorectal cancer and osteosarcoma

Colorectal cancer is a cancer that arises from the abnormal growth of cells in the colon or rectum. Osteosarcoma (OS) is a common primary bone tumor with high degree of malignancy. The configuration files for colorectal cancer dataset GSE142279 and OS datasets GSE197158 and GSE206448 were downloaded from Gene Expression Omnibus database using the platforms GPL20795, GPL20301, and GPL24676. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. Construction and analysis of protein-protein interactions (PPI) network. Functional enrichment analysis, gene set enrichment analysis (GSEA) were performed. A heat map of gene expression was drawn. The Comparative Toxicogenomics Database (CTD) was used to find the diseases most associated with the core genes. TargetScan was used to screen miRNAs regulating DEGs. According to the Gene Ontology (GO) analysis, DEGs are mainly enriched in acetylcholine binding receptor activity involved in Wnt signaling pathway, cell polarity pathway, PI3K-Akt signaling pathway, receptor regulator activity, cytokine-cytokine receptor interaction, transcriptional misregulation in cancer, and inflammation-mediated regulation of tryptophan transport. In the Metascape enrichment analysis, GO enrichment items related to the regulation of Wnt signaling pathway, regulation of muscle system process, and regulation of actin filament-based movement. Eight core genes (CUX1, NES, BCL11B, PAX6, EMX1, MCOLN2, TRPA1, TRPC4) were identified. CTD showed that 4 genes (CUX1, EMX1, TRPA1, BCL11B) were associated with colorectal neoplasms, colorectal tumors, colonic diseases, multiple myeloma, OS, and inflammation. PAX6, TRPA1, BCL11B, MCOLN2, CUX1, and EMX1 are highly expressed in colorectal cancer and OS, and the higher the expression level, the worse the prognosis.

Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma

Intra-tumoral heterogeneity (ITH) is a complex multifaceted phenomenon that posits major challenges for the clinical management of cancer patients. Genetic, epigenetic, and microenvironmental factors are concurrent drivers of diversity among the distinct populations of cancer cells. ITH may also be installed by cancer stem cells (CSCs), that foster unidirectional hierarchy of cellular phenotypes or, alternatively, shift dynamically between distinct cellular states. Ependymoma (EPN), a molecularly heterogeneous group of tumors, shows a specific spatiotemporal distribution that suggests a link between ependymomagenesis and alterations of the biological processes involved in embryonic brain development. In children, EPN most often arises intra-cranially and is associated with an adverse outcome. Emerging evidence shows that EPN displays large intra-patient heterogeneity. In this review, after touching on EPN inter-tumoral heterogeneity, we focus on the sources of ITH in pediatric intra-cranial EPN in the framework of the CSC paradigm. We also examine how single-cell technology has shed new light on the complexity and developmental origins of EPN and the potential impact that this understanding may have on the therapeutic strategies against this deadly pediatric malignancy.