Integrative analyses of bulk microarray data to discover genes, pathways, and immune infiltration characteristics associated with targeting of Ewing sarcoma

Abstract

Purpose To explore transcriptome and immunological features of patients with Ewing sarcoma (ES) using all publicly available microarray data. Methods Data of 479 ES tissues were integrated and normalized. Gene expression, immune infiltration, and cancer-specific pathways were analyzed. Genes of interest were knocked down, followed by cell proliferation and colony formation assays. Results Consistent with the previous reports of differential expressed genes (DEGs) in ES, our analysis identified CCND1, HMCN1, and NKX2-2 were among the most highly expressed, while TWNC1, MYBPC1, and CKM were among the lowest expressed genes. GO, KEGG, and GSEA enrichment analysis identified that the DEGs related to bone and muscle functioning, those that contributed to crucial cellular, and metabolism pathways such as actin binding, apoptosis, TCA cycle, and cell cycle were also significantly enriched. Immune infiltration analysis discovered that many T cell subsets including CD4T, CD8 T, and Gamma delta T cells were highly infiltrated, while monocytes and B cells were less infiltrated in tumors. A total of 138 genes were both significantly up-regulated in tumors and associated with decreased survival, while 38 significantly down-regulated genes were associated with increased survival, many of which were previously reported as oncogenes and tumor suppressors in ES and other cancers. Silencing of four newly identified top ranked up-regulated genes with decreased survivals in ES inhibited proliferation and colony formation of ES cells. Conclusion This study may provide a clear representative transcriptome profile of ES, providing diagnostic biomarkers, pathways, and immune infiltrative characteristics targets for ES.

Patient-Derived Organoids Recapitulate Pathological Intrinsic and Phenotypic Features of Fibrous Dysplasia

“…Genes encoding nuclear proteins such as HIST1H4C, H2AFZ, CENPF, and CKS2, which interact with cell-cycle regulatory proteins, were among the most highly expressed genes in these two clusters (Figure 2C, File S1). Of interest to us is the fact that these genes have been recognized as exclusive biomarkers for cell proliferation associated with a higher S and G2M score, suggesting functions in growth and cell division [71][72][73]. Moreover, TOP2A and CENPF, markers for cell-cycle regulation that were among the exclusively expressed genes in the proliferating S and G2M clusters, are reported to synergistically promote cell division, epithelial-mesenchymal transition (EMT), proliferation, and migratory phenotypes [74].…”

Dissecting the Methylomes of EGFR-Amplified Glioblastoma Reveals Altered DNA Replication and Packaging, and Chromatin and Gene Silencing Pathways

“…Cao et al found that NKX2-2-AS1 was highly expressed in Ewing sarcomas, functioning as a core co-regulator of the driver mutation fusion gene, and is recognized as a specific biomarker for Ewing sarcomas [ 26 ]. Muraguchi et al described that NKX2-2 suppresses the self-renewal of glioma-initiating cells [ 27 ].…”