The Magic Approach For 3-Methyladenine

This prompted us to investigate whether any nonmutational or epigenetic mechanisms are involved in maintaining the upregulation of subtype 2 signature genes. Given the requirements for histone demethylase KDM5A and the insulin growth factor 1 (IGF-1) signaling pathway for drug resistance in cancer stem cells (CSCs) (Sharma et?al., 2010), we also examined the expression, CNA, and promoter DNA methylation status of these genes across the subtypes. The copy number and expression of KDM5A, which are highly correlated across the 512 samples (Pearson correlation coefficient [PCC]?= 0.73), are relatively low in good-prognosis subtypes (subtypes 3 and?7) and high in other subtypes. IGF1 is specifically upregulated in subtype 2 (the metastasis subtype) and downregulated in other subtypes (Wilcoxon rank sum test, p?= 2.997e-16). Similarly, IGFBP3 is also upregulated in subtype 2 compared with the other subtypes (Wilcoxon rank sum test, p?= 3.717e-7). However, the classical CSC markers CD133 and CD44 are generally repressed in all subtypes compared with normal tissue controls (Wilcoxon rank sum test, p?= 4.212e-3 for CD133 and p?= 6.619e-6 for CD44; Figure?3). Therefore, although they lack classical CSC markers, in general, the ovarian cancer samples with a poor prognosis possess a recently discovered drug-resistant CSC feature: high expression of KDM5A and IGF1. Indeed, the poor-prognosis subtypes (subtypes 2, 4, and 5) have the worst outcomes in response to drug treatment and are more likely to be resistant to cancer drug treatments than other subtypes ( Figure?S2; Tables S3, S4, and S5). We next investigated the relationship among the signature genes of each subtype using a functional interaction network. To enrich for the ��driver�� genes (i.e., those genes in which changes are directly reflected at the gene expression level), we first removed the genes that were identified by genomic or epigenomic signatures (CNA or DNA methylations) that are not consistent with gene expression changes (PCC? ?0.3 for?promoter DNA methylations; Figure?S3; Extended Experimental Procedures). We then also removed the genes with inconsistent direction of expression changes within the featured subtype (with dominant direction in