Figure 4.

Co-occurrence of chromosome 1q gain and 6q loss is associated with an undifferentiated proliferative cellular phenotype in PFA. (A) Cytoscape clustering of gene ontologies enriched in genes overexpressed in PFA with 1q+ and/or 6q− (n = 26) versus those with wildtype 1q/6q (n = 46). (B), single sample gene set enrichment analysis (ssGSEA) of top 1q+ and/or 6q− PFA associated GOterm mitotic cell cycle process in individual patient samples grouped according to (i) 1q+ and 6q− co-occurrence (1q+ and 6q−; n = 12), (ii) 1q+ with wildtype 6q (1q+ only; n = 10), (iii) 6q− with wildtype 1q (6q− only; n = 4), and (iv) wildtype 1q and 6q (WT 1q and 6q; n = 46). C, Ontology clustering of genes underexpressed in 1q+ and/or 6q−, and (D) individual sample enrichment of GOterm gliogenesis grouped according to CNV status. (E) Overexpressed genes in 1q+ and/or 6q− PFA were compared to previously identified PFA neoplastic cluster marker genesets⁵ (top 50) by hypergeometric analysis. (F) Deconvolution of individual patient samples for UEC-A (undifferentiated EPN cell-A) neuroepithelial progenitor subpopulation using ssGSEA. (G) Corresponding neoplastic cluster gene enrichment analysis for genes underexpressed in 1q+ and/or 6q− PFA. (H) Deconvolution of individual patient samples for differentiated TEC-D (transportive EPN cell-D) subpopulation using ssGSEA.