Extended Data Fig. 5: Transcriptomic analysis of primary and rGBM post-PTP4A2 knockout.
From: Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells
(a) Row-normalized mRNA expression from pGBM (BT594) or pGBM (BT972) cells with PTP4A2 (2 gRNAs, A or B) or AAVS1 knockout (1 gRNA, control). Data from three independent biological replicates are shown. Rows and columns are sorted by hierarchical clustering. On bottom left, Venn diagram of differentially expressed genes is presented (DEGs; limma LFC| > 2 and adjusted P <0.05). (b) Gene Set Enrichment Analysis (GSEA) enrichment of axon guidance pathway gene expression in rGBM cells following PTP4A2 knockout, as compared to gRNA targeting AAVS1 (control). Hypergeometric test P values after FDR correction for multiple testing. ES, enrichment score. (c) Phospho-peptide levels of all members belonging to ROBO1-SRGAP-CDC42 signaling axis in rGBM following PTP4A-inhibition for 5 or 30 minutes. Identified dephosphorylation sites are indicated for each member. (d) GSEA enrichment plots of ROBO signaling pathway genes in CRISPR/Cas9 screens in rGBM models (BT241 and BT972). Hypergeometric test P values after FDR correction for multiple testing. (e) Immunoblotting of Myc tag in rGBM (BT972) cells electroporated with plasmids over expressing wildtype CDC42 and constitutively active CDC42 Q61L. Proteins linked with Myc tag. (f) Phospho-peptide levels of WNT signaling regulators APC, CTNNB1 (β-Catenin), and LBH in rGBM following PTP4A-inhibition for 5 or 30 minutes.
