Extended Data Fig. 5: Transcriptomic and proteomic characterization of EMT tumour cells after Rhoj deletion.
From: RHOJ controls EMT-associated resistance to chemotherapy
a, b, mRNA expression of genes upregulated (a) or downregulated (b) in EPCAM− Control shRNA compared to EPCAM− Rhoj sh KD measured by RNA seq. (Means are shown, n = 2 independent primary cultured cell lines). c,d, Gene Ontology analysis of genes that are upregulated (c) or downregulated (d) in EPCAM− control cells compared to Rhoj Sh KD EPCAM− cells (c), showing categories of genes that are significantly enriched. e-f, Gene Ontology analysis corresponding to the proteins significantly upregulated in EPCAM− WT and EPCAM− Control sh (e) and in EPCAM+ and EPCAM− Rhoj sh (f). p value is calculated according to the Benjamini–Hochberg method for multiple hypothesis testing. g, Immunofluorescence of Phalloidin (red) in EPCAM+, EPCAM− and EPCAM− Rhoj KO cells. Nuclei are counterstained with DAPI (blue) (n = 3 biological replicates; scale bar, 20μm). h-k, Western blot showing the expression of POLD (h), PCNA (i), phospho-RPA2 (S4/8), total RPA2 (j) and N-WASP (k) in EPCAM+, EPCAM− and Rhoj KO cells. Tubulin or β-Actin loading controls (n = 2, molecular weights (kDa) are indicated to the right side of the blots). l, mRNA expression of EMT transcription factors measured by RNA-sequencing in EPCAM− control cells compared to EPCAM− Rhoj sh KD cells (Means are shown, n represents the number of independent primary cell lines). m, Protein expression of selected epithelial and EMT markers in EPCAM+, EPCAM− WT, EPCAM− Control sh, EPCAM− Rhoj sh cells untreated and treated for 24h with cisplatin/5FU (n represents the number of technical replicates, Means + S.D. are shown).
