Fig. 5

Expression analysis of NA in vitro and in vivo models reveals WNT pathway activation in ALK+ ALCL patient cells. A. Principal component analysis of the RNAseq data (Dim 1 and 2). Data were scaled to unit variance before performing the representation. B. Gene set enrichment analysis of the 200 most differentially upregulated or downregulated genes obtained from the models [comparison of NPM-ALK-edited in vitro models vs. wild type cells (in vitro) or NPM-ALK in vivo models vs. wild type cells] on expression data from ALK+ ALCL patients vs. non tumoral reactive lymph nodes (CTL). UP genes: upregulated genes, DOWN genes: downregulated genes, WT: wild type. C. Gene set enrichment analysis using an ALK+ ALCL patient signature of 200 upregulated genes, on expression data from our models: NPM-ALK in vitro vs. wild type cells (upper panel), NPM-ALK in vivo models vs. wild type cells (lower panel). WT: wild type. D. Gene set enrichment analysis was performed on the Reactom and Hallmark gene lists for the following pairwise comparisons: NPM-ALK in vitro vs. wild type cells, NPM-ALK in vivo models vs. wild type cells, and NPM-ALK+ patients and non tumoral reactive lymph nodes (CTL). The overlap of significantly enriched genes is represented as Venn diagrams. WT: wild type. E. Heatmap representation of expression levels of the enriched WNT genes in the model (left panel) and the patient (right panel) datasets. F. Immunofluorescence analysis of beta-catenin in ALKIma1 and PDX cells. Blue: DAPI, green: beta-catenin, red: actin. G. Gene set enrichment analysis of the canonical and the non-canonical WNT signaling pathway gene lists to compare ALK+ ALCL patients vs. non-tumoral reactive lymph node expression data (CTL). H. Significantly upregulated WNT pathway genes in ALK+ ALCL patient cells compared with reactive lymph nodes (CTL), represented as Z scores computed from Congras et al., 2020 (Journal of Clinical Investigation) using DESeq2. p-values were adjusted for multiple comparisons with the Benjamini-Hochberg correction (*: FDR < 0.05, **: FDR < 0.01, ***: FDR < 0.001)