Fig. 2
LARGE2 mRNA levels in CRC correlate with high Wnt activity and hCoSC gene expression. (A-C)LARGE2 gene expression in consensus molecular subtypes (CMS) of the TCGA-COAD cohort (n = 373) (A), the Marisa et al. (2013) CRC cohort (n = 519) (B), and in the CRC intrinsic subtypes (CRIS) of a PDX cohort published by Isella et al. (2017) (n = 515) (C). Shown are the mean levels of LARGE2 (blue horizontal line). Asterisks indicate a significant difference between CMS2 or CRISD and the other subtypes. Significance was calculated by one-way ANOVA testing (** p < 0.01, *** p < 0.001, **** p < 0.0001). D-G) GSEA on LARGE2 gene signatures derived from TCGA-COAD and TCGA-READ RNA-Seq data sets. Shown are enrichments of Wnt target gene sets upregulated upon siRNA-mediated β-catenin silencing in CRC cells (D, E), and gene sets which specify EPHB2high(F) or PTK7high (G) hCoSCs (see method section for details). NES: normalized enrichment score, FDR-q: False discovery rate q-value. H,I) GSEA on LARGE2 gene signatures derived from microarray data of a PDX CRC cohort published by Isella et al. 2017 (H) and the 58 CRC lines included in the CCLE database (I). p.c.: positive correlation, n.c.: negative correlation. J,K) qRT-PCR analysis of LARGE2 gene expression (J) or expression of bona-fide Wnt target genes (K) in the indicated CRC cell lines. Analysis was performed in duplicates (two independent RNA samples per cell line). Error bars indicate ±SD. * gene expression not detectable by qRT-PCR