Supplementary Figure 3: Transcriptomic analysis of endometriotic organoids reveals disease-specific pathways and genes.

(a) PCA plot showing the distribution of EM-O, EUT-O and ECT-O, based on the RNA-seq data (n=4 independent donors for EM-O and EUT-O, n=7 independent donors for ECT-O). (b) Diagram of the differentially expressed genes in EM-O, EUT-O and ECT-O as identified by RNA-seq analysis. Of the 277 differentially expressed genes between EM-O/EUT-O and ECT-O, 34 are specifically expressed in EM-O/EUT-O and 243 in ECT-O. Of the 35 differentially expressed genes between EM-O and EUT-O, 15 are specifically expressed in EM-O and 20 in ECT-O (see Supplementary Tables 3–5). Relevant genes are indicated. (c) Expression of WNT ligand and Hippo pathway target genes in stage I to IV ECT-O as normalized to GAPDH and expressed as fold change relative to EM-O (mean ± s.e.m. of n=3 biologically independent experiments for stage I and IV ECT-O, n=5 for stage II ECT-O and n=4 for stage III ECT-O). *P<0.05; non-parametric Kruskal-Wallis test for multiple comparison with Dunn’s post-test (95% confidence intervals). (d) Expression of invasion and inflammatory marker genes in stage I to IV ECT-O as normalized to GAPDH and expressed as fold change relative to EM-O (mean ± s.e.m. of n=3 biologically independent experiments for stage I and IV ECT-O, n=5 for stage II ECT-O and n=4 for stage III ECT-O). *P<0.05; non-parametric Kruskal-Wallis test for multiple comparison with Dunn’s post-test (95% confidence intervals). (e) PCA plot showing the distribution of matched EUT-O and ECT-O, based on the RNA-seq data (n=4 independent donors for the EUT-O and matched ECT-O). (f) Heatmap of 75 differentially expressed genes (log₂ normalized counts) as identified by RNA-seq analysis of 4 matched ECT-O and EUT-O organoid lines as indicated. Colors range from blue (low expression) to red (high expression). LGR6 is among the top upregulated genes in the ECT-O.