Fig. 6: RNA-seq of human LECs exposed to breast cancer cell CM.

a Experimental setup for the in vitro experiments. Cells were seeded at Day 0 (D0), CM was generated on D1 to D2 (24 hours) and receiving cells were exposed on D2 to D4 (48 h). b Venn diagrams showing the number of upregulated and downregulated genes obtained by RNA-seq of CM-exposed LECs. c Heatmap showing the top DEGs in the CM-exposed LECs. Gray triangles indicate the result of unsupervised clustering for genes and cell types behaving in a similar way. d Volcano plots depicting genes upregulated and downregulated in LECs after CM exposure (two-sided Wald test). Genes indicated in red are considered mostly pro-inflammatory, whereas genes in blue are anti-inflammatory. e Pathway analysis showing the most significantly downregulated and upregulated pathways (the integrated two-sided Fisher’s exact test). LECs are from 4 different sources (n = 4) (a–e). f Gene expression changes in CM-exposed LECs (n = 3–9 HLECs). Data were analyzed with a one-way ANOVA. g Protein expression levels of MGP in LECs following CM exposure (n = 6 HLECs). Data were analyzed with a one-way ANOVA linear mixed model and Dunnett’s correction. h Protein expression of MGP and podoplanin on LECs after coculture of T47D cells with LECs compared to culture with CM. Data were analyzed with two-way ANOVA and Sidak’s multiple comparison test (n = 4 HLECs). i mRNA Expression of CDH2, CDH5, and SNAI1 in CM-exposed LECs. Data were shown as box plots (n = 5–7 HLECs). Data were analyzed using a two-way ANOVA linear mixed model and statistical significance was adjusted with Dunnett multiplicity correction. Source data, non-significant p values and detailed experiment and n-numbers (biologically independent samples of cultured cells) are provided in the Source Data file.