Fig. 3: Collagen I enhances a Yap-associated program in basal-like cells that is required to drive collective invasion.

a Differentially expressed genes in basal-like cells (Collagen I vs BME). P values, two-sided Wilcoxon rank sum test. b Enriched transcription factors (P≤0.01) based on motif analysis of the differentially expressed genes. P values, cumulative hypergeometric distribution without multiple comparisons adjustments (HOMER). c The significantly altered pathways from the gene set enrichment analysis, filtered for absolute values of NES >0.5 and enrichment P value (<0.01) produced by the GSEA. d Confocal imaging of Yap, K14 and K8 in MMTV-PyMT organoids embedded in BME/Collagen I (1 day). Arrowheads: K14-positive cells: rim (green); leader cells (white). e Yap nuclear/cytoplasmic ratio in cells located at the rim. K14-high (Hi) or -low (Lo), based on mean intensity. Red line: median from n = 407 (BME, K14 Hi), n = 92 (BME, K14 Lo), n = 627 (Collagen I, K14 Hi), n = 197 (Collagen I, K14 Lo) cells from three independent experiments. f Yap nuclear/cytoplasmic ratio in K14-high cells: rim (BME, n = 407; Collagen I n = 468) or leader cells (n = 33) from three independent experiments. g Yap, K14 and K8 in patient-derived organoids Collagen I, day 3) from 2 independent experiments. h Yap shRNA (−/+ Dox) in MMTV-PyMT organoids (Collagen I). Arrowheads: invasive strands. i–l Cumulative strand length after (i, j) Yap knockdown or (k, l) YTIP expression in MMTV-PyMT organoids (Day 3) and 4T1 spheroids (Day 2) in Collagen I. i–l Medians (black line), 25/75 percentiles (boxes) and maximum/minimum values (whiskers) from n = 30 organoids from three independent experiments (i, k), n = 15 (-Dox) n=17 (+Dox) organoids from two independent experiments (j), n = 81 (-Dox) and n = 88 (+Dox) spheroids from three independent experiments (l). m, n Patient-derived organoids invading in Collagen I, DMSO, 5 μM or 10 μM of K975 (n) resultant collective invasion after 2–3 days in Collagen I, n = 112 organoids analyzed per condition from three independent experiments. n Representation similar to (i–l). P values, (i–l) two-sided unpaired Mann–Whitney test; e, f, n two-sided Kruskal–Wallis test (Dunn’s multiple comparison). Scale bars: 50 μm (d, e, h, m), 10 μm (d, g, insets). Source data are provided as a Source Data file.