Fig. 2

Zero-passage organoids preserve short-term hormone receptor expression and reduce trans-differentiation of luminal breast cancer cells. A and B Comparison of ESR1 and PGR expression in originating tumor scrapes, zero-passage organoids, and 2D cultured cells relative to a basal control (MCF10A-5E; pink) and luminal breast cancer cell lines (MCF7, T47D, HCC1500, CAMA1, EFM19, and ZR-75–1). Shaded boxes indicate the observed range of expression among patients. Paired samples are connected with black lines. Blue highlights paired samples of tumor scrape, 2D culture, and zero-passage organoids (n = 4 independent luminal breast cancers). Paired 2D and organoid cultures were compared for ESR1 and PGR abundance by paired t test after log transformation. C. Downsampled scRNA-seq data of human breast cancers [21] used to define a CIBERSORTx signature matrix for bulk RNA-seq deconvolution [34]. D Gene-by-cell type signature matrix for deconvolving lineages in tumor scrapes, zero-passage organoids, and 2D cultures. E and F Comparison of luminal and basal lineage fractions in originating tumor scrapes, zero-passage organoids, and 2D cultured cells relative to luminal breast cancer cell lines (MCF7, T47D, HCC1500, CAMA1, EFM19, and ZR-75–1). Paired samples are connected with black lines. *P < 0.05 by paired one-sided t test after arcsine transformation of percentages