Fig. 1: BMP signaling is required for RA sensitivity in a hyper-sensitive NB cell line.
A ATRA IC50 values for all non-hematological cancer cell lines screened by GDSC1. Each dot represents a cell line (n = 759 in total). Box bounds show 25th and 75th percentiles, horizontal lines within the interquartile range (IQR) boxes indicate the median values for each group, and whiskers represent 1.5*IQR from the IQR values. Cancer types with ≤ 3 cell lines are not included. B Quantified flow cytometry results showing apoptosis in CHP-134, NB13, and D283 Med cell lines treated with ATRA (2 µM). Apoptotic cells were stained positive with annexin V and dead cells were stained positive with PI. Samples at day 9 for CHP-134 P = 1.67 × 10−7, NB13 P = 3.32 × 10−6; samples at day 6 for D283 Med P = 1.35 × 10−6. C Western blots for cleaved PARP (c-PARP) expression in CHP-134, NB13, and D283 Med cell lines treated with ATRA (2 µM). D Enrichr clustergram of CRISPR screen results (for BioPlanet 2019 pathways and GO Molecular Function 2021). Input: top 1% of genes with lowest negative and positive RRA score (191 + 191 genes). The genes and their directionality are listed in Supplementary Data 2. Red indicates screen hits. E Scatter plot highlighting top CRISPR screen hits involved in BMP signaling, ranked by positive RRA score (left, top knockouts cause resistance to ATRA) or negative RRA score (right, top knockouts sensitize to ATRA). RARA is also highlighted. F Viability of CHP-134 cells under 3-day (left) or 6-day (right) treatment with ATRA in the presence of DMSO or 0.5 µM K02288. Cell viability was measured with MTS. Data represent the mean ± SD of 4 independent replicates. For arrow indicated points, P = 3.89 × 10−6 for 3 days, P = 1.91 × 10−8 for 6 days. G. Western blots for c-PARP expression in CHP-134 treated with indicated compounds for 3 days (2 µM ATRA and 0.5 µM K02288). H Quantified flow cytometry results showing apoptosis in CHP-134 treated as in (G) for 3 days (left) and 6 days (right). For panel B and H, data represent the mean ± SD of 3 independent replicates. For panels C and G, GAPDH and β-Actin were used as loading control, the representative results of three independent experiments are shown. Two-sided t-test was used for panels B, F, and H. Source data are provided as a Source Data file.
