Fig. 2: Targeted in vivo CRISPR/Cas9 loss-of-function screen identifies synthetic lethalities with BQ in PDAC.
From: De novo pyrimidine biosynthesis inhibition synergizes with BCL-XL targeting in pancreatic cancer
a A customized CRISPR/Cas9 mini-pool library (369 genes, 4 sgRNAs per gene, 528 control sgRNA) was generated prioritizing proteomic hits with FDA-approved available drugs, CRISPR depleted/enriched hits, and genes related to DHODH in published in vitro studies. b Schematic for in vivo and in vitro CRISPR screens with customized mini-pool library (Santana-Codina, N. (2025) https://BioRender.com/t12d46e). PDAC cells were infected with the mini-pool library and implanted in a xenograft NOG mouse model (PaTu-8988T, n = 10 mice/arm). Tumor-bearing mice (80–100 mm3) were treated with either vehicle or BQ, harvested 14 days later and analyzed by NGS. PaTu-8988T and PANC-1 cells containing the sgRNA mini-library were also evaluated in in vitro screens to confirm the whole genome screen results and directly contrast to in vivo results. c, d Manhattan plot for depleted hits in a mini-pool library in vitro CRISPR/Cas9 screen in PaTu-8988T (c) and PANC-1 (d) cells at 5 μM BQ. Blue dots highlight significant genes (−log10(P) ≥ 2) in BQ versus DMSO, orange circles highlight genes related to apoptosis and cyan circles highlight genes in the nucleoside salvage pathway. e Rank-ordered graph of log2 (BQ/control) for each gene in PaTu-8988T tumors. f Manhattan plot for depleted hits in PaTu-8988T tumors. Blue dots highlight significant genes (-log10(P) ≥2) in BQ versus vehicle, orange circles highlight genes related to apoptosis and cyan circles highlight genes in the nucleoside salvage pathway. Source data are provided as a Source Data file.
