Aberrant stem cell-like activity and impaired differentiation are central to the development
of colorectal cancer (CRC). To identify functional mediators of these key cellular
programs, we engineer a dual endogenous reporter system by genome-editing the SOX9
and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting
aberrant stem cell-like and differentiation activity, respectively. By applying a
CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform,
we identify factors that contribute to stem cell-like activity and differentiation
in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate
SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation
across an array of neoplastic colon models. SMARCB1 is a dependency and required for
in vivo growth of human CRC models. These studies highlight the utility of biologically
designed endogenous reporter platforms to uncover regulators with therapeutic potential.
