Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system

Spisák, Sándor and Chen, David and Likasitwatanakul, Pornlada and Doan, Paul and Li, Zhixin and Bala, Pratyusha and Vízkeleti, Laura and Tisza, Viktoria and De Silva, Pushpamali and Giannakis, Marios and Wolpin, Brian and Qi, Jun and Sethi, Nilay S. (2024) Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. NATURE COMMUNICATIONS, 15 (1). ISSN 2041-1723

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Abstract

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.

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