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

Sandor SpisakDavid ChenPornlada LikasitwatanakulPaul DoanZhixin LiPratyusha BalaLaura VizkeletiViktoria TiszaPushpamali De SilvaMarios GiannakisBrian M WolpinJun QiNilay S Sethi
Published in: Nature communications (2024)
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.
Keyphrases
  • stem cells
  • crispr cas
  • genome editing
  • single cell
  • transcription factor
  • high throughput
  • endothelial cells
  • genome wide
  • rna seq
  • quantum dots
  • cell therapy
  • bone marrow