Genome-wide CRISPR-Cas9 screen analyzed by SLIDER identifies network of repressor complexes that regulate TRIM24
Lalit R. Patel,
Sabrina A. Stratton,
Megan McLaughlin,
Patrick Krause,
Kendra Allton,
Andrés López Rivas,
Daniela Barbosa,
Traver Hart,
Michelle C. Barton
Affiliations
Lalit R. Patel
Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA; University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX, USA; McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; Corresponding author
Sabrina A. Stratton
Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Megan McLaughlin
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Patrick Krause
Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, US
Kendra Allton
The Neurodegeneration Consortium, Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
Andrés López Rivas
School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA
Daniela Barbosa
Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, USA
Traver Hart
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Michelle C. Barton
Division of Oncological Sciences, Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, US; Corresponding author
Summary: TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and what changes in its regulation are responsible for its overexpression. Here, we perform a genome-wide CRISPR-Cas9 screen by fluorescence-activated cell sorting (FACS) that nominated 220 negative regulators and elucidated a regulatory network that includes the KAP1 corepressor, CNOT deadenylase, and GID/CTLH E3 ligase. Knocking out required components of these three complexes caused TRIM24 overexpression, confirming their negative regulation of TRIM24. Our findings identify regulators of TRIM24 that nominate previously unexplored contexts for this oncoprotein in biology and disease. These findings were enabled by SLIDER, a new scoring system designed and vetted in our study as a broadly applicable tool for analysis of CRISPR screens performed by FACS.
