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

doi:10.1016/j.isci.2023.107126

Genome-wide CRISPR-Cas9 screen analyzed by SLIDER identifies network of repressor complexes that regulate TRIM24

iScience. 2023 Jun 14;26(7):107126. doi: 10.1016/j.isci.2023.107126. eCollection 2023 Jul 21.

Authors

Lalit R Patel^{1

2

3}, Sabrina A Stratton⁴, Megan McLaughlin⁵, Patrick Krause⁶, Kendra Allton⁷, Andrés López Rivas⁸, Daniela Barbosa⁹, Traver Hart^{5

10}, Michelle C Barton¹¹

Affiliations

¹ Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
² University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX, USA.
³ McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
⁴ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
⁵ Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
⁶ Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, US.
⁷ The Neurodegeneration Consortium, Therapeutics Discovery, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
⁸ School of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA.
⁹ Department of Molecular Biology, University of Texas Southwestern, Dallas, TX, USA.
¹⁰ Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
¹¹ Division of Oncological Sciences, Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, US.

Abstract

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.

Keywords: Biochemical classification methods; Biocomputational method; Cell biology; Functional aspects of cell biology.