CRISPR/Cas9 screen for functional MYC binding sites reveals MYC-dependent vulnerabilities in K562 cells

Kazimierska, M.; Podralska, M.; Zurawek, M.; Wozniak, T.; Kasprzyk, M. E.; Sura, W.; Losiewski, W.; Ziolkowska-Suchanek, I.; Kluiver, J. L.; van den Berg, A.; Rozwadowska, N.; Dzikiewicz-Krawczyk, A.

doi:10.1101/2021.08.02.454734

bioRxiv · 10.1101/2021.08.02.454734

CRISPR/Cas9 screen for functional MYC binding sites reveals MYC-dependent vulnerabilities in K562 cells

Kazimierska, M.·Podralska, M.·Zurawek, M.·Wozniak, T.·Kasprzyk, M. E.·Sura, W.·Losiewski, W.·Ziolkowska-Suchanek, I.·Kluiver, J. L.·van den Berg, A.·Rozwadowska, N.·Dzikiewicz-Krawczyk, A.

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Abstract

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell type- and developmental stage-specific manner. To date, a comprehensive analysis of direct MYC targets with essential roles in different types of cancer is missing. To enable identification of functional MYC binding sites and corresponding target genes, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knockout protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines: K562, ST486, HepG2 and MCF7, which revealed several essential E-boxes and genes. Among them we pinpointed crucial known and novel MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach in K562 cells confirmed that E-box disruption affects MYC binding, target genes expression and cell proliferation. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.

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Kazimierska, M., Podralska, M., Zurawek, M., Wozniak, T., Kasprzyk, M. E., Sura, W., Losiewski, W., Ziolkowska-Suchanek, I., Kluiver, J. L., van den Berg, A., Rozwadowska, N., Dzikiewicz-Krawczyk, A.. 2021-08-02. CRISPR/Cas9 screen for functional MYC binding sites reveals MYC-dependent vulnerabilities in K562 cells. https://doi.org/10.1101/2021.08.02.454734

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