Kazimierska M, Podralska M, Żurawek M, Woźniak T, Kasprzyk ME, Sura W, Łosiewski W, Ziółkowska‐Suchanek I, Kluiver J, van den Berg A, Rozwadowska N, Dzikiewicz‐Krawczyk A. CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells.
Mol Oncol 2023;
17:2295-2313. [PMID:
37519063 PMCID:
PMC10620128 DOI:
10.1002/1878-0261.13493]
[Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/28/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
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 combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out 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 common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.
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