CRISPR/Cas9 screen for genome‐wide interrogation of essential MYC‐bound E‐boxes in cancer cells

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.