Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry

AD Durbin, MW Zimmerman, NV Dharia, BJ Abraham… - Nature …, 2018 - nature.com
AD Durbin, MW Zimmerman, NV Dharia, BJ Abraham, AB Iniguez, N Weichert-Leahey, S He
Nature genetics, 2018nature.com
Childhood high-risk neuroblastomas with MYCN gene amplification are difficult to treat
effectively. This has focused attention on tumor-specific gene dependencies that underlie
tumorigenesis and thus provide valuable targets for the development of novel therapeutics.
Using unbiased genome-scale CRISPR–Cas9 approaches to detect genes involved in
tumor cell growth and survival,,,–, we identified 147 candidate gene dependencies selective
for MYCN-amplified neuroblastoma cell lines, compared to over 300 other human cancer …
Abstract
Childhood high-risk neuroblastomas with MYCN gene amplification are difficult to treat effectively. This has focused attention on tumor-specific gene dependencies that underlie tumorigenesis and thus provide valuable targets for the development of novel therapeutics. Using unbiased genome-scale CRISPR–Cas9 approaches to detect genes involved in tumor cell growth and survival, , , –, we identified 147 candidate gene dependencies selective for MYCN-amplified neuroblastoma cell lines, compared to over 300 other human cancer cell lines. We then used genome-wide chromatin-immunoprecipitation coupled to high-throughput sequencing analysis to demonstrate that a small number of essential transcription factors—MYCN, HAND2, ISL1, PHOX2B, GATA3, and TBX2—are members of the transcriptional core regulatory circuitry (CRC) that maintains cell state in MYCN-amplified neuroblastoma. To disable the CRC, we tested a combination of BRD4 and CDK7 inhibitors, which act synergistically, in vitro and in vivo, with rapid downregulation of CRC transcription factor gene expression. This study defines a set of critical dependency genes in MYCN-amplified neuroblastoma that are essential for cell state and survival in this tumor.
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