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

Nat Genet. 2018 Sep;50(9):1240-1246. doi: 10.1038/s41588-018-0191-z. Epub 2018 Aug 20.

Abstract

Childhood high-risk neuroblastomas with MYCN gene amplification are difficult to treat effectively1. 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 survival2-6, 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Disease Models, Animal
  • Down-Regulation
  • Female
  • Gene Amplification
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Mice
  • Mice, Nude
  • N-Myc Proto-Oncogene Protein / genetics*
  • Neuroblastoma / genetics*
  • Transcription Factors / genetics
  • Transcription, Genetic*

Substances

  • MYCN protein, human
  • N-Myc Proto-Oncogene Protein
  • Transcription Factors