Analyses of Genes Critical to Tumor Survival Reveal Potential ‘Supertargets’: Focus on Transcription

SIMPLE SUMMARY: A variety of anticancer therapeutic targets have been identified over the decades. Nevertheless, the complexity of biological regulation dictates the necessity of knowledge about mechanisms specific to a particular tumor type. Using the DepMap CRISPR/Cas9 knockout database, we performed a comprehensive search for genes critical for tumor survival. Both established and novel markers of tumor viability were identified, many of which are transcriptional regulators. Our results substantiate new therapeutic strategies applicable to individual tumors. ABSTRACT: The identification of mechanisms that underlie the biology of individual tumors is aimed at the development of personalized treatment strategies. Herein, we performed a comprehensive search of genes (termed Supertargets) vital for tumors of particular tissue origin. In so doing, we used the DepMap database portal that encompasses a broad panel of cell lines with individual genes knocked out by CRISPR/Cas9 technology. For each of the 27 tumor types, we revealed the top five genes whose deletion was lethal in the particular case, indicating both known and unknown Supertargets. Most importantly, the majority of Supertargets (41%) were represented by DNA-binding transcription factors. RNAseq data analysis demonstrated that a subset of Supertargets was deregulated in clinical tumor samples but not in the respective non-malignant tissues. These results point to transcriptional mechanisms as key regulators of cell survival in specific tumors. Targeted inactivation of these factors emerges as a straightforward approach to optimize therapeutic regimens.