A comprehensive catalog of cancer driver mutations is essential for understanding tumorigenesis and developing therapies. The majority of cancer research so far focused on exome-sequencing studies to map the mutations in protein-coding genes. Interestingly, whole-genome sequencing (WGS) efforts have now shown that only 1% of the recurring mutations in cancer are in gene-coding regions of DNA, while the rest is in the non-coding genome and often enriched in regulatory regions. However, only a few non-coding drivers are known because genome-wide discovery and revealing the mechanistic underpinnings of these mutations is challenging. Similarly, the vast majority of cancer-related risk single-nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWASs) are located in noncoding regulatory regions, but the mechanism of action for nearly all the polymorphisms remains largely elusive.
I will introduce our efforts how to use in vivo CRISPR technologies to unravel non-coding driver mutations and show how to elucidate their mechanism of action. We previously developed a platform for multiplexed direct in vivo functional genomics knock-out screens (Loganathan et al., Science 2020; Langille et al., Cancer Discovery 2022; Yanchus et al., Science 2022). Here, we integrate our CRISPR-KO strategy with a new CRISPR-activation methodology, termed CRISPR-KOALA (CRISPR-Knock Out and Activation Linked Assay), that enables high throughput and multiplexed gene knockout and activation screens in sensitized mouse models of cancer.
Remarkably, we found that cancer-associated SNPs and frequently mutated regulatory elements (FMREs) are active in many tissues and interact with known as well as novel cancer driver genes via chromatin loops. We identified several novel non-coding cancer driver alteration and novel cancer genes and cancer circuits, that drive cancer initiation and progression and appear to be much more prevalent and potent than commonly assumed.