Crystal structure of Cas9 in complex with guide RNA and target DNA. [Hiroshi Nishimasu et al./Wikipedia]
Crystal structure of Cas9 in complex with guide RNA and target DNA. [Hiroshi Nishimasu et al./Wikipedia]

To identify weaknesses in cancer that can be targeted with new therapies, several teams of scientists are working to cut cancer genomes down to size, gene by gene. The latest team to wield the genomic broadsword is based at the University of Toronto. This team, led by Jason Moffat, Ph.D., has used a technique called deletion mutant analysis to switch off, one by one, almost 18,000 genes—almost 90% of the entire human genome. This winnowing process, which relies on the CRISPR gene-editing technique and is called deletion mutant analysis, allowed the team to identify a core set of 1,580 human core fitness genes. Moreover, the team whittled away at the genomes of five different cancer cell lines to find context-dependent fitness genes.

“It's when you get outside the core set of essential genes, that it starts to get interesting in terms of how to target particular genes in different cancers and other disease states,” explained Dr. Moffat.

The new work appeared November 25 in the journal Cell, in an article entitled “High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.” It follows similar studies that appeared online last month in the journal Science. Both of these studies, which appeared in print November 27, reported a consistent set of about 2,000 genes that are indispensable for viability in human cells. (For a news report about one of these studies, see “CRISPR-Fine Screen of Human Genome Identifies Essential Genes.”)

The new findings in Cell show that:

  • Core fitness genes are highly enriched for ancient protein complexes.
  • Context-specific fitness genes illuminate biological differences between cell types.
  • Distinct genetic signatures can be used to predict differential drug response.

Moreover, the new findings show the majority of human genes play more subtle roles in the cell because switching them off doesn't kill the cell. But if two or more of such genes are mutated at the same time, or the cells are under environmental stress, their loss begins to count.

Because different cancers have different mutations, they tend to rely on different sets of genes to survive. By turning genes off in five different cancer cell lines, including brain, retinal, ovarian, and two kinds of colorectal cancer cells, Dr. Moffatt’s team learned that each tumor relies on a unique set of genes that can be targeted by specific drugs. Essentially, the team identified distinct sets of “smoking gun” genes for each of the tested cancers. Each set may prove to be susceptible to different drugs.

“[We] demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds,” wrote the authors of the Cell article. “Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.”

The authors also demonstrated that distinct genetic signatures can be used to predict differential drug response. Specifically, they found that metformin, a widely prescribed diabetes drug, successfully killed brain cancer cells and those of one form of colorectal cancer. The same drug, however, was useless against the other cancers studied.

Similarly, the antibiotics chloramphenicol and linezolid were effective against one form of colorectal cancer, but not against brain or other cancers studied. These data illustrate the clinical potential of the data in pointing to more precise treatments for the different cancers—and suggest the value of personalized medicine.