Matching the right drug to the right tumor requires integrating tumor genotype with preclinical research about the relationship between genetic mutation and drug response. The successes of Gleevec (imatinib) against BCR-ABL leukemias, and Herceptin (trastuzamab) in HER2+ breast cancer, are testament to the power of this approach. To broaden this knowledge base, we developed CRISPR-based gene knockout screens to identify putative chemotherapeutic targets in cancer cells. To date, nearly one thousand cell lines from more than thirty different tumor lineages have been screened using this CRISPR-mediated approach, and several genotype-specific vulnerabilities have been discovered and validated....

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Matching the right drug to the right tumor requires integrating tumor genotype with preclinical research about the relationship between genetic mutation and drug response. The successes of Gleevec (imatinib) against BCR-ABL leukemias, and Herceptin (trastuzamab) in HER2+ breast cancer, are testament to the power of this approach. To broaden this knowledge base, we developed CRISPR-based gene knockout screens to identify putative chemotherapeutic targets in cancer cells. To date, nearly one thousand cell lines from more than thirty different tumor lineages have been screened using this CRISPR-mediated approach, and several genotype-specific vulnerabilities have been discovered and validated. However, there is a major disconnect between gene knockouts and drug response. Nearly all chemotherapeutic agents are “dirty;” that is, they inhibit the intended target as well as other closely related proteins. When a tumor cell relies on a single gene, this off-target effect is often unimportant, as in BCR-ABL and HER2 above. On the other hand, when a drug’s efficacy relies on its inhibition of multiple protein family members, genetic modeling fails. For example, MEK inhibitor trametinib targets the protein products of paralogs MAP2K1 and MAP2K2 simultaneously, but genetic knockout of either gene has no effect, since the other copy buffers against the loss. Drugs targeting protein families are therefore systematically missed by CRISPR screens, leaving a major blind spot in the translational potential of preclinical screening studies. Our platform seeks to alleviate this gap. We propose a state-of-the-art CRISPR multiplexing system, designed around the improved Cas12a endonuclease, that can perturb several genes simultaneously. With this technology, we can detect gene families targeted by drugs as well as interactions between buffered pathways, and rapidly match effective drugs and drug combinations to a new patient’s tumor—a transformative advance in precision medicine.

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