Center for Pediatric Genomics
Target Discovery with Forward CRISPR Genomic Screens in Leukemia Xenografts

Target Discovery with Forward CRISPR Genomic Screens in Leukemia Xenografts

Principle Investigator: Lynn Lee, MD, Division of Oncology

A photo of Lynn Lee. Acute leukemias can be probed for weaknesses by using the tool CRISPR/Cas9 with statistical modeling to simultaneously knock out individual genes across large numbers of cells. However, findings obtained through this technology in cancer models grown in a laboratory sometimes fail to perform as expected in actual human cancers. By applying CRISPR/Cas9 screening to patient leukemia samples grown in an animal model, we expect that our findings will be much more likely to successfully result in new and effective anti-leukemia therapies.

Forward genomic screens with CRISPR/Cas9 allow for the massively parallel interrogation of genes and their essentiality for a studied phenotype (such as survival or drug resistance.) This technology in particular has been applied to cancer cell lines, resulting in the discovery of a wide variety of novel vulnerabilities. However, these experiments are limited by artifacts that arise from studying legacy cell lines and biological systems in vitro. We have been able to generate patient-derived leukemia lines expressing Cas9 which successfully engraft in immunodeficient mice, with which we conducted a focused genomic screen. We thus hypothesize that CRISPR/Cas9 screening of patient-derived leukemias in vivo will facilitate the discovery of more physiologically relevant and translatable mechanistic and therapeutic targets. To test this hypothesis, we are 1) characterizing differences arising from in vitro vs. in vivo functional genomic screens with primary patient leukemias, and 2) performing focused screens in these leukemias with drug target-focused genes, and confirm their translatability to pharmacologic inhibition by treating patient-derived xenografts. This will ultimately lead to new insights into disease pathogenesis, as well as evidence for novel clinical trials which we expect will directly impact patient outcomes in relapsed/refractory leukemia.

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