Personalized Cancer Therapy

About

Summary Disease phenotypes are often regulated by interwoven genetic networks. For example, tumor genomes exhibit an extensive variety of genetic and epigenetic changes involved in tumor initiation, metastasis and ultimately, resistance to therapy. Combination therapy to target multiple pathways, as opposed to only single ones, can enhance treatment efficacy. Discovering effective combination therapies for human diseases is challenging with existing methods, due to the cost, effort, and labor required to construct and analyze each combination. There is a need for technological advances to accelerate the identification of effective combinatorial therapies. CRISPR has emerged as a new tool to systemically interrogate cancer genomes and set up the potential for personalized medicine. Personalized medicine is based upon the concept that individual differences can be identified and used to the patient’s advantage for therapy.   Description Researchers at UC San Diego have developed a CRISPR Cas9 screening methodology for targeting single and pairs of genes in high throughput which would enable systematic mapping of these genetic interaction networks. The new technology allows to knockout 2 genes at a time in high throughput, up to 105 gene pairs.  The inventors have generated dual-guide RNA library of vectors based on combination of 73 genes commonly mutated in cancer (more than 25,000 scaffolds). There is a significant value in the library itself as the constructs were carefully optimized. The library could be used as a kit for screening to identify optimal personalized (combination) therapy. In addition, the inventors also developed a novel analysis method (algorithm) specifically designed to account for the experimental characteristics of large, competitive growth interaction screens.    Applications The invention relates to an approach to map human genetic networks by using combinatorial CRISPR-Cas9 perturbation that can identify therapeutically-relevant genetic interactions in cancer. This approach would provide a superior alternative to DNA sequencing-based strategies as one would determine the optimal combinations therapy based on the actual outcomes in patient’s cells. In a matter of weeks, one would be able to run a high throughput screen of the full 25,000+ scaffold library and analyze the data to determine the critical targets/pathways for therapeutic intervention.   Advantages CRISPRi knockdowns are more specific when compared to RNAi-based methods whereby there are fewer off-target issues. The technology allows for the knockout of 2 genes at a time; not possible with current methodologies.   Stages of Development The technology has been validated in lung cancer and cervical cancer cell lines and cell viability was confirmed using drug combinations targeting predicted gene products. Additionally, the inventors have created a modified version that decreases gene expression (knockdown) rather than knocking out a gene.