PO-404 Using functional genetic screens to understand cancer immune evasion

Abstract

IntroductionWith the emerge of immunotherapy as an effective cancer therapy, there is also a growing need to identify new biomarkers of response as well as novel therapeutic targets. Functional CRISPR screens have proven to be an important tool to identify key genes in complex biological processes. We use an in vitro and in vivo CRISPR screening strategy to better understand how tumours evade the immune system.Material and methodsWe collected pre and post treatment biopsies from melanoma and lung cancer patients treated with an anti PD-1 inhibitor. Upon performing whole exome sequencing on biopsies from patients who progressed on therapy, we identified a list of candidate genes. We included genes that fell into one of the three categories: were mutated in more than one patient, were mutated only at relapse and had mutations in both alleles or had a heterozygous mutation at baseline and homozygous on progression.In addition, we also generated an adenovirus transformed mouse embryonic fibroblast cell line, which does not form tumours in the immunocompetent mice due to T-cell killing. We use this system do perform an in vivo CRISPR screen, investigating which genes are crucial for immune evasion.Results and discussionsWe have successfully generated a target gene list from sequences of patient biopsies. We have constructed a focused CRISPR library consisting of multiple gRNAs targeting each of those genes. This library will be used in a genetic screen in melanoma cells co-cultured with matched T-cells that recognise and eliminate the melanoma cells. Moreover, we will also use our in vivo adenoviral system to perform genome wide screens.ConclusionAfter the screening, we can cross validate hits from both platforms to identify robust hits. Furthermore, we can validate them in a bigger patient cohort to determine their potential as predictive biomarkers for immunotherapy response.