Abstract 2916: Delineating the radiogenomic landscape of cancer through systematic annotation of genetic variants
Authors: Yard Brian , Petty Aaron , Abazeed Mohamed 
Published: August 2019

Radiation is a fundamental pillar of treatment for many cancer patients. However, there are still no established means by which to identify patients who are more or less likely to respond to treatments. In addition, there are few synergistic drug-radiotherapy combinations currently in clinical use. To address these needs, we sought to discover genetic alterations that can predict the vulnerability of cancer to radiation. Here, we report on a large-scale study to identify and classify tumor associated genetic variants that determine survival to radiation.

To gain insight into the genetic landscape of radioresistance, we previously established a high-throughput platform that measures cellular survival to radiation. We then used this technology to analyze the radiosensitivity of more than 500 cancer cell lines and identified mutant alleles associated with radiation resistance. To functionally annotate a multitude of these variants, mutant constructs were generated using a high-throughput, site-directed mutagenesis approach and shuffled into lentiviral vectors for stable expression in immortalized BEAS2B lung cells. The effect of individual variants on radiation survival was assessed using our high-throughput platform and benchmarked against the radio-protective NRF2 E79K gain-of-function mutation and validated by colony forming assay. Radioresistant variants were further profiled in TP53 deficient BEAS2B cells and in cells across multiple lineages. For a subset of variants predicted to confer resistance by a loss of gene function, expression of the endogenous gene was knocked out by CRISPR directed to an exon-intron junction, thus allowing for the expression of the intron-less variant ORF.

We successfully generated and profiled over 550 tumor associated genetic variants. Top radioresistant conferring alleles were comprised of both rare and recurrent mutations. In many instances, rare variants were more impactful than common mutations in the same domain or even the same amino acid position. Therapeutically targetable radioresistant variants were discovered within ARAF, BRAF, CTNNB1, EGFR, MAP2K1 and PIK3CA, among others. Loss of gene function variants were profiled in KEAP1, STK11, and TP53. A subset of KEAP1 loss of gene function variants were found to confer a dominant-negative phenotype by stabilizing NRF2 levels.

Determining the impact of gene variants remains a major obstacle in the implementation of personalized radiotherapy. Here, we report on a large-scale profiling effort to identify and classify mutant alleles that govern the sensitivity of cells to radiation. We demonstrate that new genetic features responsible for mediating cellular survival to DNA damage can be discovered. We also show that a substantial proportion of variants that confer resistance to radiation are druggable, advancing drug-radiation combinations in “baskets” of patients with these alterations.

Citation Format: Brian Yard, Aaron Petty, Mohamed Abazeed. Delineating the radiogenomic landscape of cancer through systematic annotation of genetic variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2916.