Abstract LB-A03: Allele specific HLA loss and immune escape in lung cancer evolution

Cancer cells adopt a variety of mechanisms to evade the immune system and avoid T-cell recognition. Disruption of human leukocyte antigen (HLA), which may lead to reduced neoantigen presentation, has been proposed as an immune escape strategy in many cancers, including lung cancer. Mutations in HLA class I genes are infrequent in early stage non-small cell lung cancers (NSCLC), suggesting alternative mechanisms of HLA disruption may be common. To date, the polymorphic nature of the locus has precluded copy number analysis and exploration of HLA loss. To investigate the prevalence and importance of HLA disruption, we present LOHHLA (Loss Of Heterozygosity in Human Leukocyte Antigen), a computational tool to determine HLA allele-specific copy number from sequencing data. Building upon previous work imputing HLA haplotypes from sequencing data (Shukla, 2015; Szolek, 2014) and utilizing previously published datasets (Jamal-Hanjani, 2017; Brastianos, 2015), we endeavored to address the prevalence and timing of HLA LOH in lung cancer and its impact on tumor evolution and neoantigen presentation. Using LOHHLA, we find HLA LOH occurs in 40% of NSCLCs and is associated with a high subclonal neoantigen burden, APOBEC mediated-mutagenesis, upregulation of cytolytic activity and PD-L1 positivity. The focal nature of these alterations, their subclonal frequencies, enrichment in metastatic sites, and occurrence as parallel events suggest that HLA LOH is an immune escape mechanism, selected later in NSCLC tumor evolution. Characterizing HLA LOH with LOHHLA refines neoantigen prediction and may have implications for immunotherapeutic approaches targeting neoantigens. Citation Format: Nicholas McGranahan, Rachel Rosenthal, Crispin T. Hiley, Andrew J. Rowan, Thomas B.K. Watkins, Gareth A. Wilson, Nicolai J. Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero, Charles Swanton. Allele specific HLA loss and immune escape in lung cancer evolution [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A03.