Electrostatic Human Leukocyte Antigen-Neoantigen Interactions And Durable Benefit In Non-Small Cell Lung Cancer Patients Treated With Immunotherapy.

2635 Background: Human leukocyte antigen (HLA) binding relies on energy from the interaction of B-pocket residues with anchor amino acids (AA). Among HLA class I supertypes, only HLA-B has distinct electrostatic B-pocket specificities, and of 7 HLA-B supertypes, B08, B27, and B44 feature binding pockets with preferences for charged AAs (Lund Immunogen). Whether electrostatic interactions in HLA-neoepitope binding would identify superior neoantigens and associate with survival in NSCLC patients treated with immunotherapy was unknown. Methods: Forty patients with advanced NSCLC treated with single agent pembrolizumab on a clinical trial with at least 5 years follow-up underwent paired tumor-normal whole-exome sequencing (WES) with Illumina HiSeq 2000/3000. HLA typing used normal (germline) WES from peripheral blood mononuclear cells analyzed with BWA-ALN and Athlates software (Liu Nuc Acids Res); supertype was determined by 2008 criteria (Sidney BMC Immunol). Tumor nonsynonymous coding mutations were identified with GATK v3.8, annotated with Ensembl-VEP, and passed through pVAC-Seq using a NetMHC 4.0 algorithm to identify potential neoepitopes 9 AAs in length (Hundal Genome Med). Neoepitopes were characterized based on mutant AA charge (D/E negative, H/K/R positive) and position. High affinity neoepitopes (HAN) were defined as those an with IC50 < 50 nM with wildtype IC50 > 50 nM (Ghorani Annals Oncol) and a mutation to a known B-pocket supermotif (K in position 3 or 5 for B08, R in position 2 for B27, E in position 2 for B44) (Lund Immunogen). Progression-free survival (PFS) was compared with logrank tests and proportional hazards (JMPv14, Cary, NC). Results: Of the 40 patients, 29 (72.5%) had at least one B08, B27, or B44 allele. One or more supertype-matched HAN were found in 10 of the 29 (34.5%), including 6/7 with PFS > 2 years, 3 of whom continue on therapy beyond 5 years. Median PFS in those with HAN was 26.7 months (m) vs 4.3 m in those without (HR 0.34, 95% CI 0.11-0.88, p = 0.024). Conclusions: Electrostatic charge may serve as a mechanism for enhanced binding affinity in HLA-B supertypes with a preference for charged AA in their B-pockets. Identification of favorable HLA-matched neoepitopes may identify distinct prognostic groups and potentially durable responders to immunotherapy in NSCLC.