Abstract 6614: Association between immune gene signatures and neoepitopes with electrostatic charge opposite to their HLA-B binding pocket in melanoma (MEL) and lung adenocarcinoma (LUAD)
Authors: Fares Charlene M. , Cummings Amy L. , Theisen Matthew K. , Hornstein Nicholas , Gukasyan Jaklin , Akingbemi Wisdom , Li Debory , Brodrick Paige , Lisberg Aaron , Garon Edward B. 
Published: September 2020

Purpose: Immune checkpoint blockade (ICB) has revolutionized treatment of melanoma and lung cancer. Recent evidence suggests that human leukocyte antigen (HLA) B supertype influences efficacy of ICB. HLA-B27 and B44 supertypes have electronegative and electropositive binding pockets, respectively, and preferentially bind and display oppositely charged neoepitopes. We sought to evaluate the relationship between baseline immune activation and charged neoepitopes in the context of oppositely charged HLA-B binding pockets.

Methods: Datasets from a total of 466 MEL and 513 LUAD patients included in the TCGA were used. HLA type was obtained with OptiType. Nonsynonymous mutations were annotated with SnpEff, Ensembl VEP, and VAtools. Only transcribed variants were filtered for analysis. pVAC-Seq using NetMHCpan algorithm predicted nonamer neoepitopes. Favorable B27 neoepitopes were defined as having new positively charged amino acid (AA) substitutions (H/K/R) from oppositely charged or uncharged wildtype AA, while neoepitopes with new negatively charged AAs (D/E) were considered favorable for B44. Three gene signatures were evaluated with normalized RNA expression values from 14 antigen presentation, 15 immunostimulator, and 11 immunoinhibitor genes. Linear regression tests were performed between gene expression values and fraction of nonsynonymous mutations resulting in neoepitopes with new positively and negatively charged AAs. Paired t-tests were performed between the mean of Pearson's r for fraction of new positively versus negatively charged AAs compared to gene expression values, and subsetted to B27/B44. Heterozygotes for B27/B44 were excluded from analysis to avoid competing charges.

Results: 26.4% and 48.7% of MEL patients had B27 and B44, respectively. In LUAD, 28.6% had B27 and 47.2% had B44. Of new charged AAs resulting from nonsynonymous mutations, 72.6% in MEL and 75.0% in LUAD were positively charged (p=0.0053). In MEL, difference in Pearson's r values between fraction of new positively and negatively charged AAs as compared to immunostimulator (B27 p=.016; B44 p&lt;.001), immunoinhibitor (B27 p=.020; B44 p=.009), and antigen presentation (B27 p&lt;.001; B44 p&lt;.001) gene signatures showed association with positively charged AAs in B27 and negatively charged AAs in B44. In LUAD, differences in Pearson's r values between oppositely charged AAs were only significant for B27 (stimulator p=.004; inhibitor p&lt;.001; antigen presentation p&lt;.001), showing association with positively charged AAs.

Conclusion: Immune gene signatures showed association with neoepitopes that have oppositely charged AAs than their HLA-B binding pocket in both MEL and LUAD, indicating that presentation of favorable neoepitopes stimulates an immune response. The association was limited to B27 in LUAD and strongest for B44 in MEL.

Citation Format: Charlene M. Fares, Amy L. Cummings, Matthew K. Theisen, Nicholas Hornstein, Jaklin Gukasyan, Wisdom Akingbemi, Debory Li, Paige Brodrick, Aaron Lisberg, Edward B. Garon. Association between immune gene signatures and neoepitopes with electrostatic charge opposite to their HLA-B binding pocket in melanoma (MEL) and lung adenocarcinoma (LUAD) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6614.