Abstract 5647: Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy
Authors: Smart Alicia C. , Margolis Claire , Miao Diana , Liu David , Park Jihye , He Meng Xiao , Reardon Brendan , Mullane Stephanie , Schilling Bastian , Garraway Levi A. , Schadendorf Dirk , Allen Eliezer M. Van 
Published: July 2017

Background: Development of immune checkpoint inhibitors has substantially improved outcomes in patients diagnosed with metastatic melanoma. However, only a minority of patients treated experience long-term clinical benefit, and clinicians have limited ability to predict which patients will respond. Recent studies have demonstrated that the burden of tumor neoantigens generated by expressed somatic mutations is predictive of response to immunotherapy. Intron retention, which is widespread in cancer transcriptomes, represents a putative source of tumor neoantigens by generating peptides that are available for presentation through the MHC I pathway.

Methods: We developed a neoantigen prediction pipeline to identify patient-specific neoantigens from transcriptome sequencing data, which enables identification of retained intron neoantigens from clinical cohorts receiving checkpoint inhibitor therapy. This pipeline incorporates published methods for detecting intron retention events from transcriptome data, detects open reading frames that extend from normal transcripts into intronic sequences, and identifies neoepitopes predicted as strong binders based on the patient’s HLA molecules. We applied this pipeline to a cohort of 41 melanoma patients receiving checkpoint inhibitor therapy and classified patient outcomes as receiving clinical benefit (CB) (n=14), no clinical benefit (NCB) (n=22), or long-term survival without clinical benefit (LS) (n=5).

Results: Our initial analysis identified a mean retained intron neoantigen burden of 7709 per sample, without significant difference between response groups. In one patient who derived clinical benefit from checkpoint inhibition, neoantigen load from nonsynonymous mutations was low (407, 0.34 standard deviations (SD) below a mean of 1,015 among CB patients), while retained intron neoantigen load was high (14579, 1.7 SDs above a mean of 7517 among CB patients), suggesting that retained intron neoantigen load may explain response in some patients with low mutational burden. Preliminary analysis of specific neoantigens suggests that a retained intron in ZNF880 identified in patients expressing HLA-A01:01 is present in 6 of 6 patients experiencing clinical benefit, but only 2 of 7 patients not experiencing clinical benefit. The same analysis was performed on two additional cohorts of melanoma tumor samples to assess whether a larger sample size could aid in the identification of recurrent neoepitopes generated by retained introns.

Conclusions: Application of this approach to data from patients receiving checkpoint blockade with selective response identifies response-associated neoantigens that may warrant further investigation. Identification of a novel source of neoantigens associated with immunotherapy response will provide valuable prognostic information to patients and inform the development of next generation immunotherapeutics.

Citation Format: Alicia C. Smart, Claire Margolis, Diana Miao, David Liu, Jihye Park, Meng Xiao He, Brendan Reardon, Stephanie Mullane, Bastian Schilling, Levi A. Garraway, Dirk Schadendorf, Eliezer M. Van Allen. Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5647. doi:10.1158/1538-7445.AM2017-5647