Background

Somatic mutations are attractive therapeutic targets for “individuvalized neoantigen vaccines” because of lack of host central tolerance and reduced risk of autoimmunity. Here, we perform large-scale –omic analyses to assess the neoantigen landscape of colorectal cancer, a cancer largely refractory to immune-checkpoint inhibition.

Methods

We performed whole genome sequencing (WGS) (60x tumor, 30x normal) and deep whole transcriptomic sequencing (RNA-Seq) (∼200x10e⁶ reads per tumor) on 158 Colorectal cancers including 32 patients with microsatellite instability (MSI), 126 microsatellite stable (MSS). Whole Exome Sequencing (200x tumor,100x normal) was also performed on 120 tumours. HLA typing, somatic mutations, gene expression & neoepitope predictions were computationally evaluated. Inferred HLA-A alleles were orthogonally validated with Pacbio long-read sequencing.

Results

The most common HLAs were, by allele count: A*11:01: 56; A*33:03: 38; B*58:01: 33; B*46:01: 29; B*40:01: 26; C*01:02: 41; C*07:02: 33. Inferred HLA-A alleles from WGS data was largely concordant with Pacbio long-read sequencing. There were a median of 2,850 (1229-6909) [MSI] & 213 (27-13,835) [MSS] coding variants, from which 10,487 (4,307-27,365) [MSI] & 726.5 (50-59,096) [MSS] possible neoepitopes were derived, after accounting for epitope processing, the normal proteome and general population variome based on dbSNP, Of these, 5,707 (2,608-15,218) [MSI] & 320 (14-25,243) [MSS] neoepitopes are expressed (based on RNA-Seq). Epitope prediction algorithms revealed a median of 423 (17-1,056) [MSI] & 26 (0-1,102) [MSS] bound & expressed neoepitopes. 5 MSS tumors did not have any predicted bound nor expressed neoepitopes, 112 of 126 (89%) of MSS tumors had at least 5 predicted bound, expressed neoepitopes.

Conclusions

There is substantial variability in the neoantigen landscape amongst MSI & MSS Colorectal cancers. MSI contains multiple-fold higher neo-antigens. Amongst MSS tumors, 89% of patients have at least 5 predicted bound and expressed neo-epitopes that could be targeted in neoantigen-based vaccines for personalized immunotherapy.

Legal entity responsible for the study

National Cancer Centre Singapore

Funding

NMRC Clinician Scientist Award (Iain Tan), A*STAR Core Funding, NantOmics LLC

Disclosure

A. Nguyen, S. Benz, S. Rabizadeh: Employee of NantOmics LLC

All other authors have declared no conflicts of interest.