Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair–deficient colorectal cancer tissue

Tomomi Hirama,Noriyuki Sato,Munehide Nakatsugawa,Fumitake Hata,Serina Tokita,Yoshihiko Hirohashi,Yasuhito Nannya,Ichiro Takemasa,Kazuhiko Matsuo,Kenji Murata,Toshihiko Torigoe,Takayuki Kanaseki,Hidetoshi Inoko,Shinichi Hashimoto,Seishi Ogawa

doi:10.1172/jci.insight.146356

Abstract

Although CD8+ T cells recognize neoantigens that arise from somatic mutations in cancer, only a small fraction of nonsynonymous mutations give rise to clinically relevant neoantigens. In this study, HLA class I ligandomes of a panel of human colorectal cancer (CRC) and matched normal tissues were analyzed using mass spectrometry–based proteogenomic analysis. Neoantigen presentation was rare; however, the analysis detected a single neoantigen in a mismatch repair–deficient CRC (dMMR-CRC) tissue sample carrying 3967 nonsynonymous mutations, where abundant tumor-infiltrating lymphocytes (TILs) and inflamed gene expression status were observed in the tumor microenvironment (TME). Using the HLA class I ligandome data and gene expression profiles, a set of nonmutated tumor-associated antigen (TAA) candidates was concomitantly identified. Interestingly, CD8+ TILs predominantly recognized the detected neoantigen over the array of TAA candidates. Neoantigen-reactive CD8+ TILs showed PD-1 positivity and exhibited functional and specific responses. Moreover, T cell receptor (TCR) profiling identified the sequence of the neoantigen-reactive TCR clonotype and showed its expansion in the TME. Transduction of the sequenced TCR conferred neoantigen specificity and cytotoxicity to peripheral blood lymphocytes. The proteogenomic approach revealed the antigenic and reactive T cell landscape in dMMR-CRC, demonstrating the presence of an immunogenic neoantigen and its potential therapeutic applications.

Highlights

Colorectal cancer (CRC) that is mismatch repair–deficient or microsatellite instability–high (MSI-H) accounts for approximately 15% of all colorectal cancer (CRC) [1]
Neoantigen presentation was rare; the analysis detected a single neoantigen in a mismatch repair–deficient CRC tissue sample carrying 3967 nonsynonymous mutations, where abundant tumor-infiltrating lymphocytes (TILs) and inflamed gene expression status were observed in the tumor microenvironment (TME)
Despite the fact that our experimental setting was limited to the HLA-A24 ligandome, the results suggested that the antigen specificity of CRC111 patient TILs was likely biased toward the neoantigen over canonical tumor-associated antigen (TAA)

Summary

Introduction

Colorectal cancer (CRC) that is mismatch repair–deficient (dMMR) or microsatellite instability–high (MSI-H) accounts for approximately 15% of all CRCs [1]. Because somatic mutations are unique to cancer, those mutated HLA ligands, or neoantigens, are not tolerated by hosts and often elicit T cell responses [6]. Mutation-derived neoantigens are likely to be a major target of ICI-induced T cell responses [7, 8]. Neoantigen vaccination allows for the activation of inherent host T cell responses in patients with melanoma or glioblastoma [12,13,14]. All of these findings highlight the presence of clinically relevant neoantigens and their roles in patient T cell responses against tumor cells — in particular, against cells with high tumor mutation burden (TMB)

Methods

Results

Conclusion