Proteogenomic identification of an immunogenic HLA class I neoantigen in mismatch repair–deficient colorectal cancer tissue
Tomomi Hirama, … , Takayuki Kanaseki, Toshihiko Torigoe
Tomomi Hirama, … , Takayuki Kanaseki, Toshihiko Torigoe
Published June 29, 2021
Citation Information: JCI Insight. 2021;6(14):e146356. https://doi.org/10.1172/jci.insight.146356.
View: Text | PDF
Research Article Immunology

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

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.

Authors

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

×

Figure 1

CD8+ T cell infiltration and gene expression signature in a panel of CRC and patient-matched normal tissues.

Options: View larger image (or click on image) Download as PowerPoint
CD8+ T cell infiltration and gene expression signature in a panel of CRC...
(A) Numbers of CD8+ cells per HPF (an average of 10 HPFs) in a panel of CRC tumor tissues based on IHC in Supplemental Figure 1. CD8+ cells that resided in the tumor parenchyma (intraepithelial) and outside of the tumor parenchyma (stromal) were counted separately. Box-and-whisker plots represent the median (solid bars), interquartile range (boxes), and 1.5× interquartile range (vertical lines). Dots denote observations outside the range of adjacent values. (B) Estimated proportions of immune cells across the tumor and matched normal tissues calculated using MCP-counter with RNA-seq data. (C) Gene expression signature of cytotoxic granules, inflammatory cytokines, and checkpoint molecules between the tumor and matched normal tissues. The bar graphs represent the TPM values as determined via RNA-seq (n = 1).