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 2

Characterization of natural HLA class I ligands and candidates for nonmutated TAAs found in CRC tissues.

Options: View larger image (or click on image) Download as PowerPoint
Characterization of natural HLA class I ligands and candidates for nonmu...
(A) Nonredundant numbers of nonmutated HLA-A24 ligands detected in a panel of CRC tumor and matched normal tissues by HLA ligandome analysis. Analysis was performed once per sample. (B) The number of HLA-A24 ligands shared between 2 or more samples is shown in the center of the diagram. The numbers of private HLA-A24 ligands unique to each sample are shown along the rim of the circle. Tumor and normal tissues are shown in red and blue, respectively. (C) Length distribution (left) and sequence logos of 9-mer peptides (middle) of HLA-A24 ligands. In the kernel density estimation of the transcripts expressed in the indicated samples (right), the black and red lines represent the whole transcriptome and transcripts encoding the HLA-A24 ligands, respectively. (D) Venn diagram showing the number of HLA-A24 ligands overlapping between tumor and normal tissues. (E) Differential gene expression between CRC111 tumor and matched normal tissues. Only the genes encoding HLA-A24 ligands that were detected in CRC111 tumor tissue, but not in normal tissues, are plotted. Genes with a more than 20-fold increase in tumors are shown in red. (F) Candidates of nonmutated TAAs and their source genes. The numbers in the heatmap indicate the TPM values of the genes in CRC111 tumor and normal tissues.