TY - JOUR
T1 - Single-cell sequencing on CD8+TILs revealed the nature of exhausted T cells recognizing neoantigen and cancer/testis antigen in non-small cell lung cancer
AU - Komuro, Hiroyasu
AU - Shinohara, Shuichi
AU - Fukushima, Yasunori
AU - Demachi-Okamura, Ayako
AU - Muraoka, Daisuke
AU - Masago, Katsuhiro
AU - Matsui, Takuya
AU - Sugita, Yusuke
AU - Takahashi, Yusuke
AU - Nishida, Reina
AU - Takashima, Chieko
AU - Ohki, Takashi
AU - Shigematsu, Yoshiki
AU - Watanabe, Fumiaki
AU - Adachi, Katsutoshi
AU - Fukuyama, Takashi
AU - Hamana, Hiroshi
AU - Kishi, Hiroyuki
AU - Miura, Daiki
AU - Tanaka, Yuki
AU - Onoue, Kousuke
AU - Onoguchi, Kazuhide
AU - Yamashita, Yoshiko
AU - Stratford, Richard
AU - Clancy, Trevor
AU - Yamaguchi, Rui
AU - Kuroda, Hiroaki
AU - Doi, Kiyoshi
AU - Iwata, Hisashi
AU - Matsushita, Hirokazu
N1 - Publisher Copyright:
© 2023 BioMed Central Ltd.. All rights reserved.
PY - 2023/8/6
Y1 - 2023/8/6
N2 - Background CD8 + tumor infiltrating lymphocytes (TILs) are often observed in non-small cell lung cancers (NSCLC). However, the characteristics of CD8 + TILs, especially T-cell populations specific for tumor antigens, remain poorly understood. Methods High throughput single-cell RNA sequencing and single-cell T-cell receptor (TCR) sequencing were performed on CD8 + TILs from three surgically-resected lung cancer specimens. Dimensional reduction for clustering was performed using Uniform Manifold Approximation and Projection. CD8 + TIL TCR specific for the cancer/testis antigen KK-LC-1 and for predicted neoantigens were investigated. Differentially-expressed gene analysis, Gene Set Enrichment Analysis (GSEA) and single sample GSEA was performed to characterize antigen-specific T cells. Results A total of 6998 CD8 + T cells was analyzed, divided into 10 clusters according to their gene expression profile. An exhausted T-cell (exhausted T (Tex)) cluster characterized by the expression of ENTPD1 (CD39), TOX, PDCD1 (PD1), HAVCR2 (TIM3) and other genes, and by T-cell oligoclonality, was identified. The Tex TCR repertoire (Tex-TCRs) contained nine different TCR clonotypes recognizing five tumor antigens including a KK-LC-1 antigen and four neoantigens. By re-clustering the tumor antigen-specific T cells (n=140), it could be seen that the individual T-cell clonotypes were present on cells at different stages of differentiation and functional states even within the same Tex cluster. Stimulating these T cells with predicted cognate peptide indicated that TCR signal strength and subsequent T-cell proliferation and cytokine production was variable but always higher for neoantigens than KK-LC-1. Conclusions Our approach focusing on T cells with an exhausted phenotype among CD8 + TILs may facilitate the identification of tumor antigens and clarify the nature of the antigen-specific T cells to specify the promising immunotherapeutic targets in patients with NSCLC.
AB - Background CD8 + tumor infiltrating lymphocytes (TILs) are often observed in non-small cell lung cancers (NSCLC). However, the characteristics of CD8 + TILs, especially T-cell populations specific for tumor antigens, remain poorly understood. Methods High throughput single-cell RNA sequencing and single-cell T-cell receptor (TCR) sequencing were performed on CD8 + TILs from three surgically-resected lung cancer specimens. Dimensional reduction for clustering was performed using Uniform Manifold Approximation and Projection. CD8 + TIL TCR specific for the cancer/testis antigen KK-LC-1 and for predicted neoantigens were investigated. Differentially-expressed gene analysis, Gene Set Enrichment Analysis (GSEA) and single sample GSEA was performed to characterize antigen-specific T cells. Results A total of 6998 CD8 + T cells was analyzed, divided into 10 clusters according to their gene expression profile. An exhausted T-cell (exhausted T (Tex)) cluster characterized by the expression of ENTPD1 (CD39), TOX, PDCD1 (PD1), HAVCR2 (TIM3) and other genes, and by T-cell oligoclonality, was identified. The Tex TCR repertoire (Tex-TCRs) contained nine different TCR clonotypes recognizing five tumor antigens including a KK-LC-1 antigen and four neoantigens. By re-clustering the tumor antigen-specific T cells (n=140), it could be seen that the individual T-cell clonotypes were present on cells at different stages of differentiation and functional states even within the same Tex cluster. Stimulating these T cells with predicted cognate peptide indicated that TCR signal strength and subsequent T-cell proliferation and cytokine production was variable but always higher for neoantigens than KK-LC-1. Conclusions Our approach focusing on T cells with an exhausted phenotype among CD8 + TILs may facilitate the identification of tumor antigens and clarify the nature of the antigen-specific T cells to specify the promising immunotherapeutic targets in patients with NSCLC.
KW - Antigens, Neoplasm
KW - CD8-Positive T-Lymphocytes
KW - Lymphocytes, Tumor-Infiltrating
KW - Non-Small Cell Lung Cancer
UR - http://www.scopus.com/inward/record.url?scp=85166770711&partnerID=8YFLogxK
U2 - 10.1136/jitc-2023-007180
DO - 10.1136/jitc-2023-007180
M3 - 学術論文
C2 - 37544663
AN - SCOPUS:85166770711
SN - 2051-1426
VL - 11
JO - Journal for ImmunoTherapy of Cancer
JF - Journal for ImmunoTherapy of Cancer
IS - 8
M1 - e007180
ER -
