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. 2024 Jun 28;13(1):2371556.
doi: 10.1080/2162402X.2024.2371556. eCollection 2024.

Candidate tumor-specific CD8+ T cell subsets identified in the malignant pleural effusion of advanced lung cancer patients by single-cell analysis

Yusuke Sugita  1   2 , Daisuke Muraoka  1 , Ayako Demachi-Okamura  1 , Hiroyasu Komuro  1 , Katsuhiro Masago  3 , Eiichi Sasaki  3 , Yasunori Fukushima  1 , Takuya Matsui  1 , Shuichi Shinohara  1 , Yusuke Takahashi  1 , Reina Nishida  1 , Chieko Takashima  1 , Teppei Yamaguchi  4 , Yoshitsugu Horio  4 , Kana Hashimoto  5 , Ichidai Tanaka  6 , Hiroshi Hamana  7 , Hiroyuki Kishi  7 , Daiki Miura  8 , Yuki Tanaka  8 , Kousuke Onoue  8 , Kazuhide Onoguchi  8 , Yoshiko Yamashita  8 , Richard Stratford  9 , Trevor Clancy  9 , Rui Yamaguchi  10   11 , Hiroaki Kuroda  12 , Hironori Ishibashi  2 , Kenichi Okubo  2 , Hirokazu Matsushita  1   13
Affiliations

Candidate tumor-specific CD8+ T cell subsets identified in the malignant pleural effusion of advanced lung cancer patients by single-cell analysis

Yusuke Sugita et al. Oncoimmunology. .

Abstract

Isolation of tumor-specific T cells and their antigen receptors (TCRs) from malignant pleural effusions (MPE) may facilitate the development of TCR-transduced adoptive cellular immunotherapy products for advanced lung cancer patients. However, the characteristics and markers of tumor-specific T-cells in MPE are largely undefined. To this end, to establish the phenotypes and antigen specificities of CD8+ T cells, we performed single-cell RNA and TCR sequencing of samples from three advanced lung cancer patients. Dimensionality reduction on a total of 4,983 CD8+ T cells revealed 10 clusters including naïve, memory, and exhausted phenotypes. We focused particularly on exhausted T cell clusters and tested their TCR reactivity against neoantigens predicted from autologous cancer cell lines. Four different TCRs specific for the same neoantigen and one orphan TCR specific for the autologous cell line were identified from one of the patients. Differential gene expression analysis in tumor-specific T cells relative to the other T cells identified CXCL13, as a candidate gene expressed by tumor-specific T cells. In addition to expressing CXCL13, tumor-specific T cells were present in a higher proportion of T cells co-expressing PDCD1(PD-1)/TNFRSF9(4-1BB). Furthermore, flow cytometric analyses in advanced lung cancer patients with MPE documented that those with high PD-1/4-1BB expression have a better prognosis in the subset of 57 adenocarcinoma patients (p = .039). These data suggest that PD-1/4-1BB co-expression might identify tumor-specific CD8+ T cells in MPE, which are associated with patients' prognosis. (233 words).

Keywords: Advanced lung cancer; TCR; exhausted T cells; malignant pleural effusion; neoantigen; single cell analysis.

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Conflict of interest statement

This study was partly funded by NEC Corporation.

Figures

Figure 1.
Figure 1.
Phenotypic and TCR clonal analyses of CD8+ T cells from MPE.
Figure 2.
Figure 2.
Identification of tumor antigens recognized by CD8+ T cells.
Figure 3.
Figure 3.
Gene expression analysis of tumor-specific CD8+ T cells from MPE.
Figure 4.
Figure 4.
Comparison of tumor specific CD8+ T cells between MPE and TILs.
Figure 5.
Figure 5.
Associations of tumor specific CD8+ T cell fractions in MPE with patients’ prognosis.
See this image and copyright information in PMC

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