Single-Cell Transcriptomic Analysis Reveals a Tumor-Reactive T Cell Signature Associated With Clinical Outcome and Immunotherapy Response In Melanoma.

Abstract

The infiltration of tumor-reactive T cells in the tumor site is associated with better survival and immunotherapy response. However, tumor-reactive T cells were often represented by the infiltration of total CD8+ T cells, which was confounded by the presence of bystander T cells. To identify tumor-reactive T cells at the cancer lesion, we performed integration analyses of three scRNA-seq data sets of T cells in melanoma. Extensive heterogeneous functional states of T cells were revealed in the tumor microenvironment. Among these states, we identified a subset of tumor-reactive T cells which specifically expressed tumor-reactive markers and T cell activation signature, and were strongly enriched for larger T cell receptor (TCR) clones. We further identified and validated a tumor-reactive T cell signature (TRS) to evaluate the tumor reactivity of T cells in tumor patients. Patients with high TRS scores have strong immune activity and high mutation burden in the TCGA-SKCM cohort. We also demonstrated a significant association of the TRS with the clinical outcomes of melanoma patients, with higher TRS scores representing better survival, which was validated in four external independent cohorts. Furthermore, the TRS scores exhibited greater performance on prognosis prediction than infiltration levels of CD8+ T cells and previously published prognosis-related signatures. Finally, we observed the capability of TRS to predict immunotherapy response in melanoma. Together, based on integrated analysis of single-cell RNA-sequencing, we developed and validated a tumor-reactive-related signature that demonstrated significant association with clinical outcomes and response to immunotherapy.

• Authors: Min Yan, Jing Hu, Yanyan Ping, Liwen Xu, Gaoming Liao, Zedong Jiang, Bo Pang, Shangqin Sun, Yunpeng Zhang, Yun Xiao, Xia Li
• Journal: Frontiers in immunology (Front Immunol) Vol. 12 Pg. 758288 ( 2021) ISSN: 1664-3224 [Electronic] Switzerland
• PMID: 34804045 (Publication Type: Comparative Study, Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2021 Yan, Hu, Ping, Xu, Liao, Jiang, Pang, Sun, Zhang, Xiao and Li.

Chemical References

• Immune Checkpoint Inhibitors
• RNA, Neoplasm
• Receptors, Antigen, T-Cell

Topics

• Base Sequence
• CD8-Positive T-Lymphocytes (immunology, metabolism)
• Clone Cells
• Datasets as Topic
• Humans
• Immune Checkpoint Inhibitors (therapeutic use)
• Immunotherapy
• Kaplan-Meier Estimate
• Lymphocytes, Tumor-Infiltrating (immunology, metabolism)
• Melanoma (genetics, immunology)
• Prognosis
• RNA, Neoplasm (genetics)
• Receptors, Antigen, T-Cell (genetics)
• Single-Cell Analysis
• T-Lymphocyte Subsets (immunology, metabolism)
• Transcriptome
• Treatment Outcome