Tissue-resident memory T cell signatures from single-cell analysis associated with better melanoma prognosis

Chongming Jiang; Cheng-Chi Chao; Jianrong Li; Xin Ge; Aidan Shen; Vadim Jucaud; Chao Cheng; Xiling Shen

doi:10.1016/j.isci.2024.109277

Tissue-resident memory T cell signatures from single-cell analysis associated with better melanoma prognosis

iScience. 2024 Feb 20;27(3):109277. doi: 10.1016/j.isci.2024.109277. eCollection 2024 Mar 15.

Authors

Chongming Jiang^{1

2

3

4}, Cheng-Chi Chao⁵, Jianrong Li^{2

3

4}, Xin Ge¹, Aidan Shen¹, Vadim Jucaud¹, Chao Cheng^{2

3

4}, Xiling Shen^{1

6}

Affiliations

¹ Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
² Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
³ Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
⁴ Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
⁵ Department of Pipeline Development, Biomap, Inc, San Francisco, CA, USA.
⁶ Xilis, Inc., Durham, NC 27713, USA.

Abstract

Tissue-resident memory T cells (T_RM) are a specialized T cell population residing in peripheral tissues. The presence and potential impact of T_RM in the tumor immune microenvironment (TIME) remain to be elucidated. Here, we systematically investigated the relationship between T_RM and melanoma TIME based on multiple clinical single-cell RNA-seq datasets and developed signatures indicative of T_RM infiltration. T_RM infiltration is associated with longer overall survival and abundance of T cells, NK cells, M1 macrophages, and memory B cells in the TIME. A 22-gene T_RM-derived risk score was further developed to effectively classify patients into low- and high-risk categories, distinguishing overall survival and immune activation, particularly in T cell-mediated responses. Altogether, our analysis suggests that T_RM abundance is associated with melanoma TIME activation and patient survival, and the T_RM-based machine learning model can potentially predict prognosis in melanoma patients.

Keywords: Cancer; Immunology; Microenvironment.