Journal Article

A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types

Zhao, Yimin, Pulliam, Thomas H., Zhang, Boyang, Kulikauskas, Rima, Forde, Patrick M., Pardoll, Drew M., Smith, Kellie N., Li, Shuai, Topalian, Suzanne L., Ji, Hongkai, Wilson, Jordan, Zhang, Jiajia, Singh, Dipika, Zeng, Zhen, Jani, Saumya, Nghiem, Paul, Zhang, Tianbei, Connor, Sydney, Church, Candice D.

2025

Overview

Identifying tumor-specific T cell clones that mediate immunotherapy responses remains challenging. Mutation-associated neoantigen (MANA) -specific CD8+ tumor-infiltrating lymphocytes (TIL) have been shown to express high levels of CXCL13 and CD39 ( ENTPD1 ), and low IL-7 receptor ( IL7R ) levels in many cancer types, but their collective relevance to T cell functionality has not been established. Here we present an integrative tool to identify MANA-specific TIL using weighted expression levels of these three genes in lung cancer and melanoma single-cell RNAseq datasets. Our three-gene “MANAscore” algorithm outperforms other RNAseq-based algorithms in identifying validated neoantigen-specific CD8+ clones, and accurately identifies TILs that recognize other classes of tumor antigens, including cancer testis antigens, endogenous retroviruses and viral oncogenes. Most of these TIL are characterized by a tissue resident memory gene expression program. Putative tumor-reactive cells (pTRC) identified via MANAscore in anti-PD-1-treated lung tumors had higher expression of checkpoint and cytotoxicity-related genes relative to putative non-tumor-reactive cells. pTRC in pathologically responding tumors showed distinguished gene expression patterns and trajectories. Collectively, we show that MANAscore is a robust tool that can greatly enrich candidate tumor-specific T cells and be used to understand the functional programming of tumor-reactive TIL. Although individual genes that distinguish tumor-reactive CD8+ T cells from bystander T cells in tumors have been described, a functionally meaningful integrative signature has not been established. Here authors show that mutation-associated neoantigen-specific CD8+ tumor-infiltrating lymphocytes can be recognized by MANAscore, an algorithm that uses weighted expression levels of CXCL13, ENTPD1 and IL7R in single-cell RNAseq datasets of lung cancer and melanoma patients as input.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38 / 38/39 / 45 / 45/91 / 631/114/2397 / 631/250/2152/1566 / 631/250/251 / 631/67/580 / Algorithms / Antigen (tumor-associated) / Antigens / Antigens, Neoplasm - genetics / Antigens, Neoplasm - immunology / CD8 antigen / CD8-Positive T-Lymphocytes - immunology / CD8-Positive T-Lymphocytes - metabolism / Cloning / CXCL13 protein / Cytotoxicity / Datasets / Endogenous retroviruses / Functional programming / Gene expression / Gene Expression Regulation, Neoplastic / Genes / Humanities and Social Sciences / Humans / Immunological memory / Immunotherapy / Interleukin 7 receptors / Lung cancer / Lung Neoplasms - genetics / Lung Neoplasms - immunology / Lymphocytes / Lymphocytes T / Lymphocytes, Tumor-Infiltrating - immunology / Lymphocytes, Tumor-Infiltrating - metabolism / Melanoma / Melanoma - genetics / Melanoma - immunology / multidisciplinary / Mutation / Neoantigens / Neoplasms - genetics / Neoplasms - immunology / PD-1 protein / Science / Science (multidisciplinary) / Single-Cell Analysis / Tumor-infiltrating lymphocytes / Tumors