ArticleNature communications2025
A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- HLA-II Expression Marks Activated and Clonally Expanded CD8International journal of molecular sciences · 2026Article
- Article
- scXpand: Pan-cancer detection of T cell clonal expansion from single-cell RNA sequencing without paired single-cell TCR sequencing.Cell genomics · 2026Article
- Immune Spatial Organization Predicts Distant Metastasis Risk in Aggressive Localized Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- TSTScope Unifies Single-Cell Multi-Omics to Identify Functional T Cell States Predictive of Immunotherapy Response.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The Role of the T Cell Receptor Sequence in Shaping T Cell Functional Fate.Immunological reviews · 2026Review
- Phenotypic Analysis of 26 Cultured TILs Derived From Japanese Melanoma Tissues.The Journal of dermatology · 2026Article
- High-avidity TCR signaling induces a distinct KLR-positive exhaustion state in human tumor-infiltrating CD8 T cells associated with immunotherapy response.bioRxiv : the preprint server for biology · 2026Article
- Preexisting TCR Clones Drive Major Pathologic Responses in Patients with HNSCC Treated with Dual Immune Checkpoint Inhibitors.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Quantum ensembling methods for healthcare and life science.Briefings in bioinformatics · 2026Article
- Phenotype of circulating tumor-reactive T cells predicts immune checkpoint inhibitor response in non-small cell lung cancer.Nature communications · 2026Article
- Tumor reactivity assessment using clonal expression reveals tumor reactive CD8Frontiers in immunology · 2026Article
- Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.Frontiers in oncology · 2026Article
- The science of tumor-infiltrating lymphocytes (TIL): perspectives from the SITC Surgery Committee.Journal for immunotherapy of cancer · 2025Review
- Comprehensive tumor-immune profiling reveals mediators of paradoxical immune sensitivity in sarcomatoid renal cell carcinoma.Cancer cell · 2025Article
- Immunological and pathological characteristics of brain parenchymal and leptomeningeal metastases from non-small cell lung cancer.Cell discovery · 2025Article
- Functional tumor-reactive CD8 + T cells in pancreatic cancer.Journal of experimental & clinical cancer research : CR · 2025Article
- A minimal gene set characterizes TIL specific for diverse tumor antigens across different cancer types.Nature communications · 2025Article
- Tumor-infiltrating lymphocytes in cancer immunotherapy: from chemotactic recruitment to translational modeling.Frontiers in immunology · 2025Review
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
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.
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