ArticleNature genetics2016
Landscape of tumor-infiltrating T cell repertoire of human cancers.
Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 208 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
208 citing papers in PubMed, 2 syntheses or guidelines pooled it, 319 citations in OpenAlex.
- Immune-related pan-cancer gene expression signatures of patient survival revealed by NanoString-based analyses.PloS one · 2023Pooled it
- Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma.Journal for immunotherapy of cancer · 2020Pooled it
- Clinical significance of peripheral T-cell repertoire in head and neck squamous cell carcinoma treated with cetuximab and nivolumab.Cancer immunology, immunotherapy : CII · 2025Trial
- Neoadjuvant Afatinib for stage III EGFR-mutant non-small cell lung cancer: a phase II study.Nature communications · 2023Trial
- Safety and effectiveness of neoadjuvant PD-1 inhibitor (toripalimab) plus chemotherapy in stage II-III NSCLC (LungMate 002): an open-label, single-arm, phase 2 trial.BMC medicine · 2022Trial
- T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma.Journal for immunotherapy of cancer · 2022Trial
- The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival.Nature communications · 2021Trial
- Bispecific dual T cell agonist invikafusp alfa in solid tumors: the phase 1/2 START-001 trial.Nature medicine · 2026Article
- Recovering CDR3 sequences from RNA-seq data: a critical assessment of computational and experimental strategies.Genomics & informatics · 2026Review
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- 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
- Peripheral T-Cell Receptor β Repertoire Dynamics Correlate with Response to Anti-PD-L1 Therapy in Non-Small Cell Lung Cancer.Cancers · 2026Article
- Evaluation and comparison of TCR repertoire differences between patients with cervical cancer and healthy individuals.Science China. Life sciences · 2026Article
- PARP inhibition combined with a T-cell receptor β chain-directed antibody fusion molecule drives polyclonal antitumor immunity and tumor regression.Journal for immunotherapy of cancer · 2026Article
- Multiscale predictive cellular modeling: integrating hypothesis grammars, digital twins, and multi-omics for In silico oncology and precision theranostics.Functional & integrative genomics · 2026Review
- Advances in immunotherapy for colorectal cancer: overcoming resistance in mismatch repair-proficient tumors.Cancer cell international · 2026Review
- Refined phenotyping of vaccine responses reveals transcriptomic determinants of neutralizing antibody heterogeneity.NPJ vaccines · 2026Article
- Docetaxel enhances Vβ-directed T-cell activation and antitumor immunity mediated by a bifunctional TCR agonist in breast and prostate cancer models.Frontiers in immunology · 2026Article
- A reproducible pipeline for TCR β-chain repertoire analysis from thoracic tumour RNA-seq and ICI-associated cardiac immunotoxicity.Frontiers in immunology · 2026Article
- Tissue and peripheral T cell receptor repertoire predicts immunotherapy response and progression-free survival in NSCLC patients.Scientific reports · 2025Article
148 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 8 institutions in 2 countries.
Funding
Abstract
We developed a computational method to infer the complementarity-determining region 3 (CDR3) sequences of tumor-infiltrating T cells in 9,142 RNA-seq samples across 29 cancer types. We identified over 600,000 CDR3 sequences, including 15% that were full length. CDR3 sequence length distribution and amino acid conservation, as well as variable gene usage, for infiltrating T cells in many tumors, except in brain and kidney cancers, resembled those for peripheral blood cells from healthy donors. We observed a strong association between T cell diversity and tumor mutation load, and we predicted SPAG5 and TSSK6 as putative immunogenic cancer/testis antigens in multiple cancers. Finally, we identified three potential immunogenic somatic mutations on the basis of their co-occurrence with CDR3 sequences. One of them, a PRAMEF4 mutation encoding p.Phe300Val, was predicted to result in peptide binding strongly to both MHC class I and class II molecules, with matched HLA types in its carriers. Our analyses have the potential to simultaneously identify immunogenic neoantigens and tumor-reactive T cell clonotypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.