ArticleNature genetics2023
MHC II immunogenicity shapes the neoepitope landscape in human tumors.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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Who cites it
25 citing papers in PubMed, 33 citations in OpenAlex.
- Results of a phase I/IIa trial of SV-BR-1-GM inoculation with low-dose cyclophosphamide and interferon alpha (Bria-IMT) in metastatic breast cancer.Human vaccines & immunotherapeutics · 2024Trial
- Article
- Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction.Cell genomics · 2026Article
- Assessment of tumor mutation burden based on whole-exome sequencing of extracellular vesicle-derived DNA from bronchoalveolar lavage fluid in advanced non-small cell lung cancer treated with pembrolizumab: a prospective, multicenter, observational study.Translational lung cancer research · 2026Article
- Inferring translational efficiency from transcriptomes improves noncanonical neoantigen prioritization and cancer patient stratification.NPJ precision oncology · 2026Article
- Engineering polyphenol-based osteogenic system for bone and cartilage repair: Transplantation, tissue engineering, and organoid.Journal of advanced research · 2026Review
- Cytotoxic CD4Signal transduction and targeted therapy · 2026Review
- NeoPrecis: enhancing immunotherapy response prediction through integration of qualified immunogenicity and clonality-aware neoantigen landscapes.Nature communications · 2026Article
- Computational design of class II MHC binding peptide with sequence-based evolution information.Bioinformatics advances · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- B cell-reactive neoantigens boost antitumor immunity.Science advances · 2025Article
- T-SCAPE: T cell immunogenicity scoring via cross-domain aided predictive engine.Science advances · 2025Article
- Extracellular Vesicles for Clinical Diagnostics: From Bulk Measurements to Single-Vesicle Analysis.ACS nano · 2025Review
- NeoPrecis: Enhancing Immunotherapy Response Prediction through Integration of Qualified Immunogenicity and Clonality-Aware Neoantigen Landscapes.bioRxiv : the preprint server for biology · 2025Article
- pMHChat, characterizing the interactions between major histocompatibility complex class II molecules and peptides with large language models and deep hypergraph learning.Briefings in bioinformatics · 2025Article
- Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey.Briefings in bioinformatics · 2025Review
- Using major histocompatibility complex (MHC) II expression to predict antitumor response to CD4 + lymphocyte depletion.Scientific reports · 2025Article
- CapHLA: a comprehensive tool to predict peptide presentation and binding to HLA class I and class II.Briefings in bioinformatics · 2024Article
- HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses.Briefings in bioinformatics · 2024Article
- Tumor Antigens beyond the Human Exome.International journal of molecular sciences · 2024Review
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite advances in predicting physical peptide-major histocompatibility complex I (pMHC I) binding, it remains challenging to identify functionally immunogenic neoepitopes, especially for MHC II. By using the results of >36,000 immunogenicity assay, we developed a method to identify pMHC whose structural alignment facilitates T cell reaction. Our method predicted neoepitopes for MHC II and MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naive tumors with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure, particularly with high TCR clonality and MHC II expression. A similar trend was shown for MHC I neoepitopes, but only in particular tissue types. In summary, we report immune selection imposed by MHC II-restricted natural or therapeutic T cell reactivity.
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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.