ArticleImmunity2023
HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.
Article in Immunity, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- No clear evidence of PFAS-induced immunomodulation in SARS-CoV-2-specific human T cell responses following vaccination.Archives of toxicology · 2026Article
- The Ratio of Immunogenicity: A quantitative metric to identify highly immunogenic protein antigens to improve tissue-engineered biomaterials.Biomaterials · 2026Article
- PepGen: conditional generation of peptides for MHC binding.Bioinformatics (Oxford, England) · 2026Article
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- The digital keystone: how artificial intelligence is reshaping HLA research and clinical practice.Immunogenetics · 2026Review
- A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions.bioRxiv : the preprint server for biology · 2026Article
- Artificial intelligence in immunotherapy: revolutionizing diagnostic and therapeutic applications in cancer and autoimmune diseases.Clinical and experimental medicine · 2026Review
- Multidimensional risk prediction model for infant atopic dermatitis: A prospective cohort study.The World Allergy Organization journal · 2026Article
- AI-driven computational methods and benchmarking for T-cell antigen identification.Briefings in bioinformatics · 2026Review
- Landscapes of HLA Mismatching in Contemporary Unrelated Haematopoietic Cell Transplantation.HLA · 2026Article
- IFNg_DeepKG: A Novel Model for Identifying Interferon-Gamma-Inducing Epitopes Using Knowledge Graph RAG in Biomedical Applications.Journal of chemical information and modeling · 2026Article
- ProTCR: a protein language model-driven framework for decoding TCR-antigen recognition toward precision immunotherapies.Briefings in bioinformatics · 2026Article
- DSCA-HLAII: A dual-stream cross-attention model for predicting peptide-HLA class II interaction and presentation.PLoS computational biology · 2026Article
- Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors.Genome biology · 2025Article
- Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications.ACS omega · 2025Review
- The role of neoantigens and tumor mutational burden in cancer immunotherapy: advances, mechanisms, and perspectives.Journal of hematology & oncology · 2025Review
- A universal monoallelic human leukocyte antigen class II immunopeptidomic platform for defining the immunogenicity potential of therapeutic proteins.Communications biology · 2025Article
- T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.iScience · 2025Article
- HLAIIPred: cross-attention mechanism for modeling the interaction of HLA class II molecules with peptides.Communications biology · 2025Article
- Identifying T cell antigen at the atomic level with graph convolutional network.Nature communications · 2025Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.
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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.