ArticleNature communications2020
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 213 papers, 1 of them a synthesis that pooled it.
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Who cites it
213 citing papers in PubMed, 1 synthesis or guideline pooled it, 320 citations in OpenAlex.
- Predicting immunotherapy response of advanced bladder cancer through a meta-analysis of six independent cohorts.Nature communications · 2025Pooled it
- Dark matter matters: from noncoding RNA regulation to cancer immunity.Oncoimmunology · 2026Review
- Mapping the functional dark proteome in cancer.Nature reviews. Cancer · 2026Review
- Global and specific mechanisms stimulate mistranslation in cancer.Nature cell biology · 2026Article
- Inhibition of cellular NEDDylation partially alters the MHC class I immunopeptidome.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Receptor-defined targeting of a genomically unique melanoma-enriched noncanonical antigen.Signal transduction and targeted therapy · 2026Article
- Determining the dark proteome.Nature chemical biology · 2026Article
- PRMT5-mediated intron retention triggers innate and adaptive immunity against cancer.EMBO molecular medicine · 2026Article
- Review
- LINE-1 Epigenetic Repression and Regulation of Immunity.Viruses · 2026Review
- Micropeptides encoded by lncRNAs associated with cancer progression reveal novel immunogenic epitopes.Bioinformatics (Oxford, England) · 2026Article
- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
- TIPs: a deep learning-guided proteogenomic framework to expand the landscape of transposable element-derived antigens with immunopeptidomics.Genome biology · 2026Article
- Advancing proteomic discovery through optimized multi-stage scoring and deep learning-enhanced open search.Bioinformatics (Oxford, England) · 2026Article
- Targeting non-canonical antigens unlocks functional T-cell responses in renal cell carcinoma.Journal for immunotherapy of cancer · 2026Article
- A platform for parallel TCR cloning and testing enables anti-neoantigen tumor immunotherapy.JCI insight · 2026Article
- Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer.NPJ precision oncology · 2026Article
- pAnno: a comprehensive, precise, and fast proteogenomic workflow for the discovery of novel coding regions.Genome biology · 2026Article
- Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors.Molecular & cellular proteomics : MCP · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
153 more citing papers are in PubMed but not listed here.
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Authors and funding
26 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single-cell transcriptomics, ribosome profiling, and two MS/MS search tools in combination. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides, including an immunogenic peptide derived from an open reading frame downstream of the melanoma stem cell marker gene ABCB5. These findings hold great promise for the discovery of previously unknown tumor antigens for cancer immunotherapy.
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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.