ArticleGenome medicine2019
Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma.
Article in Genome medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 173 citations in OpenAlex.
- Personalized neoantigen vaccine prevents postoperative recurrence in hepatocellular carcinoma patients with vascular invasion.Molecular cancer · 2021Trial
- A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer.Frontiers in immunology · 2019Trial
- Combination of exosome vaccines, lenvatinib, and anti-PD-1 eradicates tumor in autochthonous hepatocellular carcinoma mice.Cell reports. Medicine · 2026Article
- mRNA vaccines for hepatocellular carcinoma: mechanisms, therapeutic strategies, and clinical perspectives.Hepatology international · 2026Review
- Noncanonical Transcription and Splicing Shape the Colorectal Cancer Immunopeptidome in MSI and MSS Tumors.Molecular & cellular proteomics : MCP · 2026Article
- AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity.bioRxiv : the preprint server for biology · 2026Article
- Adoptive T Cell therapy for cancer and autoimmune disease: current advances, challenges, and future directions.Oncology reviews · 2026Article
- Advancing precision immuno-oncology in melanoma: the synergistic convergence of personalized neoantigen vaccines and multi-omics biomarker profiling.Frontiers in immunology · 2026Review
- Functional Interpretation of Recurrent Genetic Variants in Hepatocellular Carcinoma: Molecular Consequences and Clinical Relevance.Human mutation · 2026Review
- Article
- Targeting the roots of myeloid malignancies with T cell receptors.Nature reviews. Cancer · 2025Review
- Harnessing alternative splicing for off-the-shelf mRNA neoantigen vaccines in hepatocellular carcinoma.Cell research · 2025Article
- HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry.Journal for immunotherapy of cancer · 2025Article
- Tumor antigens preferentially derive from unmutated genomic sequences in melanoma and non-small cell lung cancer.Nature cancer · 2025Article
- Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.Briefings in bioinformatics · 2025Article
- Comprehensive Analysis of Differentially Expressed Profiles of mRNA 5-Methylcytosine Modification in Metabolic Dysfunction-Associated Steatotic Liver Disease.Current issues in molecular biology · 2025Article
- PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development.Journal for immunotherapy of cancer · 2025Article
- Immunogenic cryptic peptides dominate the antigenic landscape of ovarian cancer.Science advances · 2025Article
- Liver biopsy in the modern era: from traditional techniques to artificial intelligence and multi-omics integration.Frontiers in medicine · 2025Review
- Multimodal reprogramming of the tumor microenvironment by MMR and dual checkpoint blockade in hepatocellular carcinoma models.Frontiers in immunology · 2025Article
29 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs.
methodsIn-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data.
resultsThe approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations.
conclusionsThis study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.
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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.