ArticleGenome medicine2023
Pervasiveness of HLA allele-specific expression loss across tumor types.
Article in Genome medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 21 citations in OpenAlex.
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- The immunology of human breast cancer.Nature reviews. Immunology · 2026Review
- Re-expression of MHC-I to treat CNS cancers.Oncotarget · 2026Review
- Association of HLA-I genotypic diversity with tumor mutational burden across cancer types in a large Chinese cohort.Discover oncology · 2026Article
- Defects in antigen processing and presentation: mechanisms, immune evasion and implications for cancer vaccine development.Nature reviews. Immunology · 2026Review
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- Immuno-epidemiologic mapping of human leukocyte antigen diversity across glioma patient cohorts.Neuro-oncology · 2025Article
- Cancer immune evasion, immunoediting and intratumour heterogeneity.Nature reviews. Immunology · 2025Review
- Review
- Vaccines for cancer prevention: exploring opportunities and navigating challenges.Nature reviews. Drug discovery · 2025Review
- Leveraging T cells for cancer immunotherapy.Immunity & inflammation · 2025Review
- Epigenetic control of antigen presentation failure in osteosarcoma: from single-cell chromatin maps to therapeutic strategies.Frontiers in immunology · 2025Review
- Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication.Computational and structural biotechnology journal · 2024Article
- Gemcitabine Modulates HLA-I Regulation to Improve Tumor Antigen Presentation by Pancreatic Cancer Cells.International journal of molecular sciences · 2024Article
- Loss of Human Leukocyte Antigen and Immune Escape in Head and Neck Cancer.The Laryngoscope · 2024Article
- Germline mechanisms of immunotherapy toxicities in the era of genome-wide association studies.Immunological reviews · 2023Review
- Pervasiveness of HLA allele-specific expression loss across tumor types.Genome medicine · 2023Article
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundEfficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact the efficacy of cancer immunotherapy, and the somatic loss of HLA-I heterozygosity has been established as a factor in immune evasion. While global deregulated expression of HLA-I has also been reported in different tumor types, the role of HLA-I allele-specific expression loss - that is, the preferential RNA expression loss of specific HLA-I alleles - has not been fully characterized in cancer.
methodsHere, we use RNA and whole-exome sequencing data to quantify HLA-I allele-specific expression (ASE) in cancer using our novel method arcasHLA-quant.
resultsWe show that HLA-I ASE loss in at least one of the three HLA-I genes is a pervasive phenomenon across TCGA tumor types. In pancreatic adenocarcinoma, tumor-specific HLA-I ASE loss is associated with decreased overall survival specifically in the basal-like subtype, a finding that we validated in an independent cohort through laser-capture microdissection. Additionally, we show that HLA-I ASE loss is associated with poor immunotherapy outcomes in metastatic melanoma through retrospective analyses.
conclusionsTogether, our results highlight the prevalence of HLA-I ASE loss and provide initial evidence of its clinical significance in cancer prognosis and immunotherapy treatment.
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