ArticleCommunications biology2021
Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 37 citations in OpenAlex.
- Identification of expressed endogenous retroviral element associated long terminal repeats in devil facial tumour cells.Open biology · 2026Article
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- Neoantigen Targeting as a Novel Approach for Therapy-Resistant Tumors.Molecular diagnosis & therapy · 2026Review
- Pan-cancer analysis reveals context-dependent roles of LINE-1 ORF1p in immune regulation and copy number alterations.bioRxiv : the preprint server for biology · 2025Article
- NovumRNA: Accurate prediction of non-canonical tumor antigens from RNA sequencing data.iScience · 2025Article
- Immunologic specificity in glioblastoma: Antigen discovery and translational implications.Neuro-oncology advances · 2025Review
- Impact of the PD-1/PD-L1 inhibitor SCL-1 on MDA-MB231 tumor growth in a humanized MHC-double knockout NOG mouse model.Scientific reports · 2025Article
- Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues.Nucleic acids research · 2025Article
- Immunogenic cryptic peptides dominate the antigenic landscape of ovarian cancer.Science advances · 2025Article
- Emerging role of endogenous peptides encoded by non-coding RNAs in cancer biology.Non-coding RNA research · 2025Review
- Integration of Bulk and Single-Cell Transcriptomics Reveals BCL2L14 as a Novel IGKC+ T Cell-Associated Therapeutic Target in Breast Cancer.Journal of inflammation research · 2025Article
- Proteogenomic analysis reveals non-small cell lung cancer subtypes predicting chromosome instability, and tumor microenvironment.Nature communications · 2024Article
- Article
- Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges.Biomarker research · 2023Review
- Proteogenomic data and resources for pan-cancer analysis.Cancer cell · 2023Review
- Pseudogenes in Cancer: State of the Art.Cancers · 2023Review
- Noncoding translation mitigation.Nature · 2023Article
- Article
- Aberrant Expression and Prognostic Potential of IL-37 in Human Lung Adenocarcinoma.Biomedicines · 2022Article
- Sources of Cancer Neoantigens beyond Single-Nucleotide Variants.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Neoantigen-based immunotherapy has yielded promising results in clinical trials. However, it is limited to tumor-specific mutations, and is often tailored to individual patients. Identifying suitable tumor-specific antigens is still a major challenge. Previous proteogenomics studies have identified peptides encoded by predicted non-coding sequences in human genome. To investigate whether tumors express specific peptides encoded by non-coding genes, we analyzed published proteomics data from five cancer types including 933 tumor samples and 275 matched normal samples and compared these to data from 31 different healthy human tissues. Our results reveal that many predicted non-coding genes such as DGCR9 and RHOXF1P3 encode peptides that are overexpressed in tumors compared to normal controls. Furthermore, from the non-coding genes-encoded peptides specifically detected in cancers, we predict a large number of "dark antigens" (neoantigens from non-coding genomic regions), which may provide an alternative source of neoantigens beyond standard tumor specific mutations.
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