ArticleJCO clinical cancer informatics2022
Intron-Retention Neoantigen Load Predicts Favorable Prognosis in Pancreatic Cancer.
Article in JCO clinical cancer informatics, 2022. 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, 10 citations in OpenAlex.
- Dark matter matters: from noncoding RNA regulation to cancer immunity.Oncoimmunology · 2026Review
- PRMT5-mediated intron retention triggers innate and adaptive immunity against cancer.EMBO molecular medicine · 2026Article
- A targetable dependency on nonsense-mediated decay for cellular homeostasis and immune control in small cell lung cancer.Molecular cancer · 2026Article
- Characterization of aberrant alternative splicing landscape in patients with metastatic renal cell carcinoma.Journal for immunotherapy of cancer · 2026Article
- Patient-derived organoid xenografts reveal the multifaceted role of the lncRNAbioRxiv : the preprint server for biology · 2026Article
- Rethinking PDAC: from immunological silence to therapeutic opportunity.Frontiers in immunology · 2026Review
- Beyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets.Frontiers in oncology · 2026Review
- Elevated intron retention implicates neuroinflammation in brains of individuals with alcohol use disorder.Brain communications · 2026Article
- Origins and implications of intron retention quantitative trait loci in human tissues.American journal of human genetics · 2025Article
- Chasing the Ghost Proteome in the Dark Matter.Molecular & cellular proteomics : MCP · 2025Review
- Analysis of SLC genes alternative splicing identifies the SLC7A6 RI isoform as a therapeutic target for colorectal cancer.Cancer science · 2025Article
- Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates.Bioinformatics advances · 2024Article
- Pan-Cancer Profiling of Intron Retention and Its Clinical Significance in Diagnosis and Prognosis.Cancers · 2023Article
- Alternative splicing: a new breakthrough for understanding tumorigenesis and potential clinical applications.Genes & genomics · 2023Review
- Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model.Communications biology · 2023Article
- Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads.Genome biology · 2022Article
- Bioinformatics detection of modulators controlling splicing factor-dependent intron retention in the human brain.Human mutation · 2022Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeHigh tumor mutation burden (TMB) in many cancer types is associated with the production of tumor-specific neoantigens, a favorable outcome and response to immune checkpoint blockade (ICB) therapy. Besides mutation-derived neoantigens, aberrant intron retention also produces tumor neopeptides that could trigger an immune response. The relationship between intron-retention-derived tumor neoantigens (IR-neoAg) and clinical outcomes in pancreatic cancer remains uncertain. Here, we quantify IR-neoAg in pancreatic cancer and evaluate whether IR-neoAg load might serve as a biomarker for selecting patients who may benefit from ICB therapy.
methodsWe developed a computational approach to estimate patient-specific IR-neoAg load from transcriptome data available in The Cancer Genome Atlas pancreatic cancer cohort. Associations between IR-neoAg load and patient overall survival were evaluated using Kaplan-Meier estimates and Cox regression. Differential expression of immune checkpoint and
resultsHigh IR-neoAg load predicted better overall survival in pancreatic cancer, although no association was found for TMB. IR-neoAg load remained a significant prognostic factor after adjusting for patient age, sex, tumor stage and grade, and TMB. Moreover, pancreatic tumors with both high IR-neoAg load and high
conclusionIR-neoAg load is associated with favorable survival in pancreatic cancer. These findings provide strong evidence for considering IR-neoAgs when selecting patients who might benefit from ICB therapy.
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