ArticleNucleic acids research2015
Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed, 194 citations in OpenAlex.
- SpliceImpactR maps alternative RNA processing events driving protein functional diversity.Nucleic acids research · 2026Article
- Aberrant splicing in human cancer shows possible functional impact on transcription factors.Oncogene · 2026Article
- TENT5A Maintains MYC mRNA Stability to Enhance Osteosarcoma Stemness.Cancer research · 2026Article
- Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.Cell genomics · 2026Article
- Glycolysis and glycolytic enzymes in acute myeloid leukemia: Warburg and beyond.Frontiers in pharmacology · 2026Review
- Long-read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons.Open biology · 2025Article
- Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves.Scientific reports · 2025Article
- Alternative Splicing of FBLN2 Generates a Prometastatic Extracellular Matrix in Gastrointestinal Cancers by Determining N-Glycosylation of Fibulin 2.Genes to cells : devoted to molecular & cellular mechanisms · 2025Article
- RNA splicing: Novel star in pulmonary diseases with a treatment perspective.Acta pharmaceutica Sinica. B · 2025Review
- iSoMAs: Finding isoform expression and somatic mutation associations in human cancers.PLoS computational biology · 2025Article
- Comparative RNA-Seq Analysis of Colon Spheroids and Patient-derived Tissues Identifies Non-Canonical Transcript Isoforms of Protein-Coding Genes Implicated in Colon Carcinogenesis.Cancer informatics · 2025Article
- Targeting splicing for hematological malignancies therapy.BMC genomics · 2024Review
- A CRISPR-dCas13 RNA-editing tool to study alternative splicing.Nucleic acids research · 2024Article
- Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma.Journal of personalized medicine · 2024Article
- Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Pan-cancer transcriptomic data of ABI1 transcript variants and molecular constitutive elements identifies novel cancer metastatic and prognostic biomarkers.Cancer biomarkers : section A of Disease markers · 2024Article
- RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing.Nature communications · 2023Article
- Pan-Cancer Profiling of Intron Retention and Its Clinical Significance in Diagnosis and Prognosis.Cancers · 2023Article
- RNA‑binding protein quaking 5 inhibits the progression of non‑small cell lung cancer by upregulating netrin‑4 expression.Oncology reports · 2023Article
- The Role of NCS1 in Immunotherapy and Prognosis of Human Cancer.Biomedicines · 2023Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The determination of the alternative splicing isoforms expressed in cancer is fundamental for the development of tumor-specific molecular targets for prognosis and therapy, but it is hindered by the heterogeneity of tumors and the variability across patients. We developed a new computational method, robust to biological and technical variability, which identifies significant transcript isoform changes across multiple samples. We applied this method to more than 4000 samples from the The Cancer Genome Atlas project to obtain novel splicing signatures that are predictive for nine different cancer types, and find a specific signature for basal-like breast tumors involving the tumor-driver CTNND1. Additionally, our method identifies 244 isoform switches, for which the change occurs in the most abundant transcript. Some of these switches occur in known tumor drivers, including PPARG, CCND3, RALGDS, MITF, PRDM1, ABI1 and MYH11, for which the switch implies a change in the protein product. Moreover, some of the switches cannot be described with simple splicing events. Surprisingly, isoform switches are independent of somatic mutations, except for the tumor-suppressor FBLN2 and the oncogene MYH11. Our method reveals novel signatures of cancer in terms of transcript isoforms specifically expressed in tumors, providing novel potential molecular targets for prognosis and therapy. Data and software are available at: http://dx.doi.org/10.6084/m9.figshare.1061917 and https://bitbucket.org/regulatorygenomicsupf/iso-ktsp.
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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.