ArticleProceedings of the National Academy of Sciences of the United States of America2011
Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in sequencing and omics studies in prostate cancer: unveiling molecular pathogenesis and clinical applications.Frontiers in oncology · 2024Pooled it
- Enhancing prostate cancer diagnosis: a machine learning-based biomarker approach.Human genomics · 2026Article
- Detection of Chimeric RNAs from RNA-Seq Data with ChiTaRS 8.0: Insights for Liquid Biopsy and Drug Target Identification.Methods in molecular biology (Clifton, N.J.) · 2026Article
- FuSViz-visualization and interpretation of structural variation using cancer genomics and transcriptomics data.Nucleic acids research · 2025Article
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.Journal of molecular biology · 2025Review
- Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis.NPJ precision oncology · 2024Article
- RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.Briefings in bioinformatics · 2024Article
- Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis.bioRxiv : the preprint server for biology · 2024Article
- Roast: a tool for reference-free optimization of supertranscriptome assemblies.BMC bioinformatics · 2024Article
- Cancer fusion transcripts with human non-coding RNAs.Frontiers in oncology · 2024Review
- Ambiguous genes due to aligners and their impact on RNA-seq data analysis.Scientific reports · 2023Article
- Overexpression of TMEM79 combined with SMG5 is related to prognosis, tumor immune infiltration and drug sensitivity in hepatocellular carcinoma.European journal of medical research · 2023Article
- Neoantigen-based cancer vaccination using chimeric RNA-loaded dendritic cell-derived extracellular vesicles.Journal of extracellular vesicles · 2022Article
- Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics.Nature reviews. Molecular cell biology · 2022Review
- Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases.Genes · 2022Review
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- Evaluating a Targeted Cancer Therapy Approach Mediated by RNAInternational journal of molecular sciences · 2022Article
- The Fusion ofInternational journal of molecular sciences · 2021Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Transcription-induced chimeric RNAs, possessing sequences from different genes, are expected to increase the proteomic diversity through chimeric proteins or altered regulation. Despite their importance, few studies have focused on chimeric RNAs especially regarding their presence/roles in human cancers. By deep sequencing the transcriptome of 20 human prostate cancer and 10 matched benign prostate tissues, we obtained 1.3 billion sequence reads, which led to the identification of 2,369 chimeric RNA candidates. Chimeric RNAs occurred in significantly higher frequency in cancer than in matched benign samples. Experimental investigation of a selected 46 set led to the confirmation of 32 chimeric RNAs, of which 27 were highly recurrent and previously undescribed in prostate cancer. Importantly, a subset of these chimeras was present in prostate cancer cell lines, but not detectable in primary human prostate epithelium cells, implying their associations with cancer. These chimeras contain discernable 5' and 3' splice sites at the RNA junction, indicating that their formation is mediated by splicing. Their presence is also largely independent of the expression of parental genes, suggesting that other factors are involved in their production and regulation. One chimera, TMEM79-SMG5, is highly differentially expressed in human cancer samples and therefore a potential biomarker. The prevalence of chimeric RNAs may allow the limited number of human genes to encode a substantially larger number of RNAs and proteins, forming an additional layer of cellular complexity. Together, our results suggest that chimeric RNAs are widespread, and increased chimeric RNA events could represent a unique class of molecular alteration in cancer.
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