ArticleCommunications biology2021
Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer.
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 15 papers.
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Who cites it
15 citing papers in PubMed, 19 citations in OpenAlex.
- A truncated TNS3 isoform expressed in metastatic triple negative breast cancer stabilizes FAK and promotes lung metastasis.Oncogene · 2026Article
- CirculatingCancers · 2026Article
- Landscape of gene fusions in hormone receptor-positive breast cancer reveals ADK fusions as drivers of progression and potential therapeutic targets.Cell discovery · 2025Article
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues.Nucleic acids research · 2024Article
- Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility.iScience · 2023Article
- Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer.Nature communications · 2023Article
- Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies.Cancers · 2023Review
- Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies.BMC genomics · 2023Article
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- Endogenous retrovirus group FRD member 1 is a potential biomarker for prognosis and immunotherapy for kidney renal clear cell carcinoma.Frontiers in cellular and infection microbiology · 2023Article
- PBSIM3: a simulator for all types of PacBio and ONT long reads.NAR genomics and bioinformatics · 2022Article
- Exploring differential exon usage via short- and long-read RNA sequencing strategies.Open biology · 2022Article
- Fusion-associated carcinomas of the breast: Diagnostic, prognostic, and therapeutic significance.Genes, chromosomes & cancer · 2022Review
- Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer.Communications biology · 2021Article
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 2 countries.
Funding
Abstract
Although transcriptome alteration is an essential driver of carcinogenesis, the effects of chromosomal structural alterations on the cancer transcriptome are not yet fully understood. Short-read transcript sequencing has prevented researchers from directly exploring full-length transcripts, forcing them to focus on individual splice sites. Here, we develop a pipeline for Multi-Sample long-read Transcriptome Assembly (MuSTA), which enables construction of a transcriptome from long-read sequence data. Using the constructed transcriptome as a reference, we analyze RNA extracted from 22 clinical breast cancer specimens. We identify a comprehensive set of subtype-specific and differentially used isoforms, which extended our knowledge of isoform regulation to unannotated isoforms including a short form TNS3. We also find that the exon-intron structure of fusion transcripts depends on their genomic context, and we identify double-hop fusion transcripts that are transcribed from complex structural rearrangements. For example, a double-hop fusion results in aberrant expression of an endogenous retroviral gene, ERVFRD-1, which is normally expressed exclusively in placenta and is thought to protect fetus from maternal rejection; expression is elevated in several TCGA samples with ERVFRD-1 fusions. Our analyses provide direct evidence that full-length transcript sequencing of clinical samples can add to our understanding of cancer biology and genomics in general.
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Registered trials
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.