ArticlePLoS genetics2022
Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver cancer.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS.bioRxiv : the preprint server for biology · 2026Article
- Beyond silencing: integrative multi-omics and spatial profiling unravel the systems-level role of piRNAs in HBV-driven Hepatocarcinogenesis.Molecular biology reports · 2026Review
- Casein kinase 2-mediated phosphorylation of the splicing factor SF3B3 plays a key role in esophageal squamous cell carcinoma progression.PLoS biology · 2026Article
- isoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization.Bioinformatics advances · 2026Article
- Peptide‑based therapeutics targeting the SLC39A14‑PIWIL2 fusion in hepatocellular carcinoma.Genomics & informatics · 2025Article
- Precision medicine in liver transplantation for hepatocellular carcinoma: applications and prospects of third-generation sequencing technology.Journal of cancer research and clinical oncology · 2025Review
- Long-read sequencing reveals novel isoform-specific eQTLs and regulatory mechanisms of isoform expression in human B cells.Genome biology · 2025Article
- Review
- 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
- The spatial and cellular portrait of transposable element expression during gastric cancer.Scientific reports · 2024Article
- Circadian-driven tissue specificity is constrained under caloric restricted feeding conditions.Communications biology · 2024Article
- Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.Molecular brain · 2024Article
- Article
- Long-read transcriptome landscapes of primary and metastatic liver cancers at transcript resolution.Biomarker research · 2024Article
- Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossGenome research · 2023Article
- Long-read sequencing reveals the complex structure of extra dic(21;21) chromosome and its biological effects.Human genetics · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.Nature computational science · 2023Article
- Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the LINE1-MET transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs. In vitro experiments on DETs showed that LINE1-MET and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis.
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