ArticleCell genomics2024
An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing.
Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Development of an isoform-discriminating RT-qPCR assay for transcript-level profiling of human ASAH2 in colorectal cancer cell models.Molecular biology reports · 2026Article
- Integrating short-read and long-read single-cell transcriptomics of pig pituitary reveals mechanisms of high-altitude hypoxia adaptation.PLoS genetics · 2026Article
- Vascular smooth muscle RbFox2 regulates the cytoskeleton and arterial stiffness by a RhoBTB1/Cullin-3 mechanism.JCI insight · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Beyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets.Frontiers in oncology · 2026Review
- MBNL1-mediated alternative splicing in cancer: underlying mechanism, isoform regulation, and translational perspectives.Frontiers in molecular biosciences · 2026Review
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Review
- Single-cell integration analysis reveals molecular signatures of the tumor microenvironment in early-onset colorectal cancer.NPJ precision oncology · 2025Article
- Assessment and applications of joint profiling of single-cell chromatin accessibility and transcriptome.Briefings in bioinformatics · 2025Review
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms.The Analyst · 2025Article
- Intron retention regulates STAT2 function and predicts immunotherapy response in lung cancer.bioRxiv : the preprint server for biology · 2025Article
- Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms.bioRxiv : the preprint server for biology · 2025Article
- A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.Nature methods · 2025Article
- Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer.Non-coding RNA · 2025Review
- Colorectal Cancer: Current and Future Therapeutic Approaches and Related Technologies Addressing Multidrug Strategies Against Multiple Level Resistance Mechanisms.International journal of molecular sciences · 2025Review
- AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level.GigaScience · 2025Article
- Advancing automated cell type annotation with large language models and single-cell isoform sequencing.Computational and structural biotechnology journal · 2025Review
- The Application of Long-Read Sequencing to Cancer.Cancers · 2024Review
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Colorectal cancer (CRC) ranks as the second leading cause of cancer deaths globally. In recent years, short-read single-cell RNA sequencing (scRNA-seq) has been instrumental in deciphering tumor heterogeneities. However, these studies only enable gene-level quantification but neglect alterations in transcript structures arising from alternative end processing or splicing. In this study, we integrated short- and long-read scRNA-seq of CRC samples to build an isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 resulting from various combinations of splicing events. Second, we characterized genes and isoforms associated with epithelial lineages and subpopulations exhibiting distinct prognoses. Among 31,935 isoforms with novel junctions, 330 were supported by The Cancer Genome Atlas RNA-seq and mass spectrometry data. Finally, we built an algorithm that integrated novel peptides derived from open reading frames of recurrent tumor-specific transcripts with mass spectrometry data and identified recurring neoepitopes that may aid the development of cancer vaccines.
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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.