ArticleScientific reports2021
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Comprehensive assessment of alternative splicing analysis methods for single-cell RNA-seq.iScience · 2026Article
- Article
- The significance of immunogenic cell death related prognostic gene markers in colorectal cancer prognosis and antitumor immunity.Scientific reports · 2026Article
- Alternative splicing immune signature for detecting HBV-related hepatocellular carcinoma in peripheral blood mononuclear cells.Biochemistry and biophysics reports · 2025Article
- Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs.PLoS computational biology · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms.Nucleic acids research · 2025Article
- Aberrant splicing in Huntington's disease accompanies disrupted TDP-43 activity and altered m6A RNA modification.Nature neuroscience · 2025Article
- Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms.bioRxiv : the preprint server for biology · 2025Article
- AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level.GigaScience · 2025Article
- Analysis of single nuclear chromatin accessibility reveals unique myeloid populations in human pancreatic ductal adenocarcinoma.Clinical and translational medicine · 2024Article
- Article
- Interleukin-17 directly stimulates tumor infiltrating Tregs to prevent cancer development.Frontiers in immunology · 2024Article
- HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).BMC medical genomics · 2023Article
- Distinct regulatory functions and biological roles of lncRNA splice variants.Molecular therapy. Nucleic acids · 2023Review
- MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data.Nucleic acids research · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Robust and annotation-free analysis of alternative splicing across diverse cell types in mice.eLife · 2022Article
- Tertiary Lymphatic Structures in Primary Hepatic Carcinoma: Controversy Cannot Overshadow Hope.Frontiers in immunology · 2022Review
- Alternative RNA splicing in tumour heterogeneity, plasticity and therapy.Disease models & mechanisms · 2022Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in single-cell RNA sequencing (scRNA-seq) have improved our understanding of the association between tumor-infiltrating lymphocyte (TILs) heterogeneity and cancer initiation and progression. However, studies investigating alternative splicing (AS) as an important regulatory factor of heterogeneity remain limited. Here, we developed a new computational tool, DESJ-detection, which accurately detects differentially expressed splicing junctions (DESJs) between cell groups at the single-cell level. We analyzed 5063 T cells of hepatocellular carcinoma (HCC) and identified 1176 DESJs across 11 T cell subtypes. Interestingly, DESJs were enriched in UTRs, and have putative effects on heterogeneity. Cell subtypes with a similar function closely clustered together at the AS level. Meanwhile, we identified a novel cell state, pre-activation with the isoform markers ARHGAP15-205. In summary, we present a comprehensive investigation of alternative splicing differences, which provided novel insights into T cell heterogeneity and can be applied to other full-length scRNA-seq datasets.
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