BGI Education Center, University of Chinese Academy of Sciences (UCAS), Shenzhen, 518083, China.
BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.
Sci Rep. 2021 Mar 5;11(1):5325. doi: 10.1038/s41598-021-84693-w.
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.
单细胞 RNA 测序 (scRNA-seq) 的最新进展提高了我们对肿瘤浸润淋巴细胞 (TILs) 异质性与癌症发生和进展之间关联的理解。然而，研究替代剪接 (AS) 作为异质性的重要调节因子的研究仍然有限。在这里，我们开发了一种新的计算工具 DESJ-detection，它可以在单细胞水平上准确检测细胞群之间差异表达的剪接连接 (DESJ)。我们分析了 5063 个肝细胞癌 (HCC) 的 T 细胞，在 11 个 T 细胞亚型中鉴定出 1176 个 DESJ。有趣的是，DESJ 在 UTR 中富集，并且对异质性具有潜在影响。具有相似功能的细胞亚型在 AS 水平上紧密聚集在一起。同时，我们鉴定出一种新的细胞状态，即具有 ARHGAP15-205 等亚型标志物的预激活状态。总之，我们对替代剪接差异进行了全面研究，为 T 细胞异质性提供了新的见解，并可应用于其他全长 scRNA-seq 数据集。
