School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
Sci Rep. 2019 Jul 2;9(1):9524. doi: 10.1038/s41598-019-45934-1.
Inter- and intra-tumour heterogeneity is caused by genetic and non-genetic factors, leading to severe clinical implications. High-throughput sequencing technologies provide unprecedented tools to analyse DNA and RNA in single cells and explore both genetic heterogeneity and phenotypic variation between cells in tissues and tumours. Simultaneous analysis of both DNA and RNA in the same cell is, however, still in its infancy. We have thus developed a method to extract and analyse information regarding genetic heterogeneity that affects cellular biology from single-cell RNA-seq data. The method enables both comparisons and clustering of cells based on genetic variation in single nucleotide variants, revealing cellular subpopulations corroborated by gene expression-based methods. Furthermore, the results show that lymph node metastases have lower levels of genetic heterogeneity compared to their original tumours with respect to variants affecting protein function. The analysis also revealed three previously unknown variants common across cancer cells in glioblastoma patients. These results demonstrate the power and versatility of scRNA-seq variant analysis and highlight it as a useful complement to already existing methods, enabling simultaneous investigations of both gene expression and genetic variation.
肿瘤内和肿瘤间异质性是由遗传和非遗传因素引起的，导致严重的临床后果。高通量测序技术为分析组织和肿瘤中单个细胞内的 DNA 和 RNA 以及探索细胞间遗传异质性和表型变异提供了前所未有的工具。然而，在同一细胞中同时分析 DNA 和 RNA 仍处于起步阶段。因此，我们开发了一种从单细胞 RNA-seq 数据中提取和分析影响细胞生物学的遗传异质性信息的方法。该方法能够基于单核苷酸变异的遗传变异对细胞进行比较和聚类，揭示基于基因表达的方法证实的细胞亚群。此外，结果表明，淋巴结转移与原始肿瘤相比，在影响蛋白质功能的变异方面，遗传异质性较低。该分析还揭示了胶质母细胞瘤患者癌症细胞中三个以前未知的常见变异。这些结果证明了 scRNA-seq 变异分析的强大功能和多功能性，并强调它是现有方法的有用补充，能够同时研究基因表达和遗传变异。
