Liu Silvia, Yu Yan-Ping, Ren Bao-Guo, Ben-Yehezkel Tuval, Obert Caroline, Smith Mat, Wang Wenjia, Ostrowska Alina, Soto-Gutierrez Alejandro, Luo Jian-Hua
Department of Pathology, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261.
High Throughput Genome Center, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, PA 15261.
bioRxiv. 2023 Aug 21:2023.03.16.532991. doi: 10.1101/2023.03.16.532991.
The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Genetic mutation is essential in species evolution and cancer development. Accurate Long-read transcriptome sequencing at single-cell level is required to decipher the spectrum of protein expressions in mammalian organisms. In this report, we developed a synthetic long-read single-cell sequencing technology based on LOOPseq technique. We applied this technology to analyze 447 transcriptomes of hepatocellular carcinoma (HCC) and benign liver from an individual. Through Uniform Manifold Approximation and Projection (UMAP) analysis, we identified a panel of mutation mRNA isoforms highly specific to HCC cells. The evolution pathways that led to the hyper-mutation clusters in single human leukocyte antigen (HLA) molecules were identified. Novel fusion transcripts were detected. The combination of gene expressions, fusion gene transcripts, and mutation gene expressions significantly improved the classification of liver cancer cells versus benign hepatocytes. In conclusion, LOOPseq single-cell technology may hold promise to provide a new level of precision analysis on the mammalian transcriptome.
哺乳动物细胞的蛋白质多样性由基因的异构体阵列决定。基因突变在物种进化和癌症发展中至关重要。需要在单细胞水平进行准确的长读长转录组测序，以解读哺乳动物生物体中蛋白质表达的谱图。在本报告中，我们基于LOOPseq技术开发了一种合成长读长单细胞测序技术。我们应用该技术分析了来自同一个体的447个肝细胞癌（HCC）和良性肝脏的转录组。通过均匀流形近似和投影（UMAP）分析，我们鉴定出一组对HCC细胞具有高度特异性的突变mRNA异构体。确定了导致单个人类白细胞抗原（HLA）分子中高突变簇的进化途径。检测到了新的融合转录本。基因表达、融合基因转录本和突变基因表达的组合显著改善了肝癌细胞与良性肝细胞的分类。总之，LOOPseq单细胞技术有望为哺乳动物转录组提供新的精准分析水平。
