PT - JOURNAL ARTICLE AU - Silvia Liu AU - Yan-Ping Yu AU - Bao-Guo Ren AU - Tuval Ben-Yehezkel AU - Caroline Obert AU - Mat Smith AU - Wenjia Wang AU - Alina Ostrowska AU - Alejandro Soto-Gutierrez AU - Jian-Hua Luo TI - Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells AID - 10.1101/2023.03.16.532991 DP - 2023 Jan 01 TA - bioRxiv PG - 2023.03.16.532991 4099 - http://biorxiv.org/content/early/2023/03/20/2023.03.16.532991.short 4100 - http://biorxiv.org/content/early/2023/03/20/2023.03.16.532991.full AB - The protein diversity of mammalian cells is determined by arrays of isoforms from genes. Protein 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.Competing Interest StatementTuval Ben-Yehezkel, Caroline Obert, and Mat Smith are employees of Element Biosciences, Inc. Silvia Liu, Yan-Ping Yu, Bao-Guo Ren, Wenjia Wang, Alina Ostrowska, Alejandro Soto-Gutierrez, and Jian-Hua Luo declare no conflict of interest.