RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling

• Published in: Cancers Vol. 12; no. 9; p. 2510
• Main Authors: Scherer, Dominique, Dávila López, Marcela, Goeppert, Benjamin, Abrahamsson, Sanna, González Silos, Rosa, Nova, Igor, Marcelain, Katherine, Roa, Juan C., Ibberson, David, Umu, Sinan U., Rounge, Trine Ballestad, Roessler, Stephanie, Lorenzo Bermejo, Justo
• Format: Journal Article
• Language: English; Norwegian
• Published: Basel MDPI AG 03.09.2020; MDPI
• Subjects: Biliary tract; Bioinformatics (Computational Biology); Bioinformatik (beräkningsbiologi); Biomarkers; Cancer; Cancer and Oncology; Cancer cells; Cancer och onkologi; Cell culture; Cell lines; Cholangiocarcinoma; DNA methylation; Epidermal growth factor receptors; exome mutations; Gallbladder; Gallbladder cancer; Gene expression; Gene mutation; Genetic aspects; Health aspects; hepatobiliary cancer; Hepatocellular carcinoma; Methods; Mutation; p53 Protein; Principal components analysis; Quality control; Researchers; Ribonucleic acid; RNA; RNA sequencing; Smad4 protein; Transcriptomics; Tumor cell lines; Tumors; Chile
• ISSN: 2072-6694; 2072-6694
• DOI: 10.3390/cancers12092510

Cancer cell lines allow the identification of clinically relevant alterations and the prediction of drug response. However, sequencing data for hepatobiliary cancer cell lines in general, and particularly gallbladder cancer (GBC), are sparse. Here, we apply RNA sequencing to characterize 10 GBC, eight hepatocellular carcinoma, and five cholangiocarcinoma (CCA) cell lines. RNA extraction, quality control, library preparation, sequencing, and pre-processing of sequencing data were implemented using state-of-the-art techniques. Public data from the MSK-IMPACT database and a large cohort of Japanese biliary tract cancer patients were used to illustrate the usage of the released data. The total number of exonic mutations varied from 7207 for the cell line NOZ to 9760 for HuCCT1. Researchers planning experiments that require TP53 mutations could use the cell lines NOZ, OCUG-1, SNU308, or YoMi. Mz-Cha-1 showed mutations in ATM, SNU308 presented SMAD4 mutations, and the only investigated cell line that showed ARID1A mutations was GB-d1. SNU478 was the cell line with the global gene expression pattern most similar to GBC, intrahepatic CCA, and extrahepatic CCA. EGFR, KMT2D, and KMT2C generally presented a higher expression in the investigated cell lines than in Japanese primary GBC tumors. We provide the scientific community with detailed mutation and gene expression data, together with three showcase applications, with the aim of facilitating the design of future in vitro cell culture assays for research on hepatobiliary cancer.