Next Generation Sequencing Facilitates Quantitative Analysis of the MDM2i and WIPi Combination Therapy in Intrahepatic Cholangiocarcinoma Transcriptomes

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized the systems-based analysis of cellular pathways. The purpose of this study is to compare the expression profiles of single and combination treatment of MDM2i and WIP1i in RBE cells by NGS-derived transcriptome profiling (RNA-seq). Methods: RBE mRNA profiles of HDM201 (MDM2i) and/or GSK2830371 (WIP1i) treatment for 6 or 24 hours were generated by deep sequencing, in triplicate, using Illumina NextSeq sequencer. The sequence of each read was trimmed based on the quality score (Q30), and read lengths less than 45 bp were dis-carded prior to further analysis. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: STAR aligner followed by ANOVA. Results: We mapped about 30 million sequence reads per sample to the RBE transcriptomes after HDM201 and/or GSK2830371 treatment. The differentially expressed genes were selected for more than 2-fold changes and p-values for differences in expression of less than 0.05. From four different comparisons, HDM201 alone and in combination with GSK2830371 for 6 h and 24 h, 26 consistently altered genes were identified (21 upregulated genes and 5 downregulated genes). Conclusions: Our study represents the detailed analysis of MDM2i and/or WIPi therapy in intrahepatic cholangiocarcinoma transcriptomes. Differentially expressed genes from combination treatment were enriched for genes involved in p53-dependent signal transduction pathways, involved in the DNA damage response, response to stress, and regulation of apoptotic processes. In addition, differentially expressed genes, analyzed using the KEGG pathway da-tabase, were enriched for genes involved in platinum drug resistance and the p53 signaling pathway and gene ontology database for protein-protein interaction using an adjusted p-values less than 0.01.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179787 | GEO | 2021/07/09

REPOSITORIES: GEO