Hyaluronan-CD44 signaling promotes pro-tumor inflammation in breast cancer

ABSTRACT: We report the application of next-generation sequencing (NGS) technology for high-throughput profiling of RNA expression in human breast cancer cells. The goal of this study was to compare NGS-derived transcriptome profiling (RNA-seq) from cells expressing either wildtype or knockout CD44 to identify key downstream signaling events of HA-CD44 interactions. Methods: This experiment was repeated for a total of three times and replicate RNA samples were extracted and submitted for Illumina Sequencing. Twelve dual-indexed Illumina TruSeq stranded mRNA libraries were pooled for sequencing on 1 lane of a HiSeq 2500 using v4 chemistry to generate 2x50 bp paired-end reads. After applying the Benjamini-Hochberg multiple hypothesis adjustment to raw p-values, differentially expressed genes were identified requiring that they had a log2 fold change > 0 and an adjusted p-value ≤ 0.01. Results: A total of 1,530 and 320 genes were impacted by CD44 KO in the Hs578T cells and MDA-MB-231 cells, respectively. When comparing each of these data sets, 40 genes were differentially expressed in both Hs578T and MDA-MB-231 cells upon deletion of CD44. Conclusions: Gene ontology (GO) analysis revealed that CD44 KO in breast cancer cells altered expression of genes involved in both cell adhesion and cytokine activity. This study provides a framework for the application of NGS to compare differential gene expression between genetically edited mammalian cell populations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE148657 | GEO | 2021/03/29

REPOSITORIES: GEO