Global characterization of prostate cancer cell expression upon treatment with media conditioned from human stromal cells epitopically expressing epiregulin (EREG)

Technical advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this study to establish the transcriptomic profiles of human prostate cancer cell lines exposed to conditioned media from human primary stromal cells engineered to express epiregulin (EREG), a typical factor of the senescence-associated secretory phenotype (SASP), the latter a hallmark of senescent cells. Overall design: Transcript profiles of prostate cancer cell lines mainly PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays