Adipocyte-driven unfolded protein response is a shared transcriptomic signature of metastatic prostate carcinoma cells

Purpose: To begin understanding molecular processes that enable tumor cells to survive and progress in difficult microenvironments such as bone, we performed unbiased examination of the transcriptome of two different prostate cancer cell lines in the absence or presence of bone marrow adipocytes. Methods: 3' RNA-seq (QuantSeq 3' mRNA) was performed. RNA from four biological replicates of PC3 and ARCaP(M) cells cultured alone or in Transwell with adipocytes was collected , and run on an Agilent TapeStation 2200 (Agilent Technologies, Santa Clara, CA) for quality control. Lexogen's QuantSeq 3'mRNA-seq Library Prep Kit (FWD for Illumina) was utilized for building RNAseq libraries. The barcoded libraries were multiplexed at equimolar concentrations and sequenced with 50 bp single reads on an Illumina HiSeq-2500 run in rapid mode. Data were demultiplexed using Illumina's CASAVA 1.8.2 software and reads were aligned to the human genomes. Differential gene expression analysis was used to detect adipocyte-mediated transcriptome changes. qRT–PCR validation was performed using TaqMan assays. Results: Our RNAseq analyses and subsequent quantitative PCR and protein-based assays reveal that upregulation of Endoplasmic Reticulum (ER) stress and Unfolded Protein Response (UPR) genes is a shared signature between two metastatic prostate carcinoma cell lines of different origin. Pathway analyses and pharmacological examinations highlight the ER chaperone BIP as an upstream coordinator of this transcriptomic signature. Conclusions: Our studies pave the way for additional mechanistic investigations and offer new clues towards effective therapeutic interventions in metastatic disease. Overall design: RNA from four biological replicates of PC3 and ARCaP(M) cells cultured alone or in Transwell with adipocytes was sequenced