AIB1 dependent transcriptome in endocrine resistance

Purpose: AIB1 expression is associated with disease progression in aromastase inhibitor (AI) treated patients in breast cancer. In order to identify genes aberrantly regulated by AIB1 in AI resistance, RNA-seq was carried out in endocrine resistant LetR cells and endocrine sensitive MCF7 cells +/- AIB1 under estrogen deprivation. Methods: RNA-seq was carried out in biological triplicate in MCF7 and LetR cells comparing NT (Scramble siRNA) cells versus cells depleted of AIB1 using a SMARTpool ON-TARGETplus siRNA. RNA was extracted using Qiagen RNeasy Kit and subjected to 100bp PE sequencing using the BGISEQ 500 platform. Briefly, clean reads were mapped to reference genome using Bowtie2 and gene expression was calculated with RSEM. Differentially expressed genes (DEGs) were detected with DEseq2. With the KEGG pathway analysis, the pathway functional enrichment was performed using phyper, a function of R. Results: 61 AIB1 differentially regulated genes were identified as unique to endocrine resistant tumor cells (logfc=1.5; Padj=0.05).MSigDB Oncogenic signature analysis of the 61 AIB1-regulated genes revealed enrichment in growth promoting endocrine resistance pathways including LTE2, RAF, ERBB2 and MEK. Conclusion: In the endocrine resistant setting, aberrant AIB1 expression regulates the expression of genes associated with growth factor signalling. Overall design: RNA-seq was carried out in biological triplicate in MCF7 and LetR cells comparing NT (Scramble siRNA) cells versus cells depleted of AIB1 using a SMARTpool ON-TARGETplus siRNA.