Global genomic and proteomic analysis of TNBC cells identifies the critical role of PELP1 in ribosome biogenesis

We examined the mechanisms by which PELP1 regulates TNBC progression. MDA-MB-231 cells were stably transfected with control non-targeted shRNA or PELP1 shRNA, and total RNA was isolated for RNA-seq analysis. Our results demonstrated that PELP1 regulates the expression of Myc, E2F and mTOR targets in TNBC. Total RNA from MDA-MB-231 control-shRNA and PELP1-shRNA cells were isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates each for knockdown and control) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.