GSE134803
Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple negative breast cancer progression
Purpose: To investigate the impact of ASAP1 depletion on the transcriptomic profile of TNBC cells using TempO-Seq-based high-throughput RNA sequencing. Methods: Three TNBC cell lines (BT549, SUM149PT and Hs578T) were treated with siRNA control or siRNA targeting ASAP1 for 72 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (TempO-Seq) was performed using Illumina high-throughput RNA sequencing. Results: We mapped about 7 million sequence reads per sample to the human genome. Normalization and differential expression analysis were performed using DESeq2 package. Genes with significant down- or up-regulation (Log2 FC = |1|) under indicated conditions were analysed by web-based functional analysis tool Metascape to visualise and annotate their biological functions and pathways. Conclusions: Genes with 2-fold changes (absolute Log2 FC = 1) in down- or up-regulation were selected in BT549 (311 down / 495 up), Hs578T (133 down / 117 up) and SUM149PT (500 down / 401 up) cells, respectively. Consequently, 95 DEGs were downregulated, and 79 DEGs upregulated in = 2/3 of the TNBC cell lines, in total 174 DEGs, which were considered as common DEGs that were susceptible to the depletion of the amplification-dependent ASAP1. 53 of  these commonly differentially expressed transcripts were linked to relapse-free survival in TNBC patients. Overall design: ASAP1 depletion-mediated transcriptional reprogramming of triple-negative breast cancer cells harboring ASAP1 amplification and high expression depletion was generated in triplicate using Illumina RNA sequencing.