A kinase inhibitor screen identifies a dual cdc7/CDK9 inhibitor to sensitise triple-negative breast cancer to EGFR-targeted therapy

Purpose: To investigate the impact of combined cdc7, CDK9 and EGFR inhibition on the transcriptomic profile of EGFR-TKI-resistant TNBC cells using high-throughput RNA sequencing. Methods: EGFR-TKI-resistant TNBC cell lines (Hs578T and SKBR7) were treated with DMSO, lapatinib (3.16 µM), PHA-767491 (1 µM) or co-treated with lapatinib (3.16 µM) & PHA-767491 (1 µM) for 6 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (RNA-Seq) was performed using Illumina high-throughput RNA sequencing. Results:we mapped about 40 million sequence reads per sample to the human genome (build hg38). RNA-Seq data was normalised by TMM using EdgeR’s normalisation-factor followed by quantile normalisation and presented in Log2 fold change (Log2 FC) scales.Genes with significant down- or up-regulation (Log2 FC ≥ |0.5|) under indicated conditions were analysed by web-based functional analysis tool Ingenuity pathway Analysis (IPA) to visualise and annotate their biological functions and pathways. Conclusions: 1387 and 2747 genes were down-regulated in co-treated Hs578T and SKBR7 cells, respectively. 2614 genes were up-regulated by co-treatment in Hs578T cells, whilst 243 genes were up-regulated by the same treatment in SKBR7 cells. We identified 845 commonly differentially expressed transcripts in both HS578T and SKBR7 cells after co-treatment of which 141 transcripts were up-regulated and 704 transcripts were down-regulated. 34 of these commonly differentially expressed transcripts were linked to metastasis-free survival in TNBC patients. Transcriptomic profiles (mRNA) of triple-negative breast cancer cells after treatment with DMSO, PHA-767491 and lapatinib or a combination of both lapatinib and PHA-767491 were generated in triplicate using Illumina RNA sequencing.