Neratinib-induced gene expression profile in breast cancer cells: A comprehensive transcriptome investigation

Breast cancer can be classified into complicated malignant subtypes based on advances of clinical and research evidence. There are still unmet needs for the more effective treatment of breast cancer patients under specific pathological conditions (stages/subtypes). Neratinib is considered as a second-generation inhibitor of the EGFR family members (EGFR, HER2 and HER4) of receptor kinases. It can irreversibly inhibit the EGFR and HER2 tyrosine kinases by targeting a cysteine residue in the ATP-binding site of the receptor. Recently neratinib has been approved by FDA for the extended adjuvant treatment of early-stage HER2+ breast cancer. In this study, to further dissect the molecular mechanisms of neratinib, the global gene expression profiling analysis of breast cancer cells treated with neratinib was performed using RNA AmpliSeq transcriptome (including 20816 gene candidates) in the Ion PI sequencing system. We selected two breast cancer cell lines, the triple negative MDA-MB-231 cell line and the low HER2-expressing, but not-amplified, ER+ MCF-7 cell line. The RNA-Seq data show differential gene profiling heatmap from these two breast cancer cell lines. The RNA-Seq data confirmed the downregulation of HER2 in MCF-7 cells, but there was no change of gene expression of EGFR, HER3 and HER4. In both MDA—MB-231 and MCF-7 cell lines, there was a panel of upregulating genes including KIAA1024, ZNF550, MESDC1, TMC8, ZNF524, AGBL2, HIST2H2BC and PPARGC1B. In contrast, with response to neratinib, another cluster of genes was downregulated in both cell lines including TAS2R5, KRT14, VWCE, LY9, PAPLN and STK4-AS1. In MDA-MB-231 cells, neratinib intended to regulate LPS/IL-1 and eNOS mediated signaling pathways. However, in MCF-7 cells, neratinib regulated ephrin receptor (EPH) signalling and PPARα activation. We then investigated the possible HER2-independent effect of neratinib in breast cancer cells such as regulation of EPH. Our data using the electric cell-substrate impedance sensing (ECIS) indicated that MCF-7 cells responded to an EphB4 inhibitor, NVP-HPG-712, by a marked reduction of cellular migration, in contrast to MDA MB-231 which does not respond to the inhibitor. Similarly, MCF-7 cells also responded to the combinational treatment of neratinib and NVP-HPG-712 with a decrease in cellular migration. Again, MDA-MB-231 failed to yield a response. In summary, differential analysis of transcripts by high throughput RNA-seq could be valuable to provide deeper insight into the gene regulation and signaling pathway prediction of breast cancer cells with response to neratinib when the large scale of patient samples and multiple types of breast cancer cell lines are integrated. Citation Format: Yuxin Cui, Alwyn Dart, Richard E. Cutler, Alshad S. Lalani, Francesca Avogadri-Connors, Richard P. Bryce, Sioned Owen, Wen G. Jiang. Neratinib-induced gene expression profile in breast cancer cells: A comprehensive transcriptome investigation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3931.