Abstract 222: RNA-seq analysis of differential gene expression in melanoma cells after combined inhibition of Plk1 and Notch
Authors: Shengqin Su, Gagan Chhabra, Mary A. Ndiaye, Chandra K. Singh, Colin N. Dewey, Nihal Ahmad
Journal: Cancer Research (2020)

Abstract Melanoma is one of the most brutal forms of skin cancer, and its increasing incidence coupled with non-lasting therapeutic options for metastatic tumor highlight the need for additional strategies for the management of this neoplasm. Using tissue microarray analysis, we previously found that the expression of polo-like kinase 1 (Plk1, a serine/threonine kinase involved in mitotic regulation) and Notch1 (a type I transmembrane protein deciding cell fate during development) were positively correlated in melanoma (Cancer Res 2018; 78 [13 Suppl]: Abstract nr 2530), and their combined inhibition resulted in a synergistic anti-proliferative response in human melanoma cells (Cancer Res 2019; 79 [13 Suppl]: Abstract nr 302). In this study, to determine the possible mechanisms behind this observed synergism, we used RNA-seq technology to obtain the differential gene expression following treatment of SK-MEL-2 human metastatic melanoma cells with Plk1 inhibitor volasertib (BI6727, 20 nM) and Notch1 inhibitor MK-0752 (100 μM) for 48 h. After data pre-processing by RSEM algorithm, the DESeq2 package was implemented to identify differentially expressed genes (DEGs, |log2-fold change| &amp;gt;= 1, false positive rate ⇐ 0.05) when comparing the individual and combined treatments to vehicle (DMSO), as well as the interaction between volasertib:MK-0752. As a result, we identified 909 DEGs from volasertib treatment, 675 DEGs from MK-0752 treatment, 2142 genes from the combined treatment of volasertib and MK-0752, as well as 304 DEGs from the interaction of volasertib and MK-0752. In addition, employing GOstats and KEGGprofile packages in R programming, we conducted Gene Ontology (GO) and KEGG pathway analysis of the various DEGs. In GO analysis (counts &amp;gt;= 2, p ⇐ 10−5), we identified 202 downregulated GO terms affected by the combined inhibition of Plk1 and Notch1, including metabolism, cell proliferation, and migration. In KEGG pathway analysis, the combined inhibition of Plk1 and Notch1 was found to be associated with downregulation of several pathways shared with single drug treatments, such as PI3K-Akt, extracellular matrix receptor interaction, and protein digestion and absorption, as well as some novel pathways that were only affected by combined treatment, such as MAPK, Ras, and Rap1 pathways. Interestingly, our analysis predicted that the combined inhibition of Plk1 and Notch may make the melanoma cells more sensitive to immune responses. Overall, our data demonstrated that not only does targeting both Plk1 and Notch1 signaling pathways alters multiple melanoma progression pathways, but it may also potentially result in an increased sensitivity to other therapeutic targets, such as immune checkpoint blockade. However, these mechanistic findings need to be validated further in other relevant in vitro and in vivo models. Citation Format: Shengqin Su, Gagan Chhabra, Mary A. Ndiaye, Chandra K. Singh, Colin N. Dewey, Nihal Ahmad. RNA-seq analysis of differential gene expression in melanoma cells after combined inhibition of Plk1 and Notch [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 222.