Identification of Integrin‐linked Kinase Downstream Effectors in Cisplatin‐Resistant Ovarian Cancer Using RNA Sequencing

Abstract

Despite good responses to first‐line treatment with platinum‐based chemotherapy such as cisplatin, most ovarian cancer patients will relapse and eventually develop chemoresistant disease with poor prognosis. Therefore, new therapies targeting key survival pathways are urgently needed for this deadly disease. Increased levels of integrin‐linked kinase (ILK), a serine/threonine kinase and adaptor protein, have been well documented in various types of cancers including ovarian cancer. Our previous findings indicate that targeting ILK with small‐interfering RNA (siRNA) inhibits cell growth and reduces invasion ability of cisplatin‐resistant ovarian cancer. The objective of the present study was to assess the signaling pathways altered as a result of siRNA‐mediated ILK targeting in cisplatin‐resistant ovarian cancer cells. To achieve this, we performed a transcriptome‐wide analysis by RNA sequencing (RNA‐Seq). Using an initial false discovery rate (FDR, q‐value) cutoff of <0.05, we identified 2,028 differentially expressed genes between Control‐siRNA and ILK‐siRNA‐transfected cells including 1,322 upregulated and 706 downregulated genes. Of these genes, 1,804 were mapped successfully by Ingenuity Pathway Analysis (IPA). To select differentially expressed genes, a log2 fold change cutoff >1.5 or <−1.5 with a p‐value ≤0.001 was used. Using these criteria, we identified a total of 77 differentially expressed genes, 68 upregulated and 9 downregulated in ILK‐siRNA compared to Control‐siRNA‐transfected cells. IPA analysis revealed that the top significantly altered canonical pathway was SAPK/JNK signaling. Top networks were associated with cell death and survival, cancer, cellular movement, cell‐to‐cell signaling and interaction, cellular development, and cellular growth and proliferation. Furthermore, cell morphology, cellular assembly and organization, and cellular function and maintenance were within the top cellular and molecular functions associated with ILK downregulation. Significant changes in the expression of cancer associated molecules including upregulation of GRIA4, TOMM40L, DUSP8, MARVELD3, and PDCD4, and downregulation of SLC4A8, TEX41, and HIPK3 were observed. The genes identified here have been previously shown to be involved in the regulation of cell proliferation, survival, migration, invasion, metastasis, drug response, and/or apoptosis, which could explain in part the biologic effects observed upon ILK depletion. Therefore, further studies are required to validate these findings and to fully understand the underlying mechanisms of ILK downstream effectors in cisplatin‐resistant ovarian cancer.Support or Funding InformationThis work was supported in part by the National Institute on Minority Health and Health Disparities CCRHD (U54MD007600) and RTRN (U54MD008149), NIGMS‐RISE (R25GM061838), PRSTRT, and institutional seed funds from the UPR‐CCC.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.