Mining Next-Generation Sequencing Data to Identify Anti-nociceptive Signaling Pathways

Abstract

AbstractCisplatin is a platinum-based chemotherapy drug which causes damage to the peripheral nerves as a toxic side effect, resulting in cisplatin-induced peripheral neuropathy (CIPN). This diminishes patients’ quality of life and possibly, their ability to work and live independently. A novel drug, CYM-5478, has been identified as a potential candidate which could ameliorate the pathology of peripheral neuropathy, although the mechanism in which it does this is not known in detail. Using RNA-Seq analysis, we identified genes in four pathways which have been shown to be significantly altered with cisplatin treatment—chemokine signaling pathway, cytokine-cytokine receptor interaction, NF-κB signaling pathway, and inflammatory medicated TRP channels. We then analyzed the genes identified in Rattus norvegicus treated with CYM-5478 to identify the pathways through which the drug exerts its protective effect. Through the characterization of genes using the data analysis method, t-test, we discovered multiple genes of interest, in particular, Gnb3 and Rac2. Finally, we validated observed pathway changes by evaluating homologous gene expression changes using an in vitro assay and performing RT-qPCR. Identified genes which were significantly altered in rats treated with cisplatin and with or without CYM-5478 did not show significant change in human astrocytes. However, we can better understand the mechanism through which CYM-5478 attenuates CIPN through the identification of these genes. This allows us to better understand the agonistic action of CYM-5478 on cisplatin toxicity, and the changes in their gene expression could be analyzed further in more vigorous future in vitro experiments involving human cells.KeywordsCisplatinCYM-5478Cisplatin-induced peripheral neuropathy (CIPN)RNA-SeqAnti-nociceptiveVolcano plotsHomologous gene expressionImmortalized normal human astrocyte (iNHA) cells