Investigating the potential molecular players and therapeutic drug molecules in carfilzomib resistant multiple myeloma by comprehensive bioinformatics analysis

Abstract

Multiple myeloma (MM), second most common hematological malignancy, still remains beyond cure because of acquirement of drug resistance. Proteasome inhibitor such as carfilzomib (Cfz) therapy which has been used as one of the key therapies against MM recently, is obstructed by the incidence of Cfz resistance. The underlying mechanism of this acquired Cfz resistance in MM is very little understood. Therefore, the current study was aimed to investigate the differentially expressed genes (DEGs), associated micro RNAs (miRNAs), and transcription factors (TFs) from the microarray datasets of Cfz resistant and Cfz sensitive MM cell lines, obtained from Gene Expression Omnibus (GEO) database. DEGs were detected using GEO2R tool from two datasets and common DEGs were identified through Venn diagram. Gene ontology (GO) and pathway enrichment analysis were performed on DAVID database. Through STRING database and Cytoscape tool, protein–protein interaction (PPI) network of DEGs was constructed. Genetic alterations in DEGs were investigated using COSMIC database. Interaction network between DEGs and miRNAs as well as TFs were obtained and constructed by using mirDIP, TRRUST, and miRNet tools. Drug gene interaction analysis was performed to identify potential drug molecules on DGIdb tool. Several common DEGs were identified in Cfz resistant MM. PDGF, VEGF, and Wnt signaling pathways were significantly enriched and might be involved in MM progression. miRNA analysis identified hsa-mir-124-3p, hsa-mir-26a-5p that can target DEGs. Various drug molecules such as dabrafenib, vemurafenib, and venetoclax that could potentially attenuate the MM pathophysiology, were detected. The entire study might provide a new understanding about the Cfz resistance in MM.

Keywords:

• Multiple myeloma
• carfilzomib resistance
• bioinformatics analysis
• differentially expressed genes
• miRNAs
• drug molecules

Consent form

All authors give consent to publish.

Author contributions

SG conceptualized the study, performed the analysis, and wrote the manuscript. SB supervised the study. All authors read and approved the final version of the manuscript.

Disclosure statement

The authors declare that they have no conflicts of interest.

Data availability statement

The datasets analyzed in this current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).