Using Drug-Induced RNA Sequencing and David Analysis to Identify Targeted Therapies for Use in Combination with Duocarmycin SA for the Treatment of Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a hematological malignancy that is associated with uncontrolled clonal expansion and the accumulation of myeloid blasts in the bone marrow. A major challenge of the treatment of AML is the high relapse rates that are often observed in patients despite advances in treatment options. Consequently, there remains a need to identify potential therapeutic candidates that can improve patient survival outcomes and reduce the risk of relapse in AML patients. The objective of this study was to utilize RNA sequencing and bioinformatic analyses to identify candidate targeted therapies for use in combination with Duocarmycin SA (DSA), a natural product antitumor antibiotic, for the treatment of AML. We hypothesized that RNA sequencing of DSA treated cells will identify novel genes that can be potentially targeted for AML drug combination studies. To test our hypothesis, human AML cell lines (Molm-14 and HL-60) were treated with high and low concentrations of DSA for 36 hours. Molm-14 cells were cultured with 100 pM (high) and 11.12 pM (low) of DSA and HL-60 cells were cultured with 500 pM (high) and 112.7 pM (low) of DSA. At 36 hours, the cells were harvested, RNA was isolated from the cells using Qiagen's RNeasy mini kit and RNA sequencing and gene expression profiling analysis were performed by the Hartwell Center for Biotechnology and the Center for Applied Bioinformatics at St. Jude Children's Research Hospital, respectively. Functional enrichment analysis was performed using the NIH's Database for Annotation, Visualization and Integrated Discovery (DAVID) tool to identify top DSA-induced pathways that were activated and target genes within the pathways for which targeted drug candidates can be identified. Overlapping differentially expressed genes (DEGs) for all four DSA treated conditions (p-value <0.05, Log >0.5) were visualized using Venny 2.1.0. Our results showed that the top pathway, oxidative phosphorylation, that is activated in all DSA treatment groups is related to mitochondrial induced cell-death. Genes that are involved include mitochondrially encoded cytochrome c oxidase 1, 2 and 3 (MT-CO1, MT-CO2, and MT-CO3). In conclusion, our findings suggest that DSA induced apoptosis in human AML cells is mediated by a mitochondrial mediated mechanisms. Additionally, the list of genes involved in the DAVID analysis provide novel therapeutic targets for which targeted drug candidates can be identified and evaluated in combination with DSA for the treatment of AML.

No relevant conflicts of interest to declare.