Integrative bioinformatics and drug response profiling identify MEK/ERK inhibition as a strategy to overcome venetoclax resistance in AML

Background Drug resistance remains a key barrier to durable remission in acute myeloid leukemia (AML). A central but poorly resolved question is whether AML cells resistant to mechanistically distinct drugs converge on shared downstream survival dependencies, and whether those dependencies can be exploited therapeutically. Methods We compared transcriptional reprogramming across 3 independent resistance models derived from the FLT3-ITD-positive MV4-11 cell line: midostaurin-resistant cells, sorafenib-resistant cells, and a novel venetoclax-resistant line generated in our laboratory. Differential expression analysis, protein -protein interaction network analysis, hub-gene prioritization across multiple network centrality algorithms, and pathway enrichment analyses were performed on shared upregulated genes. Functional validation was performed using the MEK inhibitor selumetinib, and drug combination effects with the mTOR inhibitor PP242 were quantified using the Chou-Talalay combination index method. Results Despite the distinct mechanisms through which each drug exerts its effect, differential expression analysis identified 328 upregulated genes shared across at least 2 resistance conditions, with a meaningful subset common to all 3. Protein -protein interaction network analysis of these shared genes revealed a statistically non-random and functionally cohesive network, from which 10 hub genes: TLR4, PECAM1, CYBB, CXCL8, CASP8, ICAM1, CD33, CCL5, CD36, and JUN, emerged consistently across multiple independent network centrality algorithms. Pathway enrichment analyses converged prominently on the MAPK/ERK cascade, with multiple independent terms pointing specifically to positive regulation of ERK1/2 signaling. Functional validation using the MEK inhibitor selumetinib revealed that venetoclax-resistant cells were modestly more sensitive to MAPK inhibition than parental cells, with growth suppression driven predominantly by G0/G1 cell-cycle arrest rather than apoptosis, indicating a cytostatic rather than cytotoxic mechanism. Combined MEK and mTOR inhibition produced synergistic antiproliferative effects, with greater synergy observed in resistant cells. Conclusion Collectively, these findings suggest that MV4-11 cells, despite diverging in their proximal resistance mechanisms, converge on a conserved ERK-mediated survival program, positioning the MAPK pathway as a broadly relevant therapeutic vulnerability and supporting MEK-based combination strategies to overcome acquired resistance in AML.