A Functional Profiling of Microenvironmental Factors and Small Molecules Reveals Monocyte Chemoattractant Protein-1 Mediates Drug Resistance in Acute Myeloid Leukemia

Background: The treatment of acute myeloid leukemia (AML) patients is a formidable challenge, due to disease heterogeneity and the ability to acquire secondary mutations in response to treatment. As a result, persistence and expansion of residual AML clones prevents complete remission. Emerging evidence suggests that extrinsic factors from the microenvironment protect AML cells from therapy, promote disease progression and drug resistance. Previous work from our lab highlights that higher levels of proinflammatory cytokines in the microenvironment, promote AML progression. This emphasizes the rationale to implement targeted therapies that block extrinsic signaling along with tumor intrinsic changes to overcome drug resistance in AML.

Methods and Results: To identify factors and pathways that promote drug sensitivity and resistance in AML, we quantified the levels of 41 cytokines and growth factors from the plasma of 350 newly diagnosed AML patient samples using a multiplex luminex assay. The same cohort were analyzed for drug response to 122 small molecule inhibitors using an ex vivo functional drug sensitivity assay. These data were integrated with the gene expression and reactome pathway data to identify differentially regulated pathways and markers for drug response. Data integration revealed that protein synthesis pathways were significantly enriched in venetoclax, (Bcl-2 inhibitor) resistant AML samples, whereas, cytokine and immune pathways such as aberrant activation of monocyte chemoattractant protein-1 (MCP-1; p= 4.9e-07) were correlated with resistance to trametinib, a MEK inhibitor. In contrast, trametinib sensitivity was associated with activation of IL-1 and TLR signaling, suggesting specific extrinsic pathways may drive specific drug response.

As a proof-of-concept, we dissected the role of MCP-1 activation in mediating trametinib resistance in AML. For this, we treated primary AML cells with MCP-1 in the presence of trametinib that led to a 4-fold increase in IC₅₀ (0.4 vs 2.4 µM). To model drug response in vitro, we generated trametinib resistant AML cell lines MOLM13 and MV4;11 (FLT3-ITD mutated) and OCI-AML2 (DNMT3A mutated) by culturing cells in trametinib continuously over 4 months. All the trametinib resistant AML cell lines showed 2-10-fold increase in MCP-1 levels in whole cell lysate and in the conditioned media compared to the parental cells. Further, a long-term exposure of AML cells to MCP-1 in the presence of trametinib conferred a growth advantage with a 4-fold increase in cell numbers in comparison to the cells cultured with trametinib alone (n=4/condition).

To delineate the molecular pathways driven by MCP-1 in trametinib resistance, we performed global phosphoproteomics using AML cell lines. We identified that MCP-1 activated various pro-survival pathways such as ERK, JNK, SRC, P70, and PKC kinases as well as cell cycle regulatory proteins as early as 5 mins in trametinib resistant cells. Targeting MCP-1 receptor-CCR2 by pharmacological inhibition, significantly reduced viability of trametinib resistant AML cells by 3-fold. The treatment with CCR2 inhibitor or trametinib individually reduced p-JNK levels by 3-fold in AML cells. A combined treatment with CCR2 inhibitor and trametinib, showed a 7-fold reduction in p-JNK levels. These data reinforced the role of MCP-1 in conferring trametinib resistance and that blockade of MCP-1 signaling re-sensitizes AML cells to trametinib.

Conclusion: We show that MCP-1 augments trametinib resistance in AML by triggering novel signaling pathways. These effects can be reversed by blockade of MCP-1-CCR2 axis. Such combination treatment strategy incorporating extrinsic pathways together with the intrinsic ones would aid in re-sensitizing AML cells to therapy and represent an attractive new strategy. Our functional screen identifies that these extrinsic signals modulating drug response are unique to specific targeted therapy and should be considered when designing new therapies and clinical trials. We also created a large resource with 350 primary AML samples correlating microenvironment factors and gene expression with response to 122 small molecules, many of those which are FDA approved. This resource will help identify new drug response pathways in the context of microenvironment to design novel treatment regimens for preclinical and clinical testing and to improve AML outcomes.