Genomic Analysis Defines Increased Circulating, Monocyte-Derived Macrophages That Promote Immune Suppression in Mouse Models of FGFR1-Driven Leukemogenesis and Defines a Multigene Signature That Predicts AML Outcomes

Background: The development of FGFR1-driven stem cell leukemia and lymphoma syndrome (SCLL) is accompanied by an increase in highly heterogenous myeloid derived suppressor cells (MDSCs), which leads to suppression of all immune effector cells in mouse models of the disease. This murine model provides the opportunity to define the genetic events that underly leukemia induced immune evasion.

Methods: A combination of CyTOF and scRNA-Seq was used to define the phenotypes and genotypes in leukemia induced macrophages. Pharmaceutical inhibition and correlative analysis was performed to examine the function and clinical significance of these macrophages.

Results: CyTOF analysis demonstrated an increase in levels of circulating macrophages in the peripheral blood during leukemia progression, which was further confirmed by flow cytometry. The connection between MDSC and macrophages was defined. These macrophages were derived not only from Ly6C^Hi M-MDSC, but also from the Ly6C^Int and Ly6C^Lo monocytic populations. Consistently, single cell sequencing analysis demonstrated accumulation of non-classical monocytes (ncMono) during leukemia progression, which also show increased expression of macrophage markers. Trajectory analysis revealed a transition from cMono to ncMono, and potential genes orchestrating this transition process have been identified. Furthermore, T cell suppression assays demonstrated the immune suppressive abilities of leukemia-induced circulatory macrophages. Importantly, treatment of leukemic mice with the CSF1R inhibitor GW2580, which suppresses macrophage function and reduces their viability, leads to improved survival accompanied by reduced levels of leukemia cells and increased T-cell levels. This suggests that the leukemia induced macrophages are responsible, at least in part, for the suppression of immune effector cells. In newly diagnosed AML patients, those showing a high ncMono score, which was generated based on a specific ncMono gene signature, correlated with poorer survival, compared with those with a low ncMono score.

Conclusion. Overall, we demonstrate that a major part of the immune suppression in SCLL leukemia models involves suppression of T-cell function by circulating macrophages, and targeting macrophages in this system improves survival of mice engrafted with leukemia cells. In addition, we have also defined specific genetic reprogramming that is associated with the transition of monocytes into macrophages during leukemogenesis, potentially providing opportunities to target and reverse the immune suppressive microenvironment to improve AML outcome.

Eisfeld:OncLive: Honoraria; AstraZeneca US: Membership on an entity's Board of Directors or advisory committees; VJ HemeOnc: Honoraria; Karyopharm Therapeutics: Other: Spouse employment; Dava Oncology: Honoraria; GTC: Honoraria.