m6A demethylase–driven reprogramming of leukemia-associated macrophages predicts improved outcomes in acute myeloid leukemia

TL;DR

This study shows that m6A demethylase activity in macrophages affects their function and can predict better outcomes in acute myeloid leukemia patients.

Contribution

The paper reveals a novel link between m6A demethylase activity in macrophages and improved prognosis in AML, suggesting new therapeutic strategies.

Findings

Macrophages with high eraser activity show M1-like pro-inflammatory traits and are linked to better AML patient outcomes.

Reader-high macrophages adopt an immunosuppressive M2-like phenotype, while m6A-deficient cells show functional exhaustion.

RT-qPCR validation confirms higher eraser expression in AML patients with favorable prognosis.

Abstract

N6-methyladenosine (m6A) is a dynamic mRNA modification influencing transcript fate and cellular identity, especially in cancer. While oncogenic roles of m6A regulators in AML cells are known, their impact on the leukemic immune microenvironment is unclear.

In this study, we constructed a single-cell atlas of macrophages in AML by integrating publicly available scRNA-seq datasets from 129 patient cohorts. Data were batch-corrected using Seurat and Harmony. Macrophage subpopulations were identified, and the expression and activity of 29 m6A regulators were analyzed. Pseudotime analysis (Monocle3), cell–cell communication (CellChat), and pathway enrichment (Metascape) analyses were performed to explore m6A-related functional programs. Survival analysis was conducted using Kaplan–Meier curves. RT-qPCR was used to verify the correlation between m6A regulatory molecules and prognosis.

Our findings indicated that m6A regulators are associated with macrophage fate. Writer-high macrophages showed enhanced proliferation and differentiation, maintaining monocyte-like features. Eraser-high macrophages remodeled macrophage function toward an M1-like, pro-inflammatory and antigen-presenting state. Reader-high macrophages drove macrophages toward an immunosuppressive, M2-like phenotype, while m6A-deficient cells exhibit features of functional exhaustion. Survival analysis based on bulk RNA-seq data further revealed that m6A-regulated macrophage profiles were associated with distinct prognostic stratification in AML patients. RT-qPCR analysis of macrophages isolated from clinical AML samples further validated these findings, showing that patients with favorable prognosis exhibited significantly higher expression levels of erasers compared to those with poor prognosis.

These results highlight m6A system’s role in macrophage reprogramming and suggest that targeting m6A regulators in macrophages may serve as a potential basis for prognostic stratification and a promising therapeutic strategy in AML.

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