Niche-level immune evasion in TP53 mutant AML residual disease revealed by spatial proteomics

Measurable (or minimal) residual disease (MRD) predicts relapse in patients with acute myeloid leukemia (AML). However, the biological and spatial characteristics of the AML bone marrow (BM) microenvironment (BMME) in which MRD cells survive remain largely unexplored; in particular, little is known of the BMME in TP53 mutant ( TP53 ^mut ) AML. Here, we applied sequential immunofluorescence to whole BM biopsy specimens obtained from patients with TP53 wild-type ( TP53 ^WT ) AML and TP53 ^mut AML at diagnosis and in morphological complete remission (CR) to generate a comprehensive spatial map of the hematopoietic and BMME components. We identified TP53 ^mut leukemia cells based on high p53 expression and delineated their spatial organization relative to stromal and immune niches. Biopsy-based cell composition analysis revealed marked B-cell depletion and an increased abundance of regulatory T-cells (Tregs) in TP53 ^mut BM at CR. Unlike TP53 ^WT BM, TP53 ^mut BM at CR exhibited persistent TP53 ^mut erythroid and immature leukemia cell clusters, spatially segregated from T-cell clusters, in perisinusoidal niches, suggesting niche-level immune evasion. Spatial profiling further revealed that Tregs characterized by FOXP3 upregulation were enriched near TP53 ^mut MRD cells, indicating a locally enhanced immunosuppressive activity. Single-cell RNA sequencing-based cell-cell communication analysis identified erythroid-T-cell interactions mediated by the GDF15-CD48 axis as a potential mechanism of T-cell suppression, suggesting that the erythroid differentiation of TP53 ^mut AML cells enhances local immunosuppression. Collectively, our results show a spatially organized immunosuppressive BMME in TP53 ^mut AML and highlight the potential of spatial proteomics to identify actionable MRD niches in leukemias.

TP53 mutant erythroid and immature leukemia cells form spatial clusters segregated from T-cells in complete remission. An erythroblast-centered immunosuppressive niche characterizes TP53 mutant leukemia cells.