Spatial multiomics reveal a critical role for TIM4-expressing macrophages in blast transformation of chronic myelomonocytic leukemia

Abstract The importance of bone marrow (BM) microenvironment and its immune interactions within and their role in chronic myelomonocytic leukemia (CMML) disease progression have not been well studied. Our previous work in CMML identified type 1 helper T cell (Th1) and CD4 terminal effector cell suppression in peripheral blood from untreated patients, in comparison to age-matched normal controls (Mangaonkar A et al. Blood Adv 2020). Furthermore, clonal dendritic cell (DC) aggregates in CMML are present in approximately 20-30% patients at diagnosis, display significant cell heterogeneity (plasmacytoid DCs + myeloid DCs and other myeloid/immune cells), express indoleamine 2,3-dioxygenase-1 (IDO), associate with T regulatory cell (Treg) expansion, and transformation to AML [blast transformation or BT, Lucas N et al. Leukemia 2019, Mangaonkar A et al. Blood Adv 2020, and Mangaonkar A et al. Blood 2023 (abstract)]. The purpose of this study was to define the myeloid-immune cell interactions within the BM microenvironment critical for CMML progression to AML. To phenotypically identify cell types and their interactions within the CMML BM, we used single-cell type spatial omics through two distinct modalities on archival formalin-fixed paraffin-embedded (FFPE) BM biopsy specimens. Ten serial CMML samples at chronic phase [CP, n=5, median BM blast% 5 (2-15)] and at BT [n=5, median BM blast% 60 (25-74)] were used for both techniques. Spatial transcriptomics was conducted through GeoMx Digital Spatial Profiler (DSP) platform that uses UV-photocleavable, spatial-barcoded oligo probes to profile the whole transcriptome in defined regions of interest (ROI). CD123 (marker for DC-myeloid aggregates) immunofluorescence antibody was used to identify and segment ROI. 16-color flow cytometry was done to validate cell-specific expression. Spatial cellular phenotyping of immune cells on the same samples (serial cuts) was done through multiplex imaging by co-detection by indexing (CODEX) using 27 markers: CD31, Ki67, CD11b, CD20, CD44, Ecad, CD123, CD107a, CD8, CD11c, CD45RO, FoxP3, CD14, PDL1, CD56, CD68, CD163, PD-1, CD38, HLA-DR, CD4, IDO, CD45, PanCK, Na/K/ATPase, CD3e, and DAPI. CD8T+ cell anergy was demonstrated through CFSE cell proliferation assay. Benjamini-Hochberg correction was used to adjust for multiple hypotheses. After filtering poor quality ROIs [ROIs with total read count < 1000 were removed, ROIs with trim, stitch, alignment < 80% or saturation < 50% were removed], 3rd-quartile normalization [BiocGenerics (v. 0.48.1)] and batch correction [limma (v. 3.58.1)], we compared transcriptomics signatures between CD123+ and CD123- ROIs in all samples. Results showed that LIPA, SLC4A1, HBA2, TIMD4 and HMOX1 werethe top five genes upregulated in CD123+ areas. Among all gene transcripts, TIMD4 expression increased the most (Log2FC=0.6, P-value=8.79E-10, FC=1.52, FDR=1.68E-07) when CD123+ ROIs were compared between CMML-CP and CMML-BT serial samples, suggesting a biological relevance in disease progression. Previous work in metastatic peritoneal cancer has established that TIM-4 expressing macrophages suppress Th1/Th2 ratios and impair CD8+ T cell function (Chow A et al. Cancer Cell 2021). To confirm expression at the protein level, we used a multicolor flow cytometry panel and confirmed that TIM4 is expressed on macrophages (Lineage-negative, HLA-DR+, CD68+ cells) in independent CMML BM aspirate samples (n=3). Next, we conducted spatial phenotyping using CODEX on serial cuts from the same serial samples used for spatial transcriptomics. Anatomical co-localization of macrophages with leukemic cells, monocytes and T cells was visually inspected and confirmed. Cell-interaction analysis (after Benjamini-Hochberg correction) indicated that macrophages-monocyte, macrophage-leukemic cells, and macrophage-memory CD4+T cells were significantly (P<0.05) increased in CMML-BT versus CMML-CP. CD8T+ cell anergy was confirmed through a CFSE cell proliferation assay in untreated CMML PBMC samples. In conclusion, our data suggests that TIM4-expressing macrophages and their interactions with monocytes/monocyte precursors and immune cells within a DC aggregate create a protective leukemic stem cell niche and T cell tolerance, promoting blast transformation in CMML.