Profiling the spatial architecture of multiple myeloma in human bone marrow trephine biopsy specimens with spatial transcriptomics Open Access

• The first map of human bone marrow using 5,001 gene single cell spatial transcriptomics.

• Malignant plasma cells form spatially segregated microenvironments with distinct transcriptional profiles and cell composition.

The bone marrow microenvironment is intimately linked to the biology that underpins the development and progression of multiple myeloma. However, the complex cellular and molecular features that form bone marrow niches are poorly defined. Here, we used subcellular spatial transcriptomics to profile the expression of 5,001 genes in human bone marrow in the context of multiple myeloma. Using this approach, we explored the plasma cell and stroma ecosystem in bone marrow trephines from 21 individuals, including 7 with pre-malignant disease and 10 with newly diagnosed multiple myeloma. Using spatial transcriptomics in conjunction with an optimised trephine biobanking methodology, we could resolve major components of the human bone marrow microenvironment and reliably characterise distinct plasma cell populations in samples from healthy, pre-malignant disease and active myeloma. When plasma cells were visualised in the context of location, we detected spatially restricted subpopulations of plasma cells in five of ten newly diagnosed myeloma trephines. Surprisingly, the composition of haematopoietic and stromal microenvironments varied significantly between newly diagnosed myeloma trephines. Furthermore, these differences in microenvironments were also observed within trephines that had spatially restricted plasma cell subpopulations. Thus, these data are not consistent with the hypothesis that a universal bone marrow microenvironment supports the expansion of malignant plasma cells in myeloma. Instead, we propose that myeloma subpopulations form distinct microenvironments and can vary between both patients and spatial location.