A Novel Approach to 3D Spatial Mapping of the Human Hematopoietic Microenvironment in Normal and Diseased Bone Marrow

The bone marrow hematopoietic microenvironment (HME) plays a pivotal role in regulating normal and diseased hematopoiesis. Important cellular components of the human (HME) include the bone marrow (BM) stromal cells (Li, BioRxive 2022) and other cell types, such as vascular endothelial cells (ECs), and megakaryocytes (MKs).

Perturbations of the HME can affect normal and diseased hematopoiesis. In Philadelphia-negative myeloproliferative neoplasms (MPNs), which include Essential Thrombocythemia (ET), Polycythemia Vera (PV), Primary Myelofibrosis (PMF), and its precursor, pre-fibrotic MF (pre-PMF), the HME is of critical importance for disease development and progression (Mead, Blood 2017). However, despite this important role, little is known about the spatial organization of the different HME elements in MPNs.

Therefore, we aimed to develop a novel method of immunofluorescence (IF) multiplexing with markers for HME and hematopoietic cells based on sequential staining and bleaching in combination with scanning IF microscopy and standard imaging analysis (Fig.1). Herein we show that this approach allowed us to generate 3D reconstitutions of standard biobank-stored BM samples from MPN patients and age-matched hematopoietically normal controls. Furthermore, we demonstrate how the free and open-source 3D computer graphics software toolset Blender (Stichting Blender Foundation, Amsterdam) can be utilized to analyze cell distributions and spatial relationships in 3D. BM biopsies from patients with MPN and controls were stained sequentially for CD31, CD34, CD45, and CD271 with repetitive bleaching steps to realize five color images with DAPI as a nuclear stain. Twelve subsequent slides per sample were stacked to create three-dimensional BM reconstructions with the imaging program Arivis Vision 4D. Iso-surfaces for niche cells and structures were created and exported as mesh objects for spatial distribution analysis in Blender.

We recapitulated the BM architecture using this approach and produced comprehensive 3D models of endosteal and perivascular BM niches. MPN bone marrows displayed considerable differences between the different MPN types, especially concerning megakaryocyte (MK) morphology and distribution, as well as CD271 staining density and CD271⁺ cell numbers. Whereas ET and pre-PMF were comparable to their paired normal control, we found that PMF and especially PV samples showed considerably increased numbers and densities of CD271⁺ cells. In PMF the generated MSC objects formed a thick fibrillary structure reminiscent of classic fibrosis staining that was particularly dense close to vessels, bone surfaces, and MKs. Measurements of the spatial relationships of MKs and hematopoietic stem and progenitor cells (HSPC) to vessels and bone structures, respectively, revealed the most pronounced differences in PV, with median distances of PV-MKs to vessels being significantly lower than in controls (PV 7.62 µm vs 8.20 µm control, p<0.05). Also, the median distance in PV of HSPCs to vessels (2,88 µm) and bones (52.23 µm) was less than in the controls (46.31 µm and 236.7 µm, respectively; p<0.01).

Taken together, we report a novel sequential staining and bleaching technique for multi-color analysis of normal and diseased BMs. The three-dimensional reconstruction technique developed herein revealed important aspects of the spatial HME composition in MPNs and normal BMs and provides a platform for a deeper investigation of BM pathophysiology, for example by increasing numbers of antibodies and including visualization of the expression of relevant genes and proteins.

No relevant conflicts of interest to declare.