Deep imaging of bone marrow shows hematopoietic stem cells are mainly perisinusoidal
Hematopoietic stem cells (HSCs) reside in a perivascular niche but the niche location relative to other bone marrow components remains controversial. HSCs are rare, so few can be found in tissue sections or upon live imaging, making it difficult to comprehensively localize dividing and non-dividing HSCs. Here we describe the ability to image all HSCs in large segments of optically cleared bone marrow using deep confocal imaging and digital tissue reconstruction. We discovered that in the hematopoietic system a-catulin is nearly uniquely expressed by HSCs. a-catulinGFP/+ was expressed by only 0.02% of bone marrow cells, including virtually all HSCs. One in 3.5 a-catulin-GFP+c-kit+ cells gave long-term multilineage reconstitution of irradiated mice. We systematically localized all a-catulin-GFP+c-kit+ cells in optically cleared bone marrow. HSCs were more common in the central marrow than near bone surfaces. Nearly all HSCs contacted Leptin Receptor+ and Cxcl12high niche cells. Approximately 90% of HSCs were within 10µm of a sinusoidal blood vessel. The vast majority of HSCs were distant from arterioles, transition zone vessels, and bone surfaces. This was true of Ki-67+ dividing HSCs and Ki-67- non-dividing HSCs. Dividing and non-dividing HSCs thus reside in perisinusoidal niches throughout bone marrow marked by contact with Leptin Receptor+Cxcl12high niche cells.