Hematopoietic stem cell transplantation involves the homing of stem cells to the marrow, an active process of engraftment, and the self-renewal of the blood stem cells. We have been using the zebrafish as a model to study the molecular biology of this process. Blood stem cells are born in the dorsal aorta of the developing embryo. By imaging RUNX1 GFP+ cells arriving in the next site of hematopoiesis (the caudal hematopoietic territory), engraftment can be visualized. The endothelial cells of the niche cuddle the hematopoietic stem cells, and the stem cells divide in the niche. We have used RNA tomography to find transcripts that are restricted in expression to the niche endothelial cells. After sorting these endothelial cells, we used ATAC seq to reveal regions of chromatin that are open. The regions function in enhancer assays to drive expression of GFP in the niche. By computing the binding sites in these regions, and examining RNA seq, we found transcription factors that may participate in niche endothelial development. Overexpression of three of these transcription factors is sufficient to reprogram embryonic cells to express the markers of the niche. New niches form in ectopic locations and HSPCs arrive in the new niche, akin to extramedullary hematopoiesis, are cuddled by endothelial cells and divide. Using a brainbow color barcoding system, we previously demonstrated that zebrafish produce 20-30 HSCs from the developing aorta. HSCs traffic to the embryonic niche where they exit circulation and divide. To evaluate a possible role of macrophages in attenuating HSC clone number, we depleted macrophages in our brainbow barcoding system. Unique color barcodes were induced in individual HSCs at 24 hpf, just prior to stem cell emergence, and clodronate loaded liposomes injected into circulation. On average, animals injected with clodronate liposomes had only 14 HSC color clones, compared to 24.6 HSC clones in sibling controls (p = 0.0002). Our studies show that there is a transcriptional code for niche endothelial cells and that macrophages are required for establishing clonality.

Citation Format: Leonard I. Zon. Stem cell clonality and the niche [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr SY42-02.