# Molecular Circuits in the Hematopoietic Stem Cell Niche

> **NIH NIH RC2** · BOSTON CHILDREN'S HOSPITAL · 2020 · $1,749,532

## Abstract

In mammals, hematopoietic stem cells (HSCs) first arise from a specialized hemogenic endothelium that lines
the developing embryonic aorta, migrate to and expand in the fetal liver, and ultimately colonize the bone
marrow, which supports hematopoiesis throughout adult life. These distinct anatomic locations harbor
specialized microenvironments that support the developmental maturation, expansion, and ultimately the
balance of self-renewal and differentiation of HSCs. The transcriptional programs that promote formation and
differentiation of hematopoietic stem and progenitor cells (HSPCs) have been widely interrogated, but much
remains to be learned about the supportive niche cells of the hematopoietic microenvironment and the
mechanisms of cell-cell interaction that specify HSC emergence during development, HSC migration, lodging,
and expansion in fetal niches, and the ultimate quiescence, self-renewal, and differentiation in the bone
marrow. In our preliminary data, we have gathered evidence for number of cell types, including endothelial
cells, mesenchymal cells, macrophages, neural crest derivatives, and somites as components of the
hematopoietic niche. We will gather comprehensive “omics” data to catalogue the gene expression programs
within the distinct hematopoietic niche cells that occur during development in the aorta-gonad-mesonephros
(AGM), fetal liver, bone marrow, and placenta (aim 1). Our approach begins with tomo-seq, which enables us
to discover gene expression patterns unique to cell populations like endothelium that have region-specific
specialization. We will validate cell-specific expression in FACS purified cells by single cell RNA-seq and in situ
hybridization, and will document functionality using morpholino and CRISPR knock-down in the experimentally
tractable zebrafish model. We then use ATAC-seq to define functional open chromatin around these genes,
and motif-finding software to identify DNA-binding regulatory factors that are candidate drivers of
hematopoietic cell fate. We will employ a computational pipeline and develop novel algorithms to analyze these
data (aim 2). Hypotheses emerging from aims 1 and 2 will be tested by constructing novel reporter strains of
zebrafish and mice, as well as engineered pluripotent stem cells carrying synthetic reporters and drivers (aim
3). Our goal is to define the molecular circuitry that specifies niche cells during the critical periods of HSC
emergence and expansion, and to probe cross-talk between niche elements and HSPCs. We hope to glean
unique insights into the molecular mechanisms that drive hematopoietic formation and maturation during
embryonic development, and to enhance our understanding of HSC maintenance, quiescence, self-renewal
and differentiation.

## Key facts

- **NIH application ID:** 9938198
- **Project number:** 1RC2DK120535-01A1
- **Recipient organization:** BOSTON CHILDREN'S HOSPITAL
- **Principal Investigator:** JAMES J COLLINS
- **Activity code:** RC2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,749,532
- **Award type:** 1
- **Project period:** 2020-08-15 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9938198

## Citation

> US National Institutes of Health, RePORTER application 9938198, Molecular Circuits in the Hematopoietic Stem Cell Niche (1RC2DK120535-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9938198. Licensed CC0.

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