Functional Screen Identifies Novel Regulators of Murine Hematopoietic Stem Cell Engraftment

Introduction:

Hematopoiesis involves the hierarchical generation of the major blood lineages from a common ancestor, the Hematopoietic Stem Cell (HSC). HSC also have the intrinsic ability to repopulate an ablated hematopoietic compartment when introduced into the periphery of a recipient. This has allowed Hematopoietic Stem Cell transplantation (HSCT) to be used as a cell therapy over the last 45 years, benefiting thousands of patients. Unfortunately many patients succumb to disease while waiting for an adequate donor. Others have to undergo unrelated donor transplants, putting themselves at a risk of developing graft-versus-host disease. Improving HSC engraftment could ameliorate transplant morbidity. Thus, understanding mechanisms regulating HSC engraftment is key.

Results:

We used our recently published gene expression profiles of developing HSC and other public databases to prioritize 58 genes as putative regulators of adult HSC function. We confirmed by qRT-PCR that 51/58 candidates were enriched for gene expression in Lineage-Sca-1+c-Kit+ (LSK) bone marrow cells relative to downstream progeny, suggesting a role in hematopoietic stem and progenitor cells (HSPC). To functionally assay a role for each gene of interest (GOI) in HSC engraftment, we designed and validated ≥2 independent shRNAs/GOI that effected a >75% knockdown in gene expression in LSK cells. LSK cells were lentivirally transduced with control or individual gene-specific shRNAs and transplanted into lethally irradiated recipients along with mock-transduced LSK competitor cells congenic at the CD45 allele. In contrast to previous functional screens, transplant was performed within 24-hours of LSK cell isolation, avoiding extensive ex vivo culture. This minimal manipulation allowed us to detect genes critical for efficient HSC engraftment. Peripheral blood chimerism was analyzed for at least 16 weeks post-transplant. The major bone marrow hematopoietic compartments were also analyzed. 17 of 48 genes tested were identified as necessary for optimal HSPC engraftment (i.e. knockdown induced a significant loss of repopulation) and the knockdown of three genes enhanced HSPC repopulation. shRNAs targeting each “Hit” were interrogated ex vivo for non-specific effects on LSK cell viability and expansion. A 2° screen was performed to validate the results of this primary screen. Here, CD45.2 LSK cells transduced with control or individual gene-specific shRNAs were sorted 48 hours post-transduction for mCherry+ cells and then transplanted into lethally irradiated mice with mock-transduced and mock-sorted CD45.1 congenic LSK cells. 18 “Hits” were confirmed to perturb HSC repopulating potential in this 2^° screen, including three whose loss enhanced HSPC repopulation. The transcription factor, Foxa3, is one hit identified here as necessary for HSC repopulation. We further found that that Foxa3-/- bone marrow displays a significant loss of repopulating potential >16 weeks post-transplant, confirming the results of our screen. As Foxa3-/- long-term HSC also display reduced colony forming potential in vitro and fail to contribute to downstream progenitor compartments in transplant recipients, we propose that Foxa3 is a novel regulator of HSC differentiation post-transplant. Foxa3 has never before been implicated in hematopoiesis or HSPC biology.

Conclusions:

Our novel functional screen has revealed 15 genes required for optimal HSPC engraftment and three genes whose knockdown improved HSPC engraftment. We further validated Foxa3 as a novel regulator of HSC activity by demonstrating that Foxa3^-/- HSC are also deficient in repopulating activity. We are currently investigating the molecular mechanism of Foxa3’s role in HSC and, given that Foxa genes are known transcriptional pioneering factors, pursuing the hypothesis that Foxa3 functions as a novel epigenetic regulator of HSC activation and differentiation. Each gene identified in our screen represents a window into the discovery of novel mechanisms regulating HSC biology and engraftment.