Impaired Efficacy and Durability of Hematopoietic Stem Cell Engraftment Caused By Samd9l-Deficiency within Bone Marrow Niches

Germline mutations in the SAMD9 and SAMD9L (SAMD9/L) genes on chromosome 7q drive both childhood myelodysplastic syndrome (MDS)/secondary acute myeloid leukemia (sAML) associated with monosomy 7, and adult-onset MDS/sAML associated with distinct somatic genetic alterations. The ortholog for SAMD9/L in mice is Samd9l. Gain of Function (GoF) and Loss of Function (LoF) Samd9l alleles predispose to MDS at distinct ages. LoF models show that Samd9l-deficient mice, like humans, are more likely to develop MDS during adulthood, while GoF models result in early onset bone marrow (BM) dysfunction and MDS/sAML.

Hematopoietic stem cell transplantation (HSCT) is the only curative treatment for bone marrow failure (BMF), MDS, and AML arising from germline genetic syndromes. Our previous research demonstrated that deficits in host BM microenvironment (ME) niches contribute to hematopoietic failure and poor HSC engraftment in murine models of many MDS predisposition syndromes associated with BMF. As we have observed clinical cases where poor engraftment impaired outcomes in patients with SAMD9/L mutations, we recently hypothesized, BM niche functions critical to facilitating HSC engraftment may be impaired due to niche-intrinsic deficits caused by SAMD9/L mutations. Herein, we present data testing this hypothesis, demonstrating Samd9l deficiency alters BM ME composition, extracellular matrix (ECM) regulation, and proinflammatory cytokine signaling resulting in impaired donor HSC engraftment after HSCT.

We performed primary (1^ry) and secondary (2^ry) HSCT to model impacts of SAMD9/L deficiency on BM niche function during HSCT using WT (Samd9l^+/+), Samd9l^+/-, and Samd9l^-/- mice as HSCT recipients of healthy WT GFP⁺ donor BM to measure the capacity of Samd9l LoF niches to engraft donor HSCs. To assess changes in niche composition and gene expression during HSCT, flow cytometry, multiplex ELISA, and RNASeq analysis were performed on WT, Samd9^+/- and Samd9^-/- mice.

Compared to WT control niches, Samd9^+/- and Samd9^-/- niches exhibited impaired efficiency of donor HSC engraftment at 3 weeks post-1^ry HSCT, as measured by competitive 2^ry-HSCT performed with 1^ry recipient BM harvested at this timepoint. Beyond 30 weeks post-2^ry-HSCT in this model, GFP⁺ reconstitution of GR1⁺ myeloid, RBC’s, and platelets was reduced by 25%, 18%, and 35% in 2^ry recipients of Samd9^+/- 1^ry recipient BM and by 26%, 28%, and 32% in 2^ry recipients of Samd9^-/- 1^ry recipient BM. Durability of HSC engraftment by 8 months was even more significantly impaired in Samd9^+/- and Samd9^-/- niches, with Samd9^-/- mice exhibiting low survival by this timepoint. Competitive 2^ry HSCT performed 8 months post-1^ry HSCT showed reduction in trilineage GFP⁺ blood cells out to 24 weeks post 2^ry-HSCT, including reductions in GFP⁺ Gr1⁺ myeloid cells by 50% and 83% in 2^ry recipients of Samd9l^+/- and Samd9l^-/- 1^ry recipient BM, respectively, compared to control 1^ry recipient BM. Similar reductions in BM long-term HSC and Lin^-Sca-1⁺cKit⁺ HSC/progenitor cells in 2^ry recipients of Samd9l^-/- compared to Samd9l^+/+ 1^ry recipient BM 8 months post 1^ry-HSCT.

Following TBI, Samd9l^+/- and Samd9l^-/- BM niches contained similar percentages of osteoprogenitors, mesenchymal stem cells, and endothelial cells compared to WT controls. Multiplex ELISA on BM plasma collected 48hrs post-TBI revealed that Samd9l^+/- and Samd9l^-/- deletion in the BM ME led to markedly reduced expression of IFN-γ (43% and 55% reduction in Samd9l^+/- and Samd9l^-/-), Eotaxin (33%/36%), GM-CSF (47%/47%), and IL-1a (48%/65%). In contrast, expression of niche cell extracts showed markedly increased levels of IL-17 (4 fold) and CXCL11 (1.4 fold) in Samd9l^+/- and of IL-17 (5.3 fold) IL-12p70 (1.3 fold), and CXCL11 (1.5 fold) in Samd9l^-/-, suggesting that aberrantly active Th17 responses caused by niche Samd9l deficiency may be responsible for impairing HSC function and maintenance post-HSCT. RNASeq analysis showed downregulation of ECM genes in both Samd9l^-/- and Samd9l^+/- models.

Our data demonstrates BM niche function is impaired by Samd9l deficiency in a gene dosage-dependent manner. These deficits are associated with increased expression of a specific inflammatory cytokine pathway, suggesting that aberrant growth factor receptor recycling due to Samd9l deficiency may drive stress hematopoiesis and alter HSC cell fate decisions leading to failure of durable donor HSC maintenance post-HSCT.