SWI/SNF Protein SMARCD2 Orchestrates Transcriptional Networks Controlling Hematopoiesis and Neutrophil Granulocytes in Humans, Mice and Zebrafish

Differentiation of hematopoietic stem cells follows a hierarchical program of transcriptional-regulated events. We here identify SMARCD2 (Swi/Snf-related matrix associated actin dependent regulator of chromatin, subfamily D, member 2) as critical regulator of myelopoiesis in humans, mice, and zebrafish. We studied four patients from three unrelated pedigrees presenting with a novel syndromatic phenotype comprising congenital neutropenia, specific granule deficiency, susceptibility to myelodysplasia with excess of blasts, and various skeletal anomalies. All patients had homozygous loss-of-function mutations in SMARCD2. In contrast to wildtype alleles, the variant alleles did not give rise to proteins with capacity to interact with the SWI/SNF subunits BRG1, BAF170, BAF155, and BAF47, as shown by co-immunoprecipitation experiments. In vitro, knockdown of SMARCD2 in promyelocytic NB4 cells, differentiated in the presence of ATRA, led to decreased expression of genes encoding the primary granule proteins cathelicidin (CAMP) and alpha-1-antitrypsin (AAT) as well as specific granule proteins matrix metalloproteinase-8 (MMP8), transcobalamin (TCN1) and lactoferrin (LTF). This phenotype is reminiscent of patients with specific granule deficiency, characterized by mutations in CEBPE, a known transcription factor controlling terminal neutrophil development. We therefore hypothesized that SMARCD2 may act via CEBPe and performed immunoprecipitation studies in transfected cells. Upon pull-down of SMARCD2, CEPBE could be detected, and vice versa, suggesting that both proteins physically interact to control transcriptional networks. To interrogate effects of SMARCD2 deficiency on global chromatin accessibility we made use of ATAC sequencing of undifferentiated and ATRA-differentiated NB4 cells and compared this data with comprehensive RNA-sequencing results. A specific subset of genes was found deregulated in both assays, affecting vesicular trafficking, migration and signalling pathways. To validate a role for SMARCD2 in hematopoiesis in vivo, we generated murine and zebrafish model systems. We generated Smarcd2^-/- mice by injection of Smarcd2^+/- murine ES cells into blastocysts, transfer into pseudo-pregnant mice and interbreeding of heterozygous Smarcd2^+/- offsprings. The mutant allele was inherited in a Mendelian fashion but no viable mice were born. 14.5dpc embryos were characterized by anemia and reduced size compared to their littermates. Analysis of fetal liver hematopoiesis revealed a complete absence of CD11b⁺Gr1⁺ and CD11b⁺Ly6c⁺ cells, whereas the number of LSK stem cells was not affected. Futhermore, Smarcd2^-/- embryos showed aberrations in erythroid cells such as extensive anisocytosis, multinucleated cells, and perturbed mitosis. In cytokine-driven colony forming unit assays, GM-CSF, M-CSF, and G-CSF induced myeloid cell differentiation was decreased. Transcriptional profiling of LSK stem cells revealed a striking dysbalance affecting genes involved in signaling pathways and host defence, including CEBPE-dependent genes. Among a total of 12362 detected genes, we found 4290 to be differentially expressed (DESeq2, FDR<10%). Interestingly, the majority (79%) of the 605 genes with a relatively large difference (fold-change > 1.4, FDR<1%) were up- and not downregulated. Next, we generated three Smarcd2-deficient zebrafish models using a) morpholino-mediated knockdown in Tg(mpx:EGFP)ⁱ¹¹⁴ and Tg(lyz:dsRed)^nz50 strains of the orthologous gene or b) Crisp/Cas9-mediated genomic engineering of this locus in Tg(mpx:EGFP)ⁱ¹¹⁴. In all models, the numbers of neutrophil granulocytes were significantly reduced. We conclude that SMARCD2 is a critical factor orchestrating transcriptional networks controlling hematopoiesis across species, in particular regulation and maintenance of neutrophil differentation and prevention of leukemogenesis.