A Tissue-Specific Transcriptional Element for C/ebpa Is Required for HSC Maintenance and Neutrophil Development

Background: C/EBPa is a lineage determining transcription factor, critical for terminal cell differentiation in different tissues including the bone marrow (BM), lung, liver, and adipocytes. Adequate CEBPA levels are needed to maintain the haematopoietic stem cell (HSC) pool and to promote neutrophilic differentiation. This knowledge points towards the importance of CEBPAdosage at different stages of differentiation.

Aim: To investigate how CEBPA dosage is regulated at the transcriptional level by specific enhancer(s) and to study their role in haematopoiesis.

Results: Chromatin immunoprecipitation for the active mark H3K27ac followed by deep sequencing (ChIP-seq), revealed eight putative regulatory elements within the CEBPA locus. One enhancer showed marked H3K27ac enrichment at +42Kb downstream of CEBPA particularly in CD34+ haematopoietic stem cells (HSCs), implying a role for CEBPA regulation at earlier stages of haematopoiesis. ChIP-Seq experiments revealed binding of RUNX1, ERG, PU.1, FLI1 and GATA2 to this +42Kb enhancer in CD34+ BM cells. Moreover, myeloid cell lines MOLM1 and U937 also showed H3K27ac enrichment at this enhancer, indicating that its activity is maintained upon myeloid differentiation. In contrast, active histone marks were completely devoid at this element in CEBPA expressing lung (A549) and liver (HepG2) cell lines, indicating hematopoietic specificity of this enhancer. Chromatin looping between the +42Kb enhancer and the CEBPA promoter was demonstrated by 4C-Seq, highlighting the specificity of this enhancer in CEBPA regulation. Furthermore, using CRISPR/Cas9 technology we deleted the +42Kb enhancer in the myeloid cell line THP-1 and showed 70% reduction of CEBPAmRNA levels.

The +42Kb enhancer is conserved and located at +37Kb near Cebpa in mice. Using CRISPR/Cas9 system, we deleted the +37Kb enhancer in one-cell stage zygotes. Heterozygous mice were inter-crossed and F1 generation mice were born at normal mendelian ratios. Morphological and flow-cytometric analysis of peripheral blood and BM at 8-10 weeks of age, showed 10-20 fold decrease in (MAC1⁺/GR1⁺) neutrophil counts in homozygous +37Kb^-/- mice, compared to +37Kb^wt/wt and +37Kb^-/wt controls. In line with the block of neutrophil development, flow-cytometric analysis revealed an increase (2 fold) in CD34+CD16/32^low common myeloid progenitors and a decrease (2 fold) in the CD34+CD16/32^high granulocyte/ monocyte progenitors of +37Kb^-/- mice. From these findings we hypothesized that the absence of the +37Kb enhancer disturbs the myeloid differentiation program via reduced Cebpa levels. In fact, Cebpa expression levels were reduced by 60-80% in bone marrow of +37Kb^-/- mice, but unchanged in other Cebpa-expressing tissues such as lung and liver, indicating tissue specificity of this enhancer. Diminished Cebpa expression levels were accompanied by decreasedexpression of Cebpa target genes, including Csf3r. In line with this, bone marrow progenitor cells from +37Kb^-/- mice were completely unresponsive to Csf3 in a colony forming assay.

Given the importance of Cebpa in HSCs maintenance, we investigated the HSC population and found that long-term HSCs (CD48- CD150+) and short-term HSCs (CD48- CD150-) were depleted in the bone marrow of the +37Kb^-/- mice. HSC depletion was accompanied by an increase in the CD48+/CD150- multipotent progenitors (MPPs). The +37Kb^-/- MPPs, unlike controls, were able to serially replate in vitro under IL-3, GM-CSF, IL-6, SCF growth factor conditions with minimal evidence of differentiation, suggesting a leukemogenic potential. Reintroduction of Cebpa cDNA into +37Kb^-/-MPPs fully recovered neutrophil development.

Conclusion: We conclude that the +37Kb enhancer is tissue-specific and plays a central role in haematopoiesis regulating Cebpa dosage. Our study reveals that the bone marrow maintains its integrity through the activity of the +37Kb enhancer, which (1) prevents HSC exhaustion and (2) preserves neutrophilic development. The in vitro replating capacity of MPPs isolated from +37Kb^-/- animals suggests that aberrant control of this enhancer may be a primary leukaemogenic event. In line with this, it is important to note that the conserved enhancer in humans (+42 KB) is a frequent target for oncogenic transcription factors such as AML1-ETO or EVI1, two oncogenes which are found in two distinct subtypes of AMLs with very low C/EBPa expression.