Enhancer and Transcription Factor Dynamics during Myeloid Differentiation Reveal an Early Differentiation Block in Cebpa null Progenitors

Abstract

Transcription factors PU.1 and CEBPA are required for the proper coordination of enhancer activity during granulocytic-monocytic (GM) lineage differentiation to form myeloid cells. However, precisely how these factors control the chronology of enhancer establishment during differentiation is not known. Through integrated analyses of enhancer dynamics, transcription factor binding, and proximal gene expression during successive stages of murine GM-lineage differentiation, we unravel the distinct kinetics by which PU.1 and CEBPA coordinate GM enhancer activity. We find no evidence of a pioneering function of PU.1 during late GM-lineage differentiation. Instead, we delineate a set of enhancers that gain accessibility in a CEBPA-dependent manner, suggesting a pioneering function of CEBPA. Analyses of Cebpa null bone marrow demonstrate that CEBPA controls PU.1 levels and, unexpectedly, that the loss of CEBPA results in an early differentiation block. Taken together, our data provide insights into how PU.1 and CEBPA functionally interact to drive GM-lineage differentiation.

Chronic Interleukin-1 exposure triggers selective expansion ofCebpa-deficient multipotent hematopoietic progenitors

“…This is likely due to using an HSPC-specific Cre rather than Mx1-Cre, where the effect of a differentiation block is delayed due to the slower turnover of HSCs and MPPs. This mouse model thus corroborates previous findings that C/EBPα acts during myeloid lineage specification upstream of GMP (Zhang et al, 2004) and pre-GMs (Pundhir et al, 2018).…”

“…The dependency of these gene programs on C/EBPα is consistent with its role as a key master regulator that initiates myeloid lineage priming in the LSK population (Pundhir et al, 2018). It is interesting that chronic IL-1β has been shown to induce precocious myeloid differentiation via PU.1 (Pietras et al, 2016).…”

Myeloid Lineage Enhancers Drive Oncogene Synergy in CEBPA/CSF3R Mutant Acute Myeloid Leukemia

“…Both subsets of enhancers demonstrated strong enrichment of PU.1 motifs, consistent with the known role of this transcription factor in driving myeloid development. In normal hematopoiesis, PU.1 and CEBPA cooperate to open myeloid lineage enhancers with PU.1 performing pioneering function in early progenitors and CEBPA assuming this role late 18 . Thus, it is likely that certain early myeloid lineage enhancers can be activated by CSF3R T618I in a CEBPAindependent manner via PU.1.…”

“…During normal hematopoietic development, CEBPA is responsible for establishing the enhancer landscape that permits myeloid differentiation 18 . We therefore hypothesized that CEBPA V314VW blocks differentiation by inhibiting priming or activation of myeloid lineage enhancers.…”

“…Published human CEBPA AML DNase sensitivity peaks 26 and enhancers 18 were compared with mouse CSF3R/CEBPA-specific enhancers. The coordinates for mouse enhancers converted to human coordinates using the UCSC liftover tool.…”