Epigenetic programming defines haematopoietic stem cell fate restriction

Abstract

Haematopoietic stem cells (HSCs) are multipotent, but individual HSCs can show restricted lineage output in vivo. Currently, the molecular mechanisms and physiological role of HSC fate-restriction remain unknown. We here show that lymphoid fate is epigenetically, but not transcriptionally, primed in HSCs. In multi-lineage HSCs that produce lymphocytes, lymphoid-specific upstream regulatory elements (LymUREs), but not promoters, are preferentially accessible compared to platelet-biased HSCs that do not produce lymphoid cell types, providing transcriptionally silent lymphoid lineage priming. Runx3 is preferentially expressed in multi-lineage HSCs, and re-instating Runx3 expression increases LymURE accessibility and lymphoid-primed MPP4 progenitor output in old, platelet-biased HSCs. In contrast, platelet-biased HSCs show elevated levels of epigenetic platelet-lineage priming, and give rise to MPP2 progenitors with molecular platelet-bias, which generate platelets with faster kinetics, and through a more direct cellular pathway, compared to MPP2s derived from multi-lineage HSCs. Epigenetic programming therefore predicts both fate-restriction and differentiation kinetics in HSCs. Main.Haematopoietic stem cells (HSCs) are rare bone marrow-resident cells with extensive self-renewal capacity that sustain definitive haematopoiesis lineage throughout the mammalian lifespan. While HSCs as a population continuously generate all definitive haematopoietic cell types, single cell analysis has identified HSCs that preferentially or selectively produce a subset of blood cell types 1-3 , and shown that such fate-restrictions are hierarchically organised 4 . Identification of molecular traits associated with HSC fate-restriction remains challenging, as we currently lack molecular markers that allow HSC subtypes to be prospectively isolated at a level of purity sufficient for accurate molecular Meng et al.: Epigenetic HSC priming 2 characterization. Combined barcoding and single cell RNA sequencing (scRNAseq) has been successfully used to identify transcriptional signatures associated with HSC lineage bias 5,6 . However, single cell approaches are limited by the uncertainty associated with measuring lineage output from single HSCs and the difficulty in obtaining multiple, deep genomic data sets from single cells 7 .Fluorescent barcoding of HSC clones has shown correlation between epigenetic lineage priming and lineage output, but did not allow measurement of platelet or erythroid output from HSCs, precluding identification of platelet-biased HSCs 8 . We have therefore used chromatin and transcriptome profiling of clonal HSC populations derived from single cell transplantation to define the chromatin accessibility and transcriptional programs associated with HSC fate-restriction, and their role in establishing the downstream differentiation pathways specific to HSC subtypes. Results.Fate-restricted HSC clones are transcriptionally distinct and coherent.Clonal HSC populations that arise from transplantation of single HSCs in principl...

Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells

“…Our present and previous findings 9 are compatible with Vwf -tdTomato + P-HSCs replenishing MkPs through fewer progenitor intermediates than Vwf -tdTomato − multi-HSCs. In agreement with this, Gata1 + progenitors produced from transplanted Vwf + P-HSCs replenish platelets with faster kinetics than Gata1 + progenitors from Vwf + multi-HSCs 48 . To investigate whether this might also translate into faster steady-state kinetics of MkP replenishment through the P-HSC than the multi-HSC progenitor pathway, we explored published single-cell RNA-sequencing data, in which the kinetics of progenitor replenishment were assessed after recombination induction in Hoxb5 Cre ERT2/+ R26 Tom/+ reporter mice, specifically labeling the HSC compartment 49 .…”

Platelet and myeloid lineage biases of transplanted single perinatal mouse hematopoietic stem cells

“…However, the fact that both adult 2 – 4 and perinatal LT-HSCs show similar lineage-biases upon transplantation into primary and secondary recipients, as well as transcriptional lineage priming corresponding to their lineage-bias upon transplantation, suggests that this is at least in part an intrinsically programmed and stable HSC property. The involvement of epigenetic programming in the P-bias of HSCs 16 is also compatible with an interplay between intrinsic and extrinsic cues.…”

Epigenetics of hematopoietic stem cell aging

“…HSCs with defined restricted lineage output exhibit distinct transcriptional and chromatin accessibility profiles. Their lineage output is epigenetically but not transcriptionally primed in HSCs by lineage-specific upstream regulatory elements (UREs) [53 ▪ ]. In multipotent HSCs, lymphoid-specific UREs (LymUREs), but not promoters, are preferentially accessible compared with platelet-biased HSCs which do not produce lymphocytes.…”