Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells/multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Using single cell transcriptome profiling of ~140,000 liver and ~74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the impact of tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, NK and ILC precursors in the yolk sac. We demonstrate a shift in fetal liver haematopoietic composition during gestation away from being erythroid-predominant, accompanied by a parallel change in HSC/MPP differentiation potential, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a valuable reference for harnessing the therapeutic potential of HSC/MPPs.

Key Points• GATA1 mutations are common in neonates with Down syndrome but are often unsuspected and detectable only with sensitive methods.• Multilineage blood abnormalities in all Down syndrome neonates in the absence of GATA1 mutations suggests that trisomy 21 itself perturbs hemopoiesis.Transient abnormal myelopoiesis (TAM), a preleukemic disorder unique to neonates with Down syndrome (DS), may transform to childhood acute myeloid leukemia (ML-DS). Acquired GATA1 mutations are present in both TAM and ML-DS. Current definitions of TAM specify neither the percentage of blasts nor the role of GATA1 mutation analysis.To define TAM, we prospectively analyzed clinical findings, blood counts and smears, and GATA1 mutation status in 200 DS neonates. All DS neonates had multiple blood count and smear abnormalities. Surprisingly, 195 of 200 (97.5%) had circulating blasts. GATA1 mutations were detected by Sanger sequencing/denaturing high performance liquid chromatography (Ss/DHPLC) in 17 of 200 (8.5%), all with blasts >10%. Furthermore lowabundance GATA1 mutant clones were detected by targeted next-generation resequencing (NGS) in 18 of 88 (20.4%; sensitivity ∼0.3%) DS neonates without Ss/DHPLC-detectable GATA1 mutations. No clinical or hematologic features distinguished these 18 neonates. We suggest the term "silent TAM" for neonates with DS with GATA1 mutations detectable only by NGS. To identify all babies at risk of ML-DS, we suggest GATA1 mutation and blood count and smear analyses should be performed in DS neonates. Ss/DPHLC can be used for initial screening, but where GATA1 mutations are undetectable by Ss/DHPLC, NGS-based methods can identify neonates with small GATA1 mutant clones. (Blood. 2013;122(24):3908-3917)

The 40-fold increase in childhood megakaryocyte-erythroid and B-cell leukemia in Down syndrome implicates trisomy 21 (T21) in perturbing fetal hematopoiesis. Here, we show that compared with primary disomic controls, primary T21 fetal liver (FL) hematopoietic stem cells (HSC) and megakaryocyte-erythroid progenitors are markedly increased, whereas granulocyte-macrophage progenitors are reduced. Commensurately, HSC and megakaryocyte-erythroid progenitors show higher clonogenicity, with increased megakaryocyte, megakaryocyte-erythroid, and replatable blast colonies. Biased megakaryocyte-erythroid-primed gene expression was detected as early as the HSC compartment. In lymphopoiesis, T21 FL lymphoid-primed multipotential progenitors and early lymphoid progenitor numbers are maintained, but there was a 10-fold reduction in committed PreproB-lymphoid progenitors and the functional B-cell potential of HSC and early lymphoid progenitor is severely impaired, in tandem with reduced early lymphoid gene expression. The same pattern was seen in all T21 FL samples and no samples had GATA1 mutations. Therefore, T21 itself causes multiple distinct defects in FL myelo-and lymphopoiesis.transient myeloproliferative disorder | aneuploidy | human fetus C onstitutional trisomy 21 (T21) causes Down syndrome (DS), the most common syndrome-associated chromosomal anomaly in humans (1). As well as with neurodevelopmental, cardiac, and gut anomalies (2), there is a striking increase in childhood acute leukemia in DS, even though the risk of solid tumors is much lower than with the general population (3). Intriguingly, this susceptibility to hematopoietic tumors manifests as an increased risk both of acute megakaryocyte (MK)-erythroid leukemia (known as ML-DS) by 150-fold and of acute B-lymphoblastic leukemia (B-ALL) by 33-fold (3, 4).DS leukemias display distinct characteristics that support a crucial role for T21 in their pathogenesis. Hallmarks of ML-DS are the megakaryoblastic phenotype, clinical presentation confined to the first 5 y of childhood (5, 6), an antecedent clonally linked preleukemic condition (termed transient myeloproliferative disorder, TMD) in most cases, and acquired N-terminal truncating mutations in the erythroid-MK transcription factor GATA1 (7-9). Such mutations in GATA1 are present in both ML-DS and TMD (9) but are not found in patients without DS who develop megakaryoblastic leukemia (7) and are not leukemogenic in the absence of T21 (10).Molecular, biologic, and clinical data indicate that TMD is initiated before birth (9,(11)(12)(13)(14). We previously reported that by the second trimester, the T21 fetal liver (FL) myeloid progenitor compartment is abnormal and that this occurs in the absence of GATA1 mutation (11, 12). Specifically, the MK-erythroid progenitor (MEP) population is expanded with increased cell-intrinsic MK and erythroid lineage proliferation from CD34 + cells. These data suggest that T21-mediated developmental alterations to FL myeloid progenitor development provide a cell-specific substrate for...

BackgroundRecent advances in single-cell techniques have provided the opportunity to finely dissect cellular heterogeneity within populations previously defined by “bulk” assays and to uncover rare cell types. In human hematopoiesis, megakaryocytes and erythroid cells differentiate from a shared precursor, the megakaryocyte-erythroid progenitor (MEP), which remains poorly defined.ResultsTo clarify the cellular pathway in erythro-megakaryocyte differentiation, we correlate the surface immunophenotype, transcriptional profile, and differentiation potential of individual MEP cells. Highly purified, single MEP cells were analyzed using index fluorescence-activated cell sorting and parallel targeted transcriptional profiling of the same cells was performed using a specifically designed panel of genes. Differentiation potential was tested in novel, single-cell differentiation assays. Our results demonstrate that immunophenotypic MEP comprise three distinct subpopulations: “Pre-MEP,” enriched for erythroid/megakaryocyte progenitors but with residual myeloid differentiation capacity; “E-MEP,” strongly biased towards erythroid differentiation; and “MK-MEP,” a previously undescribed, rare population of cells that are bipotent but primarily generate megakaryocytic progeny. Therefore, conventionally defined MEP are a mixed population, as a minority give rise to mixed-lineage colonies while the majority of cells are transcriptionally primed to generate exclusively single-lineage output.ConclusionsOur study clarifies the cellular hierarchy in human megakaryocyte/erythroid lineage commitment and highlights the importance of using a combination of single-cell approaches to dissect cellular heterogeneity and identify rare cell types within a population. We present a novel immunophenotyping strategy that enables the prospective identification of specific intermediate progenitor populations in erythro-megakaryopoiesis, allowing for in-depth study of disorders including inherited cytopenias, myeloproliferative disorders, and erythromegakaryocytic leukemias.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0939-7) contains supplementary material, which is available to authorized users.

SummaryUnderstanding the underlying molecular mechanisms of defined cancers is crucial for effective personalized therapies. Translocations of the mixed-lineage leukemia (MLL) gene produce fusion proteins such as MLL-AF4 that disrupt epigenetic pathways and cause poor-prognosis leukemias. Here, we find that at a subset of gene targets, MLL-AF4 binding spreads into the gene body and is associated with the spreading of Menin binding, increased transcription, increased H3K79 methylation (H3K79me2/3), a disruption of normal H3K36me3 patterns, and unmethylated CpG regions in the gene body. Compared to other H3K79me2/3 marked genes, MLL-AF4 spreading gene expression is downregulated by inhibitors of the H3K79 methyltransferase DOT1L. This sensitivity mediates synergistic interactions with additional targeted drug treatments. Therefore, epigenetic spreading and enhanced susceptibility to epidrugs provides a potential marker for better understanding combination therapies in humans.

Down syndrome (DS) children have a high frequency of acute megakaryoblastic leukemia (AMKL) in early childhood. At least 2 in utero genetic events are required, although not sufficient, for DS-AMKL: trisomy 21 (T21) and N-terminal-truncating GATA1 mutations. To investigate the role of T21 in DS-AMKL, we compared second trimester hemopoiesis in DS without GATA1 mutations to gestation-matched normal controls. In all DS fetal livers (FLs), but not marrows, megakaryocyteerythroid progenitor frequency was increased (55.9% ؎ 4% vs 17.1% ؎ 3%, CD34 ؉ CD38 ؉ cells; P < .001) with common myeloid progenitors (19.6% ؎ 2% vs 44.0% ؎ 7%) and granulocyte-monocyte (GM) progenitors (15.8% ؎ 4% vs 34.5% ؎ 9%) commensurately reduced. Clonogenicity of DS-FL versus normal FL CD34 ؉ cells was markedly increased (78% ؎ 7% vs 15% ؎ 3%) affecting megakaryocyte-erythroid (ϳ 7-fold higher) and GM and colony-forming unit-granulocyte, erythrocyte macrophage, megakaryocyte (CFU-GEMM) progenitors. Replating efficiency of CFU-GEMM was also markedly increased. These data indicate that T21 itself profoundly disturbs FL hemopoiesis and they provide a testable hypothesis to explain the increased susceptibility to IntroductionChildren with Down syndrome (DS) have a uniquely high frequency of acute megakaryoblastic leukemia (AMKL) in early childhood. [1][2][3] The leukemic cells acquire mutations in utero in the critical megakaryocyte transcription factor GATA1. [3][4][5][6][7][8][9][10] In many DS children, the first manifestation is neonatal transient myeloproliferative disorder (TMD), 1,2 which evolves to AMKL in 20% to 30% of infants. 3 TMD and AMKL represent 2 distinct steps in the pathogenesis of DS-AMKL. However, an additional necessary leukemogenic event (most probably the initiating event) is trisomy 21 (T21). T21 is essential for GATA1-associated TMD and AMKL 5,11,12 ; truncating GATA1 mutations in the absence of T21 are not leukemogenic. 13 GATA1 mutations also occur at high frequency in T21 (ϳ 5% of all DS neonates 14 ) and 25% of DS-associated AMKL patients have multiple, independent clones with GATA1 mutations. 6 These data suggest that GATA1 mutations and T21 specifically synergize to generate preleukemic TMD. The cellular and molecular mechanisms by which this occur are unclear.That a putative leukemia-initiating cell is present in T21 fetal liver (FL) is suggested both by the natural history of TMD (origin in utero, frequent liver involvement, and spontaneous resolution as FL hemopoiesis ceases 11,15 ) and by analysis of germline N-terminal mutant Gata1 phenotypes in mouse and humans. 16 To investigate the impact of T21, independent of GATA1 mutations, on human hemopoiesis, we studied myeloid progenitors from second trimester T21 FL and bone marrow. MethodsSecond-trimester FLs and marrow collected during elective surgical termination of pregnancy were processed immediately as previously described. 17 The study was approved by Hammersmith and Queen Charlotte's Hospitals Research Ethics Committee; written informed consent was obtain...

B-cell acute lymphoblastic leukemia is the commonest childhood cancer. In infants, B-cell acute lymphoblastic leukemia remains fatal, especially in patients with t(4;11), present in ~80% of cases. The pathogenesis of t(4;11)/KMT2A-AFF1 + (MLL-AF4 + ) infant B-cell acute lymphoblastic leukemia remains difficult to model, and the pathogenic contribution in cancer of the reciprocal fusions resulting from derivative translocated-chromosomes remains obscure. Here, “multi-layered” genome-wide analyses and validation were performed on a total of 124 de novo cases of infant B-cell acute lymphoblastic leukemia uniformly diagnosed and treated according to the Interfant 99/06 protocol. These patients showed the most silent mutational landscape reported so far for any sequenced pediatric cancer. Recurrent mutations were exclusively found in K-RAS and N-RAS , were subclonal and were frequently lost at relapse, despite a larger number of non-recurrent/non-silent mutations. Unlike non-MLL-rearranged B-cell acute lymphoblastic leukemias, B-cell receptor repertoire analysis revealed minor, non-expanded B-cell clones in t(4;11) + infant B-cell acute lymphoblastic leukemia, and RNA-sequencing showed transcriptomic similarities between t(4;11) + infant B-cell acute lymphoblastic leukemias and the most immature human fetal liver hematopoietic stem and progenitor cells, confirming a “pre-VDJ” fetal cellular origin for both t(4;11) and RAS mut . The reciprocal fusion AF4-MLL was expressed in only 45% (19/43) of the t(4;11) + patients, and HOXA cluster genes are exclusively expressed in AF4-MLL -expressing patients. Importantly, AF4-MLL / HOXA -expressing patients had a significantly better 4-year event-free survival (62.4% vs . 11.7%, P =0.001), and overall survival (73.7 vs . 25.2%, P =0.016). AF4-MLL expression retained its prognostic significance when analyzed in a Cox model adjusting for risk stratification according to the Interfant-06 protocol based on age at diagnosis, white blood cell count and response to prednisone. This study has clinical implications for disease outcome and diagnostic risk-stratification of t(4;11) + infant B-cell acute lymphoblastic leukemia.

Haematopoiesis in the bone marrow (BM) maintains blood and immune cell production throughout postnatal life. Haematopoiesis first emerges in human BM at 11-12 post conception weeks 1,2 , yet almost nothing is known about how fetal BM (FBM) evolves to meet the highly specialised needs of the fetus and newborn. Here, we detail the development of FBM, including stroma, using multi-omic assessment of mRNA and multiplexed protein epitope expression. We find that the full blood and immune cell repertoire is established in FBM in a short time window of 6-7 weeks early in the second trimester. FBM promotes rapid and extensive diversification of myeloid cells, with granulocytes, eosinophils and dendritic cell subsets emerging for the first time. Substantial B-lymphocyte expansion in FBM contrasts with FL at the same gestational age. Haematopoietic progenitors from FL, FBM and cord blood (CB) exhibit transcriptional and functional differences that contribute to tissue-specific identity and cellular diversification. Endothelial cell types form distinct vascular structures that we demonstrate are regionally compartmentalized within FBM. Finally, we reveal selective disruption of B-lymphocyte, erythroid and myeloid development due to cell-intrinsic differentiation bias as well as extrinsic regulation through an altered microenvironment in Down syndrome (trisomy 21).