Hematopoietic stem cells (HSCs) are important in cell-based therapies for blood-related disorders. While progress has been made in generating HSCs by directed differentiation of pluripotent stem cells (PSCs), such cultures promote hematopoietic progenitor cells (HPCs) over HSCs. Thus, elucidating markers and factors associated with HSC versus HPC development is imperative. HSCs and HPCs originate from hemogenic endothelium (HE) in a Runx1-dependent process. Here, we characterize a Runx1 enhancer (+110) that distinguishes emerging dorsal aorta HSCs from HPCs. Comparative transcriptomics reveal a 17-gene signature associated with in vivo long-term HSC potential, while single-cell multiome analysis demonstrates a clear epigenetic identity of dorsal aorta HE, preHSCs, and HPCs, providing a resource of stage-specific enhancer activity. Our study demonstrates the power of cell type-specific enhancer-reporter models to dissect cell fate decisions in development and provides new inroads to label and/or perturb HSC versus HPC potential in vivo and in vitro.

Embryonic hematopoiesis involves successive waves of progenitors from distinct anatomical sites, but the origins and contributions of early hematopoietic stem and progenitor cells (HSPCs) remain incompletely defined. Here we use genetic fate mapping in mice to temporally label hemogenic endothelium (HE) subsets and track their progeny. We show that a wave of fetal-restricted HSPCs arises from HE in the vitelline and umbilical arteries between embryonic days 8.5 and 9.5, preceding the emergence of definitive hematopoietic stem cells. Lineage tracing, single-cell transcriptomic analyses and functional assays revealed that these progenitors are transient and distinct from erythro-myeloid progenitors, contribute extensively to fetal lympho-myelopoiesis but decline postnatally. Our findings reveal a previously unrecognized early HE wave as a key source of fetal-restricted HSPCs, refining the spatial-temporal understanding of layered hematopoiesis and informing developmental origins of blood cell diversity.

Following muscle injury, a series of well-coordinated events ensures proper healing. Among these, inflammatory cells, particularly macrophages (MPs), play a fundamental role by phagocytosing damaged tissue and coordinating the actions of other cells involved in regeneration. Partial depletion of infiltrating MPs has been associated with endothelial cells (ECs) undergoing endothelial-to-mesenchymal transition (EndMT), contributing to extracellular matrix accumulation. However, the specific mechanisms linking MPs to this process, as well as their role in influencing EC fate, remain unclear. Here, we adopt a single-cell transcriptomics approach in mice to define a specific signature of the regenerating muscle niche. We show that perturbing MP recruitment upon injury results in impaired MP polarization, creating an aberrant inflammatory, non-regenerative, and less angiogenic microenvironment, which in turn drives ECs toward EndMT. Furthermore, we highlight complex signalling interactions between MPs and ECs, with SPP1 emerging as one of the critical modulators of these processes.

[This corrects the article DOI: 10.3389/fgene.2022.1056114.].

Fibrodysplasia Ossificans Progressiva (FOP) is a rare genetic disorder caused by gain-of-function mutations in ACVR1/ALK2, leading to progressive heterotopic ossification (HO) through endochondral bone formation. Inflammatory flare-ups often precede new ossification events, but the cellular and molecular mechanisms linking immune responses to progenitor cell fate remain incompletely understood. Here, using a tamoxifen-inducible Acvr1R206H mouse model of FOP and a reproducible muscle injury protocol, we combined single-cell RNA sequencing with in vitro assays to dissect early events during lesion formation. We identified an expansion of macrophages (MPs) and fibro-adipogenic progenitors (FAPs) in FOP mice, with both populations exhibiting inflammatory and osteochondrogenic transcriptional signatures. Cell–cell interaction analysis revealed a self-reinforcing network of cytokine signaling among MPs and a prominent MP–FAP communication axis centred on SPP1. Functional studies confirmed that SPP1 enhanced FAP osteogenic differentiation and that its inhibition partially reversed this phenotype in vitro and attenuated HO in vivo. Our findings highlight the critical role of inflammatory MPs in shaping the fate of resident stromal mesenchymal progenitors (e.g. FAP) and suggest that early immune–stromal interactions set the stage for HO. Targeting this immune–mesenchymal crosstalk may represent a potential complementary strategy for preventing or mitigating disease progression in FOP.

Myelodysplastic syndromes (MDS) are heterogeneous hematopoietic stem cell disorders defined by ineffective hematopoiesis, multilineage dysplasia, and risk of progression to acute myeloid leukemia. Improvements have been made to identify recurrent genetic mutations and their functional roles, but translating this into preclinical models is still difficult. Traditional murine systems lack the human-specific cytokine support and microenvironmental support that is necessary to reproduce MDS pathophysiology. Humanized mouse models, particularly those incorporating human cytokines (e.g., MISTRG, NSG-SGM3, NOG-EXL), immunodeficient backgrounds, and co-transplantation strategies, have improved the engraftment and differentiation of human hematopoietic stem and progenitor cells. These models allow the study of clonal evolution, mutation-specific disease dynamics, and response to therapies in vivo. However, difficulties persist, such as limited long-term engraftment, incomplete immune reconstruction, and limited possibilities of modeling early-stage or low-risk MDS. This review presents an overview of current humanized and genetically engineered mouse models suitable for studying MDS, evaluating their capacity to replicate disease complexity, preserve clonal architecture, and support translational research. We highlight the need to develop new approaches to improve the actual methodologies and propose future directions for standardization and improved clinical relevance.

Embryonic hematopoietic cells develop in the fetal liver (FL), surrounded by diverse non-hematopoietic stromal cells. However, the spatial organization and cytokine production patterns of the stroma during FL development remain poorly understood. Here, we characterized and mapped the hematopoietic and stromal cell populations at early (E12.5-14.5) FL stages, revealing that while hepatoblasts were the primary source of hematopoietic growth factors, other stromal cells-including mesenchymal, mesothelial, and endothelial cells-also contributed to this signaling network. Using a dedicated image analysis pipeline, we quantified cell distances to tissue structures and defined neighbor relationships, uncovering that different hematopoietic progenitors exhibit distinct preferences for neighboring stromal cells and show developmental changes in spatial distribution. Notably, our data suggest that the sub-mesothelium region plays a prominent role in early fetal hematopoiesis. This approach offers a valuable tool for studying complex cellular interactions in biological systems, providing new insights into hematopoietic niche organization during development.

C1q is released by microglia, localizes on weak synapses and acts as a tag for microglial synaptic pruning. However, how C1q tags synapses during the pruning period remains to be fully elucidated. Here, we report that C1q is delivered via extracellular vesicles by microglia to pre-synaptic sites that externalize phosphatidylserine. Using approaches to increase or reduce vesicles production in microglia, by C9orf72 knock out or pharmacological inhibition, respectively, we provided mechanistic evidence linking extracellular vesicle release to pre-synaptic remodelling in neuron-microglia cultures. In C9orf72 knockout mice, we confirmed larger production of microglial extracellular vesicles and showed augmented C1q presynaptic deposition associated with enhanced engulfment by microglia in the early postnatal hippocampus. Finally, we provide evidence that microglia physiologically release more vesicles during the period of postnatal circuit refinement. These findings implicate abnormal release of microglial extracellular vesicles in both neurodevelopmental and age-related disorders characterized by dysregulated microglia-mediated synaptic pruning.

Hemogenic endothelium (HE) is recognized as the origin of all definitive blood cells, including hematopoietic stem cells (HSCs); however, the mechanisms governing the hematopoietic progenitor versus HSC fate choice within the HE remain unknown. Here we combine differentiation assays with full-length single-cell transcriptome data for extra-embryonic yolk sac (YS) and intra-embryonic aorta–gonad–mesonephros (AGM) region HE populations. We identified and localized three differentiation trajectories, each containing a distinct HE subset: erythromyeloid progenitor-primed HE in the YS plexus, lymphomyeloid progenitor-primed HE in large YS arteries and hematopoietic stem and progenitor cell-primed HE in the AGM. Chromatin modifiers and spliceosome components were enriched in AGM HE. This correlated with a higher isoform complexity of the AGM HE transcriptome. Distinct AGM HE-specific isoform expression patterns were observed for a broad range of genes, including stemness-associated factors like Runx1. Our data form a unique resource for studying cell fate decisions in different HE populations. Neo et al. map blood emergence from three hemogenic endothelial (HE) populations biased toward distinct blood fates. HE primed for stem progenitors shows elevated chromatin and RNA splicing gene expression and greater isoform diversity.

Somatic SETBP1 mutations are found in various myeloid disorders covering both myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS). To characterize the early steps of SETBP1-mediated leukemogenesis, we generated a conditional mouse model expressing SETBP1 G870S mutant in the entire hematopoietic tissue through Cre-mediated recombination driven by the Vav1 promoter. In all mice signs of a hematological disease appeared between 30 and 90 days: longitudinal analysis revealed accumulation of white blood cells (WBC) in virtually all heterozygous SETBP1 G870S mice, with a marked imbalance between the lymphoid and myeloid lineages in favor of the latter, and an increase in mature myeloid cells in absence of circulating blasts or non-segmented myeloid precursors. Kaplan-Meier analysis revealed a dramatic decrease in event-free survival in SETBP1 G870S mice. BM histology showed overt myeloid hyperplasia with fibrosis and no evidence of dysplasia except for the megakaryocytic lineage. Exploration of visceral organs highlighted the presence of severe hepatosplenomegaly with massive infiltration by myeloid elements, disruption of normal tissue architecture, and signs of extramedullary hematopoiesis. Single-cell RNA-sequencing (scRNA) on BM Lin - cells identified Mecom, Setbp1 and Hoxa9 among the top upregulated genes in SETBP1 G870S precursors. Pseudotime analysis of scRNA data revealed the presence of 261 spatially autocorrelated genes. Of them 158 were also differentially expressed in SETBP1 G870Svs control mice. Spi1, encoding for the master regulator of hematopoietic differentiation PU.1, was significantly upregulated in SETBP1 G870S precursors. PU.1 promotes the maturation of bone marrow early precursors towards the granulocytic/monocytic lineages by directly impairing the transcription of Gata2 and Gata1. In line with these data, Gata2 and Gata1 expression was profoundly suppressed in the early myeloid precursors of SETBP1 G870S mice, which associated with the down-modulation of markers of the erythroid lineage, such as the Carbonic Anhydrase 1, in the MEP differentiation branch. Ourmouse model recapitulates many clinical features of primary myelofibrosis (PMF). As up to 10% of PMF are triple-negative for the classical JAK2, CALR, and MPL mutations (TN-PMF), we set out to assess SETBP1 mutations in this context. We analyzed 36 TN-PMF patients by exome sequencing. In 29 we did not find any evidence of somatic mutations; in the remaining 7 (7/36; 19.4%) high VAF SETBP1 degron mutations were identified. In two patients SETBP1 was found as a single somatic variant, while in the others it coexisted with ASXL1, NRAS TET2 SRSF2, RIT1 CBL or CSF3R mutations. Notably, SETBP1 mutations were the only shared alterations among all seven patients. A markedly reduced overall survival was observed for SETBP1 positive patients, with a median survival time of 24 months (median survival not reached at 60 months for SETBP1 negative patients). To dissect the clonal architecture of SETBP1 positive TN-PMF at single-cell resolution, we applied single-cell targeted DNA sequencing on 3 SETBP1-mutated TN-PMF samples using the Tapestri technology, showing that, as opposite to MDS/MPN, in all TN-PMF cases SETBP1 is a very early clonal event. Therefore, our study suggests a clear partition of TN-PMF into two groups, the first one characterized by oncogenic, high VAF SETBP1 mutations accompanied by other oncogenic variants and poor prognosis and the other one characterized by no evidence of an active clonal process or of driver oncogenic events and much lower aggressiveness. SETBP1 positive TN-PMF disorders lie in a gray zone comprised between the MPN and MPN/MDS boundary. In MDS/MPN, SETBP1 mutations are often found as mid or late events. In contrast, we show here that in TN-PMF SETBP1 appears to be one of the earliest hits, therefore highlighting a potentially relevant biological difference occurring in the two subsets. In this context the presence of early SETBP1 mutations seems to promote the occurrence of a myeloid disorder characterized by the triad: leukocytosis without differentiation block or dysplasia, BM fibrosis and progressive splenomegaly, hence recapitulating many clinical features of overt or prefibrotic/early PMF and resembling the SETBP1 mouse model.

Late fetal hematopoiesis was traditionally thought to be sustained by Hematopoietic Stem Cells (HSCs). However, recent reports have revealed how the prenatal hematopoietic hierarchy is generated independently from long-term HSCs, highlighting unexpected complexity in the establishment of the hematopoietic system. Indeed, progenitors appearing earlier than HSCs play key roles in fetal and postnatal life. However, their precise origin, identity, and the extent of their contribution need further clarification.To this end, we took advantage of a genetic fate-mapping strategy in mice, enabling in vivo labeling and tracking of discrete subsets of hemogenic endothelium (HE).We identified a wave of fetal-restricted hematopoietic stem/progenitor cells (HSPCs) that contribute the majority of lympho-myeloid cells during prenatal development before declining in adult life. Combining lineage tracing analysis with whole-mount imaging and single-cell transcriptomics, we located the source of this contribution within pre-HSCs of vitelline and umbilical arteries. Functional assays confirmed the intrinsic transient nature of this HSPC wave.We exploited this genetic system to generate new insights into the biology of Juvenile Myelomonocytic Leukemia (JMML), a rare myeloproliferative neoplasm of early childhood that often originates prenatally. Specifically, we investigated whether distinct waves of prenatal HSPCs would be differentially susceptible to leukemic transformation upon acquisition of JMML-associated driver mutations. We show that introducing the same mutation in discrete subsets of HSPCs can generate profoundly variable outcomes. Thus, clinical heterogeneity in JMML could be, at least in part, explained by differences in the cell of origin. We are currently analyzing the molecular and epigenetic mechanisms underlying this phenomenon.

Embryonic hematopoiesis consists of distinct waves originating in rapid succession from different anatomical locations. Hematopoietic progenitors appearing earlier than definitive hematopoietic stem cells (HSCs) play key roles in fetal and postnatal life. However, their precise origin, identity and the extent of their contribution need further clarification. To this aim, we took advantage of a genetic fate-mapping strategy in mice that allows labeling and tracking of distinct subsets of hemogenic endothelium (HE). Time-course labeling of hematopoietic progenitors emerging from HE between E8.5 and E9.5, before intra-embryonic definitive HSC generation, revealed a major fetal lympho-myeloid contribution which declined in the adult. Lineage tracing coupled with whole-mount imaging and single-cell RNA sequencing located its source within hematopoietic clusters of vitelline and umbilical arteries. Functional assays confirmed the transient nature of these progenitors. We therefore unveiled a hitherto unidentified early wave of fetal-restricted hematopoietic stem/progenitor cells poised for differentiation that provide a major contribution to pre-natal hematopoiesis. ### Competing Interest Statement The authors have declared no competing interest.

Topic: 23. Hematopoiesis, stem cells and microenvironment Background: In mammals, embryonic hematopoiesis takes place in discrete but overlapping waves. Hematopoietic Stem Cells (HSC) generation is preceded by the appearance of HSC-independent progenitors, both emerging from a specialized transient population of endothelial cells termed hemogenic endothelium (HE). Recently, several reports showed that HSC contribution to fetal hematopoiesis is limited and that, in contrast, HSC-independent progenitor play key roles in fetal and postnatal life. Understanding the dynamics of fetal hematopoiesis has a number of important implications. Indeed, gaining a better knowledge of the cellular and molecular processes underlying the production of hematopoietic cells in the embryo would aid establishing new methodologies for the in vitro generation of different hematopoietic cells from pluripotent stem cells. Moreover, given the prenatal origin of many pediatric blood cancers, a better understanding of fetal hematopoiesis could lead to the identification of potential cell(s) of origin and relevant therapeutic vulnerabilities. Aims: To precisely define the origin, identity and extent of contribution of the distinct waves of embryonic hematopoietic stem and progenitor cells. Methods: To this aim, we took advantage of a genetic fate-mapping strategy in mouse that allows in vivo labeling and tracking of distinct subsets of HE. We combined this strategy with whole-mount embryo imaging, single-cell RNA sequencing and a range of functional assays. Results: Time-course labeling of HE revealed that the major lympho-myeloid contribution towards the end of gestation was derived from progenitors appearing between E8.5 and E9.5, a time window in which dorsal aorta definitive-type HSCs have not yet emerged. This contribution was transient and fetal-restricted, as it exhibited a sharp decline during postnatal life. Remarkably, we were able to localize the emergence of fetal-restricted hematopoietic stem/progenitor cells (HSPCs) to Kit+ hematopoietic clusters emerging from HE in the vitelline and umbilical (extraembryonic) arteries. Lineage tracing using a different, myeloid-specific, transgenic mouse line established that these clusters contained cells other than erythro-myeloid progenitors (EMPs). Moreover, single-cell RNA sequencing showed that fetal-restricted HSPCs express a transcriptional signature characteristic of HSCs. Accordingly, ex vivo co-cultures showed that B- and T-lymphoid potential were enriched in these progenitors. Finally, transplantation assays demonstrated that fetal-restricted HSPCs are endowed with in vivo multi-lineage repopulation potential. Summary/Conclusion: In summary, here we identify a wave of fetal-restricted HSPCs that physiologically contribute the majority of lymphoid and myeloid cells other than macrophages during fetal development, and we demonstrate that its emergence is segregated in space and time from that of EMPs and adult definitive-type HSCs. Keywords: Hematopoietic stem and progenitor cells, Hematopoiesis, Development, Mouse model

In 2002 we published an article describing a population of vessel-associated progenitors that we termed mesoangioblasts (MABs). During the past decade evidence had accumulated that during muscle development and regeneration things may be more complex than a simple sequence of binary choices (e.g., dorsal vs. ventral somite). LacZ expressing fibroblasts could fuse with unlabelled myoblasts but not among themselves or with other cell types. Bone marrow derived, circulating progenitors were able to participate in muscle regeneration, though in very small percentage. Searching for the embryonic origin of these progenitors, we identified them as originating at least in part from the embryonic aorta and, at later stages, from the microvasculature of skeletal muscle. While continuing to investigate origin and fate of MABs, the fact that they could be expanded in vitro (also from human muscle) and cross the vessel wall, suggested a protocol for the cell therapy of muscular dystrophies. We tested this protocol in mice and dogs before proceeding to the first clinical trial on Duchenne Muscular Dystrophy patients that showed safety but minimal efficacy. In the last years, we have worked to overcome the problem of low engraftment and tried to understand their role as auxiliary myogenic progenitors during development and regeneration.

Infant acute myeloid leukemia (AML) is a heterogeneous disease, genetically distinct from its adult counterpart. Chromosomal translocations involving the KMT2A gene (MLL) are especially common in affected infants of less than 1 year of age, and are associated with a dismal prognosis. While these rearrangements are likely to arise in utero, the cell of origin has not been conclusively identified. This knowledge could lead to a better understanding of the biology of the disease and support the identification of new therapeutic vulnerabilities. Over the last few years, important progress in understanding the dynamics of fetal hematopoiesis has been made. Several reports have highlighted how hematopoietic stem cells (HSC) provide little contribution to fetal hematopoiesis, which is instead largely sustained by HSC-independent progenitors. Here, we used conditional Cre-Lox transgenic mouse models to engineer the Mll-Af9 translocation in defined subsets of embryonic hematopoietic progenitors. We show that embryonic hematopoiesis is generally permissive for Mll-Af9-induced leukemic transformation. Surprisingly, the selective introduction of Mll-Af9 in HSC-independent progenitors generated a transplantable myeloid leukemia, whereas it did not when introduced in embryonic HSC-derived cells. Ex vivo engineering of the Mll-Af9 rearrangement in HSC-independent progenitors using a CRISPR/Cas9-based approach resulted in the activation of an aberrant myeloid-biased self-renewal program. Overall, our results demonstrate that HSC-independent hematopoietic progenitors represent a permissive environment for Mll-Af9-induced leukemic transformation, and can likely act as cells of origin of infant AML.

During embryogenesis, yolk-sac and intra-embryonic-derived hematopoietic progenitors, comprising the precursors of adult hematopoietic stem cells, converge into the fetal liver. With a new staining strategy, we defined all non-hematopoietic components of the fetal liver and found that hepatoblasts are the major producers of hematopoietic growth factors. We identified mesothelial cells, a novel component of the stromal compartment, producing Kit ligand, a major hematopoietic cytokine. A high-definition imaging dataset analyzed using a deep-learning based pipeline allowed the unambiguous identification of hematopoietic and stromal populations, and enabled determining a neighboring network composition, at the single cell resolution. Throughout active hematopoiesis, progenitors preferentially associate with hepatoblasts, but not with stellate or endothelial cells. We found that, unlike yolk sac-derived progenitors, intra-embryonic progenitors respond to a chemokine gradient created by CXCL12-producing stellate cells. These results revealed that FL hematopoiesis is a spatiotemporal dynamic process, defined by an environment characterized by low cytokine concentrations.

Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.

Our knowledge of the complexity of the developing hematopoietic system has dramatically expanded over the course of the last few decades. We now know that, while hematopoietic stem cells (HSCs) firmly reside at the top of the adult hematopoietic hierarchy, multiple HSC-independent progenitor populations play variegated and fundamental roles during fetal life, which reflect on adult physiology and can lead to disease if subject to perturbations. The importance of obtaining a high-resolution picture of the mechanisms by which the developing embryo establishes a functional hematopoietic system is demonstrated by many recent indications showing that ontogeny is a primary determinant of function of multiple critical cell types. This review will specifically focus on exploring the diversity of hematopoietic stem and progenitor cells unique to embryonic and fetal life. We will initially examine the evidence demonstrating heterogeneity within the hemogenic endothelium, precursor to all definitive hematopoietic cells. Next, we will summarize the dynamics and characteristics of the so-called "hematopoietic waves" taking place during vertebrate development. For each of these waves, we will define the cellular identities of their components, the extent and relevance of their respective contributions as well as potential drivers of heterogeneity.