Behavior Of Hematopoietic Stem Cells Research Articles

TAF1, the Largest Subunit of Tfiid, Is Dispensable for Adult Hematopoiesis

Temporal and spatial control of gene expression is central to normal hematopoietic stem cell (HSC) biology. Many sequence-specific transcription factors have been identified as key regulators of HSC fate decision, while the function of general transcription factors in HSC behavior is poorly understood. We previously reported that TAF1, the largest subunit of the TFIID complex, plays a critical role in AML1-ETO driven acute myeloid leukemogenesis. To evaluate the function of TAF1 in normal fetal and adult hematopoiesis, we generated TAF1 conditional knockout (CKO) mice and identified an essential role of TAF1 in fetal erythropoiesis. Surprisingly, deletion of TAF1 in adult mice was not lethal to hematopoiesis; rather, we observed a marked expansion of hematopoietic stem and progenitor cell (HSPC) populations, with increased self-renewal and impaired differentiation capacity in these TAF1- null cells. Consistently, we found that TAF1-null HSPCs failed to up-regulate key differentiation-associated genes when induced to differentiate in vitro. Using a variety of genome-wide assays and biochemical approaches, we found that TAF1 loss not only disrupted TFIID complex formation and chromatin recruitment, but also reduced promoter accessibility, impaired RNA Polymerase II promoter recruitment and activity, as well as its promoter-proximal pausing mechanism. Thus, the effect of TAF1 loss on normal adult hematopoiesis primarily relates to the inability to upregulate genes involved in differentiation, while HSC self-renewal and the expression of self-renewal genes proceeds relatively normally.

Characterization of Hematopoietic Stem Cell Diversity Using Spatiotemporal Quantitative Phase Imaging

Cells undergo continual transformations, never retaining their original state. Hematopoietic stem cells (HSCs), at the apex of the hematopoietic hierarchy, are not exempt from this dynamic process. In recent years, the advent of single-cell analysis techniques such as scRNAseq has progressively unveiled the heterogeneity within cell populations previously presumed to be homogeneous. However, these techniques are limited to evaluating the cellular state at a single temporal point based on snapshot analysis, thus failing to account for temporal changes and dynamic behavior of cells. Therefore, the true diversity inherent to the ever-changing HSCs remains uncertain. In this study, we comprehensively elucidate HSC diversity, including temporal changes, by integrating our recently established ex vivo HSC expansion techniques (Wilkinson et al., Nature, Becker et al., Cell Stem Cell), single-cell quantitative phase imaging (QPI), and post-transplantation dynamics analysis. For live imaging, HSCs were harvested from hepatic leukemia factor ( Hlf)-tdTomato reporter mice, which specifically marks long-term HSCs. Index sorted single Hlf-tdTomato + HSC were expanded with a single-HSC culture system and monitored by QPI fluorescence time-lapse imaging. Surprisingly, even though the cells were derived from the same HSC fraction, significant variations in mitotic rate, motility, morphological changes, and Hlf expression levels were observed at the single-cell level. Stemness did not decrease stepwise over time, but always exhibited continuous changes. Thus, analysis including the temporal dimension illuminated the infinitely branched nature of HSC diversity. Interestingly, Hlf expression level correlated with the dynamic behavior of HSCs in the expansion culture system. Hlf-high HSCs exhibited a slow division rate, small, rounded morphology and low motility, while Hlf-low HSCs actively divided and differentiated, displayed larger morphological size with low sphericity, and exhibited high motility. Furthermore, spatiotemporal dynamics analysis of Hlf-high/low HSCs after transplantation, employing the highly sensitive in vivo imaging system Akaluc bioluminescence imaging (AkaBLI), revealed that Hlf-high HSCs initiate systemic hematopoiesis slowly, while Hlf-low HSCs expanded quickly, characterized by short-term explosive hematopoiesis in the spleen. As expected, only Hlf-high HSCs had long-term bone marrow reconstitution ability. Thus, based on the expression level of Hlf, it is possible to predict the dynamic behavior of the cells in the expansion medium and in the post-transplant body. Next, we investigated whether Hlf expression level could be predicted based on the kinetic features of cells during HSC ex vivo expansion. Interestingly, multidimensional analysis based on kinetic features extracted from time-lapse imaging showed multiple clusters, each linked to Hlf expression levels. In human HSCs, the dynamic diversity of HSCs was also observed in our recently established ex vivo expansion system (Sakurai et al., Nature). Notably, the kinetic features of human HSCs differed from those of mouse HSCs. Transplantation of human HSCs exhibiting specific morphological characteristics showed long-term reconstitution ability. Thus, classification of HSCs based on kinetic features facilitated enrichment of functional HSCs. This study demonstrates the importance of characterizing cells, including the temporal dimension, and illustrates the existence of infinite dynamic individuality in mouse and human HSCs.

CUX1 Levels Control Hematopoietic Stem Cell Fate and Plasticity

Hematopoietic stem cells (HSCs) sustain lifelong, multipotent output, however, the molecular mechanisms governing HSC homeostasis remain unclear. Elucidating this process is key to understanding the imbalanced differentiation and self-renewal evident in myeloid malignancies. CUX1 is a transcription factor that is monoallelically mutated or deleted in high-risk myeloid malignancies. We previously reported that CUX1 has critical, dose-dependent roles in hematopoiesis and myeloid neoplasia. The haploinsufficient nature of CUX1 in myeloid neoplasia and the broad dose-dependent requirement of CUX1 in hematopoiesis led us investigate the role of CUX1 in earliest stages of hematopoiesis. We generated a CUX1 reporter mouse in which mCherry is fused in-frame with the C-terminus of CUX1 to study how the level of CUX1 in HSCs affects their behavior. Overall, we find that CUX1 protein levels within the HSC compartment delineates stem cell activity. Stringently defined immunophenotypic HSCs with low CUX1 levels (CUX1 Dim) are phenotypically dormant, as assessed by transcriptional profiling and proliferation assays, as opposed to CUX1 Bright HSCs which have greater cell cycle participation. In transplantation assays, CUX1 Dim HSCs are initially platelet-biased but give rise to long-term, multilineage reconstitution. CUX1 Bright HSCs are initially erythroid-biased but lack long-term HSC activity and the capacity for self-renewal. In other words, despite immunophenotypic HSC markers, CUX1 Bright HSCs are not, by definition, HSCs. By most metrics, CUX1 Intermediate HSCs exhibit a distinct, albeit intermediate, phenotype. Therefore, along a continuous gradient of CUX1 expression, HSCs gradually lose the ability to self-renew as CUX1 expression increases. Remarkably, knockdown of CUX1 in CUX1 Bright HSCs re-endows these cells with the capacity for long-term multilineage chimerism, suggesting low levels of CUX1 are required for stem cell activity in HSCs. Inversely, overexpression of CUX1 in HSCs promotes their expansion and ultimate exhaustion, further demonstrating that the level of CUX1 controls HSC fate. Altogether, we report that low CUX1 levels are required for HSC self-renewal and implicate CUX1 as a molecular rheostat for HSC behaviors such as cell division and differentiation. Further, we describe an unprecedented capacity for cells without demonstrated HSC activity to acquire HSC capacity and a novel role for CUX1 in preventing this plasticity.

Polycom Group Protein Mel18 Inhibits Hematopoietic Stem Cell Self-Renewal through Repressing the Expression of Genes Important for Cellular Senescence and Proliferation

Polycomb group (PcG) proteins are epigenetic gene silencers that have been implicated in stem cell maintenance and cancer development. Genetic and biochemical studies indicate that Polycomb group proteins exist in at least two protein complexes, Polycomb repressive complex 2 (PRC2) and Polycomb repressive complex 1 (PRC1), that act in concert to initiate and maintain stable gene repression. Bmi1 and Mel18 are two major homologs of the PCGF subunit within the canonical PRC1 complex. While Bmi1 is a positive regulator of hematopoietic stem cell (HSC) and leukemia stem cell (LSC) self-renewal, the role of Mel18 in normal and malignant hematopoiesis is not fully understood. To further determine the role of Mel18 in hematopoiesis, we have generated Mel18 conditional knockout mice ( Mel18 f/f-Mx1Cre +). Acute deletion of Mel18 in the hematopoietic compartment did not affect the frequency and survival of hematopoietic stem and progenitor cells (HSPCs). To determine the impact of Mel18 deficiency on HSPC proliferation, we performed serial replating assays and found that loss of Mel18 increases the replating potential of HSPCs in vitro. To determine the role of Mel18 in HSC self-renewal, we first performed serial bone marrow (BM) transplantation assays and found that Mel18 null BM cells show increased engraftment in both primary and secondary transplantation assays. Limiting dilution transplantation showed that there were more functional HSCs in the BM of Mel18 knockout mice. We then performed HSC transplantation assays and found that loss Mel18 enhances HSC self-renewal. Thus, we demonstrated that Mel18 inhibits HSC self-renewal and decreases the number of functional HSCs in vivo. To understand the mechanism by which Mel18 inhibits HSC self-renewal and proliferation, we performed RNA-seq using Mel18 +/+ and Mel18 -/- HSCs. We then performed gene set enrichment analysis (GSEA) to identify potential Mel18 target genes important for HSC behavior. We found that HSC gene signatures are enriched in Mel18 -/- HSCs. We also found that leukemia stem cell gene signatures and CBF-mutant-AML genes are significantly enriched in Mel18 -/- HSCs, suggesting that loss of Mel18 may prime normal HSCs for leukemic transformation. Notably, our RNA-seq assay showed that senescence-related genes, including S100a9 and S100a8, were down-regulated in Mel18 -/- HSPCs. Importantly, loss of Mel18 significantly decreased the number of senescent HSPCs. To understand how Mel18 regulates gene transcription, we performed ATAC-seq assays in Mel18 +/+ and Mel18 -/- HSPCs. Mel18 null HSPCs showed decreased chromatin accessibility near both S100a8 and S100a9 genes. We confirmed that both S100a8 and S100a9 are downregulated in Mel18 -/- HSPCs compared to Mel18 +/+ HSPCs. Given that cell cycle arrest is a common feature of cellular senescence, we also examined the expression of cell cycle related genes in Mel18 -/- HSPCs. The expression of cell cycle regulators, including CDK4 and CCND2, is increased in Mel18 -/- HSPCs. Mel18 can bind to a specific DNA sequence, 5‘-GACTNGACT-3‘, thereby repressing the expression of target genes. Mel18 directly binds to the CCND2 gene locus as revealed by ChIP-seq assays in embryonic stem cells, suggesting that Mel18 may directly repress CCND2 expression in HSPCs. In summary, we demonstrate that Mel18 inhibits HSC self-renewal via repressing the expression of genes that are important for cellular senescence and proliferation.

Aging of the Hematopoietic Stem Cell Niche: New Tools to Answer an Old Question.

The hematopoietic stem cell (HSC) niche is a specialized microenvironment, where a complex and dynamic network of interactions across multiple cell types regulates HSC function. During the last years, it became progressively clearer that changes in the HSC niche are responsible for specific alterations of HSC behavior. The aging of the bone marrow (BM) microenvironment has been shown to critically contribute to the decline in HSC function over time. Interestingly, while upon aging some niche structures within the BM are degenerated and negatively affect HSC functionality, other niche cells and specific signals are preserved and essential to retaining HSC function and regenerative capacity. These new findings on the role of the aging BM niche critically depend on the implementation of new technical tools, developed thanks to transdisciplinary approaches, which bring together different scientific fields. For example, the development of specific mouse models in addition to coculture systems, new 3D-imaging tools, ossicles, and ex-vivo BM mimicking systems is highlighting the importance of new technologies to unravel the complexity of the BM niche on aging. Of note, an exponential impact in the understanding of this biological system has been recently brought by single-cell sequencing techniques, spatial transcriptomics, and implementation of artificial intelligence and deep learning approaches to data analysis and integration. This review focuses on how the aging of the BM niche affects HSCs and on the new tools to investigate the specific alterations occurring in the BM upon aging. All these new advances in the understanding of the BM niche and its regulatory function on HSCs have the potential to lead to novel therapeutical approaches to preserve HSC function upon aging and disease.

Scribble Is a Negative Regulator of Interferon-I Dependent Notch1 Activation in Adult Hematopoietic Stem Cells and Progenitors

Hematopoietic stem cells (HSC) are highly quiescent cells with the ability to rapidly enter cell cycle and differentiate through changes in their polarity and the disposition of intracellular molecular fate determinants in response to microenvironment (ME) cues. Interferons type 1 (IFN-I) are ME cytokines produced during the physiological response mounted to combat a viral infection. In bone marrow hematopoiesis, IFN-I induces activation and proliferation of HSC. Clinically, patients treated with IFN-I, as well as individuals suffering from IFN-I associated chronic disease, often exhibit sustained hematological cytopenias and HSC failure. The precise molecular mechanisms that govern HSC behavior in response to IFN-I are still unclear. Our data highlights that Scribble deficient HSC are less sensitive to IFN-I mediated activation. By using hematopoietic specific deletion of Scribble in murine hematopoiesis (Vav-Cre;Scribble KO); we demonstrated that Scribble deficient LSK CD150 +/CD48 - HSC are less responsive to polyinositide-polycytidine (pI:C) induced IFN-I mediated activation and retain cellular quiescence (G0:45±5.4% vs 63±2.7% in WT and Scribble KO, respectively, p<0.05). IFN-I induced upregulation of Sca-1 expression was also significantly hampered in Scribble deficient HSC. Functionally, serial transplantation experiments demonstrated that in response to poly I:C, Scribble deficient HSC display increased competitive repopulating potential (26±1.3% vs 38±1.2% BM chimerism for WT and KO BM in secondary recipients and 38±2.5% vs 48±2.7% BM chimerism in tertiary recipients, p<0.01). The maintenance of cellular quiescence and function for Scribble deficient HSC are independent of canonical IFN-I driven STAT-1 signaling, as we report no differences in STAT-1 activation, nuclear translocation or the expression of STAT-1 canonical target genes in response to pI:C. Unsupervised transcriptomics analysis of Scribble-deficient HSC supported dysregulation of Notch signaling. Furthermore, Scribble deficiency in non-activated LSK HSC and progenitors (HSPC) was associated with constitutive activation and cleavage of Notch1 (Notch1 ICD;~3 fold) at levels comparable to IFN-I mediated activation of WT HSPC. However, Scribble deficient HSPC did not exhibit further Notch1 cleavage activation upon in vivo IFN-I induction. Pharmacological in vivo γ-secretase inhibition (YO-01027) prevented the protective effect of Scribble deficiency on IFN-I dependent loss of HSC quiescence. These data indicate that Notch1 activation, and subsequent cleavage, is indispensable for Scribble deficient HSC quiescence in response to IFN-I. Active Cdc42 is a critical regulator of HSC quiescence and fate, and previous studies have demonstrated that Scribble controls HSC asymmetric division potential and fate through the PDZ mediated scaffolding of cytosolic Yap1 with activated Cdc42 (Cdc42-GTP). Next to determine whether poly I:C mediated Notch1 cleavage linked with Cdc42 activity, we analyzed the protein interactions between cleaved Notch1 and Cdc42-GTP in relation with Scribble. Our findings revealed that Scribble associates with non-cleaved, membrane bound Notch but upon in vivo IFN-I induction Notch1 is cleaved, activated and translocates with Scribble-free, activated Cdc42 to the nucleus of HSC. Deletion of HSC Scribble associated with a reduced (~45%, p<0.001) proximity interaction between cleaved Notch1 and Cdc42-GTP. Collectively our findings identify that Scribble controls IFN-I mediated HSPC activation through induction of Notch1 cleavage and Cdc42 activity, and highlight such interaction as a new potential target to dampen inflammation driven HSC exhaustion. DisclosuresCancelas: Cerus Co: Research Funding; TerumoBCT: Research Funding; Hemanext: Membership on an entity's Board of Directors or advisory committees, Research Funding; Cytosorbents Inc: Research Funding; Fresenius-Kabi LLC: Research Funding; Westat Inc: Research Funding; Vascular Solutions Inc.: Research Funding; Hemerus LLC: Research Funding; University of South Florida/MEQU Inc: Research Funding.

Polyvinyl alcohol hydrolysis rate and molecular weight influence human and murine HSC activity ex vivo

Ex vivo expansion of hematopoietic stem cells (HSCs) is one of the most promising strategies to increase the availability of transplantable HSCs and improve bone marrow transplantation outcomes. We recently demonstrated that mouse HSCs could be efficiently expanded in polyvinyl alcohol (PVA)-containing culture medium using only recombinant stem cell factor and thrombopoietin cytokines. However, the behavior of human HSCs in these simple PVA-based media was not fully elucidated. In this study, we analyzed the compatibility of PVA of different hydrolysis rates (HR) and molecular weights (MW) to support functional human and mouse HSCs ex vivo. Human and mouse HSCs proliferated more frequently in media containing PVA with lower HR than with higher HR, but both PVA types supported HSC multilineage reconstitution potential. Importantly, human HSCs cultured in PVA-containing media engrafted not only in irradiated recipients but also in non-irradiated recipients. Our results demonstrate that human HSCs can be maintained ex vivo using PVA-based culture systems and suggest approaches for future optimization of human HSC expansion.

The Role of Histone Variant H3.3 Regulation By Hira in Hematopoiesis

A large proportion of adult hematopoietic stem cells (HSCs) remain quiescent throughout life, rarely undergoing cell division. These quiescent HSCs must undergo global changes in gene expression patterns in order to leave their dormant state and differentiate. Chromatin modifiers that act independent of cell division may therefore be of particular importance in regulating the behavior of quiescent HSCs through alterations in the chromatin landscape.One such chromatin modifier is the histone variant H3.3 chaperone, Hira, which is responsible for incorporating H3.3 independent of DNA replication at poised and transcriptionally active promoters. Despite the fact that this histone variant only differs from the canonical H3 histones by four or five amino acids, its gene-specific association is required for the proper establishment of gene expression and lineage specification in murine embryonic stem cells (mESCs), post-mitotic neurons, and oocytes. Since Hira deposits H3.3 outside of S phase, we hypothesize that Hira plays a critical role in the maintenance of quiescent HSCs through the regulation of H3.3 independent of cell division.HSCs divide rapidly in the fetal liver but become quiescent in adulthood, providing an interesting opportunity to study HSCs that are vastly different in terms of cell cycle properties. In order to study the role of Hira in HSCs, we used a conditional knockout (cKO) mouse model to delete Hira in hematopoietic cells in early development (Vav-iCre; Hirafl/fl). Importantly, we observed severe depletion of adult, but not fetal, HSCs upon loss of Hira. This suggests that Hira is important for the maintenance of quiescent adult HSCs, but not rapidly dividing fetal HSCs, and supports our model of Hira as a regulator of HSC quiescence through the DNA replication-independent incorporation of H3.3. We additionally observed altered differentiation potential, reduced reconstitution capacity, and increased cycling in adult HSCs upon Hira cKO. These results demonstrate that Hira is an essential regulatory factor for the control of adult HSC function.To obtain adult Hira cKO HSCs for further analysis, we also used an inducible model of Hira deletion in the hematopoietic system upon polyinosinic-polycytidylic (pIpC) treatment (Mx1-Cre; Hirafl/fl). We performed RNA-seq analysis on adult Hira cKO HSCs, which showed widespread alterations in gene expression patterns and upregulation of PRC2 target genes. Since Hira is known to recruit polycomb repressive complex 2 (PRC2) to bivalent promoters in mESCs in an H3.3-dependent manner (Banaszynski et. al. Cell 2013), chromatin-immunoprecipitation and sequencing (ChIP-seq) for H3K27me3 will be used to show how loss of Hira affects PRC2 activity in HSCs. We have additionally performed assay for transposase-accessible chromatin and sequencing (ATAC-seq) in order to determine how patterns of DNA accessibility in HSCs are affected by Hira cKO. Altered nucleosome positioning and PRC2 activity will be discussed as potential mechanisms for the role of Hira in regulating the behavior of quiescent HSCs.Our findings reveal a novel paradigm for epigenetic state regulation in adult HSCs. Knowledge gained from this study may inform future research for clinical applications, such as for improved methods of in vitro HSC expansion. Characterizing the importance of H3.3 regulation by Hira in normal HSC activity will therefore provide invaluable information regarding the epigenetic mechanisms underlying hematopoietic homeostasis. DisclosuresNo relevant conflicts of interest to declare.

MTOR-C/EBPβ-c-Myc Axis Regulates the Behavior of Myeloid-Biased Hematopoietic Stem Cells Under Stress Conditions

In stress or regenerative conditions, hematopoietic stem cell (HSC) population drastically alters its behavior; they rapidly enter into cell cycle, differentiate to multipotent progenitors (MPPs) at the expense of self-renewal activity, and are reprogrammed toward predominantly myeloid-biased hematopoiesis. In these processes, essential roles of myeloid transcription factors in regenerating HSCs are anticipated. C/EBPβ regulates both proliferation and differentiation of granulocytic precursors in stress conditions. However, its functions in HSCs during stresses are largely unknown.In the past several years, we have been investigating the roles of C/EBPβ in HSCs under stress conditions, especially focusing on the expression pattern of C/EBPβ isoforms and their respective functions. Cebpb is a unique single exon gene, from which two long protein isoforms (LAP* and LAP) and one truncated isoform lacking N-terminal activating domain (LIP) are translated by different usage of initiating codons. To monitor the expression pattern of these isoforms in scarce cells, we have devised an intracellular double staining method for flow cytometric analysis using two distinct anti-C/EBPβ antibodies recognizing N- and C-terminus, respectively (57th ASH annual meeting, #3580).Here, we refined this method to reveal the characteristic expression pattern of C/EBPβ isoforms in HSCs in vivo in response to stresses. In regenerative conditions after either 5-FU treatment or transplantation, we detected remarkable LIP-dominant upregulation in LT-HSCs at early phases, which was followed by increase of LAP*/LAP at later phases. This stress-induced translational upregulation and alteration of C/EBPβ were significantly suppressed by short-term administration of rapamycin, a selective inhibitor of mTOR, suggesting its dependence on mTORC1 pathway at least in part.We further found that the stress-induced LIP-dominant upregulation of C/EBPβ was remarkable in LT-HSCs with higher surface CD150 expression (CD150high LT-HSCs), which possess myeloid-biased potential. Cell cycle analyses at early phases after 5-FU treatment, when LIP was predominantly expressed, revealed that CD150high HSCs were significantly less quiescent than CD150low HSCs but this difference was abolished in Cebpb-/- HSCs, suggesting that C/EBPβ specifically activated the cell cycle of CD150high “myeloid-biased” HSCs.We next examined the functions of C/EBPβ isoforms in HSCs in vivo . We transplanted WT BM cells retrovirally transduced with each C/EBPβ isoform into sublethally irradiated WT mice, and then analyzed the transduced cells in the recipients. LAP*- or LAP-transduced cells disappeared as early as 3 weeks after transplantation, probably due to their rapid myeloid differentiation. LIP-transduced HSCs were significantly less quiescent, exhibited more accelerated differentiation to MPPs, especially lymphoid-primed MPP4s, and produced more lymphoid-biased outputs. These results indicate that LIP induces cell cycle activation of HSCs and expansion of MPP pool, while antagonizing the other long isoforms that induce rapid myeloid commitment and premature exhaustion of HSCs.As a candidate for the downstream target of C/EBPβ, especially LIP, in HSCs, we focused on Myc (encoding c-Myc). LIP-transduced EML cells, a mouse HSC line, expressed 1.5-fold higher level of Myc mRNA than those transduced with control, and LIP-transduced HSCs in vivo expressed 2-fold higher than control. We next compared Myc mRNA expression between WT and Cebpb-/- HSCs at early phases of regeneration post 5-FU treatment and transplantation, when LIP was predominantly upregulated. Then, we found that significantly lower level of Myc transcripts was expressed in Cebpb-/- HSCs. When we performed a ChIP-qPCR analysis using C/EBPβ-transduced EML cells, remarkable enrichment of C/EBPβ was observed at the distal enhancer of Myc gene. These data suggest that both forced overexpression and physiological elevation of LIP positively regulate Myc transcription in HSCs likely through direct binding to Myc enhancer.In summary, our findings illustrate that stress-induced upregulation and alteration of C/EBPβ protein, mediated by mTORC1 and modulating Myc transcription, is significantly involved in stress-mode behavior of HSCs especially with myeloid bias. DisclosuresNo relevant conflicts of interest to declare.

A CRISPR RNA-Binding Protein Screen Reveals Novel Regulators of RUNX1 Alternative Polyadenylation

Alternative polyadenylation (APA) is a crucial post-transcriptional process that regulates the 3' end formation of over 75% of all human genes. Despite its prevalence and importance during development and in disease, there are few studies that focus on APA in the hematology field. Interestingly, APA affects the coding sequence of RUNX1, a pivotal transcription factor for proper hematopoiesis. Usage of the most proximal RUNX1 polyadenylation sequence (PAS) in upstream alternative terminal exon 7a results in the C-terminally truncated RUNX1a isoform. RUNX1a uniquely promotes self-renewal and expansion of hematopoietic stem cells (HSCs). In the endogenous context, usage of this proximal PAS is tightly restricted, resulting in polyadenylation at one of three distal PAS in exon 8 and producing the RUNX1b/c isoforms. RUNX1b/c are much more abundant and promote HSC differentiation and lineage commitment. Importantly, the ratio of RUNX1a to RUNX1b/c is developmentally-regulated. Therefore, it is highly significant to uncover the APA mechanism that controls the RUNX1 isoform ratio and consequently the balance of HSC self-renewal and differentiation. We hypothesize that there are enhancers and suppressors of the proximal RUNX1 PAS, tightly controlling the relative amount of RUNX1a produced during hematopoiesis.To identify RUNX1 APA regulators, we first developed a strategy to monitor RUNX1 proximal PAS usage in vitro. We cloned alternative terminal exon 7a, which contains the proximal PAS, along with 500 bp of up and downstream flanking intron between the two exons of a split GFP reporter. When we introduce this fluorescent minigene reporter into blood cells, two transcripts can be produced: (1) the first GFP exon splices and polyadenylates RUNX1 exon 7a, producing no GFP (RUNX1a formation) or (2) the two GFP exons are spliced together, skipping the proximal PAS in exon 7a, producing GFP (RUNX1b/c formation). Since RUNX1b/c are much more highly expressed than RUNX1a throughout hematopoiesis, we observed a robust GFP signal when this reporter was transfected into MDS-L, K562, and U937 cell lines. RT-PCR analysis confirmed that both transcripts are produced, albeit at dramatically different levels. We can thus use GFP fluorescence as a read-out for RUNX1 proximal PAS usage.Next, we generated a stable, clonal MDS-L cell line expressing this RUNX1 exon 7a split GFP reporter. We used this reporter line to perform a CRISPR screen using an sgRNA library that is enriched for targeting RNA-binding proteins (RBPs). We infected cells with the library, cultured in puromycin to force sgRNA and Cas9 integration, waited three weeks to ensure gene knockout, and then used fluorescence-activated cell sorting (FACS) to isolate GFP low and high cell populations. GFP low cells contained sgRNAs targeting RUNX1a suppressors since these cells exhibited enhanced proximal PAS usage. Conversely, GFP high cells contained sgRNAs targeting RUNX1a enhancers since proximal PAS usage was further diminished. We identified 44 putative RUNX1a suppressors and 41 putative enhancers (p < 0.05).We then sought to validate the genes revealed in our CRISPR screen by using individual sgRNAs targeting a subset of the candidates. One confirmed suppressor is HNRNPA1, an RBP which is upregulated and leukemogenic in BCR/ABL chronic myelogenous leukemia (CML). In HNRNPA1 knockout cells, there was a 5-fold increase in relative RUNX1a and a corresponding decrease in RUNX1b/c levels by RT-qPCR. This effect was dose-dependent as heterozygous HNRNPA1 cells exhibited an intermediate 2.5-fold increase in RUNX1a mRNA. We verified this data by performing shRNA knockdown of HNRNPA1 in MDS-L and K562 cells, again observing a significant increase in relative RUNX1a levels. Interestingly, HNRNPA1 is highly expressed throughout the course of hematopoiesis, indicating that a cooperating protein helps facilitate this suppressive effect. Indeed, numerous HNRNPA1-interacting proteins were also identified in our screen and are the subject of current studies.In summary, we devised a fluorescent minigene reporter to monitor RUNX1 APA in vitro. Using this reporter, we performed a CRISPR RBP screen and identified HNRNPA1 as the founding member of a complex that suppresses RUNX1a production during hematopoiesis. HNRNPA1 and additional regulators represent novel proteins that have the potential to regulate HSC behavior by modifying the RUNX1 isoform ratio. DisclosuresNo relevant conflicts of interest to declare.

Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.

SummarySome cancers originate from a single mutation event in a single cell. Blood cancers known as myeloproliferative neoplasms (MPNs) are thought to originate when a driver mutation is acquired by a hematopoietic stem cell (HSC). However, when the mutation first occurs in individuals and how it affects the behavior of HSCs in their native context is not known. Here we quantified the effect of the JAK2-V617F mutation on the self-renewal and differentiation dynamics of HSCs in treatment-naive individuals with MPNs and reconstructed lineage histories of individual HSCs using somatic mutation patterns. We found that JAK2-V617F mutations occurred in a single HSC several decades before MPN diagnosis—at age 9 ± 2 years in a 34-year-old individual and at age 19 ± 3 years in a 63-year-old individual—and found that mutant HSCs have a selective advantage in both individuals. These results highlight the potential of harnessing somatic mutations to reconstruct cancer lineages.

Structural organization of the bone marrow and its role in hematopoiesis.

The bone marrow is the main site for hematopoiesis. It contains a unique microenvironment that provides niches that support self-renewal and differentiation of hematopoietic stem cells (HSC), multipotent progenitors (MPP), and lineage committed progenitors to produce the large number of blood cells required to sustain life. The bone marrow is notoriously difficult to image; because of this the anatomy of blood cell production -- and how local signals spatially organize hematopoiesis -- are not well defined. Here we review our current understanding of the spatial organization of the mouse bone marrow with a special focus in recent advances that are transforming our understanding of this tissue. Imaging studies of HSC and their interaction with candidate niches have relied on ex-vivo imaging of fixed tissue. Two recent manuscripts demonstrating live imaging of subsets of HSC in unperturbed bone marrow have revealed unexpected HSC behavior and open the door to examine HSC regulation, in situ, over time. We also discuss recent findings showing that the bone marrow contains distinct microenvironments, spatially organized, that regulate unique aspects of hematopoiesis. Defining the spatial architecture of hematopoiesis in the bone marrow is indispensable to understand how this tissue ensures stepwise, balanced, differentiation to meet organism demand; for deciphering alterations to hematopoiesis during disease; and for designing organ systems for blood cell production ex vivo.

Bone Marrow (BM) Delivery of Genetically-Modified (gm) Adult CD34+ Hematopoietic Stem and Progenitor Cells (HSPC) Improves Homing and Engraftment of Short-Term Progenitors over Long-Term Repopulating Hematopoietic Stem Cells

Gene therapy/editing of CD34+ HSPC ex vivo, followed by their transplantation, can cure a variety of hematologic diseases. However, a substantial loss of HSPC occurs from collection to transplant. Losses occur during processing for HSPC enrichment, ex vivo genetic manipulation and culture, formulation, and testing prior to transplant. Further, HSPC are lost to peripheral organs during homing when delivered intravenously (IV), reducing the effective gm HSPC dose; a loss compounded by the lack of helper cells that aid in the homing and engraftment process which are removed during enrichment. Direct BM delivery of gm HSPC can overcome some of these limitations. This has been tried previously, with non-enriched whole cord blood (CB) and non-gm HSPC, with conflicting results. We hypothesized that BM delivery of a limited dose of gm adult HSPC would improve long-term repopulation over that of IV delivery by bypassing HSPC loss during homing. Using bioluminescent imaging, we determined that CB HSPC transduced with a luciferase lentiviral vector (LV) delivered by intra-femoral (IF) injection localized to the injected femur, validating our injection method. Next, we delivered mobilized peripheral blood (MPB) HSPC transduced with a GFP LV into irradiated NOD.LtSz-scid IL2rg -/- (NSG) mice via IV or IF injection in limiting dilution. Total human engraftment (hCD45+ cells), transduced human engraftment (hCD45+GFP+ cells), and multi-lineage engraftment were measured in the BM at 3- and 6-months post-transplant. HSPC gave rise to a bi-lineage (B-myeloid) graft at 3 months, suggesting hematopoietic progenitor cell (HPC) engraftment, and a multi-lineage graft (hCD33+, hCD19+, hCD3+, and hCD34+ cells) at 6 months, suggesting engraftment from a long-term repopulating cell or hematopoietic stem cell (HSC). At 3 months, IF delivery of HSPC resulted in significantly higher total and transduced human cell engraftment, measured in the non-injected femur (Table 1). The engraftment was bi-lineage. At 6 months, IF delivery of HSPC no longer significantly increased engraftment over IV delivery (Table 1). However, a multi-lineage graft was present, indicating full hematopoietic repopulation. There was no significant difference in the lineage output between either delivery method at 3 or 6 months. These data suggest that HPC homed and engrafted more efficiently than HSC, when delivered IF. Alternatively, IF delivery altered the BM microenvironment, allowing preferential homing of HPC. However, CD34- cells injected IF, to simulate pressure and passage of cells through the BM with IF delivery, followed by IV delivery of CD34+ cells (sham IF with IV HSPC delivery) resulted in similar homing patterns to CD34+ cells delivered IV (p=0.1, Figure 1A), suggesting that differences between IV and IF delivery were likely due to cell-intrinsic rather than cell-extrinsic differences between HPC and HSC. To study the mechanism of preferential engraftment of HPC over HSC with IF delivery, we analyzed expression of the major homing receptors CXCR4 and VLA-4 on HPC and HSC. CXCR4 (Figure 1B) and VLA-4 were both expressed at significantly higher levels on HPC than on HSC (CXCR4 p&amp;lt;0.01; VLA-4 p&amp;lt;0.05) and their expression increased with increasing culture time and with HSPC cycling. However, VLA-4 expression was significantly increased in GFP+ (MFI 65313 ± 4750) compared to GFP- (MFI 48969 ± 2099; p&amp;lt;0.01) HSPC. CXCR4 expression was similar in both GFP+ (MFI 4261 ± 189) and GFP- (MFI 5245 ± 1186) HSPC, mimicking the in vivo engraftment pattern of GFP+ and GFP- cells, suggesting that CXCR4 may be the molecule responsible for enhancing HPC homing and engraftment with BM delivery. An initial experiment shows that when we remove the high CXCR4 expressing CD34+38+ HPC and deliver HSC-enriched CD34+38- cells IV or IF, IF delivery results in higher long-term engraftment (additional experiments ongoing, Figure 1C, D). These data support the hypothesis that cell-intrinsic differences in the homing behavior of HSC and HPC is likely due to their differential expression of CXCR4. Studies underway on blockade of CXCR4 or VLA-4 on gm HPC and/or gm HSC followed by their IF or IV delivery will be presented. Overall, we show IV delivery of gm HSPC is comparable to BM delivery. However, as HSC-enriched cells become clinically available for genetic therapies, BM delivery of enriched gm HSC may result in superior engraftment. Disclosures Malik: Aruvant Sciences, Forma Therapeutics, Inc.: Consultancy; Aruvant Sciences, CSL Behring: Patents &amp; Royalties.

Perivascular Secretome Influences Hematopoietic Stem Cell Maintenance in a Gelatin Hydrogel.

Adult hematopoietic stem cells (HSCs) produce the body's full complement of blood and immune cells. They reside in specialized microenvironments, or niches, within the bone marrow. The perivascular niche near blood vessels is believed to help maintain primitive HSCs in an undifferentiated state but demonstration of this effect is difficult. In vivo studies make it challenging to determine the direct effect of the endosteal and perivascular niches as they can be in close proximity, and two-dimensional in vitro cultures often lack an instructive extracellular matrix environment. We describe a tissue engineering approach to develop and characterize a three-dimensional perivascular tissue model to investigate the influence of the perivascular secretome on HSC behavior. We generate 3D endothelial networks in methacrylamide-functionalized gelatin hydrogels using human umbilical vein endothelial cells (HUVECs) and mesenchymal stromal cells (MSCs). We identify a subset of secreted factors important for HSC function, and examine the response of primary murine HSCs in hydrogels to the perivascular secretome. Within 4 days of culture, perivascular conditioned media promoted maintenance of a greater fraction of hematopoietic stem and progenitor cells. This work represents an important first-generation perivascular model to investigate the role of niche secreted factors on the maintenance of primary HSCs.

In-vivo differentiation of adult hematopoietic stem cells from a single-cell point of view.

Although hematopoietic stem cell (HSC) function has long been studied by transplantation assays, this does not reflect what HSCs actually do in their native context. Here, we review recent technologic advances that facilitate the study of HSCs in their native context focusing on inducible HSC-specific lineage tracing and inference of hematopoietic trajectories through single-cell RNA sequencing (scRNA-Seq). Lineage tracing of HSCs at the population level using multiple systems has suggested that HSCs make a major contribution to steady-state hematopoiesis. Although several genetic systems and novel methods for lineage tracing individual hematopoietic clones have been described, the technology for tracking these cellular barcodes (in particular mutations or insertion sites) is still in its infancy. Thus, lineage tracing of HSC clones in the adult bone marrow remains elusive. Static snapshots of scRNA-Seq of hematopoietic populations have captured the heterogeneity of transcriptional profiles of HSCs and progenitors, with some cells displaying a unilineage signature as well as others with bi or multipotent lineage profiles. Kinetic analysis using HSC-specific lineage tracing combined with scRNA-Seq confirmed this heterogeneity of progenitor populations and revealed a rapid and early emergence of megakaryocytic progeny, followed by erythroid and myeloid lineages, whereas lymphoid differentiation emerged last. New approaches to study HSCs both in vivo through lineage tracing and at a high-resolution molecular level through scRNA-Seq are providing key insight into HSC differentiation in the absence of transplantation. Recent studies using these approaches are discussed here. These studies pave the way for integration of in-vivo clonal analysis of HSC behavior over time with single-cell sequencing data, including but not limited to transcriptomic, proteomic, and epigenomic, to establish a comprehensive molecular and cellular map of hematopoiesis.

Clonal hematopoiesis in donors and long-term survivors of related allogeneic hematopoietic stem cell transplantation

AbstractClonal hematopoiesis (CH) is associated with age and an increased risk of myeloid malignancies, cardiovascular risk, and all-cause mortality. We tested for CH in a setting where hematopoietic stem cells (HSCs) of the same individual are exposed to different degrees of proliferative stress and environments, ie, in long-term survivors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) and their respective related donors (n = 42 donor-recipient pairs). With a median follow-up time since allo-HSCT of 16 years (range, 10-32 years), we found a total of 35 mutations in 23 out of 84 (27.4%) study participants. Ten out of 42 donors (23.8%) and 13 out of 42 recipients (31%) had CH. CH was associated with older donor and recipient age. We identified 5 cases of donor-engrafted CH, with 1 case progressing into myelodysplastic syndrome in both donor and recipient. Four out of 5 cases showed increased clone size in recipients compared with donors. We further characterized the hematopoietic system in individuals with CH as follows: (1) CH was consistently present in myeloid cells but varied in penetrance in B and T cells; (2) colony-forming units (CFUs) revealed clonal evolution or multiple independent clones in individuals with multiple CH mutations; and (3) telomere shortening determined in granulocytes suggested ∼20 years of added proliferative history of HSCs in recipients compared with their donors, with telomere length in CH vs non-CH CFUs showing varying patterns. This study provides insight into the long-term behavior of the same human HSCs and respective CH development under different proliferative conditions.

Differential Alternative Polyadenylation Landscapes Mediate Hematopoietic Stem Cell Activation and Regulate Glutamine Metabolism.

Alternative polyadenylation (APA) is emerging as an important regulatory mechanism of RNA and protein isoform expression by controlling 3' untranslated region (3'-UTR) composition. The relevance of APA in stem cell hierarchies remains elusive. Here, we first demonstrate the requirement of the APA regulator Pabpn1 for hematopoietic stem cell (HSC) function. We then determine the genome-wide APA landscape (APAome) of HSCs and progenitors by performing low-input 3' sequencing paired with bioinformatic pipelines. This reveals transcriptome-wide dynamic APA patterns and an overall shortening of 3'-UTRs during differentiation and upon homeostatic or stress-induced transition from quiescence to proliferation. Specifically, we show that APA regulates activation-induced Glutaminase (Gls) isoform switching by Nudt21. This adaptation of the glutamine metabolism by increasing the GAC:KGA isoform ratio fuels versatile metabolic pathways necessary for HSC self-renewal and proper stress response. Our study establishes APA as a critical regulatory layer orchestrating HSC self-renewal, behavior, and commitment.

Inflammageing of Hematopoietic Stem Cells Is Driven By IL-1

Introduction: Lifelong blood production is sustained through a stepwise differentiation program by a limited number of self-renewing hematopoietic stem cells (HSCs) in the bone marrow (BM). Hematopoietic cell development is tightly controlled by both cell-intrinsic and -extrinsic factors and its dysregulation can lead to aplasia or neoplasia. During ageing, HSCs increase in number, reduce self-renewal capacity on a per cell basis, skew towards myeloid differentiation, and show less efficient bone marrow (BM)-homing ability. We here evaluated how and to what extend HSC-extrinsic factors determine HSC behaviour during aging. Methods, Results and Discussion: To screen for aging-associated extrinsic factors, we performed antibody based protein arrays and transcriptome analysis with total BM of young (6-8 week old) versus aged (2 year old) animals. This demonstrated that RANTES, MIP-2, IL-1α and IL-1β are significantly upregulated in aged BM at both the protein as well as the RNA level. ELISA of peripheral blood (PB) serum and BM lysates indicated that IL-1α and IL-1β are locally increased and produced in BM, but are not significantly increased in PB serum. Further, qPCR of various BM cell types of hematopoietic (myeloid, lymphoid and progenitor cells) and non-hematopoietic/stromal origin indicated that multiple cell types upregulate Il1α and Il1β, with highest increase being derived from myeloid hematopoietic cells. This raised the possibility that elevated IL-1 is a result of an inflammatory response to circulating pathogen-derived compounds, possibly of bacterial origin. Indeed, we previously demonstrated that steady-state levels of granulopoiesis in young steady-state mice depend on heat-resistant microbiota-derived compounds (M.Balmer et al., The Journal of Immunology 2014). To prospectively test the role of IL-1-induced signalling and the microbiome during aging, we investigated the ageing-associated phenotype of HSCs in young and aged IL1RIKO mice and in young and aged germ-free mice. Both IL1RIKO and germ-free aged mice had lower counts of platelets and neutrophils in PB, and lower frequency of LT-HSCs (LKS Flt3-CD34-CD48-CD150+) in BM, compared to aged WT mice. Moreover, aged IL1RIKO LT-HSCs showed improved lymphoid lineage repopulation upon transplantation into lethally irradiated WT mice, compared to LT-HSCs of aged WT mice that demonstrated the known myeloid-biased lineage output. Interestingly, LT-HSCs from aged germ-free mice also demonstrated lymphoid-biased lineage differentiation as observed from young mice. In line with this finding, no difference was observed in IL-1α and IL-1β protein concentrations in BM lysates from young and aged germ-free mice. To test if IL-1 increase in aged steady-state mouse BM is indeed dependent on ligation of pattern recognition receptors and consecutive signalling, we analysed MyD88 and Trif KO mice, respectively. Both aged KO mice showed compared to WT mice reduced BM IL-1 levels and a reduced ageing-phenotype of HSCs, with the most profound difference in Trif KO mice. Interestingly, this correlates with our previous finding on pathogen-Induced TLR4-TRIF innate immune signaling in HSCs, inducing reduced competitive fitness (Takizawa et al., Cell Stem Cell 2017). Conclusions: Our data demonstrate that ageing associated phenotype and myeloid-biased differentiation of HSCs is a result of signals derived from the microbiome, that act through increased IL-1 signalling, locally in BM. Disclosures No relevant conflicts of interest to declare.

ALTERNATIVE POLYADENYLATION REGULATES HEMATOPOIETIC STEM CELL METABOLISM

Alternative Polyadenylation (APA) is emerging as an important regulatory mechanism controlling 3’-UTRs and thereby RNA and protein isoform expression. However, the relevance of APA in stem cell hierarchies in vivo remains unexplored. Here, we show that deregulation of the APA regulator Pabpn1 results in severe hematopoietic stem cell (HSC) defects. Furthermore, we performed low input 3’-sequencing and established bioinformatic pipelines to uncover dynamic APA patterns in numerous genes of HSCs and multipotent progenitors. The 3’-UTRs of HSCs undergo shortening upon transition from quiescence to proliferation during homeostasis and in response to inflammation as well as during HSC differentiation. Strikingly, we observe APA-mediated metabolic reprogramming upon HSC activation leading to an increase in glutaminolysis. This increase is mediated by APA regulators and required for proper HSC function. Inhibition of this metabolic adjustment by targeting APA-regulators leads to impaired HSC function and a partial block in differentiation. Our study establishes APA and associated adaptations of the glutamine metabolism as novel layers of regulation that orchestrate HSC behavior and commitment in the hematopoietic cascade.

Mitochondrial metabolism and the maintenance of hematopoietic stem cell quiescence.

Hematopoietic stem cells (HSCs) are characterized by a potent multilineage regenerative capability that is dependent on their quiescence property. In the past few decades, researchers have found many intrinsic and niche-derived factors that can regulate HSCs, whereas how to precisely control HSC behaviors remains elusive. Recently, mitochondrial metabolism has been shown to be involved in the regulation of HSC biology. The purpose of this review is to overview recent advances in the relationship between mitochondrial metabolism and maintenance of HSC quiescence. On the basis of fact that HSCs are heterogeneous populations that have their unique metabolic characteristics, increasing studies have demonstrated that the quiescence and function of HSCs are closely correlated with the mitochondrial mass and activity, as well as the levels of mitochondria-derived reactive oxygen species and metabolites. Apart from that, mitochondria have been reported to undergo internal protective programs, including mitochondrial unfolded protein response, autophagy and mitochondrial dynamics, which are beneficial to maintaining HSC homeostasis. The maintenance of HSC quiescence needs a metabolic balance in mitochondria, and unraveling the metabolic complexity may provide deep understanding of the functional heterogeneity of HSCs.