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Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Mapping the chromatin dynamics of functionally defined cell populations will shed mechanistic insight into 2 major, unanswered questions in stem cell biology: how does epigenetic identity contribute to a cell type’s lineage potential, and how do cascades of chromatin remodeling dictate ensuing fate decisions? Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. Oligopotent progenitor populations operating between the HSCs and unipotent cells play essential roles in effecting hematopoietic homeostasis. To test the hypothesis that selective HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during progenitor differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points. Additionally, quantification of genome-wide peak count and size revealed overall greater chromatin accessibility in HSCs, allowing us to identify HSC-unique peaks as putative regulators of self-renewal and multilineage potential. Finally, CRISPRi-mediated targeting of ATACseq-identified putative CREs in HSCs allowed us to demonstrate the functional role of selective CREs in lineage-specific gene expression. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome engineering has emerged as a powerful tool to modify precise genomic sequences with unparalleled accuracy and efficiency. Major advances in CRISPR technologies over the last 5 years have fueled the development of novel techniques in hematopoiesis research to interrogate the complexities of hematopoietic stem cell (HSC) biology. In particular, high throughput CRISPR based screens using various "flavors" of Cas coupled with sequencing and/or functional outputs are becoming increasingly efficient and accessible. In this review, we discuss recent achievements in CRISPR-mediated genomic engineering and how these new tools have advanced the understanding of HSC heterogeneity and function throughout life. Additionally, we highlight how these techniques can be used to answer previously inaccessible questions and the challenges to implement them. Finally, we focus on their translational potential to both model and treat hematological diseases in the clinic.

Hematopoietic stem cells (HSCs) have been studied extensively since their initial functional description in 1961 when Dr. James Till and Dr. Ernest McCulloch developed the first in vivo clonal strategy, termed the "spleen colony-forming unit" (CFU-S) assay, to assess the functional capacity of bone marrow–derived hematopoietic progenitors at the single-cell level. Through transplantation of bone marrow cells and analysis of the resulting cellular nodules in the spleen, the CFU-S assay revealed both the self-renewal and clonal differentiation capacity of hematopoietic progenitors. Further development and use of this assay have identified highly proliferative, self-renewing, and differentiating HSCs that possess clonal, multilineage differentiation. The CFU-S strategy has also been adapted to interrogating single purified hematopoietic stem and progenitor cell populations, advancing our knowledge of the hematopoietic hierarchy. In this review, we explore the major discoveries made with the CFU-S assay, consider its modern use and recent improvements, and compare it with commonly used long-term transplantation assays to determine the continued value of the CFU-S assay for understanding HSC biology and hematopoiesis.

Simple Summary E-cigarettes have gained popularity as alternatives to traditional tobacco products over the past several decades. Despite being marketed as safer, they still contain several highly toxic compounds, which pose as dangers to human health. Nicotine is one of those toxic compounds and is known to have many deleterious effects on human health and disease susceptibility. Hematopoietic stem cells (HSCs) are the stem cells that give rise to the entire immune system and therefore serve as a compelling point of interrogation for the source of altered health and disease susceptibility in exposed individuals. Here we discuss how nicotine influences HSCs and the immune cells they make, as well as highlight potential mechanisms of altered immunity for life. Abstract Hematopoiesis is a tightly regulated process orchestrated by cell-intrinsic and cell-extrinsic cues. Over the past several decades, much effort has been focused on understanding how these cues regulate hematopoietic stem cell (HSC) function. Many endogenous key regulators of hematopoiesis have been identified and extensively characterized. Less is known about the mechanisms of long-term effects of environmental toxic compounds on hematopoietic stem and progenitor cells (HSPCs) and their mature immune cell progeny. Research over the past several decades has demonstrated that tobacco products are extremely toxic and pose huge risks to human health by causing diseases like cancer, respiratory illnesses, strokes, and more. Recently, electronic cigarettes have been promoted as a safer alternative to traditional tobacco products and have become increasingly popular among younger generations. Nicotine, the highly toxic compound found in many traditional tobacco products, is also found in most electronic cigarettes, calling into question their purported “safety”. Although it is known that nicotine is toxic, the pathophysiology of disease in exposed people remains under investigation. One plausible contributor to altered disease susceptibility is altered hematopoiesis and associated immune dysfunction. In this review, we focus on research that has addressed how HSCs and mature blood cells respond to nicotine, as well as identify remaining questions.

Summary Age-related morbidity is associated with a decline in hematopoietic stem cell (HSC) function, but the mechanisms of HSC aging remain unclear. We performed heterochronic HSC transplants followed by quantitative analysis of cell reconstitution. Although young HSCs outperformed old HSCs in young recipients, young HSCs unexpectedly failed to outcompete the old HSCs of aged recipients. Interestingly, despite substantial enrichment of megakaryocyte progenitors (MkPs) in old mice in situ and reported platelet (Plt) priming with age, transplanted old HSCs were deficient in reconstitution of all lineages, including MkPs and Plts. We therefore performed functional analysis of young and old MkPs. Surprisingly, old MkPs displayed unmistakably greater regenerative capacity compared with young MkPs. Transcriptome analysis revealed putative molecular regulators of old MkP expansion. Collectively, these data demonstrated that aging affects HSCs and megakaryopoiesis in fundamentally different ways: whereas old HSCs functionally decline, MkPs gain expansion capacity upon aging., Graphical abstract, Highlights • Reconstitution deficit by old HSCs was observed by chimerism and absolute cell numbers • Young HSCs did not outcompete resident HSCs in aged recipient mice • Old MkPs display remarkable capacity to engraft, expand, and reconstitute platelets • Aging is associated with changes in MkP genome-wide expression signatures, Poscablo et al. explored age-related changes to hematopoietic stem cell and megakaryocyte progenitor (MkP) function. They found an unexpected gain of in vitro expansion and in vivo reconstitution potential of MkPs upon aging. These functional changes were accompanied by differences in transcriptome profiles between young and old MkPs, suggesting progenitor cell mechanisms contributing to hematopoietic aging.

Adult hematopoietic stem and progenitor cells (HSPCs) respond directly to inflammation and infection, resulting in both acute and persistent changes to quiescence, mobilization, and differentiation. Here we show that fetal HSPCs respond to prenatal inflammation in utero, and that the fetal response shapes postnatal hematopoiesis and immunity. Heterogenous fetal HSPCs showed divergent responses to maternal immune activation (MIA), including changes in quiescence, expansion, and lineage-biased output. Single cell transcriptomic analysis of fetal HSPCs in response to MIA revealed specific upregulation of inflammatory gene profiles in discrete, transient HSC populations, that propagated expansion of lymphoid-biased progenitors. Beyond fetal development, MIA caused the inappropriate expansion and persistence of fetal lymphoid-biased progenitors postnatally, concomitant with increased cellularity and hyperresponsiveness of fetal-derived innate-like lymphocytes. Our investigation demonstrates how inflammation in utero can direct the trajectory of output and function of fetal-derived immune cells by reshaping fetal HSC establishment.

Our respiratory system is vital to protect us from the surrounding nonsterile environment; therefore, it is critical for a state of homeostasis to be maintained through a balance of inflammatory cues. Recent studies have shown that actively transcribed noncoding regions of the genome are emerging as key regulators of biological processes, including inflammation. lincRNA-Cox2 is one such example of an inflammatory inducible long intergenic noncoding RNA functioning to fine-tune immune gene expression. Using bulk and single-cell RNA sequencing, in addition to FACS, we find that lincRNA-Cox2 is most highly expressed in the lung and is most upregulated after LPS-induced lung injury (acute lung injury [ALI]) within alveolar macrophages, where it functions to regulate inflammation. We previously reported that lincRNA-Cox2 functions to regulate its neighboring protein Ptgs2 in cis, and in this study, we use genetic mouse models to confirm its role in regulating gene expression more broadly in trans during ALI. Il6, Ccl3, and Ccl5 are dysregulated in the lincRNA-Cox2–deficient mice and can be rescued to wild type levels by crossing the deficient mice with our newly generated lincRNA-Cox2 transgenic mice, confirming that this gene functions in trans. Many genes are specifically regulated by lincRNA-Cox2 within alveolar macrophages originating from the bone marrow because the phenotype can be reversed by transplantation of wild type bone marrow into the lincRNA-Cox2–deficient mice. In conclusion, we show that lincRNA-Cox2 is a trans-acting long noncoding RNA that functions to regulate immune responses and maintain homeostasis within the lung at baseline and on LPS-induced ALI.

Adult hematopoietic stem and progenitor cells (HSPCs) respond directly to inflammation and infection, causing both acute and persistent changes to quiescence, mobilization, and differentiation. Here we show that murine fetal HSPCs respond to prenatal inflammation in utero and that the fetal response shapes postnatal hematopoiesis and immune cell function. Heterogeneous fetal HSPCs show divergent responses to maternal immune activation (MIA), including changes in quiescence, expansion, and lineage-biased output. Single-cell transcriptomic analysis of fetal HSPCs in response to MIA reveals specific upregulation of inflammatory gene profiles in discrete, transient hematopoietic stem cell (HSC) populations that propagate expansion of lymphoid-biased progenitors. Beyond fetal development, MIA causes the inappropriate expansion and persistence of fetal lymphoid-biased progenitors postnatally, concomitant with increased cellularity and hyperresponsiveness of fetal-derived innate-like lymphocytes. Our investigation demonstrates how inflammation in utero can direct the output and function of fetal-derived immune cells by reshaping fetal HSC establishment.

Recovery from pneumococcal pneumonia remodels the pool of alveolar macrophages so that they exhibit new surface marker profiles, transcriptomes, metabolomes, and responses to infection. Mechanisms mediating alveolar macrophage phenotypes after pneumococcal pneumonia have not been delineated. IFN-γ and its receptor on alveolar macrophages were essential for certain, but not all, aspects of the remodeled alveolar macrophage phenotype. IFN-γ was produced by CD4+ T cells plus other cells, and CD4+ cell depletion did not prevent alveolar macrophage remodeling. In mice infected or recovering from pneumococcus, monocytes were recruited to the lungs, and the monocyte-derived macrophages developed characteristics of alveolar macrophages. CCR2 mediated the early monocyte recruitment but was not essential to the development of the remodeled alveolar macrophage phenotype. Lineage tracing demonstrated that recovery from pneumococcal pneumonias converted the pool of alveolar macrophages from being primarily of embryonic origin to being primarily of adult hematopoietic stem cell origin. Alveolar macrophages of either origin demonstrated similar remodeled phenotypes, suggesting that ontogeny did not dictate phenotype. Our data reveal that the remodeled alveolar macrophage phenotype in lungs recovered from pneumococcal pneumonia results from a combination of new recruitment plus training of both the original cells and the new recruits.

Hematopoietic stem cell (HSC) multipotency and self-renewal are typically defined through serial transplantation experiments. Host conditioning is necessary for robust HSC engraftment, likely by reducing immune-mediated rejection and by clearing limited HSC niche space. Because irradiation of the recipient mouse is non-specific and broadly damaging, there is a need to develop alternative models to study HSC performance at steady-state and in the absence of radiation-induced stress. We have generated and characterized two new mouse models where either all hematopoietic cells or only HSCs can be specifically induced to die in vivo or in vitro. Hematopoietic-specific Vav1-mediated expression of a loxP-flanked diphtheria-toxin receptor (DTR) renders all hematopoietic cells sensitive to diphtheria toxin (DT) in “Vav-DTR” mice. Crossing these mice to Flk2-Cre mice results in “HSC-DTR” mice which exhibit HSC-selective DT sensitivity. We demonstrate robust, rapid, and highly selective cell ablation in these models. These new mouse models provide a platform to test whether HSCs are required for long-term hematopoiesis in vivo, for understanding the mechanisms regulating HSC engraftment, and interrogating in vivo hematopoietic differentiation pathways and mechanisms regulating hematopoietic homeostasis.

Tissue-resident lymphoid cells (TLCs) span the spectrum of innate-to-adaptive immune function. Unlike traditional, circulating lymphocytes that are continuously generated from hematopoietic stem cells (HSCs), many TLCs are of fetal origin and poorly generated from adult HSCs. Here, we sought to further understand murine TLC development and the roles of Flk2 and IL7Rα, two cytokine receptors with known function in traditional lymphopoiesis. Using Flk2- and Il7r-Cre lineage tracing, we found that peritoneal B1a cells, splenic marginal zone B (MZB) cells, lung ILC2s and regulatory T cells (Tregs) were highly labeled. Despite high labeling, loss of Flk2 minimally affected the generation of these cells. In contrast, loss of IL7Rα, or combined deletion of Flk2 and IL7Rα, dramatically reduced the number of B1a cells, MZBs, ILC2s and Tregs, both in situ and upon transplantation, indicating an intrinsic and essential role for IL7Rα. Surprisingly, reciprocal transplants of wild-type HSCs showed that an IL7Rα−/− environment selectively impaired reconstitution of TLCs when compared with TLC numbers in situ. Taken together, our data defined Flk2- and IL7Rα-positive TLC differentiation paths, and revealed functional roles of Flk2 and IL7Rα in TLC establishment.

Summary Hematopoietic stem cell (HSC) transplantation is a curative treatment for a variety of blood and immune disorders. Currently available methods to obtain donor HSCs are suboptimal, and the limited supply of donor HSCs hampers the success and availability of HSC transplantation therapies. We recently showed that manipulation of vascular integrity can be employed to induce HSC mobilization from the bone marrow to the blood stream, facilitating non-invasive collection of HSCs. Here, we tested whether FDA-approved vasodilators are capable of mobilizing HSCs. We found that a rapid, 2-h regimen of a single oral dose of Viagra (sildenafil citrate) combined with a single injection of the CXCR4 antagonist AMD3100 leads to efficient HSC mobilization at levels rivaling the standard-of-care 5-day regimen of granulocyte-colony stimulating factor (G-CSF/Filgrastim/Neupogen). Our findings solidify vascular integrity as an essential regulator of HSC trafficking and provide an attractive, single-day regimen for HSC mobilization using already FDA-approved drugs., Graphical Abstract, Highlights • Viagra enhances AMD3100-mediated HSC mobilization • Extremely rapid and efficient HSC mobilization with two FDA-approved drugs • Vascular integrity regulates HSC trafficking, In this article, Forsberg and colleagues demonstrate that Viagra, a widely used vasodilator, enhances Plerixafor-mediated hematopoietic stem cell (HSC) mobilization from the bone marrow to the blood stream. These findings solidify vascular integrity as an essential regulator of HSC trafficking and provide an attractive, single-day regimen for HSC mobilization using already FDA-approved drugs.

Summary Hematopoiesis is arguably one of the best understood stem cell systems; however, significant challenges remain to reach a consensus understanding of the lineage potential, heterogeneity, and relationships of hematopoietic stem and progenitor cell populations. To gain new insights, we performed quantitative analyses of mature cell production from hematopoietic stem cells (HSCs) and multiple hematopoietic progenitor populations. Assessment of the absolute numbers of mature cell types produced by each progenitor cell revealed a striking erythroid dominance of all myeloid-competent progenitors assessed, accompanied by strong platelet reconstitution. All populations with myeloid potential also produced robust numbers of red blood cells and platelets in vivo. Clonal analysis by single-cell transplantation and by spleen colony assays revealed that a significant fraction of HSCs and multipotent progenitors have multilineage potential at the single-cell level. These new insights prompt an erythroid-focused model of hematopoietic differentiation., Graphical Abstract, Highlights • RBCs are the predominant cell type produced by multipotent hematopoietic progenitors • All cell types with myeloid potential also produced RBCs and platelets in vivo • Single HSCs and MPPF cells are capable of multilineage hematopoietic reconstitution • Erythroid cell production emerges as a default hematopoietic fate, In this article, Forsberg and colleagues use quantitative reconstitution assays to demonstrate that all myeloid-competent progenitor cells also contribute to erythroid and platelet production. Single-cell in vivo analyses showed that hematopoietic stem cells and multipotent progenitors are clonally multipotent. These results suggest that erythropoiesis is a default hematopoietic fate and challenges current views on hematopoietic lineage potential and fate decisions.

Hematopoietic stem cells (HSCs) have the capacity to differentiate into vastly different types of mature blood cells. The epigenetic mechanisms regulating the multilineage ability, or multipotency of HSCs are not well understood. To test the hypothesis thatcisregulatory elements that control fate decisions for all lineages are primed in HSCs, we used ATAC-seq to compare chromatin accessibility of HSCs with five unipotent cell types. We observed the highest similarity in accessibility profiles between Megakaryocyte Progenitors and HSCs, whereas B cells had the greatest number of regions withde novogain in accessibility during differentiation. Despite these differences, we identifiedcisregulatory elements from all lineages that displayed epigenetic priming in HSCs. These findings provide new insights into the regulation of stem cell multipotency, as well as a resource to identify functional drivers of lineage fate.HIGHLIGHTSHSCs have higher global chromatin accessibility than any unilineage progenyMegakaryocyte Progenitors are the most closely related unipotent cell type to HSCsB cell commitment involvesde novochromatin accessibilityEvidence ofciselement priming of lineage-specific genes in HSCs

Platelets provide life-saving functions by halting external and internal bleeding. There is also a dark side to platelet biology, however. Recent reports provide evidence for increased platelet reactivity during aging of mice and humans, making platelets main suspects in the most prevalent aging-related human pathologies, including cardiovascular diseases, stroke, and cancer. What drives this platelet hyperreactivity during aging? Here, we discuss how hematopoietic stem cell differentiation pathways into the platelet lineage offer avenues to understand the fundamental differences between young and old platelets. Recent advances begin to unravel how the cellular and molecular regulation of the parent hematopoietic stem and progenitor cells likely imbue aging characteristics on the resulting Plt progeny. The resulting mechanistic insights into intrinsic platelet reactivity will provide strategies for selectively targeting age-related pathways. This brief viewpoint focuses on current concepts on aging hematopoiesis and the implications for platelet hyperactivity during aging.

Hematopoietic stem cell (HSC) trafficking is regulated by a number of complex mechanisms. Among them are the transmembrane protein Robo4 and the vascular cell adhesion molecule, VCAM1. Endothelial VCAM1 is a well-known regulator of hematopoietic cell trafficking, and our previous studies revealed that germline deletion of Robo4 led to impaired HSC trafficking, with an increase in vascular endothelial cell (VEC) numbers and downregulation of VCAM1 protein on sinusoidal VECs. Here, we utilized two Robo4 conditional deletion models in parallel with Robo4 germline knockout mice (R4KO) to evaluate the effects of acute and endothelial cell-specific Robo4 deletion on HSC trafficking. Strikingly similar to the R4KO, the acute deletion of Robo4 resulted in altered HSC distribution between the bone marrow and blood compartments, despite normal numbers of VECs and wild-type levels of VCAM1 cell surface protein on sinusoidal VECs. Additionally, consistent with the R4KO mice, acute loss of Robo4 in the host perturbed long-term engraftment of donor wild-type HSCs and improved HSC mobilization to the peripheral blood. These data demonstrate the significant role that endothelial Robo4 plays in directional HSC trafficking, independent of alterations in VEC numbers and VCAM1 expression.

Hematopoietic stem and progenitor cell (HSPC) transplantation is the paradigm for stem cell therapies. The protocol described here enables quantitative assessment of the body-wide HSPC reconstitution of different mature hematopoietic cells in mice based on their presence in circulating blood. The method determines donor-derived mature cell populations per mouse, over time, by quantitatively obtaining their absolute numbers in the peripheral blood and utilizing previously assessed tissue-distribution factors. A Markov-based birth/death computational model accounts for the drastic differences in mature cell half-lives. By quantifying the number of cells produced and eliminating host variability, the protocol can be used to directly compare the lineage output of different types of HSPCs on a per cell basis, thereby clarifying the lineage potential and expansion capacity of different cell populations. These protocols were developed for hematopoiesis, but can readily be extended to other contexts by simply replacing the cell types and distributions.HighlightsQuantitative assessment of stem and progenitor cell reconstitution capacityElimination of cell-specific recipient variability for accurate donor cell potentialDirectly comparable lineage output within and between stem and progenitor cellsBlood-based absolute quantification of whole-body repopulation over timeMarkov modelling-based consideration of differential mature cell half-lives

Respiratory diseases are a leading cause of death worldwide, with highly varied vulnerability to disease between individuals. The underlying reasons of disease susceptibility are unknown, but often include a variable immune response in lungs. Recently, we identified a surprising novel role of the interleukin 7 receptor (IL7R), a primarily lymphoid-associated regulator, in fetal-specified, lung-resident macrophage development. Here, we report that traditional, hematopoietic stem cell-derived myeloid cells in the adult lung, peripheral blood, and bone marrow also depend on IL7R expression. Using single and double germline knockout models, we found that eosinophil numbers were reduced upon deletion of IL7Rα. We then employed two Cre recombinase models in lineage tracing experiments to test whether these cells developed through an IL7Rα+ pathway. Despite the impact of IL7Rα deletion, IL7R-Cre labeled only a minimal fraction of eosinophils. We therefore examined the intrinsic versus extrinsic requirement for IL7R in the production of eosinophils using reciprocal hematopoietic stem cell transplantation assays. These assays revealed that extrinsic, but not eosinophil-intrinsic, IL7R is required for eosinophil reconstitution by HSCs in the adult lung. To determine which external factors may be influencing eosinophil development and survival, we performed a cytokine array analysis between wild-type and IL7Rα-deficient mice and found several differentially regulated proteins. These findings expand upon our previous publication that IL7R is required not only for proper lymphoid cell development and homeostasis, but also for myeloid cell homeostasis in tissues.

Respiratory diseases are a leading cause of death worldwide, with highly varied vulnerability to disease between individuals. The underlying reasons of disease susceptibility are unknown, but often include a variable immune response in lungs. Recently, we identified a surprising novel role of the interleukin 7 receptor (IL7R), a primarily lymphoid-associated regulator, in fetal-specified, lung-resident macrophage development. Here, we report that traditional, hematopoietic stem cell-derived myeloid cells in the adult lung, peripheral blood, and bone marrow also depend on IL7R expression. Using single and double germline knockout models, we found that eosinophil numbers were reduced upon deletion of IL7Rα. We then employed two Cre recombinase models in lineage tracing experiments to test whether these cells developed through an IL7Rα+ pathway. Despite the impact of IL7Rα deletion, IL7R-Cre labeled only a minimal fraction of eosinophils. We therefore examined the intrinsic versus extrinsic requirement for IL7R in the production of eosinophils using reciprocal hematopoietic stem cell transplantation assays. These assays revealed that extrinsic, but not eosinophil-intrinsic, IL7R is required for eosinophil reconstitution by HSCs in the adult lung. To determine which external factors may be influencing eosinophil development and survival, we performed a cytokine array analysis between wild-type and IL7Rα-deficient mice and found several differentially regulated proteins. These findings expand upon our previous publication that IL7R is required not only for proper lymphoid cell development and homeostasis, but also for myeloid cell homeostasis in tissues.HighlightsLoss of IL7Rα resulted in significantly fewer eosinophils in adult miceIL7R-Cre lineage tracing revealed minimal labeling of eosinophilsIL7Rα-deficient HSCs robustly reconstituted eosinophils in a WT hostWT HSCs failed to fully reconstitute eosinophils in IL7Rα-/- hostsSeveral cytokines are differentially expressed in WT and IL7Rα-deficient mice

High-content phenotypic screening has become the approach of choice for drug discovery due to its ability to extract drug-specific multi-layered data. In the field of epigenetics, such screening methods have suffered from a lack of tools sensitive to selective epigenetic perturbations. Here we describe a novel approach, Microscopic Imaging of Epigenetic Landscapes (MIEL), which captures the nuclear staining patterns of epigenetic marks and employs machine learning to accurately distinguish between such patterns. We validated the MIEL platform across multiple cells lines and using dose-response curves, to insure the fidelity and robustness of this approach for high content high throughput drug discovery. Focusing on noncytotoxic glioblastoma treatments, we demonstrated that MIEL can identify and classify epigenetically active drugs. Furthermore, we show MIEL was able to accurately rank candidate drugs by their ability to produce desired epigenetic alterations consistent with increased sensitivity to chemotherapeutic agents or with induction of glioblastoma differentiation., eLife digest Each cell contains a complete copy of a person’s genes coded in their DNA. However, for a cell to perform its specific role, it only needs a small fraction of this genetic information. The mechanisms that control which genes a cell is using fall under the umbrella of ‘epigenetics’ (meaning beyond genetics). These mechanisms involve changes in the way that DNA is organized inside the cell nucleus and changes in how accessible different parts of the genome are to various cellular components. DNA is long and fragile so, to maintain its integrity, it is wrapped around protein complexes called histones. Adding chemical modifications to histones is one of the main epigenetic mechanisms that cells use to regulate which genes are turned on and off. Several methods allow researchers to read patterns of histone modification and use this information to derive what state a cell is in and how it might behave. Improving these methods is of particular interest in drug development, where this information could reveal the effects, and side-effects, of new treatments. Unfortunately, existing techniques are costly in both time and money, and they are not well suited to analyzing epigenetic changes caused by the large numbers of compounds tested during drug development. To overcome this barrier, Farhy et al. have developed a new system called ‘Microscopic Imaging of the Epigenetic Landscape’ (MIEL for short). The system allows them to quickly analyze the epigenetic changes caused by each of a large number of different chemical compounds when they are used on cells. MIEL tags different histone modifications by staining each with a different color, and then uses automated microscopy to produce images. It then extracts information from these images using advanced image analysis tools. The changes induced by different drugs can then be compared and categorized using machine learning algorithms. To test the MIEL system, Farhy et al. grew brain cancer cells (derived from human tumors) in the lab, and treated them with compounds that target proteins involved in histone modifications. Using their newly created pipeline, Farhy et al. were able to identify the unique epigenetic changes caused by these compounds, and train the system to correctly predict which type of drug the cells had been treated with. In a different set of experiments Farhy et al. demonstrate the utility of their new pipeline in identifying drugs that induce a set of epigenetic changes associated with a reduced ability to regrow tumors. This new system could help screen thousands of compounds for their epigenetic effects, which could aid the design of new treatments for many diseases.

Hematopoiesis is the process by which mature blood and immune cells are produced from hematopoietic stem and progenitor cells (HSCs and HSPCs). The last several decades of research have shed light on the origin of HSCs, as well as the heterogeneous pools of fetal progenitors that contribute to lifelong hematopoiesis. The overarching concept that hematopoiesis occurs in dynamic, overlapping waves throughout development, with each wave contributing to both continuous and developmentally limited cell types, has been solidified over the years. However, recent advances in our ability to track the production of hematopoietic cells in vivo have challenged several long-held dogmas on the origin and persistence of distinct hematopoietic cell types. In this review, we highlight emerging concepts in hematopoietic development and identify unanswered questions.

With the advent of automatic cell imaging and machine learning, high-content phenotypic screening has become the approach of choice for drug discovery because it can extract drug-specific multi-layered data, which could be compared to known profiles. In the field of epigenetics, such screening approaches have suffered from a lack of tools sensitive to selective epigenetic perturbations. Here we describe a novel approach, Microscopic Imaging of Epigenetic Landscapes (MIEL), which captures the nuclear staining patterns of epigenetic marks (e.g., acetylated and methylated histones) and employs machine learning to accurately distinguish between such patterns. We validated the fidelity and robustness of the MIEL platform across multiple cells lines using dose-response curves. We employed MIEL to uncover the mechanism by which bromodomain inhibitors synergize with temozolomide-mediated killing of human glioblastoma lines. To explore alternative, non-cytotoxic, glioblastoma treatment, we screen the Prestwick chemical library and documented the power of MIEL platform to identify epigenetically active drugs and accurately rank them according to their ability to produce epigenetic and transcriptional alterations consistent with the induction of glioblastoma differentiation.

Hematopoietic stem cells (HSCs) have long been considered the continuous source of all hematopoietic cells for the life of an individual. Recent findings have questioned multiple aspects of this view, including the ability of lifelong HSCs to contribute to tissue-resident immune cells. Here we discuss the most recent findings on the source of B1a cells, innatelike lymphocytes that primarily reside in serous cavities. Powerful experimental approaches including bar coding, single cell transplantation, in vivo lineage tracing, and HSC-specific pulse-chase labeling have provided novel insights on B1a-cell generation during ontogeny. We evaluate the evidence for fetal vs adult B1a-cell production capacity and the identity of putative cells of origin. Integrating these most recent findings with previous work, we propose a working model that encapsulates our current understanding of waves of immune development.

The generation of distinct hematopoietic cell types, including tissue-resident immune cells, distinguishes fetal from adult hematopoiesis. However, the mechanisms underlying differential cell production to generate a layered immune system during hematopoietic development are unclear. Using an irreversible lineage-tracing model, we identify a definitive hematopoietic stem cell (HSC) that supports long-term multilineage reconstitution upon transplantation into adult recipients but does not persist into adulthood in situ. These HSCs are fully multipotent, yet they display both higher lymphoid cell production and greater capacity to generate innate-like B and T lymphocytes as compared to coexisting fetal HSCs and adult HSCs. Thus, these developmentally restricted HSCs (drHSCs) define the origin and generation of early lymphoid cells that play essential roles in establishing self-recognition and tolerance, with important implications for understanding autoimmune disease, allergy, and rejection of transplanted organs.

During development, transient fetal hematopoietic stem cells (HSCs) are responsible for the production of "unconventional" innate-like immune cells that contribute to adult immunity. Whereas dysregulation of fetal-derived immune cells contributes to pathogenesis in a variety of immune tolerance disorders, the cellular and molecular drivers of pathogenesis are unknown. We have previously identified a transient developmentally-restricted HSC (drHSC) that specifically gives rise to innate-like lymphocytes during the perinatal period1. Under homeostatic conditions, the drHSC disappears postnatally, but its innate-like lymphocyte progeny persist into adulthood. Our discovery of a transient cell-of-origin for a specialized component of adult immunity underscores a “critical window” of immune development, during which phenotype of the adult immune system can be shaped by extrinsic inputs in early life. Here, we tested how developmental perturbation induced in utero by a single low-dose injection of poly(I:C) at mid-gestation drives both immediate and lasting changes to hematopoiesis and immunity in offspring. In utero perturbation disrupted the entrance of fetal HSCs into quiescence, causing disproportionate expansion of drHSCs, and a resultant shift in multipotent progenitor output. Postnatally, we observed sustained expansion and inappropriate persistence of the drHSC population into adulthood. These fundamental changes to the postnatal HSC compartment resulted in parallel expansion and hyperactivation of innate-like lymphocytes, thereby altering immune landscape and function in offspring. Our work validates the existence of a critical window of immune development by revealing how early perturbation of distinct fetal HSCs can drive long-term changes to immunity and disease susceptibility in offspring.

Our goal is to define the cellular and molecular mechanisms that control aging of the hematopoietic system. Given the increasing global life expectancy of people and the prevalence of age-related hematological diseases, understanding alterations to stem and progenitor cell function during aging is critical for developing preventative and restorative therapies. Previous reports have suggested that age-related morbidity is determined by functional decline of hematopoietic stem cells (HSCs). While HSCs themselves have been associated with hematopoietic aging, the role of progenitor cells during aging remains a mystery. Progenitor cells carry varied capacity to proliferate and differentiate in order to meet the demands of the blood system. Therefore, we hypothesize that progenitor cells play a significant role in the homeostatic decline associated with aging. Indeed, Megakaryocyte Progenitors (MkPs) have been shown to be consistently enriched in the aging bone marrow. Therefore, we specifically tackled the question – how might aging alter the functional and molecular regulation of MkPs? Surprisingly, and in stark contrast to the functional decline of aging HSCs, we found that old MkPs displayed greater capacity to generate platelets compared to young MkPs. These functional differences were apparent by both in vivo reconstitution and in vitro proliferation assays. To gain further insight into the changes in molecular regulation of MkP populations, we performed RNA sequencing (RNA-seq) analysis of young and old MkPs. Interestingly, their functional differences are paralleled by unique molecular regulators of old MkPs. These data demonstrate that megakaryopoiesis and MkP maintenance is fundamentally different between young and old mice, and that old MkPs gain expansion capacity whereas old HSCs functionally decline. Understanding these cellular and molecular events provides a promise for development of effective therapeutic strategies aimed at guiding differentiation and maturation toward a more youthful megakaryopoiesis.

The discovery of a fetal origin for tissue-resident macrophages (trMacs) has inspired an intense search for the mechanisms underlying their development. Here, we performed in vivo lineage tracing of cells with an expression history of IL-7Rα, a marker exclusively associated with the lymphoid lineage in adult hematopoiesis. Surprisingly, we found that IL7R-Cre labeled fetal-derived, adult trMacs. Labeling was almost complete in some tissues and partial in other organs. The putative progenitors of trMacs, yolk sac (YS) erythromyeloid progenitors (EMPs), did not express IL-7R, and YS hematopoiesis was unperturbed in IL-7R-deficient mice. In contrast, tracking of IL-7Rα message levels, surface protein expression, and IL7R-Cre-mediated labeling across fetal development revealed dynamic regulation of IL-7Rα mRNA expression and rapid upregulation of IL-7Rα surface protein upon transition from monocyte to macrophage within fetal tissues. Fetal liver monocyte differentiation in vitro produced IL-7R+ macrophages, supporting a direct progenitor-progeny relationship. Additionally, blockade of IL-7R function during late gestation specifically impaired the establishment of fetal-derived tissue macrophages in vivo. These data provide evidence for a distinct function of IL-7Rα in fetal myelopoiesis and identify IL-7R as a novel regulator of tissue-resident macrophage development.

RNA-seq is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase based Smartseq2 protocol to create RNA-seq libraries that capture the 5’ end of transcripts. The Tn5Prime method dramatically streamlines the 5’ capture process and is both cost effective and reliable. By applying Tn5Prime to bulk RNA and single cell samples we were able to define transcription start sites as well as quantify transcriptomes at high accuracy and reproducibility. Additionally, similar to 3’ end based high-throughput methods like Drop-Seq and 10X Genomics Chromium, the 5’ capture Tn5Prime method allows the introduction of cellular identifiers during reverse transcription, simplifying the analysis of large numbers of single cells. In contrast to 3’ end based methods, Tn5Prime also enables the assembly of the variable 5’ ends of antibody sequences present in single B-cell data. Therefore, Tn5Prime presents a robust tool for both basic and applied research into the adaptive immune system and beyond.

Summary Epigenetic regulation serves as the basis for stem cell differentiation into distinct cell types, but it is unclear how global epigenetic changes are regulated during this process. Here, we tested the hypothesis that global chromatin organization affects the lineage potential of stem cells and that manipulation of chromatin dynamics influences stem cell function. Using nuclease sensitivity assays, we found a progressive decrease in chromatin digestion among pluripotent embryonic stem cells (ESCs), multipotent hematopoietic stem cells (HSCs), and mature hematopoietic cells. Quantitative high-resolution microscopy revealed that ESCs contain significantly more euchromatin than HSCs, with a further reduction in mature cells. Increased cellular maturation also led to heterochromatin localization to the nuclear periphery. Functionally, prevention of heterochromatin formation by inhibition of the histone methyltransferase G9A resulted in delayed HSC differentiation. Our results demonstrate global chromatin rearrangements during stem cell differentiation and that heterochromatin formation by H3K9 methylation regulates HSC differentiation., Graphical Abstract, Highlights • Nuclease sensitivity decreases progressively with stem cell differentiation • Distinct chromatin architecture is apparent in cells of different lineage potential • Stem cell differentiation leads to perinuclear heterochromatin localization • G9a-mediated heterochromatin formation facilitates stem cell differentiation, Forsberg and colleagues use a variety of approaches to investigate global chromatin structure and architecture in pluripotent, multipotent, and differentiated cells. They show that progressive changes in nuclease sensitivity, chromatin condensation, and heterochromatin localization correlate with the lineage potential of embryonic and adult stem cells and committed cells. Functionally, inhibition of heterochromatin formation delayed hematopoietic stem cell differentiation. These data provide new insights on the epigenetic regulation of stem cell lineage potential and differentiation.

In February 2015, over 200 scientists gathered for the Keystone Hematopoiesis meeting, which was held at the scenic Keystone Resort in Keystone, Colorado, USA. The meeting organizers, Patricia Ernst, Hanna Mikkola and Timm Schroeder, put together an exciting program, during which field leaders and new investigators presented discoveries that spanned developmental and adult hematopoiesis within both physiologic and pathologic contexts. Collectively, the program highlighted the increasing pace of new discoveries and the substantial progress made in the hematopoiesis field since the last Keystone meeting two years ago. In this Meeting Review, we highlight the main concepts discussed at the conference, with an emphasis on topics relevant to developmental biology.

SummaryAlthough classified as hematopoietic cells, tissue-resident macrophages (MFs) arise from embryonic precursors that seed the tissues prior to birth to generate a self-renewing population, which is maintained independently of adult hematopoiesis. Here we reveal the identity of these embryonic precursors using an in utero MF-depletion strategy and fate-mapping of yolk sac (YS) and fetal liver (FL) hematopoiesis. We show that YS MFs are the main precursors of microglia, while most other MFs derive from fetal monocytes (MOs). Both YS MFs and fetal MOs arise from erythro-myeloid progenitors (EMPs) generated in the YS. In the YS, EMPs gave rise to MFs without monocytic intermediates, while EMP seeding the FL upon the establishment of blood circulation acquired c-Myb expression and gave rise to fetal MOs that then seeded embryonic tissues and differentiated into MFs. Thus, adult tissue-resident MFs established from hematopoietic stem cell-independent embryonic precursors arise from two distinct developmental programs.

Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After benchmarking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level., Short-read RNA-seq is limited in its ability to resolve complex transcript isoforms since it cannot sequence full-length cDNA. Here the authors use Oxford Nanopore MinION and their Mandalorion analysis pipeline to measure complex isoforms in B1a cells.

Haematopoietic stem cell (HSC) niches provide an environment essential for life-long HSC function. Intense investigation of HSC niches both feed off and drive technology development to increase our capability to assay functionally defined cells with high resolution. A major driving force behind the desire to understand the basic biology of HSC niches is the clear implications for clinical therapies. Here, with particular emphasis on cell type-specific deletion of SCL and CXCL12, we focus on unresolved issues on HSC niches, framed around some very recent advances and novel discoveries on the extrinsic regulation of HSC maintenance. We also provide ideas for possible paths forward, some of which are clearly within reach while others will require both novel tools and vision.

Selective labeling of specific cell types by expression of green fluorescent protein (GFP) within the hematopoietic system would have great utility in identifying, localizing, and tracking different cell populations in flow cytometry, microscopy, lineage tracing, and transplantation assays. In this report, we describe the generation and characterization of a new transgenic mouse line with specific GFP labeling of all nucleated hematopoietic cells, as well as platelets. This new “Vav-GFP” mouse line labels the vast majority of hematopoietic cells with GFP during both embryonic development and adulthood, with particularly high expression in hematopoietic stem and progenitor cells. With the exception of transient labeling of fetal endothelial cells, GFP expression is highly selective for hematopoietic cells, and persists in donor-derived progeny after transplantation of hematopoietic progenitor cells. Finally, we also demonstrate that the loxP-flanked reporter allows for specific GFP labeling of different hematopoietic cell subsets when crossed to various Cre reporter lines. Notably, by crossing Vav-GFP mice to Flk2-Cre mice, we obtained robust and highly selective GFP expression in HSCs. Together, these data describe a new mouse model capable of directing GFP labeling exclusively of hematopoietic cells or exclusively of HSCs.

Genetic fate-mapping approaches provide a unique opportunity to assess differentiation pathways under physiological conditions. We have recently employed a lineage tracing approach to define hematopoietic differentiation pathways in relation to expression of the tyrosine kinase receptor Flk2.1 Based on our examination of reporter activity across all stem, progenitor and mature populations in our Flk2-Cre lineage model, we concluded that all mature blood lineages are derived through a Flk2+ intermediate, both at steady-state and under stress conditions. Here, we re-examine in depth our initial conclusions and perform additional experiments to test alternative options of lineage specification. Our data unequivocally support the conclusion that onset of Flk2 expression results in loss of self-renewal but preservation of multilineage differentiation potential. We discuss the implications of these data for defining stem cell identity and lineage potential among hematopoietic populations.

Tobacco use is associated with an increase in the white blood cell (WBC) count. This association has been attributed to bronchopulmonary inflammation and/or infection. It is not known if nicotine itself may play a role. The objective of this study was to determine whether nicotine itself could affect the WBC count, and to determine whether this was due to a direct effect on hematopoietic stem cells (HSC). C57Bl6J mice received nicotine orally, and measurements of the WBC count, bone marrow and spleen cellularity, and HSC count were made. To determine the functionality of HSCs, irradiated animals received bone marrow transplants from vehicle or nicotine-treated mice. Nicotine increased leukocytes in the peripheral blood, bone marrow and spleen. The peripheral red cell and platelet count were unaffected. Nicotine increased the frequency of HSC in the bone marrow. Isolated long-term HSCs from nicotine-treated mice transplanted into irradiated mice regenerated all hematopoietic cell lineages, demonstrating the functional competence of those HSCs. HSCs expressed nicotinic acetylcholine receptors (nAChRs), as documented by FITC-conjugated alpha-bungarotoxin binding. Nicotine increased soluble Kit ligand, consistent with stem cell activation. In conclusion, the data suggest a new mechanism for the increased WBC associated with tobacco use. The effect of nicotine to activate hematopoiesis may contribute to tobacco-related diseases.

Tissue-resident macrophages play critical roles in tissue homeostasis and disease. Many populations of tissue-resident macrophages derive from fetal progenitors and self-maintain across the lifespan through in situ proliferation, independent of bone marrow hematopoiesis. However, the developmental mechanisms that specify fetal-derived tissue-resident macrophages are poorly understood. Here, we have identified a novel cytokine regulating tissue-resident macrophage development using an IL7Ra-cre lineage tracing model. Adult tissue resident macrophages in the brain, skin, liver, and lung were extensively labeled by IL7ra-cre, in the absence of IL7ra message or protein expression. To gain insight into developmental expression of IL7ra, we profiled IL7Ra surface expression, mRNA expression, and IL7ra-cre-driven labeling across fetal myeloid development. We observed rapid upregulation of IL7ra surface expression during a limited window of tissue macrophage establishment, and dynamic regulation of IL7ra message and protein levels in monocyte precursors, suggesting that IL7ra regulated the transition from fetal liver monocytes into tissue macrophages. Blockade of the IL7R using a monoclonal antibody decreased cellularity of liver, lung and skin tissue resident macrophages at birth, and increased cellularity of fetal liver monocytes. These data suggest that late in gestation, IL7Ra is upregulated as fetal monocytes exit the fetal liver and differentiate into macrophages, and provides evidence that IL-7R signaling regulates fetal tissue-resident macrophage development. Ongoing work addresses the function of IL-7 signaling in myeloid development, and the function of IL-7R marked macrophages in adult immunity.