Lineage Fate Research Articles

Generation and Characterization of Induced Pluripotent Stem Cells and Retinal Organoids From a Leber's Congenital Amaurosis Patient With Novel RPE65 Mutations.

RPE65-associated Leber congenital amaurosis (LCA) is one of highly heterogeneous, early onset, severe retinal dystrophies with at least 130 gene mutation sites identified. Their pathogenicity has not been directly clarified due to lack of diseased cells. Here, we generated human-induced pluripotent stem cells (hiPSCs) from one putative LCA patient carrying two novel RPE65 mutations with c.200T>G (p.L67R) and c.430T>C (p.Y144H), named RPE65-hiPSCs, which were confirmed to contain the same mutations. The RPE65-hiPSCs presented typical morphological features with normal karyotype, expressed pluripotency markers, and developed teratoma in NOD-SCID mice. Moreover, the patient hiPSCs were able to differentiate toward retinal lineage fate and self-form retinal organoids with layered neural retina. All major retinal cell types including photoreceptor and retinal pigment epithelium (RPE) cells were also acquired overtime. Compared to healthy control, RPE cells from patient iPSCs had lower expression of RPE65, but similar phagocytic activity and VEGF secretion level. This study provided the valuable patient specific, disease targeted retinal organoids containing photoreceptor and RPE cells, which would facilitate the study of personalized pathogenic mechanisms of disease, drug screening, and cell replacement therapy.

Aging of the Hematopoietic Stem Cell Niche: An Unnerving Matter.

The drivers of aging in the hematopoietic system remain incompletely understood. In this issue of Cell Stem Cell, Ho etal. (2019) report that functional switching of β-adrenergic nerve signaling underlies remodeling of stem cell niches, driving age-associated alterations in hematopoiesis.

SMYD2 Drives Mesendodermal Differentiation of Human Embryonic Stem Cells Through Mediating the Transcriptional Activation of Key Mesendodermal Genes.

Histone methyltransferases play a critical role in early human development, whereas their roles and precise mechanisms are less understood. SET and MYND domain-containing protein 2 (SMYD2) is a histone lysine methyltransferase induced during early differentiation of human embryonic stem cells (hESCs), but little is known about its function in undifferentiated hESCs and in their early lineage fate decision as well as underlying mechanisms. Here, we explored the role of SMYD2 in the self-renewal and mesendodermal lineage commitment of hESCs. We demonstrated that the expression of SMYD2 was significantly enhanced during mesendodermal but not neuroectodermal differentiation of hESCs. SMYD2 knockout (SMYD2-/- ) did not affect self-renewal and early neuroectodermal differentiation of hESCs, whereas it blocked the mesendodermal lineage commitment. This phenotype was rescued by reintroduction of SMYD2 into the SMYD2-/- hESCs. Mechanistically, the bindings of SMYD2 at the promoter regions of critical mesendodermal transcription factor genes, namely, brachyury (T), eomesodermin (EOMES), mix paired-like homeobox (MIXL1), and goosecoid homeobox (GSC) were significantly enhanced during mesendodermal differentiation of SMYD2+/+ hESCs but totally suppressed in SMYD2-/- ones. Concomitantly, such a suppression was associated with the remarkable reduction of methylation at histone 3 lysine 4 and lysine 36 but not at histone 4 lysine 20 globally and specifically on the promoter regions of mesendodermal genes, namely, T, EOMES, MIXL1, and GSC. These results reveal that the histone methyltransferase SMYD2 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation, but it promotes the mesendodermal differentiation of hESCs through the epigenetic control of critical genes to mesendodermal lineage commitment. Stem Cells 2019;37:1401-1415.

1019 - DECONVOLUTION OF HEMATOPOIETIC COMMITMENT DECISIONS BY GENOME-WIDE ANALYSIS OF PROGRESSIVE DNA METHYLATION CHANGES

Advances in single cell transcriptome analyses have resulted in the derivation of new models to describe the hierarchical organization of the mammalian hematopoietic system. While such an approach appears to be effective at discerning the trajectory of differentiation from hematopoietic stem cells (HSCs) to a given mature lineage, it remains a challenge to identify definitive points where specific lineage fates become restricted. 5-MeC is a stable epigenetic modification, whose remodeling is integral to the process of enforcing lineage-restricted gene expression programs. We have previously observed that the remodeling of the DNA methylome appears to be both progressive and irreversible during the process of hematopoietic differentiation, suggesting that this modification could be used to unambiguously identify molecular marks of lineage commitment. To pursue this concept, we generated a genome-wide DNA methylation map of murine hematopoiesis. This map, comprised of a total of 147,232 differentially methylated regions (DMRs), encompasses 26 different FACS-purified populations. Analysis of these DMRs revealed progressive lineage-specific DNA methylation dynamics that would be indicative of a molecular mechanism of cell fate restriction. Lineage-specific DMRs could already be identified within the early hematopoietic stem and multipotent progenitor compartments, supporting the concept that lineage restriction occurs early during differentiation. In contrast with previous studies, integration of our methylome data with single cell gene expression data encompassing the entire hematopoietic component of the bone marrow, revealed an unprecedented degree of correlation between the transcriptional program and DNA methylation levels. Both inflammatory challenge and ageing resulted in remodeling of the HSC DNA methylome in vivo, in a manner that was not predominantly associated with priming towards any particular differentiated cell fate. Rather the reprogrammed methylome may represent an epigenetic memory of gene expression programs resulting from extrinsic stimuli.

THE TRANSCRIPTION FACTOR IRF8 EPIGENETICALLY REGULATES EARLY DENDRITIC CELL SPECIFICATION

Dendritic cells (DCs) are vital for immune responses to pathogens. These cells are produced from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). Recently, DC lineage fate decisions occurring at stages much earlier than CDPs have been recognized, yet the mechanism remains unknown. In this study, we demonstrate that IRF8 regulates chromatin at the LMPP stage to induce early commitment towards DCs. Single-cell RNA-seq revealed that the expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. By in vivo transfer experiments, we showed that these IRF8 expressing LMPP (IRF8+ LMPPs) were derived from IRF8- LMPPs and predominantly produced DCs, especially classical DC1s (cDC1s). On the other hand, IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils or lymphocytes. RNA-seq and an assay for transposase-accessible chromatin (ATAC)-seq revealed that IRF8- and IRF8+ LMPPs displayed very similar global gene expression patterns; however, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8- LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs and cDC1s. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, thereby biasing their fate decision towards DCs.

Mowat-Wilson syndrome: Generation of two human iPS cell lines (UUIGPi004A and UUIGPi005A) from siblings with a truncating ZEB2 gene variant

Mowat-Wilson syndrome (MWS) is a complex developmental syndrome caused by heterozygous mutations in the Zinc finger E-box-binding homeobox 2 gene (ZEB2). We generated the first human iPSC lines from primary fibroblasts of two siblings with MWS carrying a heterozygous ZEB2 stop mutation (c.1027C > T; p.Arg343*) using the Sendai virus reprogramming system. Both iPSC lines were free from reprogramming vector genes, expressed pluripotency markers and showed potential to differentiate into the three germ layers. Genetic analysis confirmed normal karyotypes and a preserved stop mutation. These iPSC lines will provide a useful resource to study altered neural lineage fate and neuropathophysiology in MWS.

Abstract 952: Determining the contribution of cystathionine beta synthase to lung cancer lineage fate

Abstract The two major pathologies of non-small cell lung cancer, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) are historically treated as separate diseases, even though mounting evidence shows that epigenetic reprogramming from ADC to a more SCC fate allows lung cancers to evade therapies. Our team recently developed an isogenic lung cancer model in which lineage switching from ADC to SCC was epigenetically controlled through loss of Polycomb Repressive Complex 2 (PRC2) gene repression of squamous genes. Levels of S-adenosyl methionine (SAM), the methyl donor for the complex, influence PRC2 stability and activity. Steady state metabolism showed that SAM levels were decreased significantly and cystathionine levels were increased significantly in SCC cells relative to ADC cells. Our hypothesis is that increased activity of the enzyme cystathionine beta synthase (CBS) drives epigenetic reprogramming of lung ADC to an aggressive and therapy-resistant state through reduction of SAM pools and destabilization of PRC2, leading to expression of squamous genes. First, we stained a series of human lung cancer tissues for CBS and H3K27me3 and queried TCGA data to validate that CBS is up-regulated in squamous tumors. In addition, we leveraged 3-dimensional organoid cultures and traditional 2-dimensional human non-small cell lung cancer cell lines to explore the contribution of CBS to lung cancer lineage fate. With both of these systems, we used lentiviral small hairpins targeting Cbs/CBS and a lentivirus encoding a full length Cbs/CBS cDNA to modulate gene and protein levels. Lastly, we tested differential sensitivities to the common chemotherapeutic carboplatin on matched isogenic cultures that differ only in lineage state. In human tumors, SCCs have significantly higher levels of CBS and significantly lower levels of H3K27me3 than ADCs. Knock-down of CBS decreased cystathionine and increased both homocysteine and S-adenosyl methionine levels in 2-dimensional human NSCLC cultures. We also observed a global increase in H3K27me3 mark in shCBS cultures relative to shGFP controls. In contrast, CBS over-expression decreased global levels of H3K27me3. Importantly, we observed that squamous organoids are significantly less sensitive to the common chemotherapeutic carboplatin than are ADC organoids, suggesting that lineage switching driven by increased CBS activity will drive chemotherapy resistance. We are now characterizing changes in lineage fate and carboplatin sensitivity that are caused by these genetic manipulations of CBS. Our data suggest that lung cancer lineage fate may be governed in part through expression and activity of the enzyme CBS. Because CBS is a redox-sensitive enzyme, this could be the missing link between increased oxidative stress and ultimate epigenetic reprogramming to a therapy-resistant squamous state in lung cancer. Funded by ACS IRG-85-001-25, K22 CA201036 and KY LCRP to CFB Citation Format: Mojtaba Bakhtiari, Christine Fillmore Brainson. Determining the contribution of cystathionine beta synthase to lung cancer lineage fate [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 952.

Quantitative Difference in PLZF Protein Expression Determines iNKT Lineage Fate and Controls Innate CD8 T Cell Generation

Zbtb16 encodes the zinc-finger protein PLZF, which is often used as a lineage marker for innate-like Tcells and is specifically required for the generation of invariant natural killer T (iNKT) cells in the thymus. Here, we report that not only PLZF expression itself but also the relative abundance of PLZF proteins plays critical roles in iNKT cell development. Utilizing a Zbtb16 hypomorphic allele, PLZFGFPCre, which produces PLZF proteins at only half of the level of the wild-type allele, we show that decreased PLZF expression results in a significant decrease in iNKT cell numbers, which is further associated with profound alterations in iNKT lineage choices and subset composition. These results document that there is a quantitative aspect of PLZF expression in iNKT cells, demonstrating that the availability of PLZF protein is a critical factor for both effective iNKT cell generation and subset differentiation.

GMCSF-neuroantigen vaccines engender FOXP3+ regulatory T cell responses through low-efficiency self-antigen recognition events integrated through diminished CD40L-CD40 signaling

Abstract Neuroantigen (NAg)-specific tolerogenic vaccines that induce myelin-specific FOXP3+ regulatory T cells (Tregs) may be an effective treatment for Multiple Sclerosis. Previous studies showed that fusion proteins comprised of GM-CSF and NAg (GMCSF-NAg) are potent tolerogens that inhibit several rodent models of experimental autoimmune encephalomyelitis. GMCSF-NAg-induced T cell responses were investigated in vivo by use of 2D2-FIG mice, which have a FOXP3 GFP reporter (FIG) and a transgenic TCR (2D2) which recognizes myelin oligodendrocyte glycoprotein peptide 35–55 (MOG) as a low-efficiency antigen and neurofilament medium peptide 13–37 (NFM) as a high-efficiency antigen. A single subcutaneous vaccination of 2D2-FIG mice with GMCSF-MOG resulted in high numbers and percentages of Tregs in the blood, spleen, and lymph nodes, whereas GMCSF-NFM elicited a dominant conventional T cell (Tcon) response. To determine how low and high-efficiency TCR responses regulate cell lineage fate, we investigated TCR-induced CD40L expression. GMCSF-NFM, but not GMCSF-MOG, induced significant CD40L expression when cultured with 2D2 responder T cells. Pretreatment of 2D2-FIG mice with an agonistic anti-CD40 monoclonal antibody prevented GMCSF-MOG induction of Tregs and favored Tcon responses. MOG35–55 was a partial TCR antagonist that blocked NFM stimulation of CD40L expression in 2D2 T cell cultures. Similarly, GMCSF-MOG was functionally dominant and induced Tregs in 2D2-FIG mice when mixed with an equimolar dose of GMCSF-NFM. These data indicated that low-efficiency antigen recognition is a key parameter for the induction of Treg responses and is in part controlled through CD40L-CD40 signaling pathways to determine T cell lineage fate.

Epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice

AbstractDendritic cells (DCs), which are vital for immune responses, are derived from bone marrow hematopoietic stem cells via common DC progenitors (CDPs). DC lineage fate decisions occurring at stages much earlier than CDPs have recently been recognized, yet the mechanism remains elusive. By single-cell RNA-sequencing, in vivo cell transfer experiments, and an assay for transposase-accessible chromatin sequencing using wild-type, IRF8-GFP chimera knock-in or IRF8-knockout mice, we demonstrate that IRF8 regulates chromatin at the lymphoid-primed multipotent progenitor (LMPP) stage to induce early commitment toward DCs. A low but significant expression of IRF8, a transcription factor essential for DC and monocyte development, was initiated in a subpopulation within LMPPs. These IRF8+ LMPPs were derived from IRF8– LMPPs and predominantly produced DCs, especially classical DC1s, potentially via known progenitors, such as monocyte-DC progenitors, CDPs, and preclassical DCs. IRF8+ LMPPs did not generate significant numbers of monocytes, neutrophils, or lymphocytes. Although IRF8– and IRF8+ LMPPs displayed very similar global gene expression patterns, the chromatin of enhancers near DC lineage genes was more accessible in IRF8+ LMPPs than in IRF8– LMPPs, an epigenetic change dependent on IRF8. The majority of the genes epigenetically primed by IRF8 were still transcriptionally inactive at the LMPP stage, but were highly expressed in the downstream DC lineage populations such as CDPs. Therefore, early expression of the key transcription factor IRF8 changes chromatin states in otherwise multipotent progenitors, biasing their fate decision toward DCs.

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA.

Simultaneous measurement of cell lineage and cell fates is a longstanding goal in biomedicine. Here we describe EMBLEM, a strategy to track cell lineage using endogenous mitochondrial DNA variants in ATAC-seq data. We show that somatic mutations in mitochondrial DNA can reconstruct cell lineage relationships at single cell resolution with high sensitivity and specificity. Using EMBLEM, we define the genetic and epigenomic clonal evolution of hematopoietic stem cells and their progenies in patients with acute myeloid leukemia. EMBLEM extends lineage tracing to any eukaryotic organism without genetic engineering.

Loss of Polycomb Repressive Complex 2 impairs lung bronchiolar cell growth and underlies chronic obstructive pulmonary disease

EZH2, the functional enzymatic component of the Polycomb Repressive Complex 2 (PRC2), is a histone methyl transferase that tri-methylates histone H3 at lysine 27 (H3K27me3). This protein plays a significant role in maintaining tissue specificity by silencing gene programs that control lineage fate. We hypothesized that PRC2 controls cell fate of the lung stem cells. In order to test this hypothesis, we generated mice in which we can conditionally delete Ezh2 upon ingestion of doxycycline. To examine growth, differentiation and self-renewal potentials of different lung epithelial cells, we FACS-isolated distal lung bronchioalveolar stem cells (BASCs) and cultured them in air-liquid-interface Matrigel cultures. We observed a 2fold decrease in organoid number of EZH2 null vs wild type bronchiolar cells and a significant difference in organoid diameter between Ezh2 wild type, heterozygous and null bronchiolar cells. To test in vivo potential of EZH2 depleted epithelium to repair, we performed naphthalene injury, which specifically injures the bronchiolar club cells. We observed that 7 days post naphthalene injury, Ezh2 knock-out lungs had significantly less repair, as measured by repopulation of bronchiolar lung cells. Given that we observed that lung stem cells were impaired when PRC2-mediated gene repression was perturbed, we sought to learn if PRC2 is also dysregulated in Chronic Obstructive Pulmonary Disease (COPD). We first performed Gene Set Enrichment Analysis and found that genes up-regulated in COPD patients relative to healthy smokers were also up-regulated in Ezh2 knock-out adenocarcinoma cells. We next obtained lung tissue from healthy patients and patients with COPD, and performed immunohistochemistry for the PRC2 mark H3K27me3 and immunofluorescence for basal and club cells. There was a significant decrease in H3K27me3, coupled with an increase in basal cells and goblet cells that contained high expressions of club cell markers in COPD lung compared to healthy controls. Finally, to determine if loss of PRC2 function drives basal cell fate and goblet cell differentiation, EZH2 transcripts were knocked down with short hairpins in human bronchiolar epithelial cells, and basal cell differentiation capacity was analyzed. We observed an increased expression of a goblet cell marker and decreased expression of a club cell marker in EZH2 knockdown cultures. Together our results indicate that PRC2 plays an important role in lung stem cell function as well as club cell differentiation fate. These mechanisms may also be perturbed in COPD patients. ChIP-seq and RNA-seq studies to understand the transcriptional and epigenetic changes leading to these phenotypes are underway Support or Funding Information NIH grant K22 CA 20103, Molecular Mechanisms of Toxicity Training Grant T32ES07266 There was a 2-fold decrease in organoid number of EZH2 null vs wild type bronchiolar cells. There was a significant difference in organoid diameter between Ezh2 wild type, heterozygous and null bronchiolar cells. Immunohistochemistry staining of EZH2 shows distinct differences in EZH2 expression between wild type, heterozygous and null organoids. Naphthalene exposure to mouse lung has been shown to kill club cells in the trachea and bronchioles. This injury typically results in club cell regeneration and subsequent lung cell repopulation. Club cells without EZH2 were unable to regenerate and repopulate the airway after naphthalene injury. Club cells that did regenerate in the Ezh2-null lungs lacked the GFP tag, indicating that these cells were likely not responding to doxycycline to delete Ezh2. Gene Set Enrichment Analysis was used to compare gene expression between murine Ezh2-deleted adenocarcinoma cells and COPD patients. It revealed that a significant number of the same genes are highly expressed in both states when compared to healthy lungs or the Ezh2 WT setting. Immunohistochemistry shows significantly lower abundance of H3K27me3 in the nuclei of COPD bronchiolar cells compared to normal. Immunofluorescence staining of club (CCSP and SOX2) and basal cells (KRT5 and SOX2) in normal vs COPD lung airway shows a mixture of metaplasia and hyperplasia along with collapsed airways in COPD airway compared to normal. There is an increase in basal cells and goblet cells that also contain high expressions of CCSP (a club cell marker). EZH2 transcripts were knocked down in immortalized, Human Bronchiolar Epithelial Cells (HBEC) which were, then, prompted to differentiate in air-liquid-interface cultures. Acetylated-Mucin5 was highly expressed while club cell secretory protein (CCSP) was lowly expressed in EZH2 knockdown cells compared to wild type. This suggest that EZH2 plays a role in club and goblet cell differentiation. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Convergence of TGFβ and BMP signaling in regulating human bone marrow stromal cell differentiation

Targeting regulatory signaling pathways that control human bone marrow stromal (skeletal or mesenchymal) stem cell (hBMSC) differentiation and lineage fate determination is gaining momentum in the regenerative medicine field. Therefore, to identify the central regulatory mechanism of osteoblast differentiation of hBMSCs, the molecular phenotypes of two clonal hBMSC lines exhibiting opposite in vivo phenotypes, namely, bone forming (hBMSC+bone) and non-bone forming (hBMSC−Bone) cells, were studied. Global transcriptome analysis revealed significant downregulation of several TGFβ responsive genes, namely, TAGLN, TMP1, ACTA2, TGFβ2, SMAD6, SMAD9, BMP2, and BMP4 in hBMSC−Bone cells and upregulation on SERPINB2 and NOG. Transcriptomic data was associated with marked reduction in SMAD2 protein phosphorylation, which thereby implies the inactivation of TGFβ and BMP signaling in those cells. Concordantly, activation of TGFβ signaling in hBMSC−Bone cells using either recombinant TGFβ1 protein or knockdown of SERPINB2 TGFβ-responsive gene partially restored their osteoblastic differentiation potential. Similarly, the activation of BMP signaling using exogenous BMP4 or via siRNA-mediated knockdown of NOG partially restored the differentiation phenotype of hBMSC−Bone cells. Concordantly, recombinant NOG impaired ex vivo osteoblastic differentiation of hBMSC+Bone cells, which was associated with SERBINB2 upregulation. Our data suggests the existence of reciprocal relationship between TGFB and BMP signaling that regulates hBMSC lineage commitment and differentiation, whilst provide a plausible strategy for generating osteoblastic committed cells from hBMSCs for clinical applications.

Characterization of cell fate probabilities in single-cell data with Palantir.

Single-cell RNA sequencing (scRNA-seq) studies of differentiating systems have raised fundamental questions regarding the discrete versus continuous nature of both differentiation and cell fate. Here we present Palantir, an algorithm that models trajectories of differentiating cells—treating cell fate as a probabilistic process—and leverages entropy to measure cell plasticity along the trajectory. Palantir generates a high-resolution pseudotime ordering of cells and, for each cell state, assigns a probability of differentiating into each terminal state. We apply our algorithm to human bone marrow scRNA-seq data and detect important landmarks of hematopoietic differentiation. Palantir’s resolution enables the identification of key transcription factors that drive lineage fate choice and closely track when cells lose plasticity. We show that Palantir outperforms existing algorithms in identifying cell lineages and recapitulating gene expression trends during differentiation generalizable to diverse tissue types and well-suited to resolve less-studied differentiating systems.

Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer.

During neocortical development, neurons are produced by a diverse pool of neural progenitors. A subset of progenitors express the Cux2 gene and are fate restricted to produce certain neuronal subtypes; however, the upstream pathways that specify these progenitor fates remain unknown. To uncover the transcriptional networks that regulate Cux2 expression in the forebrain, we characterized a conserved Cux2 enhancer that recapitulates Cux2 expression specifically in the cortical hem. Using a bioinformatic approach, we identified putative transcription factor (TF)-binding sites for cortical hem-patterning TFs. We found that the homeobox TF Lmx1a can activate the Cux2 enhancer in vitro Furthermore, we showed that Lmx1a-binding sites were required for enhancer activity in the cortical hem in vivo Mis-expression of Lmx1a in hippocampal progenitors caused an increase in Cux2 enhancer activity outside the cortical hem. Finally, we compared several human enhancers with cortical hem-restricted activity and found that recurrent Lmx1a-binding sites are a top shared feature. Uncovering the network of TFs involved in regulating Cux2 expression will increase our understanding of the mechanisms pivotal in establishing Cux2 lineage fates in the developing forebrain.

Haematopoietic stem cell activity andinteractions with the niche.

The haematopoietic stem cell (HSC) microenvironment in the bone marrow, termed theniche, ensures haematopoietic homeostasis by controlling the proliferation, self-renewal, differentiation and migration of HSCs and progenitor cells at steady state and in response to emergencies and injury. Improved methods for HSC isolation, driven by advances in single-cellandmolecular technologies, have led to a better understanding of their behaviour, heterogeneity and lineage fate and of the niche cells and signals that regulate their function. Nicheregulatory signals can be in the form of cell-bound or secreted factors and other local physical cues. A combination of technological advances in bone marrow imaging and genetic manipulation of crucial regulatory factors has enabled the identification of several candidate celltypes regulating the niche, including both non-haematopoietic (for example, perivascular mesenchymal stem and endothelial cells) and HSC-derived (for example, megakaryocytes, macrophages and regulatory T cells), with better topographical understanding of HSC localization in the bone marrow. Here, we review advances in our understanding of HSC regulation by niches during homeostasis, ageing and cancer, and we discuss their implications for the development oftherapies to rejuvenate aged HSCs or niches or to disrupt self-reinforcing malignant niches.

Stem Cells Heterogeneity.

Adult endogenous stem cells are crucial to maintain organ homeostasis due to their particular capacity to originate more specialized cell populations in a coordinated manner based on the body necessity. Extensive studies in a variety of tissues have highlighted the importance of stem cells for the functioning of our organism, including the skin, intestine, stomach, skeletal muscle, bone marrow, and others. Although significant progress has been made in our understanding of stem cell biology, our knowledge about these cells still remains limited due to their complexity and their dynamics. The advancement of our knowledge on these essential cells will have substantial implications in our understanding of tissue homeostasis and disease. Importantly, not all stem cells are alike even within the same tissue. They differ in their cell cycle status, surface marker expression, response to various extrinsic molecules, and distinct lineage outputs after transplant. The expanding literature which backs heterogeneity within stem cells is presently of great interest and brings questions as how stem cell subpopulations are generated, why they exist, and whether stem cells heterogeneity influences disease progression or therapy options.In more recent years, the combination of fluorescent and confocal microscopy with genetic state-of-art techniques, such as fate lineage tracking and single-cell RNA sequencing, enabled remarkable advance in the discovery of multiple novel essential functions for stem cell subpopulations in health and disease, before unexpected. This book provides an overview on our knowledge of stem cell subtypes in different organs under physiological and pathological conditions and discusses the possible origins and consequences of stem cells heterogeneity. This book's initial title was Stem Cells Heterogeneity. However, due to the current great interest in this topic, we were able to assemble more chapters than would fit in one book, covering stem cell biology under distinct circumstances. Therefore, the book was subdivided into three volumes entitled: Stem Cells Heterogeneity-Novel Concepts, Stem Cells Heterogeneity in Different Organs, and Stem Cells Heterogeneity in Cancer. Here, we offer a selected compilation of comprehensive chapters on what we know so far about heterogeneity within stem cells. More than 30 chapters written by scientists in the field outline our present knowledge on stem cells heterogeneity.

Loss of Canonical Notch Signaling Affects Multiple Steps in NK Cell Development in Mice.

Within the hematopoietic system, the Notch pathway is critical for promoting thymic T cell development and suppressing the B and myeloid lineage fates; however, its impact on NK lymphopoiesis is less understood. To study the role of Notch during NK cell development in vivo, we investigated different NK cell compartments and function in Rbp-Jkfl/flVav-Cretg/+ mice, in which Rbp-Jk, the major transcriptional effector of canonical Notch signaling, was specifically deleted in all hematopoietic cells. Peripheral conventional cytotoxic NK cells in Rbp-Jk-deleted mice were significantly reduced and had an activated phenotype. Furthermore, the pool of early NK cell progenitors in the bone marrow was decreased, whereas immature NK cells were increased, leading to a block in NK cell maturation. These changes were cell intrinsic as the hematopoietic chimeras generated after transplantation of Rbp-Jk-deficient bone marrow cells had the same NK cell phenotype as the Rbp-Jk-deleted donor mice, whereas the wild-type competitors did not. The expression of several crucial NK cell regulatory pathways was significantly altered after Rbp-Jk deletion. Together, these results demonstrate the involvement of canonical Notch signaling in regulation of multiple stages of NK cell development.

Functional and Molecular Consequences of Trisomy 21 on Human Fetal Hematopoiesis

Children with Down Syndrome (DS) are at 150-fold increased risk of developing acute megakaryoblastic leukemia (ML-DS) and 33-fold increased risk of acute B-lymphoblastic leukemia. The multistep pathogenesis of DS - associated pre-leukemia and subsequent progression to ML-DS is among the most well characterized human blood malignancies. Trisomy 21 fetal liver (FL) provides a tractable model for dissecting T21-mediated pre-leukemic changes in human HSPC. Using a recently published (Notta, F. et. al., Science 2016) enhanced sorting scheme for human blood progenitors and paired normal disomic and trisomic human FL samples, we sought a more thorough understanding of the molecular and functional perturbations associated with T21 in human FL hematopoiesis by: 1) assessing the proportional frequency/absolute numbers of 12 normal and T21 FL HSPC populations, 2) examining clonal, proliferative and lineage output using single cell stroma-based myelo-erythroid (ME) and myelo-lymphoid (ML) differentiation assays, 3) performing RNA seq and ATAC seq to elucidate variations in gene expression and epigenetic alterations, 4) and generating long-term clonal xenografts from highly purified normal and T21 FL HSC followed by secondary transplantation to uncover alterations in HSC frequency, lineage output and progenitor hierarchy.Flow cytometry was performed on 4 sets of paired, gestational stage matched disomic and trisomic human fetal liver CD34+ HSPC samples to assess changes in the proportional frequency/absolute numbers of 12 HSCP populations. Our results reveal that the T21 FL hierarchy exhibits increased frequencies of HSC, LMPP, MPP F2/F3, CMP F3 and MEP F3 populations and concomitantly decreased MPP F1, CMP F1, MEP F1 and GMP populations. To assess T21-induced functional changes at the clonal level, we utilized single cell stroma-based differentiation assays. In ME assays, we observed increased Mk lineage output while oligopotent lineage output (M/E/Mk) was found to be skewed into the CD34+CD38+ compartment. Single cell ML assays demonstrated a loss of B lineage differentiation potential and greatly reduced NK lineage output that resulted in a complete loss of oligopotent clones (B/NK/M) in HSC, MPP F1 and LMPP. Despite observing increased numbers of immunophenotypic HSC in T21 FL samples, in vivo LDA xenotransplantation of highly purified CD34+CD38-CD90+CD45RA-CD49f+ HSC showed no change in the frequency of functional T21 FL HSC. Compared to control, T21 HSC produced smaller hCD45+ grafts with increased CD33+ myeloid, CD41+ Mk and platelet frequencies and reduced GlyA+ erythroid frequency. Furthermore, T21 grafts demonstrated an inverted CD14+ monocyte/CD66b+ granulocyte ratio with almost complete loss of CD66b+CD16+CD49d- neutrophils. Initial RNA seq results from highly purified disomic and trisomic HSC and MPP reveal aberrant expression of genes from pathways not previously implicated in T21 associated malignancies. These data suggest that T21 induces relatively consistent alterations in population frequency across the FL blood progenitor hierarchy. Furthermore, our data suggests that T21 FL HSC are biased toward E, M, Mk lineage fates at the expense of B, T, NK and neutrophil fates. Overall, our work provides unique and previously unrecognized insights into the pathogenesis of DS-associated leukemia. DisclosuresNo relevant conflicts of interest to declare.

Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls

Background: Myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell (HSC) disorders characterized by ineffective hematopoiesis, peripheral cytopenias and risk of transformation to acute myeloid leukemia (AML). Recently, HSC in MDS have been shown to carry acquired distinct genetic and epigenetic mutations, most frequently in epigenetic regulators or splicing machinery factors, which are considered disease-initiating events and are likely responsible for the dysplastic features observed in this disease. Hierarchies of hematopoiesis have been established for healthy HSC and their progeny but it is unclear whether MDS HSC follow the same patterns. Clonal hierarchies in MDS have been inferred on the basis of mutational data, these only constitute a snapshot of hematopoiesis in the patient at a given time and may not accurately reflect the kinetics of the disease. To understand how clonal dominance of MDS over healthy HSC is achieved, we sought to identify differences in proliferation kinetics and lineage fate decisions of MDS HSC in comparison to healthy hematopoiesis and to fit this real data into a mathematical model of MDS hematopoiesis.Methods: Lower-risk MDS (according to IPSS-R) bone marrow (BM) samples from patients harboring an SF3B1 mutation (n = 5) or higher-risk MDS BM samples from patients with an ASXL1 mutation (n = 5) were chosen for analysis to limit heterogeneity and allow for better comparability. Healthy age-matched control BM samples (n = 5) were obtained from patients undergoing routine hip replacement surgery. Distribution of stem and progenitor cell compartments (HSC, MPP, MLP, CMP, GMP, MEP) in BM on day 0 were determined by multiparameter flow cytometry. Cells were labeled with violet cell trace and HSC (Lin-CD34+CD38-CD90+CD45RA-) were sorted by flow cytometry. A fixed number of HSC as well single HSC cell cultures were set up in vitro in serum-free medium with defined growth factors (FL, KL, TPO, IL-6, G-CSF, GM-CSF and EPO). Cell divisions, proliferation rates, cell death and lineage maturation were determined by flow cytometry on days 1, 3, 5, 7 and 9. Clonogenic capacity was probed by standard CFU assays in methylcellulose on day 0 and day 7. Additional integration of genomic sequencing analyses of bulk BM and HSC was used to assess the contribution of the malignant clone to the population of proliferating cells and to each hematopoietic lineage.Results: While CFU numbers at day 0 were significantly reduced for all MDS samples compared to healthy controls, ASXL1 mutated MDS BM samples contained significantly higher numbers of HSC than SF3B1 MDS or healthy control BM samples. SF3B1 MDS samples had significantly larger CMP and GMP compartments compared to healthy controls or ASXL1 mutated samples. In cultures started with a fixed number of HSC, no apparent differences in proliferation kinetics were observed between MDS and healthy samples over time. However, cell trace labeling and sorting of single HSC into 96 well plates revealed clear differences between MDS and healthy HSC. Overall, MDS HSC were less robust, with fewer wells of the 96 plate containing cells after sorting than for healthy HSC samples. In contrast, the remaining HSC from both both ASXL1 and SF3B1 mutated MDS showed a significantly higher cell division rate than healthy HSC in vitro, suggesting MDS HSC are more active than their normal counterparts. Genotyping analyses to assess single MDS HSC contributions to proliferation are ongoing and data are currently being fitted to mathematical models.Conclusion: Detailed analysis of hematopoietic stem and progenitor cell compartments as well as time-resolved tracking of HSC revealed significant differences between MDS and healthy HSC kinetics in vitro. Integration of this data into a comprehensive mathematical model of MDS hematopoiesis may aid in dissecting the mechanisms of progression of MDS towards acute myeloid leukaemia (AML). DisclosuresGötze:Takeda: Honoraria, Other: Travel aid ASH 2017; Celgene: Honoraria, Research Funding; Novartis: Honoraria; JAZZ Pharmaceuticals: Honoraria.