Hematopoietic stem cell (HSC) development is accompanied by dynamic changes in the transcriptional program. How the corresponding transcriptional programs are related to the epigenetic mechanism is poorly understood. To fill this gap, we first profiled the transcriptomes and epigenomes using RNA-Seq and ChIP-Seq for five key developmental stages of HSC emergence in the mouse embryo. Using epigenetic markers, we identified novel 12,000~17,000 enhancers for each developmental stage. We applied a computational tool to link those enhancers to their target genes. Systematical analysis of enhancer-promoter (EP) pairs using network-based strategy reveals multiple novel key transcription factors for early specification of HSC in the mouse embryo. Second, we compared the 3D genome organization, epigenomes, and transcriptome of fetal and adult HSCs in the mouse. We found that higher-order genome structures are largely conserved between fetal and adult HSCs, including chromosomal compartments and topologically associating domains (TADs). However, chromatin interactions within TADs exhibit substantial differences. We found that promoters within 23% (242/1039) of TADs undergo interaction changes. Transcription factor motif analysis of HSC-specific enhancer-promoter loops suggests a role of KLF1 in mediating condition-specific enhancer looping and regulation of genes involved in cell cycle. Our result provides a comprehensive view of the differences in 3D genome organization, epigenome, and transcriptome between fetal and adult HSCs.

Les syndromes myélodysplasiques (MDS) sont un groupe de pathologies myéloïdes caractérisées par une hématopoïèse inefficace. Le rôle du microenvironnement médullaire (MM) dans l’histoire naturelle de ces pathologies reste incertain. Des anomalies du MM ont été décrites au cours des myélodysplasies et des modèles murins récemment publiés font penser qu’une altération du MM pourrait jouer un rôle dans le déclenchement et/ou l’évolution de ces maladies.Nous avons tenté de développer un modèle in vivo récapitulant l’histoire naturelle des myélodysplasies par des xénogreffes chez des souris NSG et NSG-S. Le faible taux de prise de greffe nous a amenés à développer un modèle in vitro de co-culture en 2D. Ce modèle est une bonne alternative pour les études de nouvelles stratégies thérapeutiques pour les patients atteints de myélodysplasies.Au cours de ce travail, nous avons également réalisé une étude systématique du stroma médullaire de patients atteints de syndromes myélodysplasiques dans le but d’identifier les anomalies fonctionnelles et moléculaires des cellules souches mésenchymateuses (CSMs), cellules centrales du MM pour leur interaction avec les cellules souches hématopoïétiques (CSHs).Les CSMs de MDS ont une clonogénécité diminuée. Nous n’avons pas observé de modification significative de leurs capacités de différenciation en ostéoblastes, adipocytes et chondrocytes ni dans leur capacité à supporter une hématopoïèse normale. Les CSMs de MDS présentent des modifications au niveau épigénétique et transcriptionnel pouvant expliquer l’altération des relations observées grâce à de l’imagerie enregistrée entre les CSMs de MDS et les CSHs dans un modèle de co-culture en 3D.Ces résultats montrent que les CSMs de MDS ont des modifications fonctionnelles et moléculaires et que ces anomalies perturbent leur relation avec les CSHs. / Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid pathologies characterized by an impaired hematopoiesis. The role of the bone marrow microenvironment (BMM) remains unclear in the natural history of these diseases. Abnormalities of the BMM have been observed in myelodysplasia and a recent published murine model implies that alterations of the BMM could play a role in the trigger/progression of these diseases.Firstly, we tried to develop an in vivo model of MDS in NSG and NSG-S mice. The low rate of engraftment pushed us to develop a 2D co-culture model in vitro. This model is a good alternative to test new therapeutic strategies for MDS patients.In this study, we analysed mesenchymal stromal cells (MSCs) from the bone marrow of pretreated MDS patients in order to identify the functional and molecular abnormalities in those cells of the BMM, central for their interactions with the hematopoietic stem cells (HSCs).MDS MSCs have an impaired clonogenic capacity. We didn’t observed modifications of their differentiation toward osteogenic, adipogenic and chondrogenic pathways and capacity to support of a normal hematopoiesis. MDS MSCs display epigenetic and transcriptomic modifications that could explain the alteration of the relationships between these cells and HSCs observed in imagery in a 3D co-culture model.These results showed that MDS MSCs have functional and molecular abnormalities and that these alterations could impair their relationship with HSCs.

No description available.

Bibliography: leaves 1-14 of section Reference / [175] leaves : / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (M.D.)--University of Adelaide, 1985

Multipotent hematopoietic stem cells (HSCs) are progenitors of all types of hematopoietic cells, and the efficient isolation and propagation of HSCs will significantly enhance our ability to manage many human disorders with bone marrow transplantation, stem cell transplantation and gene therapy. We employed "Signal Sequence Trap (SST)" method with yeast invertase to clone proteins on the surface of or secreted by stromal cells that enhance or inhibit the propagation of HSC’s in culture. AFT024, a mouse fetal liver stromal cell line that maintains stem cell activity in long-term culture, was subjected to SST analysis. We identified more than 60 signal sequences or transmembrane domain containing genes expressed by AFT024 cells. We compared their expression levels between AFT024 cells and BFC012 cells, a mouse fetal liver stromal cell line that was developed in the same way as for AFT024 cells but could not support HSC in long-term culture. Pleiotrophin, T16, Sca-1, deltalike and cytokine receptor like-1(CLF-1) are expressed significantly higher in AFT024 cells than in BFC012 cells. We recently employed Affymatrix genechip technology to study the interaction of HSCs and their microenvironment. In genechip experiments, Sca-1, deltalike, pleiotrophin and CLF-1 are among the most differentially expressed genes between AFT024 and BFC012 cells, while T16 was not represented on the chip. In addition, osteopontin, pigment epithelium-derived factor, proliferins, activin subunit, CXC chemokines GRO1 and LIX are more abundant in AFT024 cells than in BFC012 cells. Genechip technology was also applied to bone marrow stromal cell lines, including MS5, S17 and OP9 cells. Two murine multipotent hematopoietic cell lines, FDCP.mix and EML cells, were also analyzed. Data from these experiments are presented. / Singapore-MIT Alliance (SMA)

Hämatopoetische Stammzellen besitzen die Fähigkeit, die dauerhafte Erhaltung ihrer eigenen Population im Knochenmark zu gewährleisten und gleichzeitig zur Neubildung der verschiedenen Zelltypen des peripheren Blutes beizutragen. Die Sequenz von Entscheidungsprozessen, die den Übergang einer undifferenzierten Stammzelle in eine funktionale ausgereifte Zelle beschreibt, wird als Linienspezifikation bezeichnet. Obwohl viele Details zu den molekularen Mechanismen dieser Entscheidungsprozesse mittlerweile erforscht sind, bestehen noch immer große Unklarheiten, wie die komplexen phänotypischen Veränderungen hervorgerufen und reguliert werden. Im Rahmen dieser Dissertation wird ein geeignetes mathematisches Modell der Linienspezifikation hämatopoetischer Stammzellen entwickelt, welches dann in ein bestehendes Modell der hämatopoetischen Stammzellorganisation auf Gewebsebene integriert wird. Zur Verifizierung des theoretischen Modells werden Simulationsergebnisse mit verschiedenen experimentellen Daten verglichen. Der zweite Teil dieser Arbeit konzentriert sich auf die Beschreibung und Analyse der Entwick- lungsprozesse von Einzelzellen, die aus diesem integrierten Modell hervorgehen. Aufbauend auf den entsprechenden Modellsimulationen wird dazu eine topologische Charakterisierung der resultierenden zellulären Genealogien etabliert, welche durch verschiedener Maße für deren Quantifizierung ergänzt wird. Das vorgestellte mathematische Modell stellt eine neuartige Verknüpfung der intrazellulären Linienspezifikation mit der Beschreibung der hämatopoetischen Stammzellorganisation auf Populationsebene her. Dadurch wird das Stammzellm- odell von Röder und Löffler um die wichtige Dimension der Linienspezifikation ergänzt und damit in seinem Anwendungsbereich deutlich ausgedehnt. Durch die Analyse von Einzelzellverläufen trägt das Modell zu einem grundlegenden Verständnis der inhärenten Heterogenität hämatopoetischer Stammzellen bei.

Gain- and loss-of-function studies of the BCL-2 family of proteins have shown that they can impact chemotherapeutic sensitivity. However, cells contain myriad anti-apoptotic and pro-apoptotic BCL-2 family members making it difficult to predict cell fate decisions based on the initial conditions of these proteins. BH3 profiling is a tool that measures mitochondrial priming, the readiness of a cell to die through the intrinsic (or mitochondrial) apoptotic pathway. Priming is due to the cumulative effect of the BCL-2 family of proteins that act as the gate keepers of the mitochondrial apoptotic pathway. Priming is measured by determining the sensitivity of mitochondria to perturbation by peptides derived from the BH3 domains of pro-apoptotic proteins. Using BH3 profiling, we now have a functional readout that can quantify priming and assess its contribution to drug sensitivity. Here we show that priming affects the sensitivity of acute myeloid leukemia (AML) cell lines to various standard chemotherapeutics, especially topoisomerase II inhibitors. Priming predicts clinical response to conventional induction chemotherapy as well as the long term maintenance of remission in AML patients. Interestingly, the priming of normal hematopoietic stem cells (HSCs) sits at the boundary line between the priming of cured and refractory patient AML. This HSC priming likely defines the therapeutic index since AML that are lower primed than HSCs are often refractory and cannot be cured without transplantation. Additionally, our BH3 profiles revealed that AML cells are more sensitive to BCL-2 antagonism than normal HSCs, which are primarily dependent on MCL-1. Indeed, we were able to kill primary refractory AML cells in vitro with the BCL-2 antagonist ABT-737 at doses that left HSCs unharmed. Cumulatively, these findings show that priming is a major mechanistic determinant of AML response in vitro and in the clinic to standard induction chemotherapy. With the ability to predict outcome, BH3 profiling may offer physicians and patients a promising tool for treatment decision-making.

Stem cell biologists creating cells and tissues for therapies, disease modeling, and drug screening have observed that differentiating pluripotent stem cells (PSCs) tend to produce cells at an embryonic stage of development but have difficulty maturing into adult definitive cells. A better understanding of developmental maturation will provide insights into embryogenesis and permit more accurate disease modeling. In the hematopoietic system, primitive and definitive cells are distinguished by functional transplantation assays, well characterized cell surface antigens, and gene expression signatures. We examined the transition in vivo in transplanted murine hematopoietic stem cells (HSCs) and in vitro in human PSC (hPSC) derived red blood cells (RBCs). We found that the hematopoietic microenvironment of the recipient significantly affects the outcome of HSC transplantation. The earliest embryonic HSCs perform better in neonatal recipients, whereas more mature adult-like HSCs perform better in adult recipients. The preference may be related to different active hematopoietic niches in neonates and adults, as we observed adult HSCs homing to different tissues in neonatal and adult recipients. Additionally, we found that proliferation may enhance the neonatal engraftment potential of adult-like HSCs. Our data highlight the importance of the host environment on transplantation outcomes, and point to the neonatal transplant model as a tool to functionally examine the earliest HSCs and primitive derivatives of PSCs.

<p>Stem cells are defined by their ability to make more stem cells, a property known as self-renewal and their ability to generate cells that enter differentiation. One mechanism by which fate decisions can be effectively controlled in stem cells is through asymmetric division and the correct partitioning and inheritance of cell fate determinants. While hematopoietic stem cells have the capacity to divide through asymmetric division, the molecular machinery that regulates this process is unknown and whether its activity is required in vivo remains unclear. Here we show that Lis1, a dynein-binding protein and regulator of asymmetric division, is critically required for blood development and for hematopoietic stem cell renewal in fetal and adult life. In particular, conditional deletion of Lis1 led to a severe bloodless phenotype and embryonic lethality in vivo. In both fetal and adult mice, loss of Lis1 led to a failure of normal self-renewal, which included impaired colony-forming ability in vitro and defects in long-term reconstitution ability following transplantation. As a possible mechanism, we find that the absence of Lis1 in hematopoietic cells, in part, accelerates differentiation linked to the incorrect inheritance of cell fate determinants. Furthermore, using a live cell imaging strategy, we find that the incorrect inheritance of cell fate determinants observed following the loss of Lis1 is due defects in spindle positioning and orientation. Finally, using two animal models of undifferentiated myeloid leukemia, we show that Lis1 is critical for the aberrant cell growth that occurs in cancer. Deletion of Lis1 both at the early and late stages of myeloid leukemia blocked its propagation in vivo and led to a marked improvement in survival. Together, these data identify Lis1 and the directed control of asymmetric division as key regulators of normal and malignant hematopoietic development.</p> / Dissertation

The development of effective methods to cryopreserve precious cell types has had tremendous impact on regenerative and transfusion medicine. Hematopoietic stem cell (HSC) transplants from cryopreserved umbilical cord blood (UCB) have been used for regenerative medicine therapies to treat conditions including hematological cancers and immodeficiencies. Red blood cell (RBC) cryopreservation in blood banks extends RBC storage time from 42 days (for hypothermic storage) to 10 years and can overcome shortages in blood supplies from the high demand of RBC transfusions. Currently, the most commonly utilized cryoprotectants are 10% dimethyl sulfoxide (DMSO) for UCB and 40% glycerol for RBCs. DMSO is significantly toxic both to cells and patients upon its infusion. Glycerol must be removed to <1% post-thaw using complicated, time consuming and expensive deglycerolization procedures prior to transfusion to prevent intravascular hemolysis. Thus, there is an urgent need for improvements in cryopreservation processes to reduce/eliminate the use of DMSO and glycerol. Ice recrystallization during cryopreservation is a significant contributor to cellular injury and reduced cell viability. Compounds capable of inhibiting this process are thus highly desirable as novel cryoprotectants to mitigate this damage. The first compounds discovered that were ice recrystallization inhibitors were the biological antifreezes (BAs), consisting of antifreeze proteins and glycoproteins (AFPs and AFGPs). As such, BAs have been explored as potential cryoprotectants, however this has been met with limited success. The thermal hysteresis (TH)activity and ice binding capabilities associated with these compounds can facilitate cellular damage, especially at the temperatures associated with cryopreservation. Consequently, compounds that possess “custom-tailored” antifreeze activity, meaning they exhibit the potent ice recrystallization inhibition (IRI) activity without the ability to bind to ice or exhibit TH activity,are highly desirable for potential use in cryopreservation. This thesis focuses on the rational design of potent ice recrystallization inhibitors and on elucidating important key structural motifs that are essential for potent IRI activity. While particular emphasis in on the development of small molecule IRIs, exploration into structural features that influence the IRI of natural and synthetic BAs and BA analogues is also described as these are some of the most potent inhibitors known to date. Furthermore, this thesis also investigates the use of small molecule IRIs for the cryopreservation of various different cell types to ascertain their potential as novel cryoprotectants to improve upon current cryopreservation protocols, in particular those used for the long-term storage of blood and blood products. Through structure-function studies the influence of (glyco)peptide length, glycosylation and solution structure for the IRI activity of synthetic AFGPs and their analogues is described. This thesis also explores the relationship between IRI, TH and cryopreservation ability of natural AFGPs, AFPs and mutants of AFPs. While these results further demonstrated that BAs are ineffective as cryoprotectants, it revealed the potential influence of ice crystal shape and growth progression on cell survival during cryopreservation. One of the most significant results of this thesis is the discovery of alkyl- and phenolicglycosides as the first small molecule ice recrystallization inhibitors. Prior to this discovery, all reported small molecules exhibited only a weak to moderate ability to inhibit ice recrystallization. To understand how these novel small molecules inhibit this process, structure-function studies were conducted on highly IRI active molecules. These results indicated that key structural features, including the configuration of carbons bearing hydroxyl groups and the configuration of the anomeric center bearing the aglycone, are crucial for potent activity. Furthermore, studies on the phenolic-glycosides determined that the presence of specific substituents and their position on the aryl ring could result in potent activity. Moreover, these studies underscored the sensitivity of IRI activity to structural modifications as simply altering a single atom or functional group on this substituent could be detrimental for activity. Finally, various IRI active small molecules were explored for their cryopreservation potential with different cell types including a human liver cell line (HepG2), HSCs obtained from human UCB, and RBCs obtained from human peripheral blood. A number of phenolic-glycosides were found to be effective cryo-additives for RBC freezing with significantly reduced glycerol concentrations (less than 15%). This is highly significant as it could drastically decrease the deglycerolization processing times that are required when RBCs are cryopreserved with 40% glycerol. Furthermore, it demonstrates the potential for IRI active small molecules as novel cryoprotectants that can improve upon current cryopreservation protocols that are limited in terms of the commonly used cryoprotectants, DMSO and glycerol.