Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro

Subcellular localization of the Schlafen protein family

Although the first members of the Schlafen gene family were first described almost 10 years ago, the precise molecular/biochemical functions of the proteins they encode still remain largely unknown. Roles in cell growth, haematopoietic cell differentiation, and T cell development/maturation have, with some experimental support, been postulated, but none have been conclusively verified. Here, we have determined the subcellular localization of Schlafens 1, 2, 4, 5, 8, and 9, representing all three of the murine subgroups. We show that the proteins from subgroups I and II localize to the cytoplasm, while the longer forms in subgroup III localize exclusively to the nuclear compartment. We also demonstrate upregulation of Schlafen2 upon differentiation of haematopoietic cells and show this endogenous protein localizes to the cytoplasm. Thus, we propose the different subgroups of Schlafen proteins are likely to have functionally distinct roles, reflecting their differing localizations within the cell.

Long-range regulation of alpha-globin gene expression

Over the past 20 years, there has been an increasing awareness that gene expression can be regulated by multiple cis-acting sequences located at considerable distances (10-1000 kb) from the genes they control. Detailed investigation of a few specialized mammalian genes, including the genes controlling the synthesis of hemoglobin, provide important models to understand how such long-range regulatory elements act. In general, these elements contain a high density of evolutionarily conserved, transcription factor-binding sites and in many ways resemble the upstream regulatory elements found adjacent to the promoters of genes in simpler organisms, differing only in the distance over which they act. We have investigated in detail how the remote regulatory elements of the alpha-globin cluster become activated as hematopoietic stem cells (HSCs) undergo commitment, lineage specification, and differentiation to form red blood cells. In turn, we have addressed how, during this process, the upstream elements control the correct spatial and temporal expression from the alpha-gene promoter which lies approximately 60 kb downstream of these elements. At present too few loci have been studied to determine whether there are general principles underlying long-range regulation but some common themes are emerging.

Mechanical strain enhances extracellular matrix-induced gene focusing and promotes osteogenic differentiation of human mesenchymal stem cells through an extracellular-related kinase-dependent pathway

Human mesenchymal stem cells (hMSCs) are a population of multipotent bone marrow cells capable of differentiating along multiple lineages, including bone. Our recently published proteomics studies suggest that focusing of gene expression is the basis of hMSC osteogenic transdifferentiation, and that extracellular matrix proteins play an important role in controlling this focusing. Here, we show that application of a 3-5% tensile strain to a collagen I substrate stimulates osteogenesis in the attached hMSCs through gene focusing via a MAP kinase signaling pathway. Mechanical strain increases expression levels of well-established osteogenic marker genes while simultaneously reducing expression levels of marker genes from three alternate lineages (chondrogenic, adipogenic, and neurogenic). Mechanical strain also increases matrix mineralization (a hallmark of osteogenic differentiation) and activation of extracellular signal-related kinase 1/2 (ERK). Addition of the MEK inhibitor PD98059 to reduce ERK activation decreases osteogenic gene expression and matrix mineralization while also blocking strain-induced down-regulation of nonosteogenic lineage marker genes. These results demonstrate that mechanical strain enhances collagen I-induced gene focusing and osteogenic differentiation in hMSCs through the ERK MAP kinase signal transduction pathway.

Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis

Embryonic stem (ES) cells can differentiate in vitro to produce the endothelial and hematopoietic precursor, the hemangioblasts, which are derived from the mesoderm germ layer. Differentiation of Bry(GFP/+) ES cell to hemangioblasts can be followed by the expression of the Bry(GFP/+) and Flk1 genes. Proteomic and transcriptomic changes during this differentiation process were analyzed to identify mechanisms for phenotypic change during early differentiation. Three populations of differentiating Bry(GFP) ES cells were obtained by flow cytometric sorting, GFP-Flk1- (epiblast), GFP+Flk1- (mesoderm), and GFP+Flk1+ (hemangioblast). Microarray analyses and relative quantification two-dimensional LCLC-MS/MS on nuclear extracts were performed. We identified and quantified 2389 proteins, 1057 of which were associated to their microarray probe set. These included a variety of low abundance transcription factors, e.g. UTF1, Sox2, Oct4, and E2F4, demonstrating a high level of proteomic penetrance. When paired comparisons of changes in the mRNA and protein expression levels were performed low levels of correlation were found. A strong correlation between isobaric tag-derived relative quantification and Western blot analysis was found for a number of nuclear proteins. Pathway and ontology analysis identified proteins known to be involved in the regulation of stem cell differentiation, and proteins with no described function in early ES cell development were also shown to change markedly at the proteome level only. ES cell development is regulated at the mRNA and protein level.

Expression analysis of nuclear factor of activated T cells (NFAT) during myeloid differentiation of CD34+ cells: regulation of Fas ligand gene expression in megakaryocytes

OBJECTIVE

Nuclear factor of activated T cells (NFAT) transcription factors belong to a family of five proteins that are primarily known for their central role in the regulation of inducible gene expression in activated T cells. Little information exists on the expression or function of NFAT family members in hematopoietic cells, during myeloid differentiation or in myeloid cells.

MATERIALS AND METHODS

In the present study, we establish a comprehensive expression profile of all five NFAT family members in human CD34+ hematopoietic progenitor cells and during their ex vivo differentiation into neutrophil, eosinophil, erythroid, and megakaryocytic lineages. Based on the observed expression pattern, the role of NFAT in Fas ligand gene expression in megakaryocytes was investigated.

RESULTS

When CD34+ cells are induced to differentiate into neutrophil granulocytes, expression of all NFAT family members is rapidly suppressed. In contrast, regulation of NFAT expression during eosinophil, erythroid, and megakaryocytic differentiation follows a family member- and lineage-specific pattern. Most obviously, transcript and protein levels of NFATc4 are specifically upregulated about 10-fold during megakaryocytic differentiation, while they remain almost undetectable in neutrophil, eosinophil, and erythroid cells. As a first evidence for a functional role for NFAT in this cell type, NFAT was found to be strictly required for both the constitutive and inducible expression of the Fas ligand gene in megakaryocytes.

CONCLUSION

The expression pattern of NFAT and its family member- and lineage-specific regulation during myeloid differentiation will prompt further studies on the role of NFAT in myeloid cells, particularly in megakaryocytes.

Coordinate gene regulation during hematopoiesis is related to genomic organization

Gene loci are found in nuclear subcompartments that are related to their expression status. For instance, silent genes are often localized to heterochromatin and the nuclear periphery, whereas active genes tend to be found in the nuclear center. Evidence also suggests that chromosomes may be specifically positioned within the nucleus; however, the nature of this organization and how it is achieved are not yet fully understood. To examine whether gene regulation is related to a discernible pattern of genomic organization, we analyzed the linear arrangement of co-regulated genes along chromosomes and determined the organization of chromosomes during the differentiation of a hematopoietic progenitor to erythroid and neutrophil cell types. Our analysis reveals that there is a significant tendency for co-regulated genes to be proximal, which is related to the association of homologous chromosomes and the spatial juxtaposition of lineage-specific gene domains. We suggest that proximity in the form of chromosomal gene distribution and homolog association may be the basis for organizing the genome for coordinate gene regulation during cellular differentiation.

Differential contributions of haematopoietic stem cells to foetal and adult haematopoiesis: insights from functional analysis of transcriptional regulators

An increasing number of molecules have been identified as candidate regulators of stem cell fates through their involvement in leukaemia or via post-genomic gene discovery approaches. A full understanding of the function of these molecules requires (1) detailed knowledge of the gene networks in which they participate and (2) an appreciation of how these networks vary as cells progress through the haematopoietic cell hierarchy. An additional layer of complexity is added by the occurrence of different haematopoietic cell hierarchies at different stages of ontogeny. Beyond these issues of cell context dependence, it is important from a mechanistic point of view to define the particular cell fate pathway impacted by any given regulator. Herein, we advance the notion that haematopoietic stem cells (HSC), which sustain haematopoiesis throughout adult life and are specified in foetal life, have a minimal or late contribution to foetal haematopoiesis but instead largely proliferate during the foetal period. In light of this notion, we revisit published data on mouse knockouts of haematopoietically-affiliated transcription factors highlighting novel insights that may be gained from taking such a view.

Inference, validation, and dynamic modeling of transcription networks in multipotent hematopoietic cells

Identifying the transcription factor interactions that are responsible for cell-specific gene expression programs is key to understanding the regulation of cell behaviors, such as self-renewal, proliferation, differentiation, and death. The rapidly increasing availability of microarray-derived global gene expression data sets, coupled with genome sequence information from multiple species, has driven the development of computational methods to reverse engineer and dynamically model genetic regulatory networks. An understanding of the architecture and behavior of transcriptional networks should lend insight into how the huge number of potential gene expression programs is constrained and facilitates efforts to direct or redirect cell fate.

Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

Lineage specification of multipotent progenitor cells is governed by a balance of lineage-affiliated transcription factors, such as GATA1 and PU.1, which regulate the choice between erythroid and myelomonocytic fates. But how ratios of lineage-determining transcription factors stabilize progenitor cells and resolve their indeterminacy to commit them to discrete, mutually exclusive fates remains unexplained. We used a simple model and experimental measurements to analyze the dynamics of a binary fate decision governed by a gene-circuit containing auto-stimulation and cross-inhibition, as embodied by the GATA1-PU.1 paradigm. This circuit generates stable attractors corresponding to erythroid and myelomonocytic fates, as well as an uncommitted metastable state characterized by coexpression of both regulators, explaining the phenomenon of "multilineage priming". GATA1 and PU.1 mRNA and transcriptome dynamics of differentiating progenitor cells confirm that commitment occurs in two stages, as suggested by the model: first, the progenitor state is destabilized in an almost symmetrical bifurcation event, resulting in a poised state at the boundary between the two lineage-specific attractors; second, the cell is driven to the respective, now accessible attractors. This minimal model captures fundamental features of binary cell fate decisions, uniting the concepts of stochastic (selective) and deterministic (instructive) regulation, and hence, may apply to a wider range of binary fate decision points.

DNA methylation profiling of myelodysplastic syndrome hematopoietic progenitor cells during in vitro lineage-specific differentiation

Deregulated epigenetic mechanisms are likely involved in the pathogenesis of myelodysplastic syndromes (MDSs). Which genes are silenced by aberrant promotor methylation during MDS hematopoiesis has not been equivalently investigated. Using an in vitro differentiation model of human hematopoiesis, we generated defined differentiation stages (day 0, day 4, day 7, day 11) of erythro-, thrombo- and granulopoiesis from 13 MDS patients and seven healthy donors. Promotor methylation analysis of key regulatory genes involved in cell cycle control (p14, p15, p16, CHK2), DNA repair (hMLH1), apoptosis (p73, survivin, DAPK), and differentiation (RARb, WT1) was performed by methylation-specific polymerase chain reaction. Corresponding gene expression was analyzed by microarray (Affymetrix, HG-U133A). We provide evidence that p16, survivin, CHK2, and WT1 are affected by promotor hypermethylation in MDSs displaying a selective International Prognostic Scoring System risk association. A methylation-associated mRNA downregulation for specific hematopoietic lineages and differentiation stages is demonstrated for survivin, CHK2, and WT1. We identified a suppressed survivin mRNA expression in methylated samples during erythropoiesis, whereas WT1 and CHK2 methylation-related reduction of mRNA expression was found during granulopoiesis in all MDS risk types. Our data suggest that lineage-specific methylation-associated gene silencing of survivin, CHK2, and WT1 in MDS hematopoietic precursor cells may contribute to the MDS-specific phenotype

NOV (CCN3) functions as a regulator of human hematopoietic stem or progenitor cells

Clinically successful hematopoietic cell transplantation is dependent on hematopoietic stem and progenitor cells. Here we identify the matricellular protein Nephroblastoma Overexpressed (Nov, CCN3) as being essential for their functional integrity. Nov expression is restricted to the primitive (CD34) compartments of umbilical vein cord blood, and its knockdown in these cells by lentivirus-mediated RNA interference abrogates their function in vitro and in vivo. Conversely, forced expression of Nov and addition of recombinant Nov protein both enhance primitive stem and/or progenitor activity. Taken together, our results identify Nov (CCN3) as a regulator of human hematopoietic stem or progenitor cells.

Biological and molecular evidence for existence of lymphoid-primed multipotent progenitors

Studies from our and other laboratories have over the last 2 years implicated the existence of multipotent progenitors (MPPs) with combined granulocyte-macrophage, B cell, and T cell potential, but little or no megakaryocyte-erythroid (MkE) potential in the adult bone marrow Lineage(-)SCA-1(+)KIT(+) (LSK) compartment of multipotent stem and progenitor cells. The evidence for the existence of LSKCD34(+)FLT3(hi) lymphoid-primed MPPs (LMPPs) implicates that a strict separation into common myeloid and lymphoid pathways might not be the first lineage commitment step of hematopoietic stem cells (HSCs). Together with the evidence for existence of common myeloid and common lymphoid progenitors (CMPs and CLPs, respectively), the identification of LMPPs also suggests that at least the granulocyte-macrophage lineage can be generated through alternative pathways. However, the existence of LMPPs has recently been questioned, as there is evidence that at least a fraction of LSKCD34(+)FLT3(hi) cells sustains MkE potential. Thus, in more recent studies we have in more detail compared the molecular signature of adult LMPPs to populations of LSK cells enriched for cells with pluripotent HSC activity. Notably, we have found at the global as well as single-cell level that LMPPs when compared with pluripotent HSCs downregulate the transcriptional priming of genes typically expressed in cells of the MkE lineage, while upregulating early lymphoid genes. Although other studies have suggested that the earliest HSC commitment steps might differ in fetal and adult hematopoiesis, we have also obtained evidence suggesting that the LMPP is defined already during fetal development.

Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors

Recent studies implicated the existence of adult lymphoid-primed multipotent progenitors (LMPPs) with little or no megakaryocyte-erythroid potential, questioning common myeloid and lymphoid progenitors as obligate intermediates in hematopoietic stem cell (HSC) lineage commitment. However, the existence of LMPPs remains contentious. Herein, global and single-cell analyses revealed a hierarchical organization of transcriptional lineage programs, with downregulation of megakaryocyte-erythroid genes from HSCs to LMPPs, sustained granulocyte-monocyte priming, and upregulation of common lymphoid (but not B and T cell-specific) genes. These biological and molecular relationships, implicating almost mutual exclusion of megakaryocyte-erythroid and lymphoid pathways, are established already in fetal hematopoiesis, as evidenced by existence of LMPPs in fetal liver. The identification of LMPPs and hierarchically ordered transcriptional activation and downregulation of distinct lineage programs is compatible with a model for HSC lineage commitment in which the probability for undergoing different lineage commitment fates changes gradually when progressing from HSCs to LMPPs.

Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators

Deciphering the molecular basis for human erythropoiesis should yield information benefiting studies of the hemoglobinopathies and other erythroid disorders. We used an in vitro erythroid differentiation system to study the developing red blood cell transcriptome derived from adult CD34+ hematopoietic progenitor cells. mRNA expression profiling was used to characterize developing erythroid cells at six time points during differentiation (days 1, 3, 5, 7, 9, and 11). Eleven thousand seven hundred sixty-three genes (20,963 Affymetrix probe sets) were expressed on day 1, and 1,504 genes, represented by 1,953 probe sets, were differentially expressed (DE) with 537 upregulated and 969 downregulated. A subset of the DE genes was validated using real-time RT-PCR. The DE probe sets were subjected to a cluster metric and could be divided into two, three, four, five, or six clusters of genes with different expression patterns in each cluster. Genes in these clusters were examined for shared transcription factor binding sites (TFBS) in their promoters by comparing enrichment of each TFBS relative to a reference set using transcriptional regulatory network analysis. The sets of TFBS enriched in genes up- and downregulated during erythropoiesis were distinct. This analysis identified transcriptional regulators critical to erythroid development, factors recently found to play a role, as well as a new list of potential candidates, including Evi-1, a potential silencer of genes upregulated during erythropoiesis. Thus this transcriptional regulatory network analysis has yielded a focused set of factors and their target genes whose role in differentiation of the hematopoietic stem cell into distinct blood cell lineages can be elucidated.

Understanding cellular networks to improve hematopoietic stem cell expansion cultures

Efforts to develop culture technologies capable of eliciting robust human blood stem cell growth have met with limited success. Considering that adult stem cell cultures are complex systems, comprising multiple cell types with dynamically changing intracellular signalling environments and cellular compositions, this is not surprising. Typically treated as single-input single-output systems, adult stem cell cultures are better described as complex, non-linear, multiple-input multiple-output systems wherein the proliferation of subpopulations of cells leads to the formation of intercellular endogenously secreted protein interaction networks. Genomic and proteomic tools need to be applied to generate high-throughput (and ideally high-content) biological measurements of stem cell culture evolution. Datasets describing cellular interaction networks need to be integrated into predictive models of in vitro stem cell development. Ultimately, such models will serve as a starting point for the rational design of blood stem cell expansion bioprocesses utilizing dynamic system perturbations to achieve the preferential expansion of target cell populations.

Gene expression during terminal erythroid differentiation

PURPOSE OF REVIEW

Expression profiling is a powerful technique to sample cell state. This review shows how expression profiling is being applied to the study of erythroid differentiation.

RECENT FINDINGS

Expression-based studies of multipotential hematopoietic progenitor cells has shown that these cells express lineage-restricted genes from multiple lineages at low levels, and that they are in effect 'primed' to develop into all hematopoietic cell types. Expression profiling of oligopotent and committed progenitor cells has further shown that commitment to the erythroid lineage is associated with a progressive decline in the number of expressed genes. Lineage commitment is regulated by lineage-restricted transcription factors, and studies show that the erythroid transcription factor GATA1, in addition to activating a subset of genes, has global repressive effects on gene expression. Terminal erythroid differentiation is associated with further reduction in the number of expressed genes. The erythroid program is defined by those genes that are still expressed, and their high-level expression depends on specific epigenetic modifications, recruitment of transcription factors, and posttranscriptional effects.

SUMMARY

Expression profiling provides the means to identify novel targets for the therapy of erythrocytes disorders, and to obtain insights into the mechanisms of cellular differentiation.

Quantitative stem cell biology: computational studies in the hematopoietic system

PURPOSE OF REVIEW

This review is intended to provide an overview of recently published computational methods, including bioinformatic algorithms, mathematical models and simulation studies, applied to stem cell biology, with particular reference to the hematopoietic system.

RECENT FINDINGS

The analysis of molecular data is making an increased contribution to identify dynamic system responses. Specifically, there are promising computational approaches to characterizing the functional interrelation of network components regulating the process of differentiation and lineage specification of hematopoietic stem cells. Furthermore, evidence is accumulating that stem cell organization should be regarded as a flexible, self-organizing process rather than as a predetermined sequence of events. A number of mathematical models relevant to the hematopoietic (stem cell) system are applied successfully to clinical situations, demonstrating the predictive power of theoretical methods.

SUMMARY

Based on the advances in measurement technology, an increasing amount of cellular and molecular data is being generated within the field of stem cell biology. The complexity of the underlying systems, however, most often limits a direct interpretation of the data and makes computational methods indispensable. Mathematical models and simulation techniques are contributing considerably to the discovery of general regulatory principles of stem cell organization and are providing clinically relevant predictions.

Global genetic regulatory networks controlling hematopoietic cell fates

PURPOSE OF REVIEW

The gene expression profile of a cell is a consequence of transcription factor activities, which, in turn, are controlled by extra-cellular signals. The relationships between all these regulators constitute a genetic regulatory network, which can be used to predict the behavior of the cell in changing environments. We outline the progress being made to identify Genetic Regulatory Networks for hematopoiesis, using gene-by-gene approaches or emerging genomic technologies.

RECENT FINDINGS

The construction of genetic regulatory networks for single and multicellular organisms has inspired the building of genetic regulatory networks for erythropoiesis and B-cell differentiation. genetic regulatory networks are 'scale-free', whereby some genes have many connections while others have very few. The well connected genes, or hubs, correspond to master regulators of the networks, acting to integrate signals and control the sequential passage of the cells through the differentiation process. Lineage decisions are governed by cross-antagonism between two hubs. Large datasets from genome-wide analyses support the concept of multilineage priming and will increasingly refine the network topologies.

SUMMARY

As the underlying genetic regulatory networks for hematopoiesis continue to emerge, the program for lineage choice and differentiation will be revealed. More large-scale datasets identifying network components are needed alongside continued gene-by-gene analyses.

Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a broad developmental disease characterized by anemia, bone marrow (BM) erythroblastopenia, and an increased incidence of malignancy. Mutations in ribosomal protein gene S19 (RPS19) are found in approximately 25% of DBA patients; however, the role of RPS19 in the pathogenesis of DBA remains unknown. Using global gene expression analysis, we compared highly purified multipotential, erythroid, and myeloid BM progenitors from RPS19 mutated and control individuals. We found several ribosomal protein genes downregulated in all DBA progenitors. Apoptosis genes, such as TNFRSF10B and FAS, transcriptional control genes, including the erythropoietic transcription factor MYB (encoding c-myb), and translational genes were greatly dysregulated, mostly in diseased erythroid cells. Cancer-related genes, including RAS family oncogenes and tumor suppressor genes, were significantly dysregulated in all diseased progenitors. In addition, our results provide evidence that RPS19 mutations lead to codownregulation of multiple ribosomal protein genes, as well as downregulation of genes involved in translation in DBA cells. In conclusion, the altered expression of cancer-related genes suggests a molecular basis for malignancy in DBA. Downregulation of c-myb expression, which causes complete failure of fetal liver erythropoiesis in knockout mice, suggests a link between RPS19 mutations and reduced erythropoiesis in DBA.

The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation

We have examined the relationship between nuclear localization and transcriptional activity of the endogenous murine beta-globin locus during erythroid differentiation. Murine fetal liver cells were separated into distinct erythroid maturation stages by fluorescence-activated cell sorting, and the nuclear position of the locus was determined at each stage. We find that the beta-globin locus progressively moves away from the nuclear periphery with increasing maturation. Contrary to the prevailing notion that the nuclear periphery is a repressive compartment in mammalian cells, beta(major)-globin expression begins at the nuclear periphery prior to relocalization. However, relocation of the locus to the nuclear interior with maturation is accompanied by an increase in beta(major)-globin transcription. The distribution of nuclear polymerase II (Pol II) foci also changes with erythroid differentiation: Transcription factories decrease in number and contract toward the nuclear interior. Moreover, both efficient relocalization of the beta-globin locus from the periphery and its association with hyperphosphorylated Pol II transcription factories require the locus control region (LCR). These results suggest that the LCR-dependent association of the beta-globin locus with transcriptionally engaged Pol II foci provides the driving force for relocalization of the locus toward the nuclear interior during erythroid maturation.

Activation of vascular endothelial growth factor receptor-2 in bone marrow leads to accumulation of myeloid cells: role of granulocyte-macrophage colony-stimulating factor

Vascular endothelial growth factor (VEGF) is a secreted cytokine that plays a major role in the formation and maintenance of the hemopoietic and vascular compartments. VEGF and its receptors, VEGFR-1 and VEGFR-2, have been found to be expressed on subsets of normal and malignant hemopoietic cells, but the role of the individual receptors in hemopoiesis requires further study. Using a VEGFR-2 fusion protein that can be dimerized with a synthetic drug, we were able to specifically examine the effects of VEGFR-2 signaling in hemopoietic cells in vivo. Mice transplanted with bone marrow transduced with this inducible VEGFR-2 fusion protein demonstrated expansion of myeloid cells (Gr-1+, CD11b+). Levels of myeloid progenitors were also increased following VEGFR-2 activation, through autocrine and paracrine mechanisms, as measured by clonogenic progenitor assays. VEGFR-2 activation induced expression of GM-CSF and increased serum levels in vivo. Abrogation of GM-CSF activity, either with neutralizing Abs or by using GM-CSF-null hemopoietic cells, inhibited VEGFR-2-mediated myeloid progenitor activity. Our findings indicate that VEGF signaling through VEGFR-2 promotes myelopoiesis through GM-CSF-dependent and -independent mechanisms.

Transcriptional profiling of human hematopoiesis during in vitro lineage-specific differentiation

To better understand the transcriptional program that a ccompanies orderly lineage-specific hematopoietic differentiation, we performed serial oligonucleotide microarray analysis of human normal CD34+ bone marrow cells during lineage-specific differentiation. CD34+ bone marrow cells isolated from healthy individuals were selectively stimulated in vitro with the cytokines erythropoietin (EPO), thrombopoietin (TPO), granulocyte colony-stimulating factor (G-CSF), and granulocyte macrophage colony-stimulating factor (GM-CSF). Cells from each of the lineages were harvested after 4, 7, and 11 days of culture for expression profiling. Gene expression was analyzed by oligonucleotide microarrays (HG-U133A; Affymetrix, Santa Clara, CA). Experiments were done in triplicates. We identified 258 genes that are consistently upregulated or downregulated during the course of lineage-specific differentiation within each specific lineage (horizontal change). In addition, we identified 52 genes that contributed to a specific expression profile, yielding a genetic signature specific for successive stages of differentiation within each of the three lineages. Analysis of horizontal changes selected 21 continuously upregulated genes for EPO-induced differentiation (including GTPase activator proteins RAP1GA1 and ARHGAP8, which regulate small Rho GTPases), 21 for G-CSF-induced/GM-CSF-induced differentiation, and 91 for TPO-induced differentiation (including DLK1, of which the role in normal hematopoiesis is not defined). During the lineage-specific differentiation, 58 (erythropoiesis), 30 (granulopoiesis), and 37 (thrombopoiesis) genes were significantly downregulated, respectively. The expression of selected genes was confirmed by real-time polymerase chain reaction. Our data encompass the first extensive transcriptional profile of human hematopoiesis during in vitro lineage-specific differentiation.

Clonal heterogeneity in growth kinetics of CD34+CD38- human cord blood cells in vitro is correlated with gene expression pattern and telomere length

Human hematopoietic stem cells (HSCs) are characterized by an extensive proliferative capacity that decreases from fetal liver to cord blood (CB) to adult bone marrow. In previous studies, it was demonstrated that the proliferative capacity of individual CD34+CD38- HSC clones is correlated with their growth kinetics in vitro and that HSC turnover in vivo can be estimated by telomere-length measurements. The present study was aimed at the characterization of the clonal composition of CD34+CD38- human umbilical CB cells in terms of growth kinetics, telomere length, and gene expression profile. For this purpose, individual CD34+CD38- CB cells were sorted into 96-well plates containing serum-free medium supplemented with six growth factors. During expansion, cell numbers in each individual well were scored in 3-day intervals. Once sufficient cell numbers were achieved, telomere length was measured by flow fluorescence in situ hybridization (flow FISH). In a second set of experiments, gene expression and colony-forming capacity were analyzed in slowly growing clones as compared with fast-growing clones, using linear amplification and oligonucleotide microarrays (HG-U133A; Affymetrix). Individual CD34+CD38- cells from CB displayed an extensive functional heterogeneity in growth kinetics. Among highly proliferative clones, the most slowly growing clones were characterized by the longest telomeres. Furthermore, significant differences in gene expression were detected between slow- and fast-growing clones, whereas no significant difference in colony-forming capacity was observed. These data provide further evidence for a functional hierarchy in the human HSC compartment and suggest a link between telomere length and proliferation capacity of individual HSC clones.

The transcriptional program of terminal granulocytic differentiation

To characterize the transcriptional program that governs terminal granulocytic differentiation in vivo, we performed comprehensive microarray analyses of human bone marrow populations highly enriched in promyelocytes (PMs), myelocytes/metamyelocytes (MYs), and neutrophils (bm-PMNs). These analyses identified 11 310 genes involved in differentiation, of which 6700 were differentially regulated, including previously unidentified effector proteins and surface receptors of neutrophils. Differentiation of PMs toward MYs was accompanied by a marked decline of proliferative and general cellular activity as defined by down-regulation of E2 promoter binding factor (E2F) target genes; cyclin dependent kinases 2, 4, and 6; and various metabolic, proteasomal, and mitochondrial genes. Expression patterns of apoptosis genes indicated death control by the p53 pathway in PMs and by death receptor pathways in bm-PMNs. Effector proteins critical for host defense were expressed successively throughout granulocytic differentiation, whereas receptors and receptor ligands essential for the activation of the host defense program were terminally up-regulated in bm-PMNs. The up-regulation of ligand-receptor pairs, which are defined inducers as well as target genes of nuclear factor-κB (NF-κB), suggests a constitutive activation of NF-κB in bm-PMNs by autocrine loops. Overall, these results define a granulocytic differentiation model governed by a highly coordinated fail-safe program, which promotes completion of differentiation before cells gain responsiveness toward activating stimuli that accompany infections. (Blood. 2005; 105:1785-1796)

Conceptual models to understand tissue stem cell organization

PURPOSE OF REVIEW

Theoretic and, in particular, mathematic models can help biologists to select and design experiments, to highlight general principles, to discriminate similar and to link different phenomena, and to predict novel features. Specifically, they contribute to an understanding of latent mechanisms and crucial parameters of biologic processes. The following review gives an overview of recent developments in the field of hematopoietic tissue stem cell modeling.

RECENT FINDINGS

A number of experimental findings on heterogeneity, flexibility, and plasticity of hematopoietic and other tissue stem cells are challenging the classic stem cell concept of a predefined intrinsic stem cell program. Self-organizing systems provide a more elegant and comprehensive alternative to explain experimental data.

SUMMARY

Within the last few decades, modeling approaches in stem cell biology have evolved and now encompass a broad spectrum of phenomena, ranging from the cellular level to the tissue level. The application of theoretic models is currently suggesting that we abandon the classic assumption of a strict developmental hierarchy and understand stem cell organization as a dynamic, functional process. Such a perspective has implications for a prospective characterization of tissue stem cells (eg, regarding gene expression profiles and genetic regulation patterns).

The origin of hematopoietic cell type diversity

The hematopoietic system remains robust with regards to extrinsic perturbations, in sharp contrast with the stochastic behavior of hematopoeitic stem cells (HSCs) at the single cell level, suggesting that stability may be achieved within a stem cell system that undergoes constant self-renewal, commitment to differentiation and generates cell type diversification. Converging evidence at the interface of cellular, molecular and numerical studies suggests that diversity is generated by the chaotic dynamics of transcription factor networks within a cell and of the combination of growth factors and cytokines in the environment, both involving cooperation and competition. Current evidence indicates that HSCs are primed for multilineage gene expression. A subtle shift in transcription factor dosage is sufficient to perturb this equilibrium and to drive lineage commitment that involves a resolution of complexity at the molecular level and a transition towards less chaotic behavior. This dynamical instability establishes a state of responsiveness to extrinsic signals. Evolutionary conserved environmental cues that drive pattern formation or migratory behavior during embryonic development operate in the adult to influence the decision between self-renewal and differentiation in HSCs, as exemplified by the role of Notch1, Wnt proteins, BMPs and VEGF. In contrast, a network of cytokines uniquely present in mammalians influences later developmental stages, from progenitors with more restricted potentials (tri-, bi- or unipotent) to mature functional cells. These cytokines have co-opted the ancient Jak-STAT pathway but also appear to trigger lineage-affiliated transcription factors, thus linking environmental signaling to cell fate decisions.

A panorama of lineage-specific transcription in hematopoiesis

The hematopoietic system consists of more than ten differentiated cell types, all of which are derived from a single type of hematopoietic stem cell. The accessibility and interest of this system have made it a model for understanding normal and abnormal differentiation of mammalian cells. Newer techniques have generated a mass of data that requires integrative approaches for analysis and interpretation. The traditional view of the differentiation program holds that a small number of regulators are involved in each stage of cell specification. However, this may not be the case. Recent analyses have shown that almost all substantial subsets of genes, including the set of broadly expressed transcription factors, are expressed in patterns that are unique for each lineage. Further, much of this difference between lineages can be captured in two-dimensional graphs. Understanding the biologic significance, mechanisms and constraints underlying these differences is a challenge for experimentalists and computational biologists alike.