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

A life-time of hematopoietic cell function: ascent, stability, and decline

Aging is a set of complex processes that occur temporally and continuously. It is generally a unidirectional progression of cellular and molecular changes occurring during the life stages of cells, tissues and ultimately the whole organism. In vertebrate organisms, this begins at conception from the first steps in blastocyst formation, gastrulation, germ layer differentiation, and organogenesis to a continuum of embryonic, fetal, adolescent, adult, and geriatric stages. Tales of the "fountain of youth" and songs of being "forever young" are dominant ideas informing us that growing old is something science should strive to counteract. Here, we discuss the normal life stages of the blood system, particularly the historical recognition of its importance in the early growth stages of vertebrates, and what this means with respect to progressive gain and loss of hematopoietic function in the adult.

Form and function: how estrogen and progesterone regulate the mammary epithelial hierarchy

The mammary gland undergoes dramatic post-natal growth beginning at puberty, followed by full development occurring during pregnancy and lactation. Following lactation, the alveoli undergo apoptosis, and the mammary gland reverses back to resemble the nonparous gland. This process of growth and regression occurs for multiple pregnancies, suggesting the presence of a hierarchy of stem and progenitor cells that are able to regenerate specialized populations of mammary epithelial cells. Expansion of epithelial cell populations in the mammary gland is regulated by ovarian steroids, in particular estrogen acting through its receptor estrogen receptor alpha (ERα) and progesterone signaling through progesterone receptor (PR). A diverse number of stem and progenitor cells have been identified based on expression of cell surface markers and functional assays. Here we review the current understanding of how estrogen and progesterone act together and separately to regulate stem and progenitor cells within the human and mouse mammary tissues. Better understanding of the hierarchal organization of epithelial cell populations in the mammary gland and how the hormonal milieu affects its regulation may provide important insights into the origins of different subtypes of breast cancer.

Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis

BACKGROUND

A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. Recent advances in single-cell gene expression profiling have created new possibilities to characterize this heterogeneity and to dissect the potential intra-cancer cellular hierarchy.

RESULTS

Here, we apply single-cell analysis to systematically characterize the heterogeneity within leukemic cells using the MLL-AF9 driven mouse model of acute myeloid leukemia. We start with fluorescence-activated cell sorting analysis with seven surface markers, and extend by using a multiplexing quantitative polymerase chain reaction approach to assay the transcriptional profile of a panel of 175 carefully selected genes in leukemic cells at the single-cell level. By employing a set of computational tools we find striking heterogeneity within leukemic cells. Mapping to the normal hematopoietic cellular hierarchy identifies two distinct subtypes of leukemic cells; one similar to granulocyte/monocyte progenitors and the other to macrophage and dendritic cells. Further functional experiments suggest that these subtypes differ in proliferation rates and clonal phenotypes. Finally, co-expression network analysis reveals similarities as well as organizational differences between leukemia and normal granulocyte/monocyte progenitor networks.

CONCLUSIONS

Overall, our single-cell analysis pinpoints previously uncharacterized heterogeneity within leukemic cells and provides new insights into the molecular signatures of acute myeloid leukemia.

Model discrimination in dynamic molecular systems: application to parotid de-differentiation network

In modern systems biology the modeling of longitudinal data, such as changes in mRNA concentrations, is often of interest. Fully parametric, ordinary differential equations (ODE)-based models are typically developed for the purpose, but their lack of fit in some examples indicates that more flexible Bayesian models may be beneficial, particularly when there are relatively few data points available. However, under such sparse data scenarios it is often difficult to identify the most suitable model. The process of falsifying inappropriate candidate models is called model discrimination. We propose here a formal method of discrimination between competing Bayesian mixture-type longitudinal models that is both sensitive and sufficiently flexible to account for the complex variability of the longitudinal molecular data. The ideas from the field of Bayesian analysis of computer model validation are applied, along with modern Markov Chain Monte Carlo (MCMC) algorithms, in order to derive an appropriate Bayes discriminant rule. We restrict attention to the two-model comparison problem and present the application of the proposed rule to the mRNA data in the de-differentiation network of three mRNA concentrations in mammalian salivary glands as well as to a large synthetic dataset derived from the model used in the recent DREAM6 competition.

A single cis element maintains repression of the key developmental regulator Gata2

In development, lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates. Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements. It is not understood whether these elements function collectively to confer transcriptional regulation, or individually to control specific aspects of activation or repression, such as initiation versus maintenance. Here, we have analyzed cis element regulation of the critical hematopoietic factor Gata2, which is expressed in early precursors and repressed as GATA-1 levels rise during terminal differentiation. We engineered mice lacking a single cis element −1.8 kb upstream of the Gata2 transcriptional start site. Although Gata2 is normally repressed in late-stage erythroblasts, the −1.8 kb mutation unexpectedly resulted in reactivated Gata2 transcription, blocked differentiation, and an aberrant lineage-specific gene expression pattern. Our findings demonstrate that the −1.8 kb site selectively maintains repression, confers a specific histone modification pattern and expels RNA Polymerase II from the locus. These studies reveal how an individual cis element establishes a normal developmental program via regulating specific steps in the mechanism by which a critical transcription factor is repressed.

Different cell types are formed and maintained by proteins called transcription factors that directly bind to specific DNA sequences to activate or repress gene expression. While numerous DNA sequences bound by transcription factors are established, many questions remain unanswered regarding how they function at specific sites located at distinct chromosomal regions. As a model to study this process, we examined the regulation of a gene controlling red blood cell development, Gata2, by the transcription factor GATA1. In the DNA sequence upstream of Gata2, there are several sites that GATA1 is known to bind to; however, it is unclear whether these binding sites work together or independently to control expression of Gata2. To study this, we engineered mice to specifically remove one of these GATA1-binding sites. We found that removal of this single site reactivated expression of Gata2 in a specific stage of red blood cell development where Gata2 is normally not expressed, caused a block in differentiation of these cells, and changed the histone modification pattern specifically in the region upstream of Gata2. This work supports a model in which individual transcription factor binding sites within regions of multiple binding sites can independently and distinctly regulate gene expression during development.

From genes to cells to tissues--modelling the haematopoietic system

Haematopoiesis (or blood formation) in general and haematopoietic stem cells more specifically represent some of the best studied mammalian developmental systems. Sophisticated purification protocols coupled with powerful biological assays permit functional analysis of highly purified cell populations both in vitro and in vivo. However, despite several decades of intensive research, the sheer complexity of the haematopoietic system means that many important questions remain unanswered or even unanswerable with current experimental tools. Scientists have therefore increasingly turned to modelling to tackle complexity at multiple levels ranging from networks of genes to the behaviour of cells and tissues. Early modelling attempts of gene regulatory networks have focused on core regulatory circuits but have more recently been extended to genome-wide datasets such as expression profiling and ChIP-sequencing data. Modelling of haematopoietic cells and tissues has provided insight into the importance of phenotypic heterogeneity for the differentiation of normal progenitor cells as well as a greater understanding of treatment response for particular pathologies such as chronic myeloid leukaemia. Here we will review recent progress in attempts to reconstruct segments of the haematopoietic system. A variety of modelling strategies will be covered from small-scale, protein-DNA or protein-protein interactions to large scale reconstructions. Also discussed will be examples of how stochastic modelling may be applied to multi cell systems such as those seen in normal and malignant haematopoiesis.

A novel view on stem cell development: analysing the shape of cellular genealogies

OBJECTIVES

The analysis of individual cell fates within a population of stem and progenitor cells is still a major experimental challenge in stem cell biology. However, new monitoring techniques, such as high-resolution time-lapse video microscopy, facilitate tracking and quantitative analysis of single cells and their progeny. Information on cellular development, divisional history and differentiation are naturally comprised into a pedigree-like structure, denoted as cellular genealogy. To extract reliable information concerning effecting variables and control mechanisms underlying cell fate decisions, it is necessary to analyse a large number of cellular genealogies.

MATERIALS AND METHODS

Here, we propose a set of statistical measures that are specifically tailored for the analysis of cellular genealogies. These measures address the degree and symmetry of cellular expansion, as well as occurrence and correlation of characteristic events such as cell death. Furthermore, we discuss two different methods for reconstruction of lineage fate decisions and show their impact on the interpretation of asymmetric developments. In order to illustrate these techniques, and to circumvent the present shortage of available experimental data, we obtain cellular genealogies from a single-cell-based mathematical model of haematopoietic stem cell organization.

RESULTS AND CONCLUSIONS

Based on statistical analysis of cellular genealogies, we conclude that effects of external variables, such as growth conditions, are imprinted in their topology. Moreover, we demonstrate that it is essential to analyse timing of cell fate-specific changes and of occurrence of cell death events in the divisional context in order to understand the mechanisms of lineage commitment.

Transcriptome analysis of mammary epithelial subpopulations identifies novel determinants of lineage commitment and cell fate

Background

Understanding the molecular control of cell lineages and fate determination in complex tissues is key to not only understanding the developmental biology and cellular homeostasis of such tissues but also for our understanding and interpretation of the molecular pathology of diseases such as cancer. The prerequisite for such an understanding is detailed knowledge of the cell types that make up such tissues, including their comprehensive molecular characterisation. In the mammary epithelium, the bulk of the tissue is composed of three cell lineages, namely the basal/myoepithelial, luminal epithelial estrogen receptor positive and luminal epithelial estrogen receptor negative cells. However, a detailed molecular characterisation of the transcriptomic differences between these three populations has not been carried out.

Results

A whole transcriptome analysis of basal/myoepithelial cells, luminal estrogen receptor negative cells and luminal estrogen receptor positive cells isolated from the virgin mouse mammary epithelium identified 861, 326 and 488 genes as highly differentially expressed in the three cell types, respectively. Network analysis of the transcriptomic data identified a subpopulation of luminal estrogen receptor negative cells with a novel potential role as non-professional immune cells. Analysis of the data for potential paracrine interacting factors showed that the basal/myoepithelial cells, remarkably, expressed over twice as many ligands and cell surface receptors as the other two populations combined. A number of transcriptional regulators were also identified that were differentially expressed between the cell lineages. One of these, Sox6, was specifically expressed in luminal estrogen receptor negative cells and functional assays confirmed that it maintained mammary epithelial cells in a differentiated luminal cell lineage.

Conclusion

The mouse mammary epithelium is composed of three main cell types with distinct gene expression patterns. These suggest the existence of a novel functional cell type within the gland, that the basal/myoepithelial cells are key regulators of paracrine signalling and that there is a complex network of differentially expressed transcription factors controlling mammary epithelial cell fate. These data will form the basis for understanding not only cell fate determination and cellular homeostasis in the normal mammary epithelium but also the contribution of different mammary epithelial cell types to the etiology and molecular pathology of breast disease.

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major vasculature of the mouse embryo. As a pivotal factor in HSC ontogeny, its transcriptional regulation is of high interest but is largely undefined. In this study, we used a combination of comparative genomics and chromatin analysis to identify a highly conserved 531-bp enhancer located at position + 23.5 in the first intron of the 224-kb mouse Runx1 gene. We show that this enhancer contributes to the early hematopoietic expression of Runx1. Transcription factor binding in vivo and analysis of the mutated enhancer in transient transgenic mouse embryos implicate Gata2 and Ets proteins as critical factors for its function. We also show that the SCL/Lmo2/Ldb-1 complex is recruited to the enhancer in vivo. Importantly, transplantation experiments demonstrate that the intronic Runx1 enhancer targets all definitive HSCs in the mouse embryo, suggesting that it functions as a crucial cis-regulatory element that integrates the Gata, Ets, and SCL transcriptional networks to initiate HSC generation.

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.