Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

The emergence of multiple axes is an essential element in the establishment of the mammalian body plan. This process takes place shortly after implantation of the embryo within the uterus and relies on the activity of gene regulatory networks that coordinate transcription in space and time. Whereas genetic approaches have revealed important aspects of these processes(1), a mechanistic understanding is hampered by the poor experimental accessibility of early post-implantation stages. Here we show that small aggregates of mouse embryonic stem cells (ESCs), when stimulated to undergo gastrulation-like events and elongation in vitro, can organize a post-occipital pattern of neural, mesodermal and endodermal derivatives that mimic embryonic spatial and temporal gene expression. The establishment of the three major body axes in these 'gastruloids'(2,3) suggests that the mechanisms involved are interdependent. Specifically, gastruloids display the hallmarks of axial gene regulatory systems as exemplified by the implementation of collinear Hox transcriptional patterns along an extending anteroposterior axis. These results reveal an unanticipated self-organizing capacity of aggregated ESCs and suggest that gastruloids could be used as a complementary system to study early developmental events in the mammalian embryo.

In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture

Stefano Davide Vianello

In humans, mice, and other mammals key internal organs such as the gut, the lungs, the pancreas, and the liver all derive from the same embryonic tissue: the endoderm. The development of all of these structures thus depends on a same set of early cells, and on the developmental instructions provided to them by the embryo. One approach to study what these instructions might be is to study the behaviour of endoderm cells when they can not rely on embryonic instructions. That is, when they are generated and made to develop outside of the embryo. The rationale behind this approach, widely embraced by the field of synthetic embryology, is that the unguided development of specific embryonic cell types can provide a window to the observation of intrinsic characteristics of these cells and of fundamental developmental principles which might not be executed or manifested within the regulated environment of the embryo. Accordingly, in the work here described I use gastruloids, synthetic models of development made by aggregation of mouse embryonic stem cells in vitro to characterise the developmental behaviour of endoderm cells, in the absence of embryonic cues and in the absence of the extraembryonic tissues that they would usually rely on in vivo. In the first chapter of this thesis, I provide an introduction, overview, and review of our current understanding of the developmental biology of mouse endoderm as this develops in the embryo. I also introduce gastruloids as stem-cell-based experimental systems to study developmental mechanisms in vitro, decoupled from the constraints of experimental work with animals and animal embryos. Chapter 2 is dedicated to the earliest steps of endoderm development in gastruloids. I show when and where these cells appear, and how they sort as the gastruloid starts to mature. I find that endoderm cells follow similar spatial and temporal developmental patterns as those they would follow if they were in the embryo. I notably find that they always remain in an epithelial state, even as other cell types undergo mesenchymal transition. In Chapter 3 I describe surprising dynamics of endoderm cells over time, and how they self-organise into complex architectures at the core of the gastruloids. The epithelial domain that forms is dynamic and plastic, and partitions the gastruloids into interfacing compartments. Importantly, I reveal a significant endodermal component to this in vitro system, usually considered to be unstructured and neural/mesodermal in character. In Chapter 4 I show how the core endoderm compartment that I see forming in gastruloids is patterned along the longitudinal axis of the aggregate, with different cellular identities at different anterior-posterior position of the domain. By comparison with published embryonic datasets, I identify endodermal identities corresponding to the full spectrum of those that make up the gut tube in the embryo. Specifically, I describe how most endodermal cells adopt an early intestinal fate, and how many acquire anterior foregut identities. The work described in this thesis presents gastruloids as promising in vitro systems for the study of endoderm biology, morphogenesis, and mature fate specification, filling a gap within the field of synthetic embryology. It also notably opens translational possibilities to the use of gastruloids to produce endodermal cell types which may be otherwise difficult to generate using conventional directed differentiation methods.

EPFL2022

Assessing the role of Hes1 and identification of target genes in human and murine T-ALL

Silvia Wirth

The Notch signalling pathway is an ancient cell signalling mechanism that enables short-range communications between cells and controls a broad spectrum of cell fates and developmental processes. In the haematopoietic system Notch signalling has been linked to physiological, but also to pathological phenotypes of T cell development. Identification of numerous activating mutations within the NOTCH1 receptor in human T cell acute lymphoblastic leukaemia (T-ALL) patient samples demonstrated that aberrant activation of this signalling pathway is a frequent event in T-ALL. Active Notch signalling leads to the expression of a plethora of genes that might be drivers or passengers in tumorigenesis including Hes1, which encodes a transcriptional repressor. We have therefore studied Hes1 in the context of T-ALL in mouse models that mimic human disease and in human T-ALL cell lines with the aim to evaluate whether Hes1 affects disease development and disease maintenance and to characterize its function on a molecular level. The first part of this study is dedicated to the functional characterisation of Hes1 in vivo in T-ALL mouse models and in vitro in human T-ALL cell lines. Using a retroviral bone marrow transplant model of T-ALL in which progenitor cells are transduced with a retrovirus expressing constitutive active Notch1 intracellular domain (NICD) we could show that Hes1 is not required in established, late stage T-ALL cells, but that it promotes tumour progression in the early stages of the disease. We have also investigated the function of HES1 in human T-ALL and can show that the overexpression of dominant negative versions of Hes1 in two patient derived cell lines (T-ALL1, CUTLL-1) does not affect proliferation or apoptosis, emphasising that HES1 does not affect cell viability once cells are fully transformed to the leukemic state. In the second part of the study we set out to systematically delineate the gene regulatory networks down-stream of Hes1 by combining RNA-seq and ChIP-seq analysis. Comparing the gene expression of murine premalignant, early stage NICD induced CD4+CD8+ DP cells in the presence and absence of Hes1 by RNA-seq, we unexpectedly found a predominant upregulation of genes in cells expressing Hes1 indicating that Hes1 might rather act as a positive regulator of transcription than as a transcriptional repressor of distinct target genes. Hes1 might influence transcription through secondary or indirect effects as combinatorial analysis of RNA-seq and ChIP-seq led to the identification of only a small number of potential direct target genes that are transcriptionally regulated by Hes1. In summary, the role of Hes1 in promoting the early stages of the disease appears to be highly complex and is likely to involve both direct and indirect control of gene regulatory networks.

EPFL2014

Assessing the role of Hes1 and identification of target genes in human and murine T-ALL

Silvia Wirth

EPFL2014

In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture

Stefano Davide Vianello

EPFL2022