Exploring the potency of normal and pathological human thymic epithelial cells

Thymic epithelial cells (TECs) are organised in a unique 3D network that is critical for the development of efficient and self-tolerant T-cells. We report for the first time that the human thymus of all ages, even old and involuted, contains a significant number (up to 30%) of clonogenic TECs with extensive growth potential. All clonogenic TECs derive from a common EpCAM+ precursor, which within 48h in culture undergoes a molecular switch and gives rise to refringent EpCAM- colonies and stratified EpCAM+ colonies. The latter two subpopulations can be distinguished based on their morphology, their expression of genes implicated in epidermal stratification and their expression of genes implicated in epithelia-mesenchymal transition. Clonal analysis revealed that clonogenic cells are hierarchically organised, refringent cells being higher in the hierarchy than stratified cells. Although the thymus normally involutes with age, it can be the site of uncontrolled proliferation, resulting in the formation of thymic tumours including thymomas. Thymomas are classified by the WHO based on histological criteria as type A, B and AB and are frequently associated with Myasthenia Gravis, an autoimmune disease affecting the neuromuscular junction. The biology of thymomas is poorly understood, because of the rarity of the tumours and because of the lack of a reliable in vitro model. We report for the first time, that clonogenic cells can be isolated from all thymoma subtypes as well as from thymic hyperplasia and mediastinal teratoma. The latter cells displayed many similarities with normal TECs but also differences in terms of morphology, gene expression and genetic profile. Importantly, all thymic tumours studied contained refringent-like EpCAM- cells and stratified EpCAM+ cells, supporting the hypothesis that thymic tumour-initiating cells arise from clonogenic TECs. We have not succeeded yet in developing an appropriate assay to support the growth of clonogenic epithelial cells from thymic tumours in vivo. Finally, we report that the SY5 monoclonal antibody raised against human involucrin reproducibly cross-reacts with a molecule present in the Golgi apparatus of refringent cells derived from normal and pathological thymi. Immunocytochemistry and knock-down experiments revealed that the latter molecule is not involucrin. Epitope mapping by phage-display experiments and data base search identified putative candidate proteins, including nesprin-1, a player of the neuromuscular junction, which could be the key to understand the frequent association of thymomas with Myasthenia Gravis.

Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells

Onur Tidin

Cells live in ever-changing environments, thereby facing a variety of dynamic environmental signals. Environmental stimuli elicit intracellular responses through signaling pathways, which converge on transcriptional activation or repression of target genes. Despite intensive research, dissecting the complex interactions between pathway components that modulate mRNA and protein production still remains a difficult task. To this end, single-cell approaches provide unique insights into intracellular processes and cell responses to environmental stimuli, otherwise inaccessible with traditional bulk studies. Single-cell measurements have revealed that isogenic cells sharing the same environment display substantial heterogeneity in both transcript and protein level. As the initial step in gene expression, transcription is an important source of such variability in eukaryotic cells due to low number of molecules involved, transcription factor dynamics and the discrete nature of biochemical reactions. Notably, production of mRNA during transcription occurs in short periods of activity, termed as transcriptional bursts, followed by longer periods of inactivity. Despite widespread observations of transcriptional dynamics in mammals, upstream molecular mechanisms shaping the eukaryotic transcription remained elusive. In this study, we quantitatively linked upstream factors and transcriptional kinetics by developing an experimental system to temporally monitor, simultaneously, inputs (transcription factors) and outputs (target gene expression) in mammalian cells, in response to stimulus. We established two Tet-On inducible stable cell lines each expressing a fusion protein of a luminescence (Nanoluciferase) reporter to either SMAD4 or SMAD2, the two main transcrip- tion factors downstream of the TGF-Î² pathway. These cell lines that also contain a short-lived firefly luciferase reporter for the expression of the target endogenous connective tissue growth factor (ctgf ) gene allowed us to quantitatively link nuclear accumulation of SMADs upon TGF-Î² stimulation to the target gene expression in real-time single cell measurements. Time- lapse luminescence microscopy and image analysis with the custom developed CAST (Cell Automated Segmentation and Tracking platform) platform provided quantitative single-cell data to link the upstream transcription factor profile to its target gene activity. The data revealed weak single-cell correlations between translocation level and the target gene expression response which suggests a mechanism in which the translocation of SMADs initiates the transcriptional response but affects the response amplitude minimally. However, SMAD4 expression levels influenced the target gene response dynamics such that cells with high SMAD4 abundance favored to respond in a more sustained and even oscillatory manner. This suggests a mechanism consisting of a dynamic interplay between the transcriptional activators and feedback mechanisms in TGF-Î² signaling. We explored further the effect of different factors such as ligand concentration, ligand type on both signaling and target gene response. Taken together, this study proposes an experimental and quantitative framework that dissect mechanisms underlying transcriptional response to stimulus.

EPFL2018

A conserved transcriptional enhancer that specifies Tyrp1 expression to melanocytes

Friedrich Beermann

Pigment cells of mammals originate from two different lineages: melanocytes arise from the neural crest, whereas cells of the retinal pigment epithelium (RPE) originate from the optic cup of the developing forebrain. Previous studies have suggested that pigmentation genes are controlled by different regulatory networks in melanocytes and RPE. The promoter of the tyrosinase-related family gene Tyrp1 has been shown to drive detectable transgene expression only to the RPE, even though the gene is also expressed in melanocytes as evident from Tyrp1-mutant mice. This indicates that the regulatory elements responsible for Tyrp1 gene expression in the RPE are not sufficient for expression in melanocytes. We thus searched for a putative melanocyte-specific regulatory sequence and demonstrate that a bacterial artificial chromosome (BAC) containing the Tyrp1 gene and surrounding sequences is able to target transgenic expression to melanocytes and to rescue the Tyrp1b (brown) phenotype. This BAC contains several highly conserved non-coding sequences that might represent novel regulatory elements. We further focused on a sequence located at -15 kb, which we identified as a melanocyte-specific enhancer as shown by cell culture and transgenic mice experiments. In addition, we show that the transcription factor Sox10 can activate this conserved enhancer. The presence of a distal Tyrp1 regulatory element, which specifies melanocyte-specific expression, supports the idea that separate regulatory sequences can mediate differential gene expression in melanocytes and RPE.

2006

Tissue engineering of the bladder

Catharina Adelöw

Stem cell use in bladder tissue engineering is a recently addressed area of investigation that has generated excitement as a novel way to restore and regenerate lost or damaged urinary bladder tissue. The remodelling of smooth muscle plays a significant role in bladder repair and regeneration. De-differentiation of smooth muscle cells from a contractile phenotype to a synthetic proliferative phenotype is characterised by smooth muscle hypertrophy and fibrosis, and leads to a poorly compliant bladder. To elucidate the underlying mechanisms of such phenomena, recent efforts in bladder tissue engineering have focused on understanding smooth muscle biology and associated mechanisms of bladder diseases. In this thesis we have designed a synthetic poly (ethylene glycol) (PEG) hydrogel for stem cell and drug delivery aimed to enhance control smooth muscle cell phenotype and thus assist in bladder repair and regeneration. We began by developing a method for isolation of cells from the bladder wall. Traditionally urothelium and smooth muscle cells are separated by dissection, and primary cultures are initiated in distinctly different medium formulations to obtain homogenous cultures and limit contaminating cells. However, the bladder wall harbours, apart from urothelial and smooth muscle cells, fibroblasts that have similar nutritional requirements and are likely candidates to contaminate smooth muscle cell cultures. Isolation of these three cell types by conjugation to magnetic beads and repeated separations allowed us to obtain pure cell populations. Furthermore, this technique permitted us to freely choose any specific medium formulation we wished to utilise. We then turned our attentions to engineering a materials system, by chemically and physically tuning a PEG hydrogel in terms of ligand concentration and matrix stiffness, to provide a three-dimensional environment for optimal spreading of human smooth muscle cells and mesenchymal stem cells. Cell viability, proliferation and differentiation were assessed in optimised hydrogels. Compared to cultures on traditional two-dimensional plastic, mesenchymal stem cells cultured within our three-dimensional hydrogels acquired a smooth muscle cell-like phenotype and smooth muscle cells obtained a less de-differentiated phenotype. In addition, we demonstrated cell-demanded gel degradation and deposition of newly synthesised extracellular matrix proteins. In order to modulate cell phenotypes further, we hypothesised that cell differentiation could be directed by the adhesion ligands made available within the matrix. In this manner, cells that were exposed to a matrix presenting certain integrin-binding ligands would begin expressing the corresponding integrins in order to adhere to the matrix. Consequently, we explored the effect of various specific integrin-binding ligands on mesenchymal stem cell integrin expression and differentiation. Fibronectin (FN) fragments engineered to demonstrate specificity to different integrins, namely α5β1 (FNIII910) and αvβ3 (FNIII10), were conjugated to PEG functionalised with vinyl sulfone and compared to fibronectin wild type (FNIIIWT) fragment and the RGD peptide, which both provide binding sites for a range of integrins. We found that assembly of focal adhesions and formation of stress fibres were altered due to the specific fragments provided, and expression of integrin- and smooth muscle cell specific genes varied in mesenchymal stem cells cultured within hydrogels functionalised with different fragments. Moreover, these fibronectin fragments turned out to be especially helpful for improved attachment of urothelial cells on top of hydrogels. With this biomaterial system in hand, we sought to develop a co-culture model of the bladder wall that permitted mesenchymal stem cells and urothelial cells cultured within / on top of PEG hydrogels, and to explore the combinatorial effect of ligand binding and cell-cell interactions on mesenchymal stem cell fate. Interestingly, we found that co-culturing with urothelial cells influenced gene expression of mesenchymal stem cells differently, depending on the protein fragment to which they were adhering. Mesenchymal stem cells cultured within PEG-FNIIIWT hydrogels were shown to up-regulate smooth muscle cell specific genes, while down-regulation was demonstrated in PEG-RGD, PEG-FNIII910 and PEG-FNIII10 hydrogels. Again, mesenchymal stem cells cultured within PEG-FNIIIWT hydrogels were shown to up-regulate integrin expressions α5, αv, β1 and β3, while down-regulation of the same genes was demonstrated for cells cultured within PEG-FNIII9*10 hydrogels, and a more complex pattern of integrin regulation was found for cells cultured within PEG-RGD and PEG-FNIII10 hydrogels. Finally, we investigated a novel approach to growth factor delivery in a controlled release manner, by providing cell- and growth factor binding protein fragments. In this system we show that transforming growth factor beta 1 (TGF-β1) release from PEG hydrogels influence smooth muscle cell specific gene expressions differently depending on the integrin- and growth factor binding proteins available within the hydrogel. Delivery of TGF-β1 within PEG-FNIIIWT hydrogels was shown to up-regulate smooth muscle specific genes in mesenchymal stem cells, while the other conditions displayed more complex patterns of gene expression. Further experiments are required to characterise the conjugation of PEGprotein-growth factor, and the release profiles for the growth factor in the different conditions. In conclusion, this thesis investigates the effect of various chemical and physical signals on mesenchymal stem cell-to-smooth muscle cell differentiation in an in vitro model to further understand cell-cell and cell-extracellular matrix interactions and create improved artificial microenvironments for directing and / or maintaining cell differentiation. The PEG hydrogel that we designed permits the co-culture of cells as well as the incorporation of peptides and proteins such as cell adhesion- and growth factor binding ligands, and growth factors for directing the differentiation of human mesenchymal stem cells into smooth muscle cells. Here, we explore these features and their effects on cell differentiation in vitro. Hence, our PEG hydrogel system can serve both as an in vitro model for studying basic cell biology, and as a cell delivery vehicle for improved bladder tissue regeneration.