Prostate cancer (PCa) is the second most common cancer in men with more than 1 million new cases worldwide each year. While some of the genomic, genetic and molecular events characterizing PCa have been functionally associated with tumor onset, development and resistance to therapy, the meaning of many other molecular alterations remains poorly understood. Recent development of organoids technology and prostate organoid cultures has established an innovative and valuable model for the study of adult tissue homeostasis, physiology and disease. In this project we combined prostate organoids technology with genetic engineering and CLICK-chemistry coupled Mass Spectrometry approaches in order to better characterize molecular features of wild type and genetically engineered mouse prostate organoids modeling early steps of human prostate tumorigenesis. In details, by manipulating mPrOs to proxy ETS-related gene (ERG) precursor PIN/HGPIN lesions of human prostate, we identified possible novel pro-tumorigenic roles of ERG which unleashes cells proliferation from the tight control of growth stimuli, and, even more interesting, corrupts immune system components to escape immune surveillance. In conclusion, this project shows that coupling innovative biological systems and technological approaches can lead to significant improvements in the analysis and understanding of disease mechanisms.

Textbook accounts of vertebrate embryonic development have been based largely upon experiments on amphibian embryos, which have shown that the tissues of the trunk and tail are organised from distinct precursors that existed during gastrulation. In the mouse and chick, however, retrospective clonal analyses and transplantation experiments have demonstrated that the amniote body instead arises progressively from a population of axial precursors that are common to both the neural and mesodermal tissues of the trunk and tail. For this reason, they are known as neuro-mesodermal progenitors (NMps). Detailed studies of NMps have been precluded by their lack of a unique gene expression profile and the technical difficulties associated with isolating them from the embryo. Mouse embryonic stem cells (ESCs) provide the possibility of instead deriving them in vitro. ESCs have been used to model developmental processes, partly through large cellular aggregates known as embryoid bodies. These structures do not, however, resemble the axial organisation of the embryo and they develop in a disordered manner. This thesis presents a novel culture system of small, three-dimensional aggregates of ESCs (gastruloids) that can recreate the events of early post-implantation development, including axial elongation. Gastruloids are the first ESC-based model for axial elongation morphogenesis; this body of work characterises their development and identifies a candidate population of NMps within their elongating tissues. Additionally, this work establishes a xenotransplantation assay for testing the functional properties of in vitro-derived NMp populations in the chicken embryo and applies it to NMps from gastruloid cultures. The results of this assay show that gastruloids are a credible source of NMps in vitro and therefore offer a new experimental means to interrogate their properties. The use of gastruloids to recreate embryonic development has implications for basic research as a synthetic system and for the therapeutic derivation of other embryonic progenitors through bioengineering.

The maintenance of the airway/respiratory epithelium during adult homeostasis and repair and its construction during embryonic development require tightly regulated cell fate decisions. This regulation takes the form of complex transcription factor and signalling cascades, much of which are unknown, particularly in human lung development. Multiciliogenesis describes the process of specification/differentiation of airway epithelial progenitors/stem cells into mature multiciliated cells (MCCs). Here, I have identified 2 novel transcription factors, Fank1 and Jazf1 which form part of the transcription factor cascade regulating multiciliogenesis in adult and embryonic mouse tracheas. Mouse tracheal epithelium is representative of epithelium lining the entire human airway and it is possible that we will also be able to extrapolate these findings to the human airway. It is not until we fully understand the regulation of multiciliogenesis that it will be possible to look at ways of pushing basal cells towards a MCC fate for purposes of cell replacement therapy, for example in patients with mucociliary disease. As well as exploring cell fate decisions in the mouse upper airway epithelium using embryonic tracheal explants and mouse tracheal epithelial cell (MTEC) cultures, I have also explored the regulation of cell fate decisions in distal human lung epithelium at the pseudoglandular stage of development. At this stage SOX9+ distal tip cells are self-renewing and multipotent and give rise to SOX2+ stalk descendents, which differentiate into airway epithelium. The regulation of SOX9+ lung tip cell multipotency and migration of SOX2+ stalk descendents during human lung development is poorly understood. I have compared human tip (SOX9+) versus stalk (SOX2+) transcriptomes using gene ontology (GO), which has highlighted some key signalling pathways enriched in tip cells which could be important in maintaining distal tip cell multipotency. These pathways have been utilised in optimising conditions for propagating self-renewing tip-derived organoids. These organoids have the potential to be differentiated into bronchiolar and alveolar fates and as such are an invaluable research tool for studying human lung epithelial development, whilst minimising the use of human embryos and its associated ethical implications. I have also performed human tip versus mouse tip transcriptome GO analysis which highlights that although there are many similarities, there are also differences between human and mouse lung epithelium development, emphasising the need for research on human tissue.

Transporters dynamically expressed at the mammary gland transport critical nutrients into the breast milk of nursing mothers to meet the nutritional demands of the suckling infant. However, xenobiotics may interact with these transporters to potentially alter the nutrient composition of milk and compromise neonatal nutrition. The aim of the present study was to quantitatively evaluate the constitutive expression of various nutrient transporters in whole mammary gland tissue and mammary epithelial organoids (MEO) isolated from female Sprague-Dawley rats at various stages of pregnancy, lactation, and involution. Furthermore, the studys aim was to determine if appropriately cultured mammary epithelial organoids (MEO) maintain in vivo transporter expression to lay down critical groundwork for the development of an in vitro screening tool assessing xenobiotic-nutrient transporter interactions. The following transporters were evaluated using quantitative real-time reverse transcription polymerase chain reaction (QRT-PCR): multidrug resistance protein (Mdr) 1a, 1b; multidrug resistance-like protein (Mrp) 1; organic cation transporter (Oct) 1; organic cation/carnitine transporter (Octn) 1, 2, and 3; concentrative nucleoside transporter (Cnt) 1, 2, and 3; equilibrative nucleoside transporter (Ent) 1, 2, and 3; nucleobase transporter (Ncbt) 1 and 2; oligopeptide transporter (Pept) 1 and 2; methotrexate carrier (Mtx) 1; divalent metal transporter (Dmt) 1; and the milk protein ?-casein. Transporter expression patterns in MEO differed from whole tissue for ?-actin, Mdr1a, Mdr1b, Oct1, Octn3, Ent3, Cnt1, Cnt3, Ncbt1, Pept2, Mtx1, and ?-casein. This brings into question whether whole mammary gland tissue is truly appropriate for an understanding of transporter expression in the mammary epithelium. Nevertheless, four general transporter expression patterns emerged in isolated MEO: decline throughout lactation (Mdr1a, Mdr1b, Mrp1 & Dmt1), increase throughout lactation (Cnt1 & Octn3), increase in early lactation (Oct1, Octn2, Ent1, Cnt2, Cnt3, Pept2 & Mtx1) and constant expression throughout lactation (Octn1, Ent2, Ent3, Ncbt1, Ncbt2 & Pept1). These expression patterns will provide insight into the critical windows of nutrient delivery to the breast milk to provide adequate nutritional stimuli to the suckling infant. Furthermore, MEO cultured in an extracellular matrix-rich environment maintained transporter expression at the mRNA level, which underscores the potential of the primary MEO in vitro model system as a screening tool for xenobiotic-transporter interactions at the mammary gland. Transporter expression patterns in MEO were unique for each transporter evaluated. This information accompanied by an in vitro screening tool may allow for predictions of xenobiotic interference with breast milk composition to help safeguard infant health.

Transporters dynamically expressed at the mammary gland transport critical nutrients into the breast milk of nursing mothers to meet the nutritional demands of the suckling infant. However, xenobiotics may interact with these transporters to potentially alter the nutrient composition of milk and compromise neonatal nutrition. The aim of the present study was to quantitatively evaluate the constitutive expression of various nutrient transporters in whole mammary gland tissue and mammary epithelial organoids (MEO) isolated from female Sprague-Dawley rats at various stages of pregnancy, lactation, and involution. Furthermore, the studys aim was to determine if appropriately cultured mammary epithelial organoids (MEO) maintain in vivo transporter expression to lay down critical groundwork for the development of an in vitro screening tool assessing xenobiotic-nutrient transporter interactions. The following transporters were evaluated using quantitative real-time reverse transcription polymerase chain reaction (QRT-PCR): multidrug resistance protein (Mdr) 1a, 1b; multidrug resistance-like protein (Mrp) 1; organic cation transporter (Oct) 1; organic cation/carnitine transporter (Octn) 1, 2, and 3; concentrative nucleoside transporter (Cnt) 1, 2, and 3; equilibrative nucleoside transporter (Ent) 1, 2, and 3; nucleobase transporter (Ncbt) 1 and 2; oligopeptide transporter (Pept) 1 and 2; methotrexate carrier (Mtx) 1; divalent metal transporter (Dmt) 1; and the milk protein ?-casein. Transporter expression patterns in MEO differed from whole tissue for ?-actin, Mdr1a, Mdr1b, Oct1, Octn3, Ent3, Cnt1, Cnt3, Ncbt1, Pept2, Mtx1, and ?-casein. This brings into question whether whole mammary gland tissue is truly appropriate for an understanding of transporter expression in the mammary epithelium. Nevertheless, four general transporter expression patterns emerged in isolated MEO: decline throughout lactation (Mdr1a, Mdr1b, Mrp1 & Dmt1), increase throughout lactation (Cnt1 & Octn3), increase in early lactation (Oct1, Octn2, Ent1, Cnt2, Cnt3, Pept2 & Mtx1) and constant expression throughout lactation (Octn1, Ent2, Ent3, Ncbt1, Ncbt2 & Pept1). These expression patterns will provide insight into the critical windows of nutrient delivery to the breast milk to provide adequate nutritional stimuli to the suckling infant. Furthermore, MEO cultured in an extracellular matrix-rich environment maintained transporter expression at the mRNA level, which underscores the potential of the primary MEO in vitro model system as a screening tool for xenobiotic-transporter interactions at the mammary gland. Transporter expression patterns in MEO were unique for each transporter evaluated. This information accompanied by an in vitro screening tool may allow for predictions of xenobiotic interference with breast milk composition to help safeguard infant health.

The adult mammary gland is comprised of a bi-layered epithelium of luminal and myoepithelial cells surrounded by an adipocyte-rich fat pad, a highly collagenous extra-cellular matrix (ECM) and a number of other stromal and endothelial cell types. Mammary stem cells (MaSCs) reside within the epithelium and these are capable of repopulating a mammary fat pad that is devoid of epithelium, upon transplantation. It was sought to recapitulate this process of MaSCs repopulating a fat pad using a synthetic fat pad, engineered from a collagen scaffold invested with adipocytes, to provide an in vitro 3D model. Fluorescently tagged murine Axin2-expressing cells were obtained from transgenic mice and seeded into these scaffolds and cultured, mimicking the process of fat pad repopulation. Immunohistochemical analysis demonstrated that Axin2+ myoepithelial cells were rarely capable of forming bi-layered structures that expressed correct myoepithelial localisation and resemblance to a luminal morphology. Breast tumours surrounded by anisotropic (directional) collagen fibres running perpendicular to the tumour boundary are more aggressive and associated with poor patient prognosis. To recapitulate this anisotropic collagen phenotype in vitro, an ice-templating technique was used to modify the structure of the collagen scaffolds producing both non-directional (isotropic) and anisotropic internal architectures. Tumour cells from various breast cancer cell lines were seeded into both isotropic and anisotropic scaffolds to investigate whether this approach could distinguish cell type-specific migratory ability and whether anisotropy affected migration efficiency. Following analysis by confocal microscopy and ImageJ, anisotropic scaffolds were observed to enhance the migratory potential of MDA-MB-231 breast cancer cells. These results highlight the importance of collagen alignment and provide a reproducible method to quantitatively measure cell migration in 3D for cells derived from different breast cancer subtypes. Building on these data, the protocol was adapted to permit the direct investigation of tumour biopsy material. Given the heterogeneity of breast tumours, it was considered important to maintain tumour architecture and stromal components. Thus, murine mammary tumour fragments from two different established mammary cancer models were utilised and cultured in anisotropic collagen scaffolds in the presence or absence of adipocytes to allow an investigation of their influence on tumour cell migration. Further experiments included addition of various therapeutic drugs followed by immunofluorescence microscopy coupled with an optical clearing technique. These data demonstrated the utility of the model in determining both the rate and capacity of tumour cells to migrate through the engineered stroma while shedding light also on the mode of migration. Moreover, the response of different mammary tumour types to chemotherapeutic drugs could be could be readily quantified. To humanize the fat pad for subsequent human tissue analysis, human mesenchymal stem cells (MSC) were obtained from reduction mammoplasties and immortalised, before differentiating them into adipocytes within anisotropic collagen scaffolds. Human breast cancer cells were fluorescently tagged for tracking using lentiviral methods and were seeded into scaffolds invested with differentiated MSCs. Both cell types were successfully co-cultured for 7 days and imaged using multiphoton methods.

No description available.

No description available.

Les principales maladies neurodégénératives humaines, qui reposent toutes sur des mécanismes de type prion (auto-propagation d’agrégats protéiques pathogéniques), représentent un risque sociétal majeur avec une augmentation de leur prévalence directement corrélée avec l’augmentation de la longévité de la population mondiale. Il n’existe à ce jour aucun traitement curatif ni aucun modèle expérimental suffisamment pertinent pour ces maladies.L'objectif de ce travail a été d'utiliser le potentiel des mini-cerveaux humains comme modèle in vitro auto-assemblé en trois dimensions (3D) capable de restituer la complexité du cortex cérébral et d’étudier les mécanismes de type prion en développant une méthodologie de validation basée sur la microscopie 3D. Ces nouvelles structures 3D qui peuvent être obtenues à partir de cellules adultes reprogrammées de patients en cellules souches pluripotentes induites (iPSC), offrent des possibilités uniques pour accéder, observer et perturber les processus biologiques dans le cerveau humain sans les biais ni les complications des modèles animaux ou des échantillons de cerveau humain ex vivo. Ce modèle permet notamment d’observer l’apparition d’agrégats d’Aß et de Tau phosphorylée, deux protéines qui s’accumulent et se propagent de cellule en cellule dans la maladie d’Alzheimer.Nous avons été en mesure de rendre le modèle des mini-cerveaux compatible avec une future approche de criblage de molécules thérapeutiques en modifiant la méthodologie de différenciation pour augmenter leur rendement de production. D’autre part, nous avons pu tester différentes modalités de modélisation pour la Maladie d’Alzheimer, la maladie de Parkinson, la Démence Fronto-Temporale et la maladie de Creutzfeldt-Jakob : à l’aide de molécules d’induction chimique, à l’aide de cellules issues de patients, par modification génétique et par mise en contact de matériel infectieux. Ces différentes approches nous ont permis d’établir que le modèle d’organoïde cérébral permet de reproduire des aspects-clés retrouvés dans l’apparition de la pathologie chez les patients. Pour compenser l’hétérogénéité de notre modèle, nous avons réalisé une analyse in toto par imagerie, c’est-à-dire dans sa totalité sans coupes préalables. La modalité retenue pour cette acquisition est la microscopie à feuillet de lumière utilisée après marquage et clarification des mini-cerveaux. Pour ce faire, nous avons évalué et développé différentes stratégies en vue d’obtenir une plateforme d’analyse à haut contenu pour nos organoïdes cérébraux.Cette plateforme centrée autour de l’organoïde cérébral, sous-tendue par l’analyse en microscopie 3D, a été développée dans le cadre du projet « Investissements d’Avenir » 3DNeuroSecure. Ce projet a pour ambition d’apporter des solutions de calcul haute performance au domaine de la biologie, notamment avec la possibilité de traiter des informations de très grand volume, dit « exascale », telles que celles que nous obtenons avec la microscopie 3D. Le développement de cet aspect nous permettrait à terme de pouvoir établir les bases d’un outil de criblage thérapeutique par les organoïdes cérébraux pour les maladies neurodégénératives. Nous avons démontré que les mécanismes de type prion pouvaient être étudiés dans ce modèle de mini-cerveaux humains et de multiples voies de recherche fondamentale et appliquée sont désormais possibles. A plus long terme, une telle plateforme pourrait accueillir tout type d’organoïdes pour modéliser l’ensemble du corps humain et s’inscrire comme un compagnon biologique dans le cadre des futurs développements de la médecine personnalisée. / Human neurodegenerative diseases, which are all based on prion-like mechanisms (self-propagation of pathogenic protein aggregates), represent a major societal risk with the increase of their prevalence directly correlated to the increasing longevity of the world population. There is to date neither any cure nor any pertinent experimental model for their study.The objective of this work was to use the potential of human mini-brains, a self-assembled three-dimensional in vitro model able to restitute the complexity of the cerebral cortex. This model will allow us to study prion-like mechanism by developing a validation methodology based on 3D microscopy. These novel 3D structures can be obtained from reprogrammed adult cells into induced pluripotent stem cells (iPSCs) and offer unique possibilities to access, observe and disrupt biological processes in the human brain without bias nor complications as in animal models and ex vivo human brain samples. This model makes it possible to observe the development of aggregates of Aβ and hyper-phosphorylated Tau, two proteins that accumulate and propagate from cell to cell during Alzheimer’s disease.We have been to able to adapt the cerebral organoid model for a future screening approach by modifying the differentiation methodology to enhance its production ratio. We also have been able to test different modalities for disease modeling for Alzheimer’s disease, Parkinson’s disease, Fronto-Temporal Dementia and Creutzfeldt-Jakob disease: with chemical induction, with patient specific cells, through genetic modification and through contact with infectious material. These different approaches allowed us to validate that the cerebral organoid can indeed reproduce key aspects found during pathological development within patients. To compensate for the heterogeneity of the cerebral organoid, we performed an in toto analysis through microscopy, meaning in its totality without prior slicing. The chosen method of acquisition is fluorescence light-sheet microscopy used after staining and optical clearing of cerebral organoids. To do so, we have evaluated and established different strategies in order to obtain a high content screening platform for our cerebral organoid model.This platform centered around the cerebral organoid model, underpinned by 3D microscopy analysis, was developed during the “Investissements d’Avenir” project 3DNeuroSecure. This project has for ambition to bring high performance computing to the biological sciences, notably with the possibility to deal with large scale data, also called “exascale”, like the ones obtained with 3D microscopy. The development of this aspect would allow us to establish the basis for a therapeutic screening tool based on cerebral organoids for neurodegenerative diseases. We have demonstrated that prion-like mechanisms can be studied in a human mini-brain model and multiple research avenues are now opened for both fundamental and applied research. This platform could in turn become the basis for any kind of organoids derived from patients to model the whole human body and become a biological companion for personalized medicine.

During the last years, important progress has been made in modeling early brain development using 3-dimensional in vitro systems, so-called cerebral organoids. These can be grown from pluripotent stem cells of different species such as our closest living relatives, the chimpanzees and from patients carrying disease mutations that affect brain development. This offers the possibility to study uniquely human features of brain development as well as to identify gene networks altered in neurological diseases. Profiling the transcriptional landscape of cells provides insights into how gene expression programs have changed during evolution and are affected by disease. Previously, studies of this kind were realized using bulk RNA-sequencing, essentially measuring ensemble signals of genes across potentially heterogeneous populations and thus obscured subtle changes with respect to transient cell states or cellular subtypes. However, remarkable advances during the last years have enabled researchers to profile the transcriptomes of single cells in high throughput. This thesis demonstrates how single-cell transcriptomics can be used to dissect human-specific features of the developing and adult brain as well as cellular subpopulations dysregulated in a malformation of the cortex.