Human pluripotent stem cells (hPSCs) have the ability to self-renew and differentiate into all specialized body cells, providing material suitable for studying basic biology, modeling disease, and for regenerative medicine. The differentiation of hPSCs into functional cell types has been further enhanced by the production of organoids, miniature 3D organ-like structures that mimic the architecture and function of their in vivo counterparts, representing more physiologically relevant models of native tissues than monolayer cultures. Our initial aim was to differentiate hPSCs into lung epithelial organoids in vitro, and we hypothesized that applying knowledge of signaling cues during embryonic development to the dish would produce lineage-specific tissue. Using a multi-stage differentiation strategy, we derived organoids sharing properties with the developing lung as well as intestine. From this work, we learned the importance of purification, selection, and using singularized precursor cells to produce populations of bona fide lineage-restricted organoids. Upon developing a type of intestinal organoid technology from hPSCs not reported before, we shifted our focus to the intestine. We generated cystic intestinal epithelial organoids called enterospheres (hEnS) in vitro from hPSCs, which mimic structural and cell type properties of the native small intestinal epithelium. hEnS growth, differentiation, and long-term culture can be controlled by modulating media conditions. Importantly, hEnS are functional in that they elicit an innate immune response upon treatment with enteric pathogens. We established hEnS as an attractive in vitro model system for studying human gastrointestinal biology. We then developed an automated hEnS imaging assay to measure responses to growth factors, bacterial products, and enteric bacteria themselves. In doing so, we demonstrated the utility of hEnS as a germ-free system for studying host-microbe interactions and intestinal maturation. Finally, we investigated the expression of protein markers of intestinal maturation in tissue sections of primary human intestine spanning gestation, and made observations that are different from those reported in mice. Overall, our work provides new and important insights into hPSC differentiation, organoid technologies, and intestinal development in humans. / Thesis / Doctor of Philosophy (PhD)

The intestinal tissue is charged with a delicate immunological task. The intestinal immune system needs to be tolerant towards nutrients and microbiota present in the intestinal lumen, while simultaneously detecting and responding to dangers such as pathogens. A single-cell layer of intestinal epithelial cells (IECs) acts as a first line of defence. There is a T cell population located between the IECs that have been named intraepithelial lymphocytes (IELs). As the main lymphoid population within the intestinal barrier, IELs are thought to have an important role in intestinal homeostasis maintenance, as well as a role in intestinal inflammatory and autoimmune diseases such as inflammatory bowel disease and celiac disease. Despite extensive research on IEL biology, there are still questions remaining in terms of the development, maintenance and activation of IELs. Furthermore, IELs survive poorly in vitro, which hinders mechanistic insights. In this thesis, a co-culture system between IELs and intestinal organoids, "mini-guts", provides an in vitro model for IELs. With this IEL-organoid co-culture system, IELs associated with the organoids survive for at least 4 days. Additional findings suggest that IELs are kept in a poised state of activation due to differences in their mitochondria compared to other T cells found in spleen, lung and skin. Upon activation or intestinal inflammation, the mitochondrial mass in IELs increases. This increase correlates with effector functions such as cytokine production and proliferation. In addition, the composition of the mitochondria-specific lipid, cardiolipins, alters drastically in IELs after activation. These data support a model of mitochondria-dependent activation of IELs. The mitochondria-dependent activation in IELs appears to have at least two pathways: one T cell receptor-dependent and one microbiota-dependent. The latter pathway suggests a model in which IELs can become activated regardless of the cause of intestinal epithelial barrier damage.

In adult mammals, the gastrointestinal (GI) epithelium exhibits the highest turnover rate among the endodermal tissues. The harsh luminal environment of the GI tract necessitates replenishment of epithelial cells to maintain organ structure and function during routine turnover and injury repair. This delicate balance between gain and loss of cells is called tissue homeostasis, and multipotent tissue specific adult stem cells serve as the continuous source of self-renewal. Due to their important contribution to homeostatic maintenance the proliferative capacity of the stem cells needs to be tightly controlled, as an imbalance can result in diverse pathologies such as cancer or insufficient injury repair. Despite the crucial role for regulatory processes the molecular mechanisms and the genes governing these processes remain poorly understood. Rnf43 and its paralogue Znrf3 (RZ) act as tumour suppressors in the intestine, but their role in the gastric epithelium has not been previously investigated. Using a novel unpublished stomach specific CreERT2 expressing mouse line I found that simultaneous knockout of RZ (RZ DKO) result in gastric hyperplasia of the corpus epithelium. Gastric RZ DKO organoids show independence from the essential growth factor Rspondin-1 but require exogenous Wnt. A similar exogenous Wnt dependence was identified in a human gastric cancer cell line harbouring homozygous Rnf43 inactivating mutations. Thus, Wnt secretion inhibition might provide a new treatment paradigm for a subset of patients carrying Rnf43 mutations. The prominent role of the E3s Rnf43 and Znrf3 in the intestinal and gastric epithelial led to the question of whether other E3s either closely related to RZ or specifically expressed in stem or niche cells could play a role in homeostatic regulation, specifically in the small intestine. Using a retroviral overexpression screen I identified Rnf24 and Rnf122, two E3s that rendered intestinal organoids insensitive to withdrawal of the BMP inhibitor Noggin. Moreover, potential substrate candidates located at the cell surface membrane were identified and the generation of in vivo models initiated to provide a basis for further studies investigating the role of these E3s. In trying to address the function of the abovementioned genes using in vitro functional genetics I identified gaps in the current technology for organoid genetic engineering. I therefore developed two gene editing methods; a gRNA concatemer system allowing simultaneous knockout of multiple genes and CRISPR-FLIP enabling generation of conditional gene knockouts In summary, this thesis describes the first stomach specific knockout of Rnf43 and Znrf3 in the gastric epithelium, showing that it results in gastric hyperplasia located to the corpus epithelium. The dependence of the Rnf43 and Znrf3 knockout epithelium on exogenous Wnt signalling provides a potential treatment strategy for a subset of patients harbouring Rnf43 mutations. Next, it identifies Rnf24 and Rnf122 as E3 ubiquitin ligases involved in intestinal stem cell regulation and provide preliminary data and a basis for future studies. Finally, it describes the establishment of two advanced genetic engineering approaches which can be applied to various in vitro culture systems such as 3D organoids, mouse embryonic stem cells and conventional cell lines. Collectively this work and the developed methods will contribute to our understanding of the mechanisms regulating adult stem cell homeostasis.

This thesis reports investigations of the interactions between the intestinal epithelial barrier and the intracellular apicomplexan Eimeria spp., both in vivo and in vitro. Initially, conventional in vivo studies using genetically modified animals were used to investigate the contribution of innate lymphoid cells (ILCs) to immune protection of the intestinal barrier. Additionally, to understand complex epithelial host-pathogen interactions a novel in vitro model of small intestine organoids was developed. Data suggest that immunoprotection against Eimeria vermiformis infections is mediated by T cells. Furthermore, there is an indication that ILCs have a detrimental effect in Eimeria vermiformis-infected immunocompromised animals. However, the role for ILCs in the regulation of the immune response remains unclear. The life cycles of Eimeria vermiformis and Eimeria falciformis are highly complex, comprising multiple schizogonies followed by a gametogony. In vitro life cycle completion has not been achieved to date due to the limitations of monolayer cell line models. It is likely that for a successful parasite development the interaction of the different epithelial cell types present in intestinal organoids is required. The development of intestinal organoids by Sato and colleagues gave rise to a breakthrough in cellular studies, providing the tools to study complex interactions between host tissues and invading pathogens in vitro. I showed that small intestine-derived organoids grow exponentially after passage and that each organoid contains distinct specialised epithelial cell types, such as Paneth, Goblet or enteroendocrine cells, suggesting that the organoid model closely resembles the native intestinal epithelium and that Eimeria spp. benefit from the three-dimensional structure and physiological characteristics of the organoid model. Intestinal organoids were infected with E. vermiformis or E. falciformis sporozoites. These completed several rounds of asexual replication but did not proceed to the final gametogony. Despite the need for the development of sensitive techniques applicable to three-dimensional cell culture models, these results indicate that intestine-derived organoids are a promising model to study host-parasite interactions at the intestinal epithelial barrier at the cellular and molecular levels.

Considering that both cardiovascular disease (CVD) and congenital heart diseases (CHD) are still the leading cause of morbidity and mortality worldwide, there is a need for a robust and reliable cardiac model. Cardiac organoids are complex, three-dimensional cellular constructs that recapitulate the processes of the human embryonic heart. However, certain vital morphological features within the fetus are not yet replicable with cardiac organoids. Here we report our investigation to generate cardiac organoids with chamber formations. Our method involves modulating the Wnt pathway at two different instances while also implementing two cell seeding densities, all to determine the most optimized that to produce chamber formations within cardiac organoids.

Tgf-β ligands induce cell cycle arrest in a variety of mammalian epithelia, including in the prostate. Genetic deregulation of the downstream canonical Smad-dependent pathway is an early well-studied event in tumorigenesis, yet, in prostate cancer such mutations are rare, leaving unexplained how Tgf-β represses prostate cell proliferation. Here, we adopted a variety of pharmacological and genetic approaches to dissect the pathways controlling proliferation in mouse prostate organoids. We found that Egf signalling is a potent proliferative stimulus through the concomitant activation of both Pi3k/Akt and Mapk/Erk pathways. However, the autocrine release of the Tgf-β family ligand Activin A has a dominant role over Egf-induced proliferation by promoting the non-canonical Tak1-p38α/β axis, which leads to Mapkapk2, p16, p21, and Stat1/2 activation and cell-cycle arrest. Bypass of the proliferation barrier can spontaneously occur upon long-term culture and it is associated to aberrant Activin A signalling and DNA replication stress. Finally, orthotopic transplantation of adapted organoids into immunocompetent hosts, leads to aberrant outgrowth and the emergence of prostatic intraepithelial neoplasia (PIN). Overall, our experiments unveil how Activin A limits mouse prostate progenitor cells proliferation and provide a rationale for the frequent MAP3K7 (TAK1) and ACVR2A (Activin A type II receptor) deletions observed in human primary prostate cancers (20% in the TCGA 2015 dataset).

La microcéphalie est une maladie neurologique du nouveau-né qui se traduit par une circonférence réduite de la tête, une déficience intellectuelle et des défauts anatomiques du cerveau. La microcéphalie peut être la conséquence d’une infection, de stress environnementaux ou de mutations génétiques.Le cerveau commence à se former dès la cinquième semaine de grossesse et est majoritairement constitué de cellules souches neuronales, cellules qui conservent une capacité a se reproduire a l’identique sans se spécialiser. Cette première phase de prolifération est importante pour générer suffisamment de cellules. Suit une phase de différenciation, durant laquelle les cellules préalablement formées se différencient en deux groupes : les neurones, qui permettent de partager l’information grâce à des influx électriques, et les cellules gliales, qui soutiennent activement les fonctions des cellules neuronales.Je m’intéresse à un gène en particulier, KNL1, muté chez certains patients microcéphales. Grace aux nouvelles techniques d’édition du génome, j’ai reproduit la mutation retrouvée chez les patients dans des cellules souches pluripotentes humaines. En utilisant un modèle tridimensionnel (mini-cerveaux en culture), à partir de cellules souches neuronales, j’ai analysé de manière quantitative les étapes-clés de développement: les phases de prolifération et de différenciation.Mes travaux de recherche ont montré que les cellules souches neuronales portant la même mutation que les patients prolifèrent moins, réduisant le nombre de cellules initiales nécessaires au développement cérébral normal. Par ailleurs, les cellules souches neuronales se différencient prématurément en neurones et cellules gliales, ce qui réduit davantage le nombre le nombre final de cellules. Cette hypothèse a été confirmée par l’utilisation du modèle tridimensionnel, ou les mini-cerveaux sont plus petits que la normale.Cette étude est essentielle non seulement pour comprendre le développement de la maladie, mais également pour comprendre les étapes clés du développement du cerveau humain, et ne pourrait pas être mener à bien sur des modèles animaux. En outre, l’utilisation de cellules souches induites nous permet de ne pas utiliser de cellules embryonnaires, si nécessaire pour raisons d’éthique. / Microcephaly is a neurological condition, resulting in patients having a small head circumference, intellectual impairment and brain anatomical defects. A pre-requisite for achieving a better understanding of the cellular events that contribute to the striking expansion of the human cerebral cortex is to elucidate cell-division mechanisms, which likely go awry in microcephaly. Most of the mutated genes identified in microcephaly patient encode centrosomal protein, KNL1 is the only gene that encodes a kinetochore protein, it plays a central role in kinetochore assembly and function during mitosis. While the involvement of centrosome functions is well established in the etiology of microcephaly, little is known about the contribution of KNL1.In an attempt to assess the role of KNL1 in brain development and its involvement in microcephaly, we generated isogenic human embryonic stem cell (hESC) lines bearing KNL1 patient mutations using CRISPR/Cas9-mediated gene targeting. We demonstrated that the point mutation leads to KNL1 reduction in neural progenitors. Moreover, mutant neural progenitors present aneuploidy, an increase in cell death and an abrogated spindle assembly checkpoint. Mutant fibroblasts, derived from hESC, do not have a reduced expression of KNL1 and do not present any defect in cell growth or karyotype, which highlight a brain-specific phenotype.The subsequent differentiation of mutant neural progenitors into two-dimensional neural culture leads to the depletion of neural progenitors in the favor of premature differentiation. We developed a three-dimensional neural spheroids model from neural progenitors and reported a reduced size of mutant neural spheroids, compare to control. Lastly, using knockdown and rescue assays, we proved that protein level of KNL1 is responsible of the premature differentiation and the reduced size.These data suggest that KNL1 has a brain-specific function during the development. Changes in its expression might contribute to the brain phenotypic divergence that appeared during human evolution.

The neocortex is the most recently evolved part of the mammalian brain which is involved in a repertoire of higher order brain functions, including those that separate humans from other animals. Humans have evolved an expanded neocortex over the course of evolution through a massive increase in neuron number (compared to our close relatives-­‐‑ the chimpanzees) in spite of sharing similar gestation time frames. So what do humans do differently compared to chimpanzees within the same time frame during their development? This dissertation addresses this question by comparing the developmental progression of neurogenesis between humans and chimpanzees using cerebral organoids as the model system. The usage of cerebral organoids, has enabled us to compare the development of both the human neocortex, and the chimpanzee neocortex from the very initiation of the neural phase of embryogenesis until very long periods of time. The results obtained so far suggest that the genetic programs underlying the development of the chimpanzee neocortex and the human neocortex are not very different, but rather the difference lies in the timing of the developmental progression. These results show that the chimpanzee neocortex spends lesser time in its proliferation phase, and allots lesser time to the generation of its neurons than the human neocortex. In more scientific terms, the neurogenic phase of the neocortex is shorter in chimpanzees than it is in humans. This conclusion is supported by (1) an earlier onset of gliogenesis in chimpanzees compared to humans which is indicative of a declining neurogenic phase, (2) an earlier increase in the chimpanzee neurogenic progenitors during development, compared to humans, (3) a higher number of stem cell– like progenitors in human cortices compared to chimpanzees, (4) a decline in neurogenic areas within the chimpanzee cerebral organoids over time compared to human cerebral organoids.

La thrombine, une protéase à sérine connue pour être l'acteur clé de la cascade de coagulation, a été décrite pour réguler les processus apoptotiques au niveau du côlon via l'activation de récepteurs activés par des protéases ou PARs (Protease-Activated Receptors). Cependant, les effets de la thrombine sur la cellule épithéliale colique n'ont été étudiés qu'en utilisant des lignées cellulaires. Les conséquences d'une exposition à différentes doses de thrombine sur un épithélium complexe, composés de différents types cellulaires plus ou moins différenciés sont inconnues à ce jour. Un nouveau modèle cellulaire, nommé organoïde, permet de reconstituer un épithélium colique fonctionnel en 3-dimensions (3D) à partir de résections ou de biopsies humaines, et ce, grâce aux capacités d'auto-renouvellement et de différenciation des cellules souches issues des cryptes coliques. Le 1er objectif de ma thèse a été d'évaluer les effets de la thrombine sur la survie, la prolifération, l'apoptose et la différenciation de l'épithélium colique humain, en utilisant le modèle organoïde. Puis, de déterminer l'implication des récepteurs PAR1 et PAR4 activés par la thrombine dans ces effets. Ainsi, l'ajout de thrombine (à faible dose : 10mU/mL et à forte dose : 50mU/mL) sur une culture d'organoïdes établis à partir de tissus colorectaux normaux entraîne une diminution de moitié de l'activité métabolique et de la prolifération cellulaire. Ces effets sont bloqués en présence d'un antagoniste de PAR1. Le processus apoptotique est, cependant, augmenté d'un facteur 8 en réponse à la thrombine (aux deux doses). Ce processus est inhibé en présence d'antagoniste de PAR1 ou de PAR4. Concernant la différenciation épithéliale, la thrombine diminue le nombre de colonosphères (structures immatures), au profit d'une augmentation du nombre de structures apoptotiques et de colonoïdes (structures plus matures présentant des néo-cryptes). Cet effet est dû à l'activation à la fois de de PAR1 et de PAR4 dans les cellules épithéliales coliques. Mes résultats démontrent que la thrombine exogène agit sur les processus d'apoptose, de prolifération et de différenciation sur un épithélium complexe, issu de la culture de tissus humains. L'utilisation de ce modèle ex vivo permet de comparer les organoïdes pathologiques et normaux, voire de tester les effets d'approches pharmacologiques et de nouveaux médicaments sur ces cultures. Ainsi, la 2nde partie de ce travail de thèse a été d'aborder la mise en place des conditions de culture et d'imagerie nécessaires pour réaliser un screening à haut débit robuste et reproductible, HCS (High-Content Screening), appliquée aux organoïdes. Les conditions de culture d'organoïdes en plaques 96-puits ont été mises au point de même que les conditions permettant d'acquérir des images répondant aux critères nécessaires pour une analyse via un système HCS. Le système Operetta HCS couplé au logiciel d'analyse Harmony (PerkinElmer) a été utilisé pour mettre en place une procédure d'analyse permettant de reconnaître les organoïdes, de les dénombrer, de les classer selon leur état de différenciation et de suivre leur croissance tout au long de la culture. Pour conclure, ces travaux de thèse ont permis de mettre en évidence les effets de la thrombine sur l'état métabolique, l'apoptose et la différenciation de l'épithélium colique humain, grâce au modèle 3D ex vivo d'organoïdes colorectaux. L'utilisation de ce modèle complète les approches jusque-là effectuées dans des modèles de lignées de cellules épithéliales, proposant une vision intégrée du comportement d'un épithélium complexe humain. L'approche HCS initiée lors de ces travaux de thèse pourrait permettre d'analyser de façon robuste et automatisée dans ce modèle, les effets d'autres composés et avoir ainsi un impact majeur sur notre compréhension des pathologies épithéliales et sur les tests de nouvelles approches thérapeutiques. / Thrombin, a serine protease known for its role in the coagulation cascade, was described for its effects on the induction of apoptosis in colonic epithelial cell lines, through the activation of Protease Activated Receptors (PARs). However, the effects of thrombin on complex epithelial structures such as the human intestinal epithelium composed of different cell types and cells at different stages of differentiation, has never been investigated. A new cellular model, named organoid, enables to reconstitute a functional epithelium in 3-dimensions (3D), from human resections or biopsies, thanks to the self-renewal and differentiation properties of stem cells isolated from colonic crypts. The first objective of this thesis was to evaluate thrombin's effects on survival, proliferation, apoptosis and differentiation in human colonic epithelium, using the organoid model. Then, we aimed to determining the implication of PAR1 and PAR4 in the thrombin's effects. Thus, thrombin added (at low dose: 10mU/mL and higher dose: 50mU/mL) to organoid cultures from control patients, led to a decrease by half of metabolic activity and cell proliferation. These effects were blocked by the addition of a PAR1 antagonist. Apoptotic process was 8-fold higher in organoid cultures exposed to thrombin (both doses) and this effect was inhibited by the addition of a PAR1 or a PAR4 antagonist. As per epithelial differentiation, thrombin decreased the number of colonospheres (immature structures) favoring the increase of apoptotic structures and colonoids (budding structures considered as more mature). This effect was due to PAR1 and PAR4 activation as again, it was blocked both by PAR1 and PAR4 antagonist. Taken together, these results reveal that exogenous thrombin acts on apoptosis, proliferation and differentiation processes in complex human colonic epithelium. The use of this ex vivo model will allow to compare pathological versus normal organoid cultures, but also to test the effects of pharmacological approaches and new treatment options directly in cultured human tissues. Thus, the 2nd part of this thesis was to setup the best culture conditions and the best imaging conditions to perform a robust and reproducible screening approach, HCS (High-Content Screening), using organoid cultures. Culture conditions in 96-well plates were set up and allowed to acquire images with the HCS system. Operetta HCS coupled to an analysis software (Harmony, PerkinElmer) was used to develop a specific program enabling the recognition of organoids, their counting, their classification according to their differentiation status and enabling to follow organoid growth in cultures. To sum up, the work performed allowed to highlight the effects of thrombin on metabolic status, apoptosis and differentiation of human colon epithelium, using an ex vivo 3D organoid model. The use this model nicely completed epithelial cell line approaches, offering an integrated view of the complex behavior of human epithelium. The HCS approach initiated within this thesis should allow the automated analysis of a number of drugs and treatments. It should help our understanding of epithelial pathologies and the testing of new therapeutic approaches.

The biliary tree is a series of ductular tissues responsible for the drainage of bile produced by the liver and pancreatic secretions from the pancreas. The biliary tree is affected by a diversity of life- threatening diseases collectively called cholangiopathies. Cholangiopathies show regionalization, with some diseases such as biliary atresia predominantly targeting extrahepatic bile ducts (EHBDs) outside of the liver. Despite this, little is known on whether anatomical location within the biliary tree contributes to differences in functionality of biliary epithelium, especially in the EHBD compartment. Additionally, reports have demonstrated the possibility for in vitro culture of bile duct stem/progenitor cell organoids from both intrahepatic (IHBD) and EHBD sources. The relation of these organoid systems to each other, and to their tissue of origin, is largely unknown. In this dissertation, I address these major questions by combining transcriptional analyses and in vitro culture of human bile duct organoids derived from primary IHBD and EHBD epithelium. First, I show that in vitro organoids can be derived from four regions of the human biliary tree: gallbladder, common bile duct, pancreatic duct, and intrahepatic bile ducts. Characterization of these organoids demonstrated expression of adult stem cell (LGR5/PROM1) and ductal (KRT19/KRT7) markers suggesting these cultures contained cells with a biliary stem/progenitor phenotype. Further, I show that IHBD organoids are distinct from EHBD organoids requiring different conditions for sustained growth. Using RNA-Sequencing, I demonstrate that primary tissues from different regions of the extrahepatic biliary tree display unique expression profiles and identify novel tissue-specific markers. I also show that only a limited number of these tissue specific differences are maintained in the in vitro organoids and that the organoids are very different from their tissue of origin. Finally, I demonstrate that IHBD, but not EHBD organoids, express a low-level of hepatocyte-specific markers under differentiation conditions. Taken together, the work in this dissertation has uncovered regional specific markers for different anatomical regions of the human biliary tree. Further, I demonstrate that major differences exist between IHBD organoids and EHBD organoids in vitro and discover that only IHBD organoids have the capacity to express hepatocyte markers under differentiation conditions. Ultimately, these results may help to identify new targets for therapeutic development for cholangiopathies and regenerative medicine. They have also provided important insight to the understanding of both basic biliary physiology and also the field of biliary stem/progenitor cell organoids.