T-Helfer-9-(Th9-)Zellen produzieren große Mengen Interleukin-(IL-)9 und lösen bei Wurm- und Tumorerkrankungen protektive Immunantworten aus. Sie sind aber auch maßgeblich an der Pathogenese chronisch entzündlicher Darmerkrankungen beteiligt. Im Widerspruch zu diesen entzündungsauslösenden Eigenschaften steht ihre Rolle bei der Erzeugung von Toleranz gegenüber allogenen Transplantaten. Diese gegensätzlichen inflammatorischen Eigenschaften deuten eine bisher nicht untersuchte funktionelle Heterogenität an. In vitro-differenzierte allo-reaktive Th9-Zellen zeigten sich in ihrer Gesamtheit pro-inflammatorisch. Dies äußerte sich nach Transfer in recombination activating gene-defiziente (Rag-/-) Mäuse durch einen akut einsetzenden Gewichtsverlust mit intestinaler Entzündung und durch die Abstoßung allogener Hauttransplantate. Mittels Einzelzell-Genexpressionsanalyse wurden zwei Th9-Subpopulationen identifiziert, die sich vor allem in ihrer CD96-Expression unterschieden (CD96low versus CD96high Th9-Zellen). Die differenzielle Expression von CD96 spiegelte sich auch im inflammatorischen Potenzial der Zellen wider. Während der Transfer von CD96low Th9-Zellen in Rag-/- Mäuse einen Gewichtsverlust mit Darmentzündung sowie die Transplantatzerstörung verursachte, zeigten CD96high-rekonstituierte Tiere kaum Entzündungsanzeichen im Transplantat bzw. im Darm. Dementsprechend verloren sie auch kein Gewicht. Es zeigte sich, dass CD96low Th9-Zellen ein höheres Potenzial zur Produktion von IL-4 und IL-9 sowie zur Expansion besaßen als CD96high Th9-Zellen. Eine Blockade von CD96 in vivo stellte die inflammatorischen Eigenschaften von CD96high Th9-Zellen wieder her, wodurch die funktionelle Relevanz der CD96-Expression unterstrichen wurde. Diese Daten belegen, dass es sich bei Th9-Zellen um eine funktionell heterogene Zellpopulation handelt. Weiterhin zeigen sie, dass CD96 – ein Molekül mit bislang unklarer Funktion in CD4+ T-Zellen – die Aktivität von Th9-Zellen negativ beeinflusst. / T helper 9 (Th9) cells are potent producers of interleukin(IL-)9 driving host immunity against worm infections and tumors. Furthermore, they are predominantly involved in the pathogenesis of chronic inflammatory bowel diseases. However, they also induce tolerance in allogeneic transplantation, which contrasts with their pro-inflammatory properties. These observations indicate a functional heterogeneity of Th9 cells not examined so far. Total in vitro differentiated allo-reactive Th9 cells injected into recombination activating gene-deficient (Rag-/-) mice caused weight loss, intestinal inflammation and rejection of allogenic skin grafts which proofed their inflammatory character. However, using single cell profiling, two subsets of Th9 cells mainly differing in their CD96 expression were identified (CD96low versus CD96high Th9 cells). Transfer of CD96low Th9 cells into Rag-/- mice induced severe weight loss, intestinal inflammation and graft destruction. In contrast, transfer of CD96high Th9 cells did cause neither weight loss nor resulted in graft rejection. Transcriptional profiling revealed a higher IL-9 and IL-4 expression potential as well as an increased expansion capacity in CD96low Th9 cells compared to CD96high Th9 cells. Blockade of CD96 in vivo restored the inflammatory properties of CD96high Th9 cells demonstrating, that expression of CD96 controls effector functions in Th9 cells. Thus, Th9 cells are heterogeneous in function. Moreover, this study suggests an inhibitory role for the co-signaling receptor CD96 – a molecule with so far unknown function in CD4+ T cells – in Th9 cells.

Lors du développement, la coordination d’évènements moléculaires et cellulaires mène à la production du cortex qui orchestre les fonctions sensori-motrices et cognitives. Son développement s’effectue par étapes : les cellules gliales radiaires (RGs) – les cellules souches neurales (NSCs) du cerveau en développement – et les cellules progénitrices de la zone ventriculaire (VZ) et de la zone sous ventriculaire (SVZ) génèrent séquentiellement des vagues distinctes de nouveaux neurones qui formeront les différentes couches corticales. Autour de la naissance, les RGs changent de devenir et produisent des cellules gliales. Cependant, une fraction persiste tout au long de la vie dans la SVZ qui borde le ventricule, perdant au passage leur morphologie radiale. Ces NSCs produisent ensuite les différents sous types d’interneurones du bulbe olfactif ainsi que des cellules gliales en fonction de leur origine spatiale dans la SVZ. Ces observations soulèvent d’importantes questions non résolues sur 1) le codage transcriptionnel régulant la régionalisation de la SVZ, 2) le potentiel des NSCs postnatales dans la réparation cérébrale, et 3) le lignage et les spécificités transcriptionnelles entre les NSCs et leur descendants. Mon travail de doctorat repose sur une étude transcriptionnelle des domaines de la SVZ postnatale. Celle-ci soulignait le fort degré d’hétérogénéité des NSCs et progéniteurs et identifiait des régulateurs transcriptionnels clés soutenant la régionalisation. J’ai développé des approches bio-informatiques pour explorer ces données et connecter l’expression de facteurs de transcription (TFs) avec la genèse régionale de lignages neuraux distincts. J’ai ensuite développé un modèle d’ablation ciblée pour étudier le potentiel régénératif des progéniteurs postnataux dans divers contextes. Finalement, j’ai participé au développement d’une procédure pour explorer et comparer des progéniteurs pré et postnataux à l’échelle de la cellule unique. Objectif 1 : Des expériences de transcriptomique et de cartographie ont été réalisées pour étudier la relation entre l’expression régionale de TFs par les NSCs et l’acquisition de leur devenir. Nos résultats suggèrent un engagement précoce des NSCs à produire des types cellulaires définis selon leur localisation spatiale dans la SVZ et identifient HOPX comme un marqueur d’une sous population biaisé à générer des astrocytes. Objectif 2 : J’ai mis au point un modèle de lésion corticale qui permet l’ablation ciblée de neurones de couches corticales définies pour étudier la capacité régénérative et la spécification appropriée des progéniteurs postnataux. Une analyse quantitative des régions adjacentes, incluant la région dorsale de la SVZ, a révélé une réponse transitoire de progéniteurs définis. Objectif 3 : Nous avons développé la lignée de souris transgénique Neurog2CreERT2Ai14, qui permet le marquage de cohortes de progéniteurs glutamatergiques et de leurs descendants. Nous avons montré qu’une large fraction de ces progéniteurs persiste dans le cerveau postnatal après la fermeture de neurogénèse corticale. Ils ne s’accumulent pas pendant le développement embryonnaire mais sont produits par des RGs qui persistent après la naissance dans la SVZ et qui continuent de générer des neurones corticaux, bien que l’efficacité soit faible. Le séquençage d’ARN sur cellule unique a révélé une dérégulation transcriptionnelle qui corrèle avec le déclin progressif observé in vivo de la neurogénèse corticale. Ensemble, ces résultats soulignent le potentiel des études transcriptomiques à résoudre mais aussi à soulever des questions fondamentales comme les changements trancriptionnels intervenant dans une population de progéniteurs au cours du temps et participant aux changements de leur destinée. Cette connaissance sera la clé du développement d’approches novatrices pour recruter et promouvoir la génération de types cellulaires spécifiques, incluant les sous-types neuronaux dans un contexte pathologique. / During development, a remarkable coordination of molecular and cellular events leads to the generation of the cortex, which orchestrates most sensorimotor and cognitive functions. Cortex development occurs in a stepwise manner: radial glia cells (RGs) - the neural stem cells (NSCs) of the developing brain - and progenitor cells from the ventricular zone (VZ) and the subventricular zone (SVZ) sequentially give rise to distinct waves of nascent neurons that form cortical layers in an inside-out manner. Around birth, RGs switch fate to produce glial cells. A fraction of neurogenic RGs that lose their radial morphology however persists throughout postnatal life in the subventricular zone that lines the lateral ventricles. These NSCs give rise to different subtypes of olfactory bulb interneurons and glial cells, according to their spatial origin and location within the postnatal SVZ. These observations raise important unresolved questions on 1) the transcriptional coding of postnatal SVZ regionalization, 2) the potential of postnatal NSCs for cellular regeneration and forebrain repair, and 3) the lineage relationship and transcriptional specificities of postnatal NSCs and of their progenies. My PhD work built upon a previously published comparative transcriptional study of defined microdomains of the postnatal SVZ. This study highlighted a high degree of transcriptional heterogeneity within NSCs and progenitors and revealed transcriptional regulators as major hallmarks sustaining postnatal SVZ regionalization. I developed bioinformatics approaches to explore these datasets further and relate expression of defined transcription factors (TFs) to the regional generation of distinct neural lineages. I then developed a model of targeted ablation that can be used to investigate the regenerative potential of postnatal progenitors in various contexts. Finally, I participated to the development of a pipeline for exploring and comparing select populations of pre- and postnatal progenitors at the single cell level. Objective 1: Transcriptomic as well as fate mapping were used to investigate the relationship between regional expression of TFs by NSCs and their acquisition of distinct neural lineage fates. Our results supported an early priming of NSCs to produce defined cell types depending of their spatial location in the SVZ and identified HOPX as a marker of a subpopulation biased to generate astrocytes. Objective 2: I established a cortical lesion model, which allowed the targeted ablation of neurons of defined cortical layers to investigate the regenerative capacity and appropriate specification of postnatal cortical progenitors. Quantitative assessment of surrounding brain regions, including the dorsal SVZ, revealed a transient response of defined progenitor populations. Objective 3: We developed a transgenic mouse line, i.e. Neurog2CreERT2Ai14, which allowed the conditional labeling of birth-dated cohorts of glutamatergic progenitors and their progeny. We used fate-mapping approaches to show that a large fraction of Glu progenitors persist in the postnatal forebrain after closure of the cortical neurogenesis period. Postnatal Glu progenitors do not accumulate during embryonal development but are produced by embryonal RGs that persist after birth in the dorsal SVZ and continue to give rise to cortical neurons, although with low efficiency. Single-cell RNA sequencing revealed a dysregulation of transcriptional programs, which correlates with the gradual decline in cortical neurogenesis observed in vivo. Altogether, these data highlight the potential of transcriptomic studies to unravel but also to approach fundamental questions such as transcriptional changes occurring in a population of progenitors over time and participating to changes in their fate potential. This knowledge will be key in developing innovative approaches to recruit and promote the generation of selected cell types, including neuronal subtypes in pathologies.

Zusammenfassung Die molekularbiologischen Untersuchungen der variablen Genabschnitte der Immunglobulingene von Lymphomzellen zweier Patienten mit kutanen B-Zell-Lymphomen wurden in der vorliegenden Arbeit mittels Einzel-Zell-PCR-Technik durchgeführt. Die erfolgte Analyse galt bevorzugt dem Aspekt der intraklonalen Diversität. Die Sequenzanalysen der Ig-Gene für die leichte Kette aus den insgesamt 100 untersuchten Tumorzellen des Patienten WS ergaben, daß zwischen den Zellen aus drei voneinander entfernt lokalisierten Gewebeproben intraklonale Diversität vorlag. Aufgrund der Mutationsanalysen und der Zuordnung der Subklone zu den Entnahmeorten ist eine evtl. antigengetriebene Entwicklung des Tumorklons zu vermuten. Bei Patient LB konnte trotz des großen Aufwandes, der Untersuchung von insgesamt 126 Zellen aus acht räumlich getrennten Biopsien, keine intraklonale Diversität für die schwere Kette der Immunglobulingene aufgezeigt werden. Die Sequenzunterschiede der leichten Kette beruhen auf einer einzigen stummen Mutation im Bereich der CDR 1, die keinen funktionellen Einfluß auf die Aminosäuresequenz hat und deshalb geringe prognostische Bedeutung besitzt. In beiden Fällen lagen hypermutierte Immunglobulingene vor. Die Tumorzellen des Patienten WS sind aus molekularbiologischer Sicht Keimzentrumszellen, die des Patienten LB eher Nachkeimzentrumszellen zuzuordnen. Die gewonnenen Erkenntnisse zeigen, daß bei der Untersuchung und Erforschung der Pathogenese von kutanen B-Zell-Lymphomen eine gewonnene Gewebeprobe nicht repräsentativ für den gesamten Tumor sein muß. Veröffentliche Ergebnisse, bei denen Monoklonalität anhand einer Biopsie postuliert wurde, müssen daher initial überdacht werden (74;76;77;84). Es ist folglich in Betracht zu ziehen, daß bei einer exakten molekularbiologischen Zuordnung der Tumorzellen zu ihrem Entwicklungsstadium und ihrer Herkunft räumliche als auch zeitliche Faktoren zu beachten sind. Eine chronologische Untersuchung könnte aufzeigen, ob andauernde Mutationen in den Tumorzellen stattfinden. Die Mikromanipulation und die Einzel-Zell-PCR-Technik sind elegante Methoden, um intraklonale Sequenzunterschiede aufzuzeigen und einen Beitrag für die molekularbiologische Erforschung der Pathogenese von kutanen B-Zell-Lymphomen zu leisten. Eine Kontrolle von malignoproliferativen Krankheiten, ob es unter den heutigen Therapiemöglichkeiten gelingt, den malignen Tumorklon vollständig zu beseitigen oder Aussagen über Progredienz und Prognose zu treffen, wäre ein interessanter Einsatzbereich dieser Methode. / abstract The molecularbiological investigation of the immunoglobulin variable region genes of two patients suffering on primary cutaneous B-cell-lymphoma was carried out using single-cell- PCR technic. The main focus lay on the aspect on the aspect of detecting intraclonal diversity. The sequence nucleotid-analysises of the immunoglubulin light chain genes obtained from a total of 100 investigated tumor B-cells in patient WS revealed intraclonal diversity among cells isolated from three spatially separated tissue samples. Considering the mutational pattern and the subclones in dependence on the tumorcells, taken from different topographical tumorsides, an antigen-driven clonal expansion could be supposed. Despite extensive efforts and the analysis of altogether 126 tumor B-cells out of eight spatially different localised biopsies, no intraclonal diversity could be observed for the immunoglobulin heavy chain rearrangement of second patient LB. Sequence differences of the Ig light chain based on only a single silent mutation within the CDR1 region. This mutation has no functional affect of the amino acid sequence and therefore little prognostical significance. In both cases the immunoglobulin genes were somatically hypermutated in compromise to the germ-line gene. From the molecularbiological point of view, the tumor cells of patient WS descended from germinal center cells, whereas the tumor B-cells of patient LB rather can be characterized as post-germinal center cells. The results clearly demonstrate, that the investigation of a single tissue sample of primary cutaneous B-cell lymphoma using micromanipulation and single cell-PCR technic may not be representative for the whole tumor. Publications concluding monoclonality with no intraclonal diversity from the analysis of a single biopsie therefore have to be interpreted with caution (74;76;77;84). Accordingly, an appropiate molecularbiological characterization of tumor B-cells regarding their developmental stage and origin has to consider spatial and time dependant aspects. Only the investigation of sequential biopsies may reliably detect ongoing mutations in tumor B-cells. The combination of micromanipulation and single cell PCR represents an elegant method to observe intraclonal diversity. The technic will give contribution to molecularbiological investigation of the pathogenesis of primary cutaneous B-cell lymphomas. It could be of interest to apply this method to the evaluation of current therapies with respect to its capability to eradicating the malignant cell clone completely, and to draw conclusions on disease progression and prognosis.

L'expression des gènes dans une cellule a longtemps été observable uniquement à travers des quantités moyennes mesurées sur des populations. L'arrivée des techniques «single-cell» permet aujourd'hui d'observer des niveaux d'ARN et de protéines dans des cellules individuelles : il s'avère que même dans une population de génome identique, la variabilité entre les cellules est parfois très forte. En particulier, une description moyenne est clairement insuffisante étudier la différenciation cellulaire, c'est-à-dire la façon dont les cellules souches effectuent des choix de spécialisation. Dans cette thèse, on s'intéresse à l'émergence de tels choix à partir de réseaux de régulation sous-jacents entre les gènes, que l'on souhaiterait pouvoir inférer à partir de données. Le point de départ est la construction d'un modèle stochastique de réseaux de gènes capable de reproduire les observations à partir d'arguments physiques. Les gènes sont alors décrits comme un système de particules en interaction qui se trouve être un processus de Markov déterministe par morceaux, et l'on cherche à obtenir un modèle statistique à partir de sa loi invariante. Nous présentons deux approches : la première correspond à une approximation de champ assez populaire en physique, pour laquelle nous obtenons un résultat de concentration, et la deuxième se base sur un cas particulier que l'on sait résoudre explicitement, ce qui aboutit à un champ de Markov caché aux propriétés intéressantes / Gene expression in a cell has long been only observable through averaged quantities over cell populations. The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells: it turns out that even in an isogenic population, the molecular variability can be very important. In particular, an averaged description is not sufficient to account for cell differentiation. In this thesis, we are interested in the emergence of such cell decision-making from underlying gene regulatory networks, which we would like to infer from data. The starting point is the construction of a stochastic gene network model that is able to explain the data using physical arguments. Genes are then seen as an interacting particle system that happens to be a piecewise-deterministic Markov process, and our aim is to derive a tractable statistical model from its stationary distribution. We present two approaches: the first one is a popular field approximation, for which we obtain a concentration result, and the second one is based on an analytically tractable particular case, which provides a hidden Markov random field with interesting properties

Les progrès technologiques récents en imagerie par résonance magnétique (IRM) ont ouvert la voie à une résolution spatiale de l’ordre de quelques microns, et donc à l’imagerie de cellules biologiques. Dans le cadre de ce projet, nous avons réalisé des expériences de microscopie IRM sur le système nerveux de l’aplysie (Aplysia californica), particulièrement adapté de par sa simplicité et de par la très grande taille de ses neurones, en vue d’étudier des processus à échelle cellulaire avec divers contrastes IRM. Les expériences d’imagerie ont été effectuées sur un aimant horizontal 17.2 Tesla, à des résolutions spatiales jusqu’à 25 µm isotrope. Le travail initial a consisté en la conception et fabrication de micro-antennes radiofréquences adaptées à la taille de neurones uniques et de ganglions. La première partie du projet a porté sur l’utilisation de l’ion manganèse (Mn2+) comme traceur de réseaux neuronaux dans le ganglion buccal de l’aplysie. Le manganèse (Mn) est un agent de contraste IRM qui pénètre dans les neurones par les canaux de calcium. La cartographie des projections axonales des neurones moteurs du ganglion dans chacun des nerfs périphériques a été établie. Il a également été démontré l’existence d’un transport actif du Mn2+ au sein du réseau neuronal activé par le neurotransmetteur dopamine. Dans un second temps, on s’est intéressé à deux méthodes de mesure de diffusion par IRM, à échelle microscopique. D’une part, un mécanisme de pondération en diffusion, DESIRE (Diffusion Enhancement of SIgnal and REsolution), original et particulièrement adapté à des échantillons petits, a été exploré. La séquence DESIRE a été implémentée en deux dimensions et testée avec succès sur fantôme. Le rehaussement mesuré était en accord avec les prévisions théoriques. Le grand défi à venir sera d’utiliser cette séquence pour acquérir des images de tissu biologique pondérées en diffusion avec un contraste unique. D’autre part, une séquence plus « classique » a été implémentée pour mesurer le coefficient de diffusion apparent (ADC) dans le tissu nerveux. Il s’agit d’une DP-FISP (Diffusion Prepared Fast Imaging with Steady-state free Precession) en trois dimensions, qui répond aux critères de résolution spatiale et de rapidité, avec un minimum d’artefacts. Cette séquence a permis d’étudier l’évolution de l’ADC de l’eau à différentes échelles du tissu nerveux en réponse à un stress cellulaire. Les deux sollicitations retenues étaient un choc hypotonique ou l’ajout d’ouabaïne. Des mesures d’ADC ont été effectuées sur des corps neuronaux isolés et sur du tissu de ganglion, avant et après sollicitation. Les deux types de stress ont entraîné une augmentation de l’ADC dans la cellule et une diminution globale de l’ADC dans le tissu. Ces résultats soutiennent l’hypothèse que la diffusion ralentie de l’eau habituellement observée dans un tissu ischémié (ou dans d’autres conditions associées à un gonflement cellulaire) est due à l’augmentation de surface membranaire. / Recent progress in magnetic resonance imaging (MRI) has opened the way for micron-scale resolution, and thus for imaging biological cells. In this thesis work, we performed magnetic resonance microscopy (MRM) on the nervous system of Aplysia californica, a model particularly suited due to its simplicity and to its very large neuronal cell bodies, in the aim of studying cellular-scale processes with various MR contrasts. Experiments were performed on a 17.2 Tesla horizontal magnet, at resolutions down to 25 µm isotropic. Initial work consisted in conceiving and building radiofrequency microcoils adapted to the size of single neurons and ganglia. The first major part of the project consisted in using the manganese ion (Mn2+) as neural tract tracer in the buccal ganglia of Aplysia. Manganese is an MR contrast agent that enters neurons via voltage-gated calcium channels. We performed the mapping of axonal projections from motor neurons into the peripheral nerves of the buccal ganglia. We also confirmed the existence of active Mn2+ transport inside the neural network upon activation with the neurotransmitter dopamine. In the second major part of the project, we tested the potential of two diffusion MRI sequences for microscopy. On the one hand, we explored a very original mechanism for diffusion weighting, DESIRE (Diffusion Enhancement of SIgnal and REsolution), particularly suited for small samples. The two-dimensional DESIRE sequence was implemented and successfully tested on phantoms. The measured enhancement was consistent with theoretical predictions. Using this sequence to produce diffusion weighted images with an unprecedented contrast in biological tissue remains a challenge. On the other hand, a more “standard” sequence was implemented to measure the apparent diffusion coefficient (ADC) in nervous tissue with MRM. This sequence was a three-dimensional DP-FISP (Diffusion Prepared Fast Imaging with Steady-state free Precession), which met criteria for high resolution in a short acquisition time, with minimal artifacts. Using this sequence, we studied the changes in water ADC at different scales in the nervous system, triggered by cellular challenges. The challenges were hypotonic shock or exposure to ouabain. ADC measurements were performed on single isolated neuronal bodies and on ganglia tissue, before and after challenge. Both types of stress produced an ADC increase inside the cell and an ADC decrease at tissue level. The results favor the hypothesis that the increase in membrane surface area associated with cell swelling is responsible for the decrease of water ADC in tissue, typically measured in ischemia or other conditions associated with cell swelling.

The loss of efficiency and performance of bioprocesses on scale-up is well known, but not fully understood. This work addresses this problem, by studying the effect of some fermentation gradients (pH, glucose and oxygen) at a larger scale in a bench-scale two compartment reactor (PFR + STR) using the cadaverine-producing recombinant bacterium, Corynebacterium glutamicum DM1945 Δact3 Ptuf-ldcC_OPT. The initial scale down strategy increased the magnitude of these gradients by only increasing the mean cell residence time in the plug flow reactor (τ_PFR). The cell growth and product related rate constants were compared as the τ_PFR was increased; differences were significant in some cases, but only up to 2 min residence time. For example, losses in cadaverine productivity when compared to the control fed-batch fermentation on average for the τ_PFR of 1 min, 2 min and 5 min were 25 %, 42 % and 46 % respectively. This indicated that the increasing the τ_PFR alone does not necessarily increase the magnitude of fermentation gradients. The new scale-down strategy developed here, increased the magnitude of fermentation gradients by not only increasing the τ_PFR, but also considering the mean frequency at which the bacterial cells entered the PFR section (f_m). The f_m was kept constant by reducing the broth volume in the STR. Hence, the bacterial cells also spent shorter times in the well mixed STR, as the τ_PFR was increased (hypothesised as giving the bacterial cells less time to recover the non-ideal PFR section of the SDR). On adoption of this strategy cadaverine productivity decreases for the τ_PFR of 1 min, 2 min and 5 min were 25 %, 32 % and 53 % respectively. Thus, highlighting that loss in performance is most likely to occur as the magnitude of heterogeneity within the fermentation environment increases. However, Corynebacterium glutamicum DM1945 Δact3 Ptuf-ldcC_OPT did show some resilience in its biomass productivity. It was only marginally affected in the harshest of conditions simulated here.

The two defining features of mouse embryonic stem (ES) cells are self-renewal and naive pluripotency, the ability to give rise to all cell lineages in the adult body. In addition to being a unique and interesting cell type, pluripotent ES cells have demonstrated their potential for continued advancements in biomedical science. Currently, there is an improved understanding in the chemical signals and the gene regulatory network responsible for the maintenance of ES cells in the naive pluripotent state. However, less is understood about how ES cells exit pluripotency. My main aim is to study the dynamics and the factors affecting the irreversible exit from pluripotency. Expression of the reporter Rex1-GFPd2, which is inactivated upon exit from naive pluripotency, was analyzed by quantitative long-term single-cell imaging over many generations. This technique allowed chemical, physical, and genealogical information to be recorded during the transition to exit. Culture conditions that provided homogeneous populations were used in all assays and these data were validated against bulk-culture data where appropriate. Changes in real-time cell behavior were seen in cell-cell contact, motility, and cell-cycle duration. Undifferentiated ES cells form tightly joined colonies, with cells that exhibit low motility and a constant cell-cycle duration. Exit is associated with increasing cell motility, decreased cell-cell contact, and an acceleration in cell proliferation. The onset of exit is associated with a sudden and irreversible inactivation of the Rex1-GFPd2 reporter. This inactivation is asynchronous, as it occurs at different times and in different generations during ES cell differentiation. However, examination of daughter cells generated from the same mother revealed a high level of synchronicity. Further investigation revealed that high levels of correlation in cell-cycle duration and Rex1-GFPd2 expression exist between differentiating sister and cousin cells, providing strong evidence that cell potency is inherited symmetrically in cell divisions during exit $\textit{in vitro}$. How cells change fate is a fundamental question in developmental biology. Knowing the cellular dynamics during the transition out of naive pluripotency is important for harnessing the potential of ES cells and understanding how cell fate decisions are made during embryonic development. The quantification of the timing of exit from naive pluripotency coupled with identifiable changes in cellular behaviors, such as motility, cell size, and cell-cycle duration, enhances the understanding of how cell fate changes are regulated during directed differentiation.

Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug response studies in patient-derived xenograft models of triple-negative breast cancer are also discussed. Taken together, data from these studies highlight LCI’s versatility as a tool for clinical, translational, and basic research applications.

Der Tumorsuppressor p53 spielt eine wichtige Rolle bei der Aufrechterhaltung der zellulären Homöostase und verhindert die Bildung und Entwicklung von Krebs. Frühere Studien auf Einzelzellebene haben gezeigt, der p53 nach dem Auftreten von DNS Schäden in einer Serie gleichförmiger Pulse im Kern akkumuliert. Um den Einfluss von Temperatur, dem Zustand des NFκB Weges oder dem Vorhandensein von Wachstumsfaktoren auf die p53 Dynamiken nach DNS-Schäden zu untersuchen, wurden in dieser Arbeit A549 und MCF10A p53 Reporter-Zelllinien verwendet. Um Daten mit hoher zeitlicher und räumlicher Auflösung auf Einzelzellebene zu erhalten, wurde Zeitraffer-Fluoreszenzmikroskopie verwendet. Überraschenderweise zeigten A549 Zellen, die mit γ-Strahlung behandelt wurden, eine höhere p53 Akkumulation und ein verlängertes Zeitintervall zwischen den p53 Pulsen, wenn sie bei 30°C inkubiert wurden im Vergleich zu Zellen unter physiologischen Bedingungen. Hingegen zeigten Zellen bei 40°C eine höhere p53 Pulsfrequenz. Außerdem wurde die p53 Zielgen-Expression durch die Änderungen in der Dynamik beeinflusst. In den beiden Zelllinien, A549 und MCF10A, wurde die p53 Dynamik durch Inhibierung des NFκB Signalweges verändert, nicht aber durch dessen Aktivierung mittels TNF. So verlängert die Inhibierung des NFkB Signalweges das Zeitintervall zwischen p53 Pulsen, was sich auch in der Expression von p53 Zielgenen wiederspiegelt. Weiterhin konnte in MCF10A Zellen durch Experimente mit verschiedenen Medien-Bedingungen gezeigt werden, dass p53 Dynamiken vor allem durch die Anwesenheit von EGF und Hydrocortison geprägt werden. So führt EGF zu einem pulsierenden p53 Verhalten, während Hydrocortison alleine die p53 Antwort vollständig aufhebt.. Diese Studie macht deutlich, wie wichtig es ist, das Verhältnis von zellulärem Zustand und p53 Antwort systematisch zu untersuchen, um Krebstherapien wirksamer zu machen / The tumor suppressor p53 plays important roles in maintaining cellular homeostasis and in preventing the formation and development of cancer. Previous studies on p53 activation after DNA damage have reported that it shows a series of regular discrete pulses of protein accumulation over time at the single cell level. In this work A549 and MCF10A p53 reporters cell line were used to investigate how p53 dynamics after DNA damage were affected by changes in temperature, by changes in the state of the NFκB pathway and changes in the provided growth factors. Time-lapse florescent microscopy was used to obtain single cell data with high temporal and special resolution at the single cell level. Surprisingly A549 cells treated with γ-irradiation showed higher level of p53 accumulation and increased time between p53 pulses when imaged at 30°C than cells imaged under physiological conditions. Cells imaged at 40°C showed instead higher p53 pulse frequency. P53 target gene expression was also affected by these changes in dynamics. In both A549 and MCF10A cells, p53 dynamics were changed by NFκB pathways inhibition but not activation via TNFα. Upon inhibition of the NFκB pathway the timing between p53 pulses was increased leading to changes also in p53 target genes expression. In MCF10A cells experiments done under different medium conditions proved that p53 dynamic in this cell line was shaped mainly by the presence of EGF and hydrocortisone that are usual components of the media. EGF leads to a more pulsatile p53 behavior while hydrocortisone completely abrogates the p53 response. These discoveries pointed out the need to study more systematically the relationship between the p53 response to a given stress and the cellular state in order to make cancer therapies more effective.

The occupational exposures of sewage workers are complex and variable, and include a great variety of biological and chemical agents. Previous research has focused mostly on infections and various symptoms among sewage workers, e.g. abdominal and respiratory symptoms. At several sewage plants in Sweden, concern arose about occupational cancer, specifically cancer of the stomach, the kidney, and the lung. The aim of this study was to study the cancer incidence among municipal sewage workers, some exposures that might be connected with cancer risk, and self reported abdominal and respiratory symptoms. In a cohort of municipal sewage workers there was no increase in the overall incidence of cancer when compared with the general population. However, there was a slight increase in the incidence of prostate cancer, but not in the sites of original concern among the workers. Infection by the gastric carcinogen Helicobacter pylori (determined from the presence of IgG antibodies in serum against H pylori) was no more prevalent in sewage workers than in comparable referents. Neither were sewage workers more exposed to genotoxic agents than comparable referents, as measured by the alkaline single cell gel electrophoresis (SCG) assay performed on peripheral lymphocytes. There was no increase in the three-month prevalence of abdominal symptoms when compared with other municipal workers. Specifically, there was no difference in prevalence of the common disorders dyspepsia and irritable bowel syndrome. Sewage workers reported adult bronchial asthma significantly more than the referents.