RNA-binding proteins play a central role in the post-transcriptional regulation of gene expression; however, little is known about the endogenous transcripts to which they bind. Here, I have used the ultra-violet cross-linking and immuno-precipitation (CLIP) technique to identify RNA targets directly bound to two RNA-binding proteins: Acinus and hnRNP A1. Acinus (apoptotic chromatin condensation inducer in the nucleus) contains a region that is homologous to the RNA binding domain of the Drosophila splicing regulator sex-lethal, and a serine and arginine rich region similar to that seen in the SR family of proteins, which function extensively in splicing. Furthermore it is a component of the multi-protein spliceosome complex, and I have demonstrated it can directly bind polyadenylated RNA. I have shown that Acinus displays a diffuse nuclear localisation pattern, however, overexpression of an epitope-tagged protein results in its accumulation in enlarged nuclear speckles. Together these results suggest a role in pre-mRNA splicing. Acinus is cleaved during apoptosis by caspase-3, resulting in a truncated protein with chromatin condensation inducing activity (Sahara et al., 1999). Accordingly, I have demonstrated that overexpression of epitope-tagged Acinus results in an increased number of cells exhibiting an apoptotic phenotype. The proteolytic fragment contains the RNA binding region, and to determine if the role of Acinus in apoptosis is mediated by RNA interactions I utilised CLIP to identify in vivo RNA targets. I have identified several mRNA targets of Acinus and found that the binding sites in those mRNA targets predominantly map to constitutively expressed exons. This is in agreement with the exon junction complex, of which Acinus is a component, being deposited on mRNAs after splicing. These results may indicate that Acinus is a core RNA binding factor of the exon junction complex. To complement this approach, I also performed CLIP with a known alternative splicing regulator, hnRNP A1. In this manner, the binding site preferences could be compared between the two proteins. As expected, the majority of hnRNP A1 binding sites are located in introns, corresponding with their identified role of antagonizing pre-mRNA splicing by binding intronic splicing elements. Interestingly, a number of the CLIP tags are located in, or adjacent to, alternatively spliced events suggesting a role for hnRNP A1 in the regulation of alternative splicing of these specific pre-mRNAs. In addition to pre-mRNA splicing hnRNP A1 also functions in the cellular stress response. Upon environmental stresses it relocates to the cytoplasm and accumulates in cytoplasmic foci known as stress granules (Guil et al., 2006). Here I show some of the targets identified by CLIP are regulated by hnRNP A1 in times of cellular stress. In summary, I have identified two novel subsets of RNAs, bound by Acinus or hnRNP A1 in vivo. I have shown these proteins exhibit distinct binding preferences, which correspond to their biological function. This work is consistent with hnRNP A1 acting as an alternative splicing regulator, and provides evidence for a dual role of Acinus in mRNA splicing and apoptosis. This study also demonstrates the power of the CLIP technique, as identification of in vivo RNA targets allows greater understanding of the mechanisms by which RNA-binding proteins exert their regulatory control.

Pancreatic Ductal Adenocarcinoma (PDAC) continues to have a dismally low survival rate due to late diagnosis and poor treatment options. Therefore, there is a need to understand the early stages and progression of the disease. PDAC is known to have two types of cells of origin: ductal cells or acinar cells. Since acinar-derived PDAC is thought to be the more malignant of the two, it was chosen as the focus of this work. Most studies of acinar cells as they relate to PDAC are accomplished by using animal models such as genetically engineered mouse models. While this method yields a large amount of insight into the progression of the disease and the role of specific genes, it has the drawbacks of being very time and resource intensive. The quicker and less costly alternative is <i>in vitro </i>culture. Specifically, here we have developed a microfluidic model which can incorporate a key aspect of the extracellular matrix (ECM), type I collagen, and mimics the 3D geometry of an <i>in vivo </i>acinus. Most attempts at <i>in vitro </i>culture have been limited by the fact that isolated acinar cells show a decrease in the amount of digestive enzymes they secrete as culture continues. For this reason, we are using a reprogrammed cancer cell line. These cells can be induced with doxycycline to express PTF1a, which allows the cells to adapt acinar characteristics, such as the production of digestive enzymes. We were able to successfully culture and induce PTF1a in these cells within our chip. We showed that the cells exhibit no invasion into the collagen matrix once PTF1a is expressed, thus eliminating a key aspect of cancer cell culture. The cells grown in the chip are confirmed to be producing PRSS2, the digestive enzyme trypsinogen. Collectively, this suggests that we have produced healthy acinar cells growing in the same configuration that they would <i>in vivo. </i>This has many applications in the study of pancreatic ductal adenocarcinoma, as we have developed way to culture reprogramed cancer cells as their benign precursors and maintain acinar characteristics <i>in vitro.</i> It will also have applications in the study of many other pancreatic diseases by providing an <i>in vitro</i> model of a healthy, functional acinus.

Cette thèse a pour cadre la modélisation du dépôt de particules dans le poumon humain afin d'optimiser l'administration de médicaments par voie inhalée. La région alvéolaire du poumon jouant un rôle physiologique et fonctionnel crucial, l'objectif de ce travail est de mettre en place un modèle de dépôt au sein de la région acinaire qui soit intégrable à un modèle intégrant le poumon complet. Les deux premiers chapitres rappellent les caractéristiques anatomiques et fonctionnelles du poumon et en particulier de la région alvéolaire ainsi que les principes physiques mis en jeu lors de l'écoulement de l'air et du transport de particules dans l'arbre pulmonaire. Puis un modèle numérique d'écoulement dans une géométrie alvéolaire simplifiée est présenté. Le transport d'un bolus d'aérosol y est étudié par une approche eulérienne, au cours de plusieurs cycles respiratoires ; l'impact des irréversibilités de l'écoulement sur la dispersion du bolus est ensuite quantifié. Le dernier chapitre présente l'intégration des résultats précédents au sein d'un modèle analytique de dépôt de particules dans le poumon. Les résultats générés par ce modèle sont ensuite comparés aux données expérimentales issues de la littérature ou obtenues lors d'une étude clinique en cours, spécifiquement orientée sur la mesure du dépôt de particules dans les voies aériennes. Les résultats du modèle montrent une augmentation du dépôt de particules dans la région acinaire, présentant un bon accord avec les données expérimentales. Ce modèle pourrait aider à la conception de thérapies ciblant spécifiquement la région alvéolaire du poumon / The context of this thesis is the modelling of particle deposition in the human lung in order to optimise the administration of inhaled drugs. As the alveolar region plays a crucial role both physiologically and functionally, especially for systemic delivery, the objective of this work is to set-up a particle deposition model specific to the acinar region which could be integrated in whole lung deposition model. The first two chapters concentrate on the anatomical and functional aspects of the lung and on the physical principles involved in the flow and particle transport mechanisms in the lung. Then a computational fluid dynamics model was setup in a simplified alveolar geometry. Aerosol bolus transport was studied through an Eulerian approach, for one or several breathing cycles. The impact of flow irreversibilities on bolus dispersion was quantified. The last chapter deals with the integration of the previous results in an analytical model of particle deposition in the whole lung. The results generated by this model are then compared to experimental data from the literature or obtained from an ongoing clinical trial. The results of the new theoretical model show an increase of particle deposition in the acinar region which improves correlation of theory with experimental data. This model could favourably help designing therapies targeting the alveolar region of the lung

L'acinus pulmonaire constitue l'unité d'échange gazeux entre l'air et le sang dans les voies aériennes pulmonaires. Dans le cadre de cette thèse, nous nous sommes plus particulièrement intéressés à l'oxygène. Plusieurs mécanismes sont mis en jeu depuis son entrée dans l'acinus jusqu'à sa capture par l'hémoglobine : les mécanismes de transport de l'oxygène dans l'air : convection et diffusion, le transfert par diffusion passive de l'oxygène à travers la membrane alvéolo-capillaire et sa capture par l'hémoglobine. Par la détermination de la capacité diffusive pulmonaire DL, il est possible d'évaluer cliniquement le fonctionnement et l'efficacité de ces mécanismes. Cette mesure est couramment employée pour le diagnostic, notamment pour mettre en évidence les détériorations de la membrane alvéolo-capillaire ou encore les pertes de surface d'échange. Expérimentalement, la DL s'exprime à partir des deux mesures cliniques suivantes: la pression alvéolaire PA et la consommation de gaz V. Plus particulièrement, dans le cas qui nous intéresse ici soit celui de l'oxygène, il s'agit de la pression partielle en oxygène contenue dans les alvéoles pulmonaires PA,O2 et de la quantité d'oxygène échangée en une minute VO2. Il est possible de déterminer une valeur théorique de la capacité diffusive pulmonaire grâce à une formulation classique et empirique très utilisée en médecine. Celle-ci est aujourd'hui encore le sujet de nombreuses publications car elle ne reproduit pas exactement les résultats de l'expérience. Nous avons mis en place un modèle numérique dynamique du transport et du transfert de l'oxygène au sein de l'acinus pulmonaire permettant de restituer les valeurs de PA,O2 et VO2 chez les sujets sains. Ce modèle dépend d'un unique paramètre physique ajustable qu'on appelle la perméabilité $W$. Celle-ci traduit toute la complexité du transfert de l'oxygène vers le sang. Elle se définit comme une conductance équivalente imposée par les trois mécanismes acteurs du transfert vers le sang. Par cette approche numérique, nous avons donc construit un acinus artificiel qui, à partir de la seule détermination de la perméabilité $W$ est capable de reproduire le fonctionnement de l'acinus réel. A partir de ce modèle, nous avons pu étudier l'influence de la géométrie asymétrique de l'acinus pulmonaire sur le transport et l'échange. Cette étude a mis en évidence une forte hétérogénéité de la répartition du flux d'oxygène échangé vers le sang dans l'acinus pulmonaire. Ceci peut s'expliquer grâce à un phénomène physique appelé masquage diffusionnel, responsable du fait que la pression partielle en oxygène dans l'acinus diminue. Ce phénomène est gouverné, notamment, par l'absorption à travers la membrane alvéolaire et la diffusion le long de la structure irrégulière de l'acinus. Cet effet entraîne que les parties profondes de l'acinus sont très peu alimentées en oxygène, la majorité ayant été absorbée dans les premières générations. Au repos, l'influence du masquage est élevée et le flux d'oxygène ne dépend que très peu du volume (proportionnel à la surface alvéolaire). A l'effort, l'effet du masquage est moindre, notamment grâce à la vitesse de convection plus élevée. Ainsi, la quasi-totalité de la surface alvéolaire est utilisée.

Retinoic acid receptor (RAR), a member of the steroid/thyroid hormone nuclear receptor superfamily, functions as a RA-dependent transcription activator bound to the RA response element (RARE) within the promoter or enhancer region of target genes. The transcriptional activity of RAR is modulated by a large number of coregulators including coactivators and corepressors. Acinus is a nuclear protein with three isoforms (Acinus-L, Acinus-S and Acinus-S'). Acinus-S' interacts with the A/B domain of RAR and represses RAR-regulated genes expression. Acinus (without isoform definition) has been identified as a component of nuclear speckles, the spliceosome and the exon junction complex (EJC), suggesting its localization in nuclear speckles and involvement in RNA processing. Acinus-S has been shown to localize in nuclear speckles. However, it is unclear whether the other two isoforms also localize in nuclear speckles. In addition, the role of Acinus in regulating pre-mRNA splicing is unclear. The goal of these studies was to examine the nuclear localization of Acinus-L and Acinus-S' and to determine the role of Acinus isoforms in RAR-dependent splicing. The sub-nuclear localization of Acinus-L and Acinus-S' was determined using fluorescence microscopy. Acinus-S' colocalizes with SC35 in nuclear speckles while Acinus-L localizes diffusely throughout the nucleoplasm. RA treatment has little effect on the sub-nuclear localization of Acinus-L and Acinus-S'. The domains/regions necessary for the distinct sub-nuclear localization of Acinus-L and Acinus-S' were identified. The speckled sub-nuclear localization of Acinus-S' is dependent on its C-terminal RS- and RD/E-rich region but is independent of the phosphorylation status of Ser-453 and Ser-604 within this region. The unique N-terminal SAP-motif of Acinus-L is responsible for its diffuse localization in the nucleus. Moreover, the sub-nuclear localization of Acinus isoforms is affected by each other, which is determined by the combinatorial effect of the more potent SAP motif of Acinus-L and the C-terminal RS- and RD/E-rich region in all Acinus isoforms. The C-terminal RS- and RD/E-rich region of Acinus mediates the colocalization of Acinus isoforms as well as with its interacting protein RNPS1. The role of Acinus isoforms in regulating pre-mRNA splicing was explored using in vivo splicing assays. Both Acinus-L and Acinus-S', with the activity of Acinus-L higher than that of Acinus-S', increase the splicing of a RA-responsive minigene containing a weak 5' splice site but not a RA-responsive minigene containing a strong 5' splice site. RA treatment further enhances the splicing activity of Acinus in a dose- and time-dependent manner, suggesting a RA-dependent activity in addition to a RA-independent activity of Acinus. The RA-independent effect of Acinus on the splicing of pre-mRNAs containing the weak 5' splice site occurs to varying degrees using minigene constructs containing several different promoters while the RA-dependent splicing activity of Acinus is specific for transcripts derived from the minigene driven by the RARE-containing promoter. This suggests that the ligand-dependent splicing activity of Acinus is related to the RA-activated RAR bound to the RARE. The ligand-dependent splicing activity of Acinus was further shown to be promoter-specific, depending on the ligand-dependent transcription activator. The RRM domain was identified to be necessary for the RA-dependent splicing activity of Acinus. The RA-independent splicing activity of Acinus is repressed by RNPS1. Unexpectedly, the C-terminal RS- and RD/E rich region is dispensable for the splicing activity of Acinus in regulating the minigene containing a weak 5' splice site. Importantly, measurement of the splicing of endogenous human RARâ and Bcl-x in vivo demonstrates that Acinus stimulates the use of the weaker alternative 5' splice site of these two genes in a RA-dependent manner for RARâ and in a RA-independent manner for Bcl-x. Taken together, these studies demonstrate the distinct sub-nuclear localization of Acinus-L and Acinus-S', and identified the domains that are responsible for their sub-nuclear localization, which shed light on possible distinct functions between Acinus isoforms. In addition, both Acinus-L and Acinus-S' have been shown to be splicing cofactors (with the activity of Acinus-L higher than that of Acinus-S') that facilitate constitutive splicing of pre-mRNAs containing a weak 5' splice site and regulate alternative splicing in favor of the isoform generated from the weaker alternative 5' splice site. Both Acinus-L and Acinus-S' have a RA-dependent splicing activity specific for RA-responsive genes, which suggests that Acinus functions in RAR-dependent splicing. / Biochemistry

The characterization of the normal pulmonary acinus is a necessary first step in understanding the nature of respiratory physiology and in assessing the etiology of pulmonary pathology. Murine models play a vital role in the advancement of current understanding of the dynamics of gas exchange, particle deposition and the manifestations of diseases such as COPD, Cystic Fibrosis and Asthma. With the advent of interior tomography techniques, high-resolution micro computed tomography (μCT) systems provide the ability to nondestructively assess the pulmonary acinus at micron and sub-micron resolutions. With the application of Systematic Uniform Random Sampling (SURS) principles applied to in-situ fixed, intact, ex-vivo lungs, we seek to characterize the structure of pulmonary acini in mice and study the variations across dimensions of age, location within the lung and strain phenotypes. Lungs from mice of three common research strains were perfusion fixed in-situ, and imaged using a multi-resolution μCT system (Micro XCT 400, Zeiss Inc.). Using lower resolution whole lung images, SURS methods were used for identification of region-specific acini for high-resolution imaging. Acinar morphometric metrics included diameters, lengths and branching angles for each alveolar duct and total path lengths from entrance of the acinus to the terminal alveolar sacs. In addition, other metrics such as acinar volume, alveolar surface area and surface area/volume ratios were assessed. A generation-based analysis demonstrated significant differences in acinar morphometry across young and old age groups and across the three strains. The method was successfully adapted to large animals and the data from one porcine specimen has been presented. The registration framework provides a direct technique to assess acinar deformations and provides critical physiological information about the state of alveolar ducts and individual alveoli at different phases of respiration. The techniques presented here allow us to perform direct assessment of the three-dimensional structure of the pulmonary acinus in previously unavailable detail and present a unique technique for comprehensive quantitative analysis. The acinar morphometric parameters will help develop improved mathematical and near-anatomical models that can accurately represent the geometric structure of acini, leading to improved assessment of flow dynamics in the normal lung.

The context of this thesis is the modelling of particle deposition in the human lung in order to optimise the administration of inhaled drugs. As the alveolar region plays a crucial role both physiologically and functionally, especially for systemic delivery, the objective of this work is to set-up a particle deposition model specific to the acinar region which could be integrated in whole lung deposition model. The first two chapters concentrate on the anatomical and functional aspects of the lung and on the physical principles involved in the flow and particle transport mechanisms in the lung. Then a computational fluid dynamics model was setup in a simplified alveolar geometry. Aerosol bolus transport was studied through an Eulerian approach, for one or several breathing cycles. The impact of flow irreversibilities on bolus dispersion was quantified. The last chapter deals with the integration of the previous results in an analytical model of particle deposition in the whole lung. The results generated by this model are then compared to experimental data from the literature or obtained from an ongoing clinical trial. The results of the new theoretical model show an increase of particle deposition in the acinar region which improves correlation of theory with experimental data. This model could favourably help designing therapies targeting the alveolar region of the lung

Two isoforms of the tick Ixodes ricinus digestive peptidases cathepsins L1 and L3 are expressed also in salivary glands. In order to assess their role in this tissue, the specific antibodies against these peptidases were prepared by affinity chromatography and used for their detailed immuno-localization using cutting-edge methods of electron microscopy.