<p dir="ltr">Skeletal muscle accounts for 40% of total body weight and the homeostasis of muscle tissue is critical in maintaining proper body function. Skeletal muscle develops during the embryonic stages from the muscle progenitor cells derived from the dermomyotome structure. The myogenic progenitor cells contribute to the primary myogenesis by forming the primary myotubes which are the founding structures that the secondary myogenesis continues to build on. A portion of the myogenic progenitor cells makes up the adult muscle stem cells residing in homeostatic muscle tissue. The adult muscle stem cells contribute substantially for the adult muscle regeneration. Due to the significance of the muscle tissue and the importance of muscle stem cells, dysregulation of the muscle homeostasis or the muscle stem cell homeostasis will result in severe pathological conditions such as myopathy.</p><p dir="ltr">Mitochondria are cellular organelles that are responsible for generating energy needed for cellular processes, especially for muscle tissue where muscle contraction requires the presence of ATP. On the other hand, mitochondria also serve as signaling molecules and provide macromolecules for the biosynthesis. FAM210A (Family With Sequence Similarity 210 Member A) protein was shown to impact the lean mass of human subjects yet a detailed study on the effect of FAM210A in skeletal muscle was not performed, nor has the molecular mechanisms through which FAM210A function been elucidated. Therefore, I take on the task to unveil the function of FAM210A in muscle development, muscle homeostasis and muscle stem cell behavior by using a combination of mouse models with different myogenic promoters to target <i>Fam210a</i> at different developmental stages.</p><p dir="ltr">In the first part of the thesis, I investigated the role of FAM210A in post differentiation myofibers. Using the <i>Myl1</i>^<em>Cre</em> driven deletion of <i>Fam210a</i>, I found that <i>Fam210a</i>^<em>MKO</em> had normal development before 3 weeks of age, but the growth was stagnant from 4 weeks on, and the mice did not survive past 8 weeks of age. I found that the assembly of the ribosomes in the <i>Fam210a</i>^<em>MKO</em> was defective, leading to impaired translation which attenuated the muscle atrophy phenotype. I identified through proteomics that the mitochondrial autophagy and proteostatic control pathways were significantly induced yet mitochondrial organization and energetic proteins were downregulated. Metabolomics analysis showed that the signaling metabolite acetyl-CoA was increased in the <i>Fam210a</i>^<em>MKO</em> which led to increased protein acetylation, specifically, we showed that the ribosomal proteins were hyperacetylated, and that the acetylation increase was elicited by the <i>Fam210a</i>-null mitochondria.</p><p dir="ltr">In the second part of the thesis, I investigated the function of FAM210A in muscle progenitor cells. In the <i>FamMKO</i> mice, I found that deletion of <i>Fam210a</i> from embryonic myogenic progenitor cells led to developmental arrest and postnatal death at day 6. In the <i>FamPKO</i> mice, I found that <i>Fam210a</i> is needed for adult muscle stem cell to contribute to regeneration. Loss of <i>Fam210a</i> leads to the regenerative defects when the muscle was exposed to injury cues. We further showed that <i>Fam210a</i> deletion in muscle stem cells resulted in disruption of the proteostatic control over muscle stem cell activation, thereby forbidding the translational increase necessary to facilitate activation and proliferation. Furthermore, I showed that <i>Fam210a</i> deletion leads to excessive OPA1 cleavage, which contributes to the regenerative failure of muscle stem cells as fusion is required for the mitochondrial network remodeling during regeneration. Therefore, <i>Fam210a</i> safeguards the mitochondrial network and proteostasis during regeneration.</p><p dir="ltr">In summary, my studies characterized the functional contribution of FAM210A during embryonic muscle development, muscle mass maintenance and adult muscle stem cell homeostasis. The regulation of FAM210A in these three processes impinge on the translational regulation. My studies further demonstrated the importance of mitochondrial regulated protein translation in skeletal muscle and muscle stem cells.</p>

<p dir="ltr">Newborn animals undergo a lot of early-life stress that heavily impact on their long-term growth, performance, and welfare. Typically, the stress would indirectly interfere with the capacity of these neonates to utilize dietary nutrients and consequently impact tissue growth and development. In piglets, weaning is a stressful situation characterized by disruption of intestinal epithelial cell development which causes poor digestion of solid feed and a negative impact on absorption of nutrients especially in the post-gastric region. In addition, weaning in piglets could cause an increase in cellular assault by reactive oxygen species thereby potentially causing gut leakiness and paracellular loss of nutrients along the intestinal tract. In broiler chickens, access to feed may take up to 72 h following hatching which may affect their gut development as well as their gut microbiota. After the first feed ingestion, there is a sharp increase in the gut microbiota which triggers an increase in the development of the immune system as well as the gut. There is continuous attention on the strategies and nutritional interventions to mitigate or ameliorate the adverse effects of early life stressors in these food animals, especially in broiler chickens and piglets. In the studies described in this dissertation, myo-inositol (purely supplemented or phytase-induced) and luteolin were tested as nutritional strategies to mitigate the effects of early-life stressors on growth and the potential mechanisms by which myo-inositol and luteolin regulate growth were investigated.</p><p dir="ltr">In study I, the effect of myo-inositol on growth in 128 postweaning piglets fed protein-deficient corn-soy diets was tested. There were 4 dietary treatments in a randomized complete block design with body weight as the blocking factor. The treatments consisted of 1 positive control (PC) diet formulated to meet all the nutrient requirements of the piglets with a 20% crude protein (CP); the remaining 3 diets were the negative control (NC) diets with a 3% reduction in CP, a 2 g/kg myo-inositol supplemented negative control diet (NC+INO), and phytase (3,000 FTU/kg) supplemented negative control (NC+PHY) diet. The results showed that phytase enhanced the apparent total tract digestibility (ATTD) of P in the weanling pigs. Myo-inositol supplementation in a protein-deficient diet improved (P < 0.05) porcine plasma myo-inositol concentration while an in vitro myo-inositol incubation with intestinal epithelial cells increased the expression of genes that encode for Claudin-1, Claudin-3, Claudin-4, ZO-1, NaPiIIb, GLUT2, and SLC7A2. The in vitro analysis of tight junction integrity in the IPEC-J2 cells indicated by the transepithelial electrical resistance and FITC-Dextran permeability showed an enhancement in response to myo-inositol treatment. Although the in vivo study found that myo-inositol did not improve growth performance or ATTD, the in vitro myo-inositol enhanced markers of gut health and function.</p><p dir="ltr">In study II, the effect of myo-inositol on the growth of broiler chickens was tested. In this study, there were 6 experimental treatments based on two dietary protein levels (PC and NC) and three supplement types (BASAL, INO, and PHY) resulting in a 2 x 3 factorial arrangement in a completely randomized design. A total of 384 broiler chickens comprising 6 treatments with eight replicates per treatment and 8 birds per replicate were used. The birds were fed a common starter diet for the initial 7 days after they arrived at the poultry unit followed by a 14-day trial. The protein-deficient diet decreased the feed efficiency of the birds. Phytase addition increased (P < 0.05) the apparent ileal digestibility (AID) and ATTD of P and Ca in both PC and NC groups. The jejunal gut morphology was enhanced by supplemental phytase as indicated by an increase in villus height and the ratio of the villus height-to-crypt depth, coupled with an increase in serum myo-inositol concentration caused by both myo-inositol and phytase. In conclusion, myo-inositol showed a differential influence on growth performance, nutrient digestibility, and gut morphology.</p><p dir="ltr">In study III, the effects of luteolin on weanling pigs and IPEC-J2 cells were examined. A total of 48 piglets were randomly allotted to two dietary treatments consisting of a control group and a luteolin (LUT)-supplemented dietary group for a 4-week trial. A weekly assessment of the growth performance and expression of specific proteins in the jejunal mucosa was performed. In each dietary group, 8 piglets were slaughtered at weeks 1, 2, and 4 postweaning to collect blood, jejunal and ileal mucosa, and tissues. Luteolin supplementation numerically improved the ADG and G:F of the pigs. Luteolin feeding altered the jejunal and ileal gut morphology with increased villi height (P < 0.05) and villus height-to-crypt depth ratio (VCR, P < 0.05) in the jejunum and decreased crypt depth in the ileum. The effect of luteolin on IPEC-J2 global proteome and phosphor-proteome showed that luteolin could potentially improve intestinal barrier integrity by enhancing the abundance of proteins important in cell growth and survival. </p><p dir="ltr">In summary, dietary supplementation with myo-inositol and luteolin could regulate growth and nutrient digestibility in broiler chickens and weanling pigs by enhancing the integrity of intestinal cells and facilitating the expression of nutrient transporters that are significant in the uptake of nutrients across the lining of the gastrointestinal tract. Phytase supplementation improves the P release from phytate in the diets thereby alleviating its loss.</p>

Thesis summary The process of B cell lymphogenesis in swine remains uncertain. Some reports indicate that pigs belong to a group of animal that use ileal Peyers's patches (IPP) for the generation of B cells while others point to the possibility that the bone marrow is functional throughout life. The functional subpopulations of B cells in swine are also unknown. Together with other ruminants, and also birds, γδ T cells in swine may account for >70% of all T cells which is in apparent contrast with humans and mice. The purpose of this thesis was to address these discrepancies and unresolved issues. The results disprove the existing paradigm that the IPP is primary lymphoid tissue and that B cells develop in IPP in an antigen-independent manner. On the other hand, it shows that bone marrow is fully capable of B cell lymphogenesis and remains active at least for the same period of time as it had been speculated for the IPP. This thesis also identified functionally different subsets of porcine peripheral B cells, and shows that CD21 molecules can be expressed in differential forms. Finally, this thesis identifies two lineages of γδ T cells that differ in many functional and phenotype features. This finding may explain why γδ T cells constitute of minority of lymphocytes in circulation of humans and mice.

L’allogreffe des cellules souches hématopoïétiques (CSH) dans les situations d’incompatibilité HLA partielle représente une option thérapeutique irremplaçable pour des patients nécessitant une greffe de cellules souches hématopoïétiques, en absence d’un donneur HLA-identique. Toutefois, le retard de la restauration du système immunitaire en particulier dans du compartiment lymphocytaire après greffe est l'une des complications majeures. Une nouvelle stratégie pour promouvoir la reprise de la thymopoïèse à partir des CSH provenant du donneur et d'accélérer la reconstitution cellulaire T chez des patients après greffe de CSH consiste en le transfert adoptif des progéniteurs T générés in vitro. L’identification de Notch1 comme le régulateur-clé du développement lymphocytaire T a permis l’établissement de systèmes de culture à base de ligands de Notch, qui permettent la génération efficace de progéniteurs lymphoïdes T in vitro. L'efficacité des progeniteurs T-lymphoïdes murins pour promouvoir la reconstitution des lymphocytes T a été bien démontrée dans des modèles de greffe chez la souris. De même, des progéniteurs T-lymphopoïétiques humains générés in vitro et greffés aux souris humanisées favorisent la reprise de la thymopoïèse. Pourtant, aucune donnée n’a encore démontré leur capacité à donner naissance à un compartiment lymphocytaire T périphérique. De plus, les systèmes de co-culture à base de ligand de Notch actuellement utilisés consistent en des lignées stromales murines génétiquement modifiées. Afin d'établir un système cliniquement applicable, il est donc indispensable d’établir des systèmes de culture qui soutiennent la génération de progéniteurs T en absence d’un support des cellules nourricières. Au cours de mon projet de thèse, j'ai développé un nouveau système de culture pour la génération des progéniteurs T-lymphopoïétiques humains T basé sur l’immobilisation du ligand de Notch Delta-like-4 (DL-4) sous sa forme protéique. La culture des progéniteurs hématopoïétiques CD34+ issue de sang en présence de DL-4 immobilisé permet la génération d’un grand nombre de cellules ayant un phénotype de progéniteurs thymiques précoces (early thymic progenitor: ETP) et de prothymocytes (proT). Les cellules ETP et ProT ainsi générées expriment à des niveaux élevés des gènes impliqués dans le développement lymphocytaire précoce (i.e. pTa, Rag1, IL7Ra et BCL11b). Elles montrent des signes de réarrangement du récepteur des cellules T (TCR) similaires à leurs homologues thymiques. Par des expériences de dilution limite sur une co-culture OP9/DL-1 secondaire, j’ai pu montrer que les progéniteurs générés sur DL-4 possédaient un potentiel lymphoïde T très augmenté, qui pourrait être entièrement attribué aux sous populations ETP et ProT. Suite à leur transfert dans des souris NOD/SCID/γc-/-, les progéniteurs lymphoïde T générés par exposition a DL-4 sont capable de migrer dans le thymus, d’y poursuivre des étapes ultérieures de leur développement et d’accélérer la différentiation T intra thymique ainsi que l’émergence des lymphocytes T mature, polyclonaux et fonctionnels en périphérie. Dans une approche de co-transplantation, qui se rapproche des conditions cliniques envisagées, j’ai simultanément injecté dans le même récipient des progéniteurs générées sur DL-4 et des cellules CD34+ non traitées (d’un 2èm donneur HLA-incompatible). Cette procédure a permis une reconstitution des lymphocytes T encore plus rapide et plus. Etant donné que les progéniteurs T générées sur DL-4 et les cellules CD34+ non-traitées étaient issue de deux donneurs avec un HLA différent, cette expérience a permis de montrer que les progéniteurs préalablement exposés à DL-4 reconstituaient spécifiquement les compartiments lymphoïdes T alors que les autres lignées hématopoïétiques provenaient des progéniteurs CD34+ non-traités... / Human leukocyte antigen (HLA)-mismatched haematopoietic stem cell transplantation (HSCT) represents an important therapeutic option for patients lacking suitable donors. Delayed posttransplant immune recovery constitutes one of its major complications and is most pronounced in the T cellular compartment. A novel strategy to promote de novo thymopoiesis from donor derived HSCs and to accelerate T cellular reconstitution in patients after HSCT consists in the adoptive transfer of in vitro generated T cell progenitor cells. Identification of Notch1 as the key regulator of early T-lineage development has allowed the generation of Notch ligand-based culture systems, which provide a powerful tool to generate T-lymphoid progenitors in vitro. The efficacy of murine T-lymphoid progenitors to promote T cell reconstitution has been well demonstrated in conventional mouse models. In consistency, in vitro-generated human T cell progenitors were demonstrated to promote thymic recovery in humanized mice. Yet, positive effects of in vitro generated human T cell precursors on peripheral T cell reconstitution have not been demonstrated. Moreover currently used Notch-based co-culture systems consist of genetically modified murine cell lines. With view to establishing a clinically applicable system, feeder-cell-free Notch-ligand culture systems for the generation of T-lymphopoietic progenitors are warranted. During my PhD project I developed a new culture system based on the immobilized Notch ligand Delta-like-4 (DL-4). Exposure of human CD34+ cord blood cells to immobilized DL-4 enabled the in vitro generation of high number of T cell progenitors, which harboured the phenotype of immature early thymic progenitor cells (ETP) and prothymocytes (proT). ETP and proT cell generated during DL-4 culture upregulated essential genes involved in early T-lymphoid development (i.e. IL7Rα, PTα, RAG1 and BCL11b) and had undergone stage-specific recombination of the T cell receptor (TCR) locus in a similar way as in native human thymopoiesis. In limiting dilution analysis after secondary OP9/DL-1 co-culture, DL-4 progenitors displayed a highly increased T-lymphoid potential, which could be entirely attributed to the ETP and proT subset. When transferred into NOD/SCID/γc-/- mice, DL-4 primed T cell progenitors migrated to the thymus and accelerated intrathymic T cell differentiation and emergence of functional, mature and polyclonal αβ T cells in the periphery. In a co-transplantation approach, which more closely mimics a clinical setting, DL-4 progenitors and untreated CD34+ cells from HLA-disparate donors were simultaneously injected in the same recipient. This procedure allowed even more rapid and more robust T cell reconstitution. HLA-tracking of the distinct graft sources further showed, that DL-4 progenitors specifically reconstituted the T-lymphoid compartments. This work provides further evidence for the ability of in vitro-generated human T cell progenitors to promote de novo thymopoiesis and shows for the first time, that these cells accelerate peripheral T cell reconstitution in humanized mice. The availability of the efficient feeder-cell-free DL-4 culture technique represents an important step towards the future clinical exploitation translation of in vitro generated T-lymphoid progenitor cells to improve posttransplant immune reconstitution / Die Wiederherstellung der T-lymphozytären Immunität nach T-Zell depletierter hämatopoetischer Stammzelltransplantation (HSZT) ist ein langwieriger Prozess. Eine potentielle Strategie zur Beschleunigung der Neubildung von T-Zellen aus den transplantierten Stammzellen besteht in der Gabe von T-lymphozytären Vorläuferzellen. Die Entdeckung von Notch1 als wichtigster Regulator der frühen T-Zell-Entwicklung hat zur Etablierung Notchligand-basierter Zellkulturen geführt, mit deren Hilfe T-lymphoide Vorläuferzellen aus hämatopoetischen Stammzellen in vitro gebildet werden können. Das therapeutische Potential dieses Zelltyps wurde eindrucksvoll in konventionellen, syngenen und allogenen Maustransplantationsmodellen belegt, in denen nach Injektion in vitro generierter, muriner T-Vorläuferzellen eine Verbesserung der Neubesiedlung des Thymus sowie eine beschleunigte Wiederherstellung der T-zellulären Immunität erreicht werden konnte. Notchbasierte Co-Kultursysteme wurden ebenfalls für die invitro Herstellung humaner T-lymphoider Vorläuferzellen verwendet. Das in-vivo Potential humaner T Vorläuferzellen ist bislang jedoch nur lückenhaft charakterisiert: Zwar konnte gezeigt werden, dass humane T-Vorläuferzellen den hypoplastischen Thymus von immundefizienten NOD/SCID/γc-/- Mäusen besiedeln können. Ihre Wirksamkeit, die Wiederherstellung eines funktionellen, peripheren T-Zellkompartiments zu beschleunigen, gelang bislang jedoch nicht. Darüber hinaus werden Notchliganden in derzeit verwendeten Kultursystemen von genetisch modifizierten, murinen Stromazellen präsentiert. Die Entwicklung stromazellfreier, proteinbasierter Notchligand-Kultursysteme ist daher von grosser Bedeutung für eine mögliche therapeutische Nutzung in vitro generierter T-Vorläuferzellen. Durch Immobilisierung von Notchligand Delta-like 4 (DL-4) habe ich im Rahmen meines PhD Projekts ein stromazellfreies Kultursystem zur Züchtung T-zellulärer Vorläuferzellen aus humanen CD34+ Nabelschnurblutzellen etabliert. In DL-4 Kultur generierte Zellen besitzen phänotypische und molekulare Eigenschaften von frühen thymischen Vorläuferzellen (ETP) und Prothymocyten (proT). ETP und proT Zellen aus DL-4 Kulturen exprimieren wesentliche Geneder frühen T-Zellentstehung (z.B. IL7Ra, PTa, RAG1 und BCL11b). Die entwicklungsstadiumspezifischen TCR-Rekombinationsprozesse in DL-4 Zellen erfolgen nach dem gleichen Muster wie in der nativen Thymusentstehung. Die in DL4 Kultur generierten T-Vorläuferzellen können sich in reife T-Zellen weiterentwickeln und durchlaufen die weitere T-Zelldifferenzierung innerhalb kürzerer Zeit als native CD34+ hämatopoetische Vorläuferzellen. 13 Darüber hinaus können DL-4 generierte T-Vorläuferzellen nach Xenotransplantation den hypoplastischen Thymus von immundefizienten NOD/SCID/γc-/- Mäusen besiedeln, intrathymische T-Zellentwicklung begünstigen und die Neubildung reifer und funktionaler TZellen in der Peripherie beschleunigen. Zur Simulation einer klinischen Anwendung führte ich weiterhin Co-Transplantationen mit DL-4 Vorläuferzellen und unbehandelten CD34+ Zellen in gleiche Empfänger durch und konnte hiermit eine weitere Verbesserung der Immunrekonstitution erzielen. Durch Verwendung HLA-divergenter Spender in diesen Versuchen konnte ich zeigen, dass DL-4 Zellen sich vornehmlich in T-Zellen weiterentwickelten, während die restlichen Blutzellreihen von unbehandelten CD34-poitiven Zellen gebildet wurden. Im Rahmen dieses Projekts konnte ich mit einem für die klinische Anwendung geeigneten Kulturmodell wichtige präklinische Belege für das therapeutische Potential in vitro generierter TVorläuferzellen erbringen. Diese Arbeit bildet somit eine wichtige Grundlage für eine zukünftige klinische Anwendung von T-Vorläuferzellen zur Verbesserung der T-Zell-Immunität nach HSZT

<p dir="ltr">The BRG1/BRM-associated factor (BAF) complexes, also called SWI/SNF, are multi-subunit chromatin remodelers that regulate chromatin compaction in an ATP-dependent manner. In the past decade, BAF complexes have been under the spotlight in cancer research, especially after proteomic analyses revealed the genes encoding the subunits are amongst the most frequently mutated genes in cancer. The present dissertation focuses on prostate cancer (PCa), a disease in which the role of the BAF subunits is increasingly being explored but is yet to be defined as a potential therapeutic target. According to the GLOBOCAN report, PCa is the second most frequent cancer in males worldwide. Since most of the variants of PCa rely on the androgen receptor (AR) axis, surgical or chemical castration and androgen deprivation therapy (ADT) are the main treatment strategies for PCa patients. Even though these therapeutic approaches prolong survival, reduce tumor burden, and relieve symptoms, PCa patients eventually relapse and develop castration resistant PCa (CRPC). At present, the mechanisms underlying ADT resistance are not fully understood, current efforts focus on finding new targets for PCa treatment.</p><p dir="ltr">In the projects included in this dissertation we explored the function of the PBAF complex, a BAF subtype, in a variety of models of PCa and its potential as a therapeutic target by inhibiting or depleting its different subunits. To do so we (i) developed the first inhibitors for BRD7 (a subunit unique to PBAF) and (ii) established cell-based assays in multiple PCa cell lines to study BRD7 and other PBAF unique subunits.</p><p dir="ltr">Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer. Bromodomain-containing protein 7 (BRD7) has been implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease. Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a binding pocket exclusive to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two inhibitors with increased selectivity towards BRD7, 1-78 and 2-77, which bind with submicromolar affinity to the BRD7 BD. Our binding mode analyses indicate that these ligands occupy a uniquely accessible binding cleft in BRD7 and maintain key interactions with the asparagine and tyrosine residues critical for acetylated lysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.</p><p dir="ltr">There are three BAF complexes that have been biochemically characterized up to date: canonical BAF (cBAF), polybromo-associated BAF (PBAF) and GLTSCR1/like-containing BAF (GBAF or ncBAF). All BAF complexes are characterized by containing an ATPase and accessory subunits that may be shared between them or unique to each subtype. PBAF, the BAF subtype of interest of this dissertation, contains four unique subunits: BRD7, PBRM1, ARID2 and BAF45A. We showed that knocking down BRD7 and ARID2 leads to reduction of cell viability in PCa cells with ligand-dependent and independent AR signaling, while knocking down PBRM1 leads to reduction in viability of cells with only ligand-dependent AR signaling. We also performed a chromatin immunoprecipitation assay with BAF45A and observed that it does not colocalize with AR binding sites, indicating that the mechanism by which PBAF regulates AR signaling is indirect. This observation was further supported by the fact that knocking down BRD7 prevents expression of genes related to adaptive processes, but not AR target genes, in response to androgen treatment. Further mechanistic studies will aid in understanding the function of PBAF in PCa. However, overall, our results indicate that PBAF is a promising therapeutic target in PCa models expressing AR, including CRPC systems.</p>