Macrophages belong to the mononuclear phagocyte system and they perform fundamental roles to maintain homeostasis in the organism. Macrophage development, survival, proliferation and functionality depend upon the colony stimulating factor 1 (CSF1) and interleukin-34 (IL-34), which signal through the CSF1 receptor (CSF1R). CSF1R is a type III tyrosine kinase receptor that is present in the plasma membrane of monocytes and macrophages. Mutations in Csf1r in mice produce the loss of many tissue macrophage populations and multiple developmental abnormalities. In humans, abnormal enhancement of CSF1R expression has been correlated to adverse prognosis in a subset of carcinomas; and mutations in the human CSF1R are associated with an autosomal-dominant neurodegenerative disease. CSF1R is encoded by the c-fms proto-oncogene and its expression is partially controlled by the fms-intronic regulatory element (FIRE). The FIRE sequence is highly conserved across species and contains binding motifs for multiple transcription factors, which are relevant for haematopoiesis. Previous results from murine Csf1r transgenes showed that FIRE is essential for driving Csf1r expression, and that interactions between FIRE and multiple myeloid transcription factors contribute to maximal regulatory activity. This project aimed to study the role of FIRE in its normal chromatin context, in vivo. A FIRE knockout (FIRE-/-) mouse model was generated using the CRISPR/Cas9 technology in mouse embryonic stem cells (ESCs) and in mice. In ESCs, the deletion severely compromised the differentiation of macrophages from embryoid bodies generated in vitro. In mice, the frequency of the FIRE- /- genotype in the progeny does not follow a Mendelian distribution and about 5% of the offspring developed hydrocephalus. Unlike Csf1r -/-mice, which die before weaning, most surviving FIRE-/- mice grew normally and were fertile. The impact of the mutation on macrophage populations is selective. FIRE-/- mice are not monocyte deficient (identified as F4/80+ Csf1r+ cells in peripheral blood), although these cells have reduced levels of Csf1r mRNA and do not bind porcine CSF1 Fc fusion protein. The development of peritoneal macrophages and Iba-1+ microglia was abolished, but Adgre1+ (F4/80+) macrophage populations in liver and spleen were unaffected. Csf1r was greatly reduced in bone marrow progenitors, but about 30% of these cells were able to differentiate into macrophages in vitro, upon exposure to recombinant human CSF1 (rhCSF1). This study shows that FIRE is essential for the development of a subset of tissue-resident macrophage populations. In FIRE-/- mice, potential compensation from additional regulatory elements within Csf1r might underlie the development of unaffected tissue-resident macrophages.

Η geminin είναι ένα σχετικά καινούριο μόριο το οποίο διαθέτει καίριο ρόλο κατά την ανάπτυξη και την διαφοροποίηση, εξαιτίας του νευροποιητικού δυναμικού της, της ικανότητάς της να αλληλεπιδρά με μέλη των Hox και polycomb πρωτεϊνών, καθώς επίσης και να δρα σαν ρυθμιστής του κυτταρικού κύκλου, λειτουργώντας ως αναστολέας του παράγοντα αδειοδότησης της αντιγραφής του DNA, CDT1. Στα πλαίσια της εργασίας αυτής, κλωνοποιήσαμε το γονίδιο της geminin στο ποντίκι το οποίο αποτελείται από 7 εξώνια και καλύπτει μία περιοχή γύρω στα 10Kb. Σχεδιάσαμε και κλωνοποιήσαμε ένα πλασμιδιακό όχημα στόχευσης για το γονίδιο της mgeminin και εισήγαμε 3 θέσεις loxP στο γενωμικό locus αυτής, με σκοπό να δημιουργήσουμε υπό συνθήκη ελλειμματικούς ποντικούς για το γονίδιό της. Χρησιμοποιώντας το συγκεκριμένο φορέα στόχευσης αδρανοποιήσαμε το γονίδιο της Geminin σε pc3 (protamine Cre 3) πολυδύναμα κύτταρα ποντικού, δημιουργώντας ετερόζυγους ES κλώνους που φέρουν το «floxed» αλληλόμορφο, καθώς επίσης και το αλληλόμορφο αγρίου τύπου. Το μεταλλαγμένο αλληλόμορφο ελέγχθηκε τόσο με PCR όσο και με ανάλυση κατά Southern για την ορθότητα του ομόλογου ανασυνδυασμού. Ταυτοποιήσαμε 15 ορθά ανασυνδυασμένους ES κλώνους, οι οποίοι μπορούν να χρησιμοποιηθούν για τη δημιουργία υπό συνθήκη knockout ποντικών για το γονίδιο της geminin, μετά από έγχυση σε B6 βλαστοκύστεις και επακόλουθη μεταφορά αυτών σε θετές μητέρες. / Geminin is a novel bifunctional molecule with a pivotal role in the processes of differentiation and cell cycle regulation, due to its neuralizing potential, its ability to interact through Hox and polycomb group members, as well as in the inhibition of cell cycle progression through protein-protein interactions with the licensing factor Cdt1. We have cloned the mouse Geminin gene, which consists of 7 exons and spans approximately a region of 10Kb. We have generated a vector and introduced 3 loxP sites in the Geminin locus, in order to create conditional knockout mice. Using this knockout construct we inactivated the geminin locus in pc3 mouse embryonic stem cells, creating heterozygous ES clones, carrying a “floxed” and a “WT” allele for geminin. The mutant allele in the targeted ES cells has been verified with Southern blotting and PCR for the correct homologous recombination events. We identified 15 correctly targeted ES clones, which can be used for the generation of conditional geminin knockout mice, upon injection into B6 blastocysts and subsequent transfer to foster mothers.

Telomeres are fundamental structures found at the end of all eukaryotic chromosomes that function to protect the end of chromosomes from end-to-end fusion, erosion and subsequent telomere dysfunction. Telomerase and alternative lengthening of telomere (ALT) mechanisms maintain the telomeres by compensating natural telomeric loss. ALT is found to be present in 15% of human tumours lines and it may be expressed at low levels in the normal mouse tissues. However, the exact mechanism behind ALT depression and/or activation in the mammalian cells is not fully understood. Previous studies have highlighted the role of BRCA1 in telomere dysfunction. Also, it has recently been shown that BRCA1 co-localises at telomeres in the ALT + human cells through BLM and Rad50. However, it is still unclear whether BRCA1 plays a direct role on telomere length maintenance and integrity. The aim of this project was to examine the role of BRCA1 in telomere maintenance associate with ALT in BRCA1 defective mammalian cells. Therefore to achieve this, we have set up series of experiments to look at, (a) hallmarks of ALT activity at the cytological level, (b) measuring of ALT activity using biochemical and immunocytochemistry techniques and (c) understanding the role of BRCA1 in DNA damage response mechanism and telomere dysfunction. Firstly, we found elevated levels of recombination at telomeres in the two human BRCA1 carrier cell lines and mouse embryonic stem cell with deficiency in Brca1-/-. Secondly, our data showed that human and mouse BRCA1 defective cells are significantly more sensitive to ionizing radiation in line with the DNA repair function of BRCA1. Moreover, we found persistent DNA damage at telomeres in the BRCA1 defective environment when after exposure of cells to ionizing radiation. Thirdly, we found evidence of ALT activity in some mouse cell lines, and elevated ALT in mouse cells defective in Brca1. Finally, we examined some other ALT markers using immunofluorescence. Our data indicate differences between human and mouse cells in regulating ALT. Taken together data presented in this thesis revealed that (i) BRCA1 plays a major role in telomere maintenance and defective BRCA1 mammalian cells show evidence of telomere dysfunction and telomere length shortening in line with previous publish data, (ii) BRCA1 defective mouse cells have elevated levels of ALT, (iii) the mouse lymphoblastoid LY-S cells have complete absence of ALT.

Le contrôle de l'expression des programmes géniques orchestrant le développement précoce et l'homéostasie des cellules souches fait l'objet de recherches intenses. En effet, les cellules souches embryonnaires (CSE) sont caractérisées par des propriétés comme leur clonogénicité (la capacité à proliférer dans le même état indifférencié) et leur pluripotence (la capacité à se différencier et à former les tissus embryonnaires et adultes). Au niveau moléculaire, l'identité des CSE est orchestrée par le contrôle de l'expression génique aux niveaux épigénétique, transcriptionnel, post- transcriptionnel et traductionnel en réponse à l'activation de voies de signalisation spécifiques. Dans ce contexte, des données récentes suggèrent un rôle de la machinerie traductionnelle les ribosomes et de la régulation de leur biogenèse, dans le maintien de l'homéostasie de cellules souches de différentes espèces. À partir de l'analyse de données transcriptomiques à haut débit (RNAseq), mon équipe d'accueil a ainsi identifié un ensemble de protéines associées aux ribosomes (PaR) significativement enrichies dans les cellules souches embryonnaires murines (CSEm) en comparaison à des lignées cellulaires murines différenciées et à des tissus. Parmi ces candidats, mes travaux de thèse ont consisté à la caractérisation d'une PaR particulièrement enrichie : Rsl24d1. Rsl24d1 est une protéine de biogenèse des ribosomes décrites exclusivement chez la levure. Son profil d'expression dans différentes lignées de CSEm suggère une fonction spécifique: enrichissement au niveau transcriptionnel et protéique dans les CSE à l'état de pluripotence naïf et diminution importante au cours de la différenciation. En effet, des approches de perte d'expression de Rsl24d1 m'ont permis d'établir l'importance de cette PaR dans l'homéostasie des CSEm. Rsl24d1 contribue au maintien de la prolifération cellulaire des CSE, de leur clonogénicité et plus modérément à leur pluripotence. Rsl24d1 semble être une protéine majoritairement nucléaire mais également associée aux sous- unités 60S libres des ribosomes cytoplasmiques. D'autre part, la perte d'expression de Rsl24d1 affecte spécifiquement la biogenèse des particules ribosomiques 60S. Ainsi, comme chez la levure, dans les CSEm, Rsl24d1 est un facteur navette orchestrant la maturation des particules ribosomiques pré-60S. Par ailleurs, Rsl24d1 semble permettre le maintien d'un taux de synthèse protéique élevé permettant notamment le renouvellement des protéines ayant une demi-vie courte parmi lesquels on recense des facteurs de transcription de la pluripotence comme Oct4 (Oct3/4), Nanog et Esrrb. Mes travaux de thèse ont donc permis d'identifier et de caractériser un facteur de biogenèse de la sous-unité 60S, Rsl24d1, impliqué dans l'homéostasie des CSEm / Embryonic stem cells (ESC) possess clonogenic and pluripotency abilities i.e. they are able to self-renew indefinitely in the same developpemental state and to differentiate in all the cell types composing embryonic and adult tissues. ESC homeostasis is coordinated by complex networks which are regulated at different levels of gene expression regulation, including epigenetic, transcriptional and post-transcriptional levels. Furthermore, emerging evidences point out that the translational machinery, ribosomes, are directly implicated in the control of adult and embryonic stem cell homeostasis in different model organisms. Along this line, we have identified Rsl24d1, a ribosomal associated protein (RaP), which is strongly expressed in naïve murine ESCs compared to their differentiated progenies. We demonstrated that Rsl24d1 actively contributes to ESC homeostasis and its expression is essential for ESC proliferation and clonogenic capacities. Finally, we have also demonstrated that Rsl24d1, like Rlp24 its yeast ortholog, is associated to pre-ribosomes in ESCs from the nucleus to the cytoplasm and is required for the biogenesis of the large ribosomal subunit

L’acétylation des histones est associée à une activation transcriptionnelle. Cette acétylation est mise en place par des histone acétyltransférases (HATs) qui sont le plus souvent les sous-unités catalytiques de complexes multiprotéiques. Mon travail concerne plus particulièrement deux complexes contenant l’acétyltransférase Mof, MSL et NSL, ainsi que le complexe HAT Tip60-p400 dans les cellules souches embryonnaires de souris (mESCs). Nos analyses de localistaion sur l’ensemble du génome par ChIP-seq indiquent que MSL, NSL et Tip60-p400 se lient aux gènes activement transcrits et agissent comme des co-activateurs transcriptionnels majeurs dans les mESCs. MSL, NSL et Tip60-p400 ont des rôles à la fois chevauchants mais aussi distincts dans la régulation transcriptionnelle dans les mESCs. Chaque complexe présent un profil distinct de liaison à la chromatine. NSL lie principalement des gènes de ménage. MSL et Tip60-p400 sont également présent les gènes impliqués dans le développement. MSL est directement impliqué dans l’augmentation de l’expression de ces gènes au cours de la différenciation des mESCs. / Histone acetylation is involved in transcriptional activation of genes and is carried out by histone acetyltransferases (HATs), which are part of molecular protein complexes. This study focuses on the genome-wide role of Mof-containing MSL and NSL complexes and the Tip60-p400 complex in mouse embryonic stem cells (mESCs). I have analysed these complexes by ChIP-seq, shRNA knockdown and biochemical approaches. The genome-wide binding studies show that NSL, MSL and Tip60-p400 have a global overlap at promoters, but also bind to specific gene sets. There distinct binding profiles propose distinct roles in transcriptional regulation. MSL is the main H4K16 acetylase in mESCs.NSL binds mainly to housekeeping genes, whereas MSL and Tip60 are also present at developmental genes. Importantly, these developmental genes are directly regulated by MSL during cellular differentiation.

Indiana University-Purdue University Indianapolis (IUPUI) / Embryonic stem cells (ESCs) are unique in that they have potential to give rise to every cell type of the body. Little is known about stimuli that promote mouse (m)ESC differentiation and proliferation. Therefore the purpose of this study was to determine the role of Toll Like Receptor (TLR) ligands in mESCs proliferation, survival, and differentiation in the presence of Leukemia Inhibitory Factor (LIF). We hypothesized that TLRs are expressed and functional, and when activated by their ligand will induce survival, proliferation, and prevent differentiation. In this study, mESC line E14 was used to determine the expression of TLRs at the mRNA level and three mESC lines, R1, CGR8, and E14, were used to determine cell surface protein levels. We found expression of TLRs 1, 2, 3, 5, and 6 at the mRNA level, but no expression of TLRs 4, 7, 8, and 9 in the E14 mESC line. We confirmed the presence of TLR-2 but not of TLR-4, protein on the cell surface using flow cytometric analysis for all three cell lines. We focused our studies mainly on TLR-2 using the E14 cell line. Pam3Cys, is a synthetic triacyl lipoprotein and a TLR-2 ligand, which induced a significant increase in mESC proliferation on Days 3, 4, and 5 and enhanced survival of mESC in a dose dependent manner in the context of delayed addition of serum. All the latter experiments were performed in triplicate and student T-test was performed to establish significant differences. Next, we demonstrated functionality of TLR-2 via the MyD88/IKK pathway, where MyD88 was expressed and IKKα/β phosphorylation was enhanced. This was associated with increased NF-κB nuclear translocation upon activation by Pam3Cys. Finally, we showed that there were no changes in expression of mESCs markers Oct-4, KLF-4, Sox-2, and SSEA-1, thus illustrating that the mESCs may have remained in a pluripotent state after activation with the TLR-2 ligand in the presence of LIF. These results demonstrate that mESCs can respond to microbial products, such as Pam3Cys, and can induce proliferation and survival of the mESCs. This finding expands the role of TLRs and has some implications in understanding embryonic stem cell biology.

Embryonic stem (ES) cells offer a valuable source for generating insulin-producing cells. However, current differentiation protocols often result in heterogeneous cell populations of various developmental stages. Here we show the activin A-induced differentiation of mouse ES cells carrying a homologous dsRed-IRES-puromycin knock-in within the Sox17 locus into the endoderm lineage. Sox17-expressing cells were selected by fluorescence-assisted cell sorting (FACS) and characterized at the transcript and protein level. Treatment of ES cells with high concentrations of activin A for 10 days resulted in up to 19% Sox17-positive cells selected by FACS. Isolated Sox17-positive cells were characterized by defini- tive endoderm-specific Sox17/Cxcr4/Foxa2 transcripts, but lacked pluripotency-associated Oct4 mRNA and protein. The Sox17-expressing cells showed downregulation of extraembryonic endoderm (Sox7, Afp, Sdf1)-, mesoderm (Foxf1, Meox1)- and ectoderm (Pax6, NeuroD6)-specific transcripts. The presence of Hnf4α, Hes1 and Pdx1 mRNA demonstrated the expression of primitive gut/foregut cell-specific markers. Ngn3, Nkx6.1 and Nkx2.2 transcripts in Sox17-positive cells were determined as properties of pancreatic endocrine progenitors. Immunocytochemistry of activin A-induced Sox17-positive embryoid bodies revealed coexpression of Cxcr4 and Foxa2. Moreover, the histochemical demonstration of E-cadherin-, Cxcr4-, Sox9-, Hnf1β- and Ngn3-positive epithelial-like structures underlined the potential of Sox17-positive cells to further differentiate into the pancreatic lineage. By reducing the heterogeneity of the ES cell progeny, Sox17-expressing cells are a suitable model to evaluate the effects of growth and differentiation factors and of culture conditions to delineate the differentiation process for the generation of pancreatic cells in vitro. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Die dreidimensionale Organisation des Chromatins verändert sich während der Zelldifferenzierung als Reaktion auf die Umgebung und ist bei Krankheiten oftmals verändert. Das Zusammenspiel zwischen Chromatinzustand, Chromatinorganisation und Genexpression ist insbesondere bei Neuronen nach wie vor nur geringfügig erforscht. In dieser Arbeit untersuchte ich die Organisation und den Zustand des Chromatins im Zusammenhang mit der Transkription in embryonalen Stammzellen (ESCs) und dopaminergen Neuronen (DNs) der Maus. Dazu habe ich die Organisation des Chromatins mittels Genome Architecture Mapping (GAM) bestimmt und zelltypspezifische Genexpressionsprofile zur Klassifizierungen von Promotoren, Enhancern und Super-Enhancern (SEs) erzeugt. Anschließend habe ich diese linearen Chromatinprofile mit den verschiedenen Stufen der Chromatinorganisation kombiniert und konnte so Unterschiede zwischen den 3D-Genomstrukturen von ESCs und DNs aufzeigen. Zudem konnte ich verstärkt Dreifach-Wechselwirkungen zwischen zelltypspezifischen SEs und/oder exprimierten Genen nachweisen, die bei DNs besonders oft neuronale Signalgene darstellen und oftmals bei neurologischen Störungen betroffen sind. Ich fand auch heraus, dass die Grenzen topologisch assoziierter Domänen (TADs) oft mit Genen zur zellulären Differenzierung zusammen fallen und zudem zelltyp-spezifische Eigenschaften aufweisen, was von Bedeutung für zukünftige funktionelle Untersuchungen solcher Grenzen sein dürfte. Schließlich konnte ich zeigen, dass Chromatinkompartimente zwischen ESCs und DNs in Abhängigkeit vom Chromatinzustands und der Chromatinexpression variieren und dass eine Gruppe transkriptionell aktiver DN Gene, die für die neuronale Aktivität wichtig sind, in B-Kompartimenten liegt. Mit diesen neuen Erkenntnissen erweitert meine Arbeit das Verständnis der Chromatinorganisation bei der Regulierung der Genexpression in Maus ESCs und DNs. / The three-dimensional organization of chromatin changes during cell differentiation, in response to the environment, and is often altered in disease. The interplay between chromatin state, chromatin organization and gene expression remains poorly understood, particularly in neurons. In this work, I examined the organization and state of chromatin associated with transcription in mouse embryonic stem cells (ESCs) and dopaminergic neurons (DNs). To do this, I determined the organization of chromatin using genome architecture mapping (GAM) and generated cell type-specific gene expression profiles to classify promoters, enhancers and super-enhancers (SEs). I then combined these linear chromatin profiles with the different levels of chromatin organization and was able to show differences between the 3D genome structures of ESCs and DNs. In addition, I was able to demonstrate increased triple interactions between cell type-specific SEs and/or expressed genes, which are often neuronal signalling genes in DNs and affected in neurological disorders. I also found that the boundaries of topologically associated domains (TADs) often coincide with cellular differentiation genes and also exhibit cell type-specific properties, which may be important for future functional studies of such boundaries. Finally, I was able to show that chromatin compartments between ESCs and DNs vary depending on chromatin state and chromatin expression, and that a group of transcriptionally active DN genes important for neuronal activity are located in B compartments. With these new findings, my work expands the understanding of chromatin organization in regulating gene expression in mouse ESCs and DNs.

No description available.

Tot i que es coneix l’involucrament de les cèl·lules pancreàtiques acinars en patologies exocrines (pancreatitis i càncer de pàncrees), la manca de models normals basats en cèl·lules ha limitat l’estudi de les alteracions que succeeixen en el programa de diferenciació pancreàtica. Hem demostrat prèviament que les cèl·lules mare embrionàries murines, que són pluripotents, poden adquirir un fenotip acinar in vitro. Això es va aconseguir, en part, amb una combinació de senyals que provenien del cultiu de pàncrees fetals que no era, però, específic del llinatge pancreàtic. L’objectiu d’aquest treball ha estat el de desenvolupar un protocol selectiu pel llinatge acinar basat en l’activació seqüencial de vies de senyalització que recapitulin el desenvolupament pancreàtic in vivo, a través de la formació definitiva de l’endoderm, l’especificació pancreàtica i acinar i l’expansió/diferenciació de progenitors acinars. El tractament de cossos embrionaris amb Activina A va promoure l’expressió de gens d’endoderm com està prèviament descrit. El tractament subsegüent amb àcid Retinoic, FGF10 i Ciclopamina, un inhibidor de la via de Hedgehog, va resutar en la inducció dels marcadors de progenitors pancreàtics Pdx1, Ptf1a i Cpa1 però també d’aquells expressats en el llinatge pancreàtic, que van ser reduïts amb la inhibició de BMPs. Les cèl·lules van ser a continuació cultivades en Matrigel utilitzant un sistema de cultiu en 3D en presència de fol·listatina, dexametasona i KGF comportant una inducció significativa dels nivells de mRNA i proteïna de marcadors acinars i una disminució de l’expressió dels de marcadors acinars. A més, es va veure que Amyl es secretava en el medi. Aquestes dades indiquen que l’activació selectiva del programa de diferenciació acinar en cèl·lules mare embrionàries es pot dur a terme mitjançant una inducció esgraonada de vies de senyalització involucrades en el desenvolupament pancreàtic exocrí proporcionant una eina potencial per estudiar la diferenciació pancreàtica i malalties relacionades amb el pàncrees. / Despite known involvement of pancreatic acinar cells in exocrine pathologies (pancreatitis and pancreatic cancer), the lack of normal cell-based models has limited the study of the alterations that occur in the acinar differentiation program. We have previously shown that mESC (murine embryonic stem cells), which are pluripotent, can acquire an acinar phenotype in vitro. This was achieved, in part, by a combination of signals provided by the culture of foetal pancreases which was, however, no specific for the acinar lineage. The aim of this work was to develop a protocol selective for the acinar lineage based on the sequential activation of signaling pathways that recapitulate pancreatic development in vivo, through the definitive endoderm formation, the pancreatic and acinar specification and the expansion/differentiation of acinar progenitors. Treatment of embryoid bodies with Activin A enhanced the expression of endodermal genes as previously described. Subsequent treatment with Retinoic acid, FGF10 and Cyclopamine, an inhibitor of the Hedgehog pathway, resulted in the enhancement of pancreatic progenitor markers Pdx1, Ptf1a and Cpa1 but also of those expressed in the hepatic lineage, which were reduced by BMPs inhibition. Cells were further cultured in Matrigel using a 3D culture system in the presence of follistatin, dexamethasone, and KGF leading to a significant enhancement of the mRNA and protein levels of acinar markers while decreasing the expression of endocrine ones. Moreover, active Amyl was released into the medium. These data indicate that the selective activation of the acinar differentiation program in ES cells can be achieved by stepwise induction of signaling pathways involved in pancreatic exocrine development providing a potential tool for studying pancreatic differentiation and pancreas-related diseases.