Morphogens of the Wnt and Hedgehog families are secreted signaling molecules that coordinate growth and patterning of many different tissues. Both, Wingless and Hedgehog spread across long distances in developing wing of Drosophila melanogaster. However, both proteins are covalently modified with lipid moieties. The mechanisms that allow long-range movement of such hydrophobic molecules are unclear. Like Wingles and Hedgehog, glycosylphosphatidylinositol (gpi)-linked proteins also transfer between cells with their lipid anchor intact. It has been speculated that gpi-linked proteins and lipid-linked morphogens travel together on a membranous particle, which was termed an argosome. As yet however, no functional link between argosome production and dispersal of lipid-linked proteins has been established. The topic of this thesis is to understand the cell biological nature of the argosome and thus contribute to understanding of morphogen gradient formation. To address the question of argosome biosynthesis, at least two models have been proposed. One possibility is that argosomes are membranous exovesicles with a complete membrane bilayer. Alternatively, argosomes might resemble lipoprotein particles that comprise on of a family of apolipoproteins scaffolded around a phospholipid monolayer that surrounds a core of esterified cholesterol and triglyceride. Lipid-modified proteins of the exoplasmic face of the membrane (like GFPgpi, Wingless or Hedgehog) might fit well into the outer phospholipid monolayer of such a particle. Here, I utilize biochemical fractionation to determine the sort of particle that lipid-linked proteins associate with. I show that Wingless, Hedgehog and gpi-linked proteins bind Drosophila lipoprotein particles in vitro, and colocalize with them in wing imaginal discs. Next, I use genetic means to address the functional importance of this association. I demonstrate that reducing Lipophorin levels in Drosophila larvae perturbs long-range but not shor-range Wingless and Hedgehog signaling, and increases the sequestration of Hedgehog by Patched. I propose that Lipophorin particles are vehicles for the long-range movement of lipid-linked morphogens and gpi-linked proteins.

Morphogens of the Wnt and Hedgehog families are secreted signaling molecules that coordinate growth and patterning of many different tissues. Both, Wingless and Hedgehog spread across long distances in developing wing of Drosophila melanogaster. However, both proteins are covalently modified with lipid moieties. The mechanisms that allow long-range movement of such hydrophobic molecules are unclear. Like Wingles and Hedgehog, glycosylphosphatidylinositol (gpi)-linked proteins also transfer between cells with their lipid anchor intact. It has been speculated that gpi-linked proteins and lipid-linked morphogens travel together on a membranous particle, which was termed an argosome. As yet however, no functional link between argosome production and dispersal of lipid-linked proteins has been established. The topic of this thesis is to understand the cell biological nature of the argosome and thus contribute to understanding of morphogen gradient formation. To address the question of argosome biosynthesis, at least two models have been proposed. One possibility is that argosomes are membranous exovesicles with a complete membrane bilayer. Alternatively, argosomes might resemble lipoprotein particles that comprise on of a family of apolipoproteins scaffolded around a phospholipid monolayer that surrounds a core of esterified cholesterol and triglyceride. Lipid-modified proteins of the exoplasmic face of the membrane (like GFPgpi, Wingless or Hedgehog) might fit well into the outer phospholipid monolayer of such a particle. Here, I utilize biochemical fractionation to determine the sort of particle that lipid-linked proteins associate with. I show that Wingless, Hedgehog and gpi-linked proteins bind Drosophila lipoprotein particles in vitro, and colocalize with them in wing imaginal discs. Next, I use genetic means to address the functional importance of this association. I demonstrate that reducing Lipophorin levels in Drosophila larvae perturbs long-range but not shor-range Wingless and Hedgehog signaling, and increases the sequestration of Hedgehog by Patched. I propose that Lipophorin particles are vehicles for the long-range movement of lipid-linked morphogens and gpi-linked proteins.

Despite tremendous advances in mass spectrometry instrumentation and mass spectrometry-based methodologies, global protein profiling of organellar, cellular, tissue and body fluid proteomes in different organisms remains a challenging task due to the complexity of the samples and the wide dynamic range of protein concentrations. In addition, large amounts of produced data make result exploitation difficult. To overcome these issues, further advances in sample preparation, mass spectrometry instrumentation as well as data processing and data analysis are required. The presented study focuses as first on the improvement of the proteolytic digestion of proteins in in-gel based proteomic approach (Gel-LCMS). To this end commonly used bovine trypsin (BT) was modified with oligosaccharides in order to overcome its main disadvantages, such as weak thermostability and fast autolysis at basic pH. Glycosylated trypsin derivates maintained their cleavage specifity and showed better thermostability, autolysis resistance and less autolytic background than unmodified BT. In line with the “accelerated digestion protocol” (ADP) previously established in our laboratory modified enzymes were tested in in-gel digestion of proteins. Kinetics of in-gel digestion was studied by MALDI TOF mass spectrometry using 18O-labeled peptides as internal standards as well as by label-free quantification approach, which utilizes intensities of peptide ions detected by nanoLC-MS/MS. In the performed kinetic study the effect of temperature, enzyme concentration and digestion time on the yield of digestion products was characterized. The obtained results showed that in-gel digestion of proteins by glycosylated trypsin conjugates was less efficient compared to the conventional digestion (CD) and achieved maximal 50 to 70% of CD yield, suggesting that the attached sugar molecules limit free diffusion of the modified trypsins into the polyacrylamide gel pores. Nevertheless, these thermostable and autolysis resistant enzymes can be regarded as promising candidates for gel-free shotgun approach. To address the reliability issue of proteomic data I further focused on protein identifications with borderline statistical confidence produced by database searching. These hits are typically produced by matching a few marginal quality MS/MS spectra to database peptide sequences and represent a significant bottleneck in proteomics. A method was developed for rapid validation of borderline hits, which takes advantage of the independent interpretation of the acquired tandem mass spectra by de novo sequencing software PepNovo followed by mass-spectrometry driven BLAST (MS BLAST) sequence similarity searching that utilize all partially accurate, degenerate and redundant proposed peptide sequences. It was demonstrated that a combination of MASCOT software, de novo sequencing software PepNovo and MS BLAST, bundled by a simple scripted interface, enabled rapid and efficient validation of a large number of borderline hits, produced by matching of one or two MS/MS spectra with marginal statistical significance.

Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designerrecombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designerrecombinases. We gather the sequence information of over one million Crelike recombinase sequences evolved for 89 different target sites with whichwe train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases.

Das Multiple Myelom (MM) ist eine hämatologische Erkrankung, welche sich durch eine Akkumulation von malignen Plasmazellen im Knochenmark auszeichnet und eine gestörte Hämatopoiese und Osteolyse zur Folge hat. Komplexe molekulare Interaktionen zwischen MM-Zellen und der Mikroumgebung/Nische im Knochenmark (bone marrow microenvironment, BMM) führen zu einer Aktivierung von verschiedenen Wachstums-, Überlebens- und anti-apoptotischen Signalwegen, die zur Entstehung bzw. Wirkstoffresistenz von MM-Zellen beitragen. IL-6R/STAT3, Ras/MAPK und PI3K/Akt sind die drei wichtigsten Signalwege, die mit dem Wachstum und der Entwicklung des MM assoziiert sind. Auf der anderen Seite sind Myelomzellen insensitiv gegenüber einer Blockade des IL6R/STAT3-Signalweges bzw. des Ras/MAPK-Signalwegs in der Gegenwart von Knochenmarksstromazellen (bone marrow stroma cells, BMSCs), was die Entbehrlichkeit dieser beiden Signalwege unter Ko-Kultur-Bedingungen nahelegt. Interessanterweise aber induziert die gleichzeitige Unterbrechung der IL6R/STAT3 und Ras/MAPK Signalwege Apoptose in MM-Zellen. Ziel der Arbeit war die Identifizierung und Analyse von Zielgenen, die von beiden Signalwegen und nicht durch einen Signalweg alleine reguliert werden. Genexpressionsanalysen zeigten eine deutliche Herunterregulierung der Proteine Hsp90alpha und Hsp90beta nach einer gleichzeitigen Inhibition der IL6R/STAT3 und Ras/MAPK Signalwege. In Hinblick auf die zentrale Rolle von Hsp90 in der Tumorbiologie fokussiert sich die vorliegende Arbeit auf die Erforschung der Rolle von Hsp90 im Multiplen Myelom. Die siRNA-vermittelte Herunterregulation der Proteinexpression von Hsp90-Proteinen zeigte, daß das Ausschalten von HsP90alpha alleine nur zu einer moderaten Apoptoseinduktion in INA-6- und MM.1s-Zellen führte. Die gleichzeitige Herunterregulation von HsP90beta hingegen führte zu einer Verstärkung dieses Effektes und deutet darauf hin, daß beide Proteine miteinander kooperieren. Die pharmakologische Inhibition der Hsp90-Funktion mittels eines neuen Hsp90-Inhibitors (17-DMAG) führte zu einer Verringerung von phospho-ERK1/2, zur Degradation von STAT3 und zu einem verminderten Überleben von MM-Zellen. Die pro-apoptotischen Effekte der gestörten Hsp90-Funktion konnten weder durch BMSCs und Osteoklasten noch durch ECs (??) abgeschwächt werden, obwohl für ECs beschrieben wurde, daß sie zum Wachstum und Überleben von MM-Zellen beitragen können. Diese Beobachtungen deuten auf einen positiven Rückkopplungskreislauf zwischen HsP90alpha/beta und den wichtigsten Signalwegen hin, welcher das Überleben von MM-Zellen gewährleistet. Desweiteren zeigten immunhistologische Analysen, daß Hsp90-Proteine im Vergleich zu MGUS (??) bzw. normalen Plasmazellen in MM-Plasmazellen hochreguliert sind. Zusammengefasst zeigen die Ergebnisse der vorliegenden Arbeit die essentielle Rolle von Hsp90-Proteinen für die Überlebensfähigkeit von MM-Zellen. Ein neuer Mechanismus der Hsp90-Regulation durch das Zusammenwirken der Signalwege IL6R/STAT3 und Ras/MAPK in MM-Zellen konnte gezeigt werden. Darüber hinaus deuten die Ergebnisse darauf hin, daß ein positiver Rückkopplungskreislauf zwischen Hsp90-Proteinen und den wichtigsten Signalwegen existiert, welcher zum Wachstum und zur Entwicklung von MM-Zellen beiträgt. Die Inhibition der Hsp90-Funktion durch den pharmakologischen Inhibitor 17-DMAG führte zum Absterben von MM-Zellen und der pro-apoptotische Effekt der Hsp90-Depletion konnte nicht durch unterstützende BMM-Zellen aufgehoben werden. Diese Beobachtungen untermauern die multifunktionelle Rolle von Hsp90 in der MM-Biologie und zeigen die Wichtigkeit der Entwicklung neuer therapeutischer Wirkstoffe zur Inhibition der Hsp90-Funktion bei der Behandlung des MM. / Multiple myeloma (MM) is a haematological malignancy characterised by the accumulation of malignant plasma cells in the bone marrow leading to impaired haematopoiesis and osteolytic bone destruction. Intricate molecular interactions between MM cells and the BMM activate a diverse set of growth, survival and anti-apoptotic signaling cascades that mediate tumor progression and drug resistance. IL-6R/STAT3, Ras/MAPK and PI3K/Akt are the three major signal transduction pathways that are associated with MM growth and progression. However, myeloma cells have shown independence from IL-6R/STAT3 blockade or insensitivity towards Ras/MAPK pathway inhibition in the presence of BMSCs, indicating the dispensability of both in co-culture conditions. Interestingly, concomitant disruption of both IL-6R/STAT3 and Ras/MAPK pathways was successful to drive MM cells into significant apoptosis. This study aimed to identify and analyse the downstream target genes that are regulated by both pathways and not by either pathway alone. Gene expression profiling revealed prominent downregulation of Hsp90alpha and Hsp90beta proteins after combined inhibition of the IL-6R/STAT3 and Ras/MAPK pathways. Owing to the important role played by Hsp90 in cancer biology, this study was narrowed down to investigate the role of Hsp90 in MM. Specific siRNA-mediated knockdown of Hsp90 proteins showed that although knockdown of Hsp90beta was sufficient to induce moderate apoptosis in INA-6 and MM.1s cells, the effect was more pronounced when both Hsp90 proteins were targeted, indicating co-operation between them. Pharmacological inhibition of Hsp90 function by using a novel Hsp90 inhibitor (17-DMAG) down-regulated the levels of pERK1/2 and led to degradation of STAT3 and decreased viability of MM cells. The pro-apoptotic effects of compromised Hsp90 function could not be alleviated by either BMSCs, OCs or ECs, which are well-known to support myeloma growth and survival. These observations point to the existence of a positive feedback loop consisting of Hsp90alpha/beta and major signaling pathways supporting MM cell survival. Furthermore, immunohistochemical analysis unveiled the up-regulated status of Hsp90 proteins in MM PCs as compared to MGUS or normal PCs. Taken together, the results of this study explain the critical contribution of Hsp90 proteins to MM cell survival. A novel mechanism of Hsp90 regulation by co-operation between the IL-6R/STAT3 and Ras/MAPK pathways was discovered in myeloma cells. There is also strong evidence of the existence of a positive feedback loop between Hsp90alpha/beta proteins and major signaling pathways supporting MM growth and progression. Inhibition of Hsp90 function by using the Hsp90 inhibitory drug 17-DMAG proved to be lethal for myeloma cells and the pro-apoptotic effects of Hsp90 blockade could not be reversed by the presence of cells from the supportive BMM. These observations highlight a multi-functional role of Hsp90 in MM biology and strongly strengthen the notion that therapeutic strategies targeting Hsp90 may open new perspectives for anti-myeloma drug development.

Das Verständnis der Mechanismen, nach denen biologische Systeme ablaufen, ist ein wichtiger Fokus der aktuellen Strukturbiologie. Kernmagnetische Resonanzspektroskopie (NMR) ist eine geeignete Technik, um solche Ziele anzustreben sowie Struktur und Dynamik von Biomolekülen zu erforschen, um komplementäre Informationen zum Verständnis von Proteinfunktionalität zu erhalten. Rasante Fortschritte sind vor nicht langer Zeit auf dem Gebiet biologischer Festkörper-NMR (ssNMR) erzielt worden, was zu vollständiger Strukturaufklärung zahlreicher Peptide und kleiner Proteine, der Beschreibung von Protein-Komplexbildung sowie der der dynamischen Eigenschaften kleiner Proteine geführt hat. Festkörper-NMR ist die Methode der Wahl bei struktureller und dynamischer Charakterisierung von Membranproteinen und aggregierten amyloidogenen Systemen, die schwer löslich und kaum mit Lösungs-NMR oder Röntgenkristallographie zugänglich sind. Moderne Festkörper-NMR ist noch immer limitiert, was Auflösung und Empfindlichkeit betrifft, und macht weitere Entwicklungen auf den Gebieten der Probenpräparation und des Pulssequenz-Designs erforderlich. In meiner Arbeit untersuche ich die potenzielle Verwendung von Deuterierung in der Protein Festkörper-NMR zur Erhöhung von Empfindlichkeit und Auflösung in 15N-1H Korrelationsexperimenten. Der erzielte Fortschritt auf diesen Gebieten erlaubt die Verfolgung von Proteinrückgratbewegungen mit hoher Genauigkeit, die vorher nicht verfügbar war. Wir zeigen zum ersten Mal, dass TROSY Experimente für Festkörper-NMR gewinnbringend sind. Außerdem wurde eine Pulssequenz für 13C-13C J Kopplung zur Erhöhung der Auflösung in der Kohlenstoff-Dimension entwickelt. / Understanding the mechanisms how biological systems work is an important objective of current structural biology. Nuclear magnetic resonance (NMR) spectroscopy is a well suited technique to approach these goals and to study structure and dynamics of biomolecules in order to obtain complimentary information for understanding functionality of proteins. Recently, rapid progress has been made in the field of biological solid state NMR (ssNMR), which resulted in complete structure elucidation of several peptides and small proteins, the characterization of protein complex formation and the characterization of dynamic properties of small proteins. Solid state NMR is the method of choice for structural and dynamic characterization of membrane proteins and aggregated amyloidogenic systems, which are poorly soluble and can not be easily studied by solution state NMR and X-ray spectroscopy. Modern solid state NMR is still limited in resolution and sensitivity, and requires developments in sample preparation and pulse sequence design. In my thesis, I study the potential use of deuteration in protein solid state NMR for sensitivity, as well as for resolution enhancement in 15N-1H correlation experiments. Achieved progress in these fields allows to monitor backbone motion with high accuracy, which has not been available before. We show for the first time that TROSY type experiments can be beneficial for solid state NMR. In addition, a pulse sequence for 13C-13C J decoupling was developed to increase resolution in the carbon dimension.

No description available.

Hintergrund: Endothelzellen spielen sowohl in Homöostase als auch in Stresssituationen eine wesentliche Rolle bei der Regulation und der Erhaltung der hämatopoetischen Stammzellen (HSC). Viele Zytokine und Wachstumsfaktoren werden für die natürliche HSC-Aktivität benötigt und von den Endothelzellen exprimiert. Neben der Unterstützung der hämatopoetischen Stammzellaktivität stellen Endothelzellen ein Gefäßversorgungsnetzwerk zur Verfügung, um eine ausreichende Sauerstoffversorgung zu gewährleisten. Fragestellung: In der hier vorgestellten Arbeit habe ich die Hypothese verfolgt, dass eine Veränderung der Sauerstoffsensorik in Endothelzellen eine Modifizierung der Aktivität hämatopoetischer Stammzellen ermöglicht. Material und Methoden: Trotz des Wissens um die Bedeutung von Sauerstoff für die Endothelzellen fehlt uns das Verständnis dafür, wie die Sauerstoffsensorik der Endothelzellen die lokalen Knochenmark-Nischenzellen und die HSCs reguliert. Um einen Einblick in diesen Mechanismus zu erhalten, haben wir ein Mausmodell mit einem endothelzellenspezifischen Knockout des zentralen Sauerstoffsensors PHD2 entwickelt. Mit diesem in vivo-Ansatz habe ich versucht, den Einfluss von Veränderungen der Hypoxie-Signalwegproteine in Endothelzellen auf HSCs und ihre Nische zu untersuchen. Ergebnisse: Ich konnte in der vorliegenden Arbeit zeigen, dass die Morphologie der sinusförmigen Endothelzellen des Knochenmarks nach Verlust von PHD2 verändert ist. Außerdem konnte ich eine ausgeprägte Gefäßvasodilatation, begleitet von reduzierten hypoxischen Bereichen im angrenzenden Knochenmark beobachten. Zudem stellte ich fest, dass die Inaktivierung von PHD2 in Endothelzellen zu einem Rückgang des Knochenvolumens und zu einer Verminderung der an das Endothel angrenzenden Perizyten führt. Auffallend ist, dass sich gravierende Unterschiede in den hämatopoetischen Zellen der Peripherie zeigten, insbesondere war ein deutlicher Anstieg der zirkulierenden Leukozyten bei den KO-Mäusen zu erkennen. Dieser Phänotyp ist mit einer Vermehrung der hämatopoetischen Stamm- und Vorläuferzellen in Knochenmark und Milz verbunden. Darüber hinaus konnte ich zeigen dass die B-Zelldifferenzierung in der Milz vollständig zum Erliegen kommt, was zu einem signifikanten Rückgang der B-Zellen in der Marginalzone führt. Um die Funktionalität von Endothelzellen mit deletiertem PHD2 zu beurteilen, habe ich die Mäuse mit einer nicht-tödlichen Dosis ionisierender Strahlung behandelt. Die Analyse der endothelialen Zellregeneration im KO-Knochenmark zeigte eine Verminderung der Gefäßneubildung ohne Einfluss auf das gesamte Gefäßlumen im Vergleich zu unbehandelten Wurfgeschwistern. Außerdem stellte ich fest, dass sich in den ersten 3 Wochen nach der Bestrahlung bei Mäusen mit fehlendem PHD2 auf der Endothelzellenoberfläche das RBC-Kompartiments schneller regeneriert. Ich konnte ausschließen, dass dieser Effekt auf eine erhöhte Produktion von RBCs zurückzuführen ist, was zu der Hypothese führte, dass eine Verminderung des endothelialen PHD2 entweder zu einem längerfristigen Überleben der RBCs oder zu einer beeinträchtigten RBC-Clearance führt. Zusätzlich habe ich einen Anstieg in der Anzahl der quieszenten hämatopoetischen Vorläuferzellen bei Mäusen mit endothelialer PHD2-Deletion beobachtet, was darauf hindeutet, dass das endotheliale PHD2 Downstream-Signaling den Zellzyklus von hämatopoetischen Vorläuferzellen bei myeloablativen Stress beeinflusst. Abschließend konnte ich zeigen, dass ein Großteil der beobachteten Phänotypen bei KO-Mäusen durch den nachgeschalteten Transkriptionsfaktor HIF-2α vermittelt wird. Die Verwendung meiner selbstgenerierten Doppel-Knockout-Mauslinie, bei der erstmalig gleichzeitig PHD2 und HIF-2 in den Endothelzellen deletiert sind, führte zu eine vollständige Umkehrung des hämatopoetischen Phänotyps der bei den PHD2-Knockout-Mäusen im Steady-State beobachtet wurde. Zusätzlich wird der zuvor beobachtete signifikante Anstieg der Lymphozyten und der Rückgang der Erythrozyten- und Thrombozytenzahl in den Doppel-Knockout-Mäusen genetisch wiederhergestellt. Gleichzeitig reduziert sich die Entwicklung der marginalen B-Zellen im stationären Zustand wieder auf das Wildtyp-Niveau. Des Weiteren habe ich nach der Bestrahlung von Mäusen mit ionisierender Strahlung keine signifikanten Unterschiede zwischen WT und KO in ihrer hämatopoetischen Zellregeneration mehr feststellen können. Schlussfolgerungen: Zusammengenommen konnte ich in meiner Dissertation neue Eigenschaften von Hypoxie-Pathway-Proteinen in Endothelzellen mit Einfluss auf hämatopoetische Stamm- und Vorläuferzellen sowie auf verschiedene Kompartimente ihrer Nische demonstrieren; sowohl im stationären Zustand als auch nach Belastung durch Bestrahlung. Abschließend unterstreicht meine Arbeit die entscheidende Bedeutung der Sauerstoffsensorik im Knochenmark und gibt neue Einblicke in das Zusammenspiel zwischen dem Knochenmark-Endothel und dem hämatopoetischen System.:1 Introduction 1.1 Oxygen is necessary for survival of multicellular organisms 1.2 Oxygen sensing is necessary for induction of rapid cellular response 1.3 Endothelial and hematopoietic tissues together deliver oxygen 1.4 Hematopoietic stem cells give rise to blood cells 1.5 Regulation of HSCs is dependent on cells of the hematopoietic niche 1.6 Types of HSC regulation 1.7 Cancer therapy affects all highly proliferating cells 1.8 Irradiation stress disrupts hematopoietic stem cell niche signaling 1.9 Hypoxia induced signaling during recovery after irradiation 2 Aims of the thesis Aim 1: Determination of the role of endothelial PHD2 on the signaling towards the hematopoietic stem cells and its niche. 3 Materials and methods 3.1 Mice. 3.2 Histology, immunohistochemistry and immunofluorescence staining 3.2.1 Tissue processing prior to staining: 3.2.2 Staining: 3.3 Endothelial cell sorting 3.4 Mature hematopoietic cell isolation 3.5 Expression analysis 3.6 Hypoxyprobe 3.7 Quantitative image analysis 3.8 Bone structure analysis 3.9 Blood analysis 3.10 FACS analysis 3.11 Cell cycle analysis 3.12 RBC transfusion 3.13 Statistics. 4 Results 4.1 Determination of the role of endothelial PHD2 on the signaling towards the hematopoietic stem cells and its niche 4.1.1 Validation of the Flk1:cre line endothelial cell targeting 4.1.2 Characterization of the endothelial cell morphology and vessel function upon PHD2 inactivation 4.1.3 Loss of endothelial PHD2 leads to a decrease in bone marrow niche 4.1.4 Loss of PHD2 in endothelial cells leads to alterations of hematopoietic cells in the periphery 4.1.5 Significant increase of white blood cells in the periphery upon loss of endothelial PHD2 4.1.6 Loss of endothelial PHD2 does not impact the hematopoietic stem cells in the bone marrow. 4.1.7 Loss of PHD2 leads to increase in hematopoietic stem cells in the spleen 4.1.8 Loss of endothelial PHD2 impacts lineage-committed progenitors in bone marrow and the spleen 4.1.9 Loss of PHD2 in endothelial cells leads to an increase in frequency and activity of myeloid progenitors in bone marrow and the spleen 4.1.10 Loss of endothelial PHD2 impacts lymphocyte progenitors in secondary lymphatic organs but not in the bone marrow 4.2 Defining the impact of radiation exposure on the recovery of PHD2-deficient endothelial cells and its hematopoietic compartment. 4.2.1 Characterization of the non-lethal ionizing radiation damage to bone marrow endothelial and hematopoietic recovery 4.2.2 Loss of PHD2 from endothelium impacts endothelial recovery after myeloablative assault 4.2.3 Loss of PHD2 in endothelial cells and its subsequent effect on hematopoietic recovery following ionizing radiation exposure 4.2.4 Mechanism of increased RBC numbers is not due to an increase in hematopoietic stem cell frequency or activity in bone marrow or the spleen, 2 weeks after irradiation 4.3 Characterization of the influence of the transcription factor HIF-2α in mice lacking EC PHD2 4.3.1 The molecular signal transduction upon PHD2 inactivation is mediated by the HIF-2 transcription factor. 4.3.2 Loss of PHD2 and HIF-2α from endothelial cells partially rescues alterations in bone marrow endothelial cell morphology 4.3.3 Simultaneous loss of PHD2 and HIF-2α in endothelial cells completely reverses the hematopoietic phenotype observed in KO mice. 4.3.4 HIF-2α transcription factor induce signaling on endothelial cells that leads to marginal zone B cell impairment 4.3.5 Loss of PHD2 and subsequent stabilization of the HIF-2αtranscription factor is responsible for the increased recovery of RBCs following ionizing radiation 5 Discussion 6 References 7 List of abbreviations 8 Abstract 9 Zussamenfassung 10 Acknowledgements 11 Deklarations / Background: Endothelial cells have an essential role in hematopoietic stem cell (HSC) regulation and maintenance during homeostasis and stress. Many cytokines and growth factors are required for normal HSC activity and are expressed by the endothelial cells. Along the support of hematopoietic stem cell activity, endothelial cells provide vessel delivery network to ensure proper oxygen delivery. Despite the importance of oxygen on endothelial cells, we lack the understanding of how oxygen sensing in endothelial cells regulates the local bone marrow niche cells and HSCs. Hypothesis: I have hypothesized that by modulating oxygen sensor in endothelial cells I will be able to modify the activity of hematopoietic stem cells Material and methods: To gain insight into this system, we developed a mouse model with an endothelial cell-specific knockout of the central oxygen sensor PHD2. Using this in vivo approach I sought to determine the impact of changes in hypoxia pathway proteins in endothelial cells on HSCs and their niche. Results: First, I revealed that the morphology of bone marrow sinusoidal endothelial cells is altered upon loss of PHD2. I observed prominent vessel vasodilation accompanied by reduced hypoxic areas in their adjacent marrow. Moreover, I determined that inactivation of PHD2 in endothelial cells led to a decrease in bone volume and pericytes adjacent to endothelium. Remarkably, I observed profound differences in the hematopoietic cells of the periphery. Specifically, I observed a profound increase in circulating leukocytes of KO mice. This phenotype was related to an increase in hematopoietic stem and progenitor cells in bone marrow and spleen. Moreover, I found a complete impairment of B cell differentiation in the spleen, which consequently led to a profound decrease in marginal zone B cells. To assess the functionality of endothelial cells lacking PHD2, I subjected the mice to a non-lethal dose of ionizing radiation. Analysis of endothelial cell recovery in KO bone marrow revealed a decrease in the formation of new vessels without an impact on the overall vascular lumen compared to WT littermates. Similarly, I found an enhanced recovery of the RBC compartment during the first 3 weeks after irradiation in mice lacking PHD2 on endothelial cells. I excluded the possibility that this effect was due to an increased RBC production, which led to hypothesis that inhibition of endothelial PHD2 results in prolonged RBC survival or impaired RBC clearance. Additionally, I observed an increase in quiescent hematopoietic progenitors cells in mice lacking PHD2 in endothelial cells that implies that endothelial PHD2 downstream signaling impact cycling of hematopoietic progenitors upon myeloablative stress. Finally, I demonstrated that a majority of the observed phenotypes in KO mice are mediated by the downstream HIF-2α transcription factor. Using my unique self-made double knockout mouse line simultaneously lacking PHD2 and HIF-2 in their endothelial cells, I was able to reveal a reversal of the hematopoietic phenotypes observed in the single PHD2 knockout mice during steady state. Additionally, the previously observed significant increase in lymphocyte and decrease in erythrocyte and thrombocyte numbers was genetically rescued in double knockout mice. Similarly, marginal zone B cell development returned to wild-type levels during steady state. Moreover, after subjecting mice to ionizing radiation I did not observe any significant differences between WT and KO in their hematopoietic cell recovery. Conclusions: Taken together, during my thesis I was able to demonstrate novel properties of hypoxia pathway proteins in endothelial cells having an impact on hematopoietic stem and progenitor cells as well as different compartments of their niche; both during steady state and radiation stress. In conclusion, my work underscores the critical importance of oxygen sensor signaling in the bone/bone marrow and provides new insight into the interplay between the bone marrow endothelium and the hematopoietic system.:1 Introduction 1.1 Oxygen is necessary for survival of multicellular organisms 1.2 Oxygen sensing is necessary for induction of rapid cellular response 1.3 Endothelial and hematopoietic tissues together deliver oxygen 1.4 Hematopoietic stem cells give rise to blood cells 1.5 Regulation of HSCs is dependent on cells of the hematopoietic niche 1.6 Types of HSC regulation 1.7 Cancer therapy affects all highly proliferating cells 1.8 Irradiation stress disrupts hematopoietic stem cell niche signaling 1.9 Hypoxia induced signaling during recovery after irradiation 2 Aims of the thesis Aim 1: Determination of the role of endothelial PHD2 on the signaling towards the hematopoietic stem cells and its niche. 3 Materials and methods 3.1 Mice. 3.2 Histology, immunohistochemistry and immunofluorescence staining 3.2.1 Tissue processing prior to staining: 3.2.2 Staining: 3.3 Endothelial cell sorting 3.4 Mature hematopoietic cell isolation 3.5 Expression analysis 3.6 Hypoxyprobe 3.7 Quantitative image analysis 3.8 Bone structure analysis 3.9 Blood analysis 3.10 FACS analysis 3.11 Cell cycle analysis 3.12 RBC transfusion 3.13 Statistics. 4 Results 4.1 Determination of the role of endothelial PHD2 on the signaling towards the hematopoietic stem cells and its niche 4.1.1 Validation of the Flk1:cre line endothelial cell targeting 4.1.2 Characterization of the endothelial cell morphology and vessel function upon PHD2 inactivation 4.1.3 Loss of endothelial PHD2 leads to a decrease in bone marrow niche 4.1.4 Loss of PHD2 in endothelial cells leads to alterations of hematopoietic cells in the periphery 4.1.5 Significant increase of white blood cells in the periphery upon loss of endothelial PHD2 4.1.6 Loss of endothelial PHD2 does not impact the hematopoietic stem cells in the bone marrow. 4.1.7 Loss of PHD2 leads to increase in hematopoietic stem cells in the spleen 4.1.8 Loss of endothelial PHD2 impacts lineage-committed progenitors in bone marrow and the spleen 4.1.9 Loss of PHD2 in endothelial cells leads to an increase in frequency and activity of myeloid progenitors in bone marrow and the spleen 4.1.10 Loss of endothelial PHD2 impacts lymphocyte progenitors in secondary lymphatic organs but not in the bone marrow 4.2 Defining the impact of radiation exposure on the recovery of PHD2-deficient endothelial cells and its hematopoietic compartment. 4.2.1 Characterization of the non-lethal ionizing radiation damage to bone marrow endothelial and hematopoietic recovery 4.2.2 Loss of PHD2 from endothelium impacts endothelial recovery after myeloablative assault 4.2.3 Loss of PHD2 in endothelial cells and its subsequent effect on hematopoietic recovery following ionizing radiation exposure 4.2.4 Mechanism of increased RBC numbers is not due to an increase in hematopoietic stem cell frequency or activity in bone marrow or the spleen, 2 weeks after irradiation 4.3 Characterization of the influence of the transcription factor HIF-2α in mice lacking EC PHD2 4.3.1 The molecular signal transduction upon PHD2 inactivation is mediated by the HIF-2 transcription factor. 4.3.2 Loss of PHD2 and HIF-2α from endothelial cells partially rescues alterations in bone marrow endothelial cell morphology 4.3.3 Simultaneous loss of PHD2 and HIF-2α in endothelial cells completely reverses the hematopoietic phenotype observed in KO mice. 4.3.4 HIF-2α transcription factor induce signaling on endothelial cells that leads to marginal zone B cell impairment 4.3.5 Loss of PHD2 and subsequent stabilization of the HIF-2αtranscription factor is responsible for the increased recovery of RBCs following ionizing radiation 5 Discussion 6 References 7 List of abbreviations 8 Abstract 9 Zussamenfassung 10 Acknowledgements 11 Deklarations

Zellen sind in der Lage, gleichzeitig ganz unterschiedliche biochemische Prozesse zu bewältigen. Dies gelingt ihnen durch eine Einteilung ihres Inneren in Kompartiemente, sogennante Organellen, die die jeweils geeignete biochemische Umgebung für die unterschiedlichen Aufgaben schaffen. Bei membranumschlossenen Kompartimenten ist leicht vorstellbar, dass sie eine andere biochemische Zusammensetzung als ihre Umgebung haben können. Jedoch existieren auch Organelle ohne Membran die durch eine flüssig-flüssig Phasenseparation entstehen. Manche dieser Kompartiemente haben die Fähigkeit, RNA zu binden und Proteinkomplexe auszubilden, während andere auf die Veränderungen innerhalb der Zelle, wie z.B. die Veränderung des pH-Werts und der damit Verbunden Änderung ihres Protonierungszustands, reagieren können. Um diese Prozesse theoretisch analysieren zu können, entwickeln wir zunächst ein allgemeingültiges, thermodynamisches Gerüst, um Systeme zu untersuchen, die im chemischen Gleichgewicht flüssig-flüssig hasensepariert vorliegen können. Dies erlaubt, basierend auf den Erhaltungsgrößen, im chemischen Gleichgewicht thermodynamisch konjungierten Variablen zu identifizieren, welche aus den erhaltenen Komponenten und den zugehörigen chemischen Potentialen bestehen. Mithilfe des obig erwähnten Gerüsts können wir den Einfluss des pH-Wertes auf die flüssig-flüssig Phasenseparation in einem minimalen Modell untersuchen. Dies beschreibt die makromolekulare Phasenseparation, kontrolliert durch Protonierungs- und Deprotonierungreaktionen, welche wiederum vom pH-Wert abhängig sind. Unsere Untersuchung der pH-Abhängigkeit der Phasenseparation kommt zu folgenden Ergebnissen: Erstens liegt die größte Region von Phasenseparation im Phasendiagramm typischerweise im Bereich des isoelektrischen Punkts. Zweitens zeigt das Modell eine Fähigkeit der erneuten Mischung auf. Drittens ist die Topologie des Phasendiagrams von der dominantesten Interaktion bestimmt. Unser Modell stimmt mit experimentellen Beobachtungen zur Phasenseparation von intrinsisch ungeordneten, Proteinen, deren Struktur sich pH abhängig verändern, überein. Das Modell ist außerdem konsistent mit Beobachtungen von Phasenseparation von Proteinen im Zytosol von Hefezellen, die entsteht, wenn der intrazellulare pH-Wert in die Nähe des isoelektrischen Punkt dieser Proteine gebracht wird. Des Weiteren geht diese Arbeit auf den physikalischen Mechanismus ein, mit dem flüssigkeitsähnliche Organellen, sog. P granules, im Organismus Caenorhabditis elegans positioniert werden. Um dieses Phänomen zu analysieren, stellen wir zunächst experimentelle Beobachtungen vor, die zeigen, dass PGL-3, eine Hauptkomponente der P granules, flüssigkeitsähnliche Tropfen bildet, deren Zusammensetzung von RNA moduliert werden kann. Darüber hinaus zeigen wir Daten, die großen Unterschiede zwischen der RNA-Bindungsaffinität von Proteinen wie Mex-5, die für die Positionierung der P granules relevant sind, und solchen, die P granules bilden, wie PGL-3, zeigen. Dies deutet darauf hin, dass eine Konkurrenz zwischen den Bestandteilen der P Granula und MEX-5 um die zur Bindung zur Verfügung stehende RNA besteht, die die Kondensation und Auflösung von P Granula räumlich kontrollieren könnte. Auf diesen experimentellen Befunden aufbauend führen wir ein minimalles Modell ein, in dem wir die Phasenseparation von PGL-3 an Bindungsreaktionen der MEX-5 Proteine und RNA koppeln. Um die experimentellen Beobachtungen beschreiben zu können, muss die Neigung des PGL-3 Proteins zur Phasenseparation zunehmen, wenn es Komplexe mit RNA bildet. Dies unterstützt die Idee, dass MEX-5 diese Phasenseparation unterdrückt, indem es die Anzahl an möglichen RNA-Bindungspartner für PGL-3 herabsetzt und damit die weitere Entstehung derartiger Protein-RNA-Komplexe erschwert. Dieser einfache Mechanismus scheint die Hauptursache dafür zu sein, dass P granules auf der posterioren Seite des Caenorhabditis elegans Embryos zu finden sind. / One of the main features of cells is their incredible ability to control biochemical processes in space and time. They do so by organizing their interior in sub-compartments called organelles, each of them with a different biochemical environment that allows them to perform specific tasks in the cell. It is sometimes believed that these compartments need a membrane in order to have a stable biochemical environment and regulat their compositions. However, there are some organelles which lack a membrane and seem to form and organize via liquid-liquid phase separation. Some of the components that form these membraneless organelles have the ability to bind to RNA and form complexes, while some others react to changes in the intracellular environment such as pH variations, which in turn affects their protonation state. In order to study these processes from a theoretical perspective, we develop a generic thermodynamic framework to study systems exhibiting liquid-liquid phase separation at chemical equilibrium. This framework, based on the use of conservation laws in chemical reactions, allow us to identify thermodynamic conjugate variables at chemical equilibrium, which are given by a set of conserved quantities and the corresponding conjugate chemical potentials. Within the aforementioned framework, we introduce a minimal model to study the effect of pH on liquid-liquid phase separation. Our model explains macromolecular phase separation controlled by protonation and deprotonation reactions, which are tuned by the pH of the system. We study the phase behavior of the system as a function of pH. Our main findings are: Firstly, the broadest region of phase separation is typically found at the isoelectric point. Secondly, the system exhibits reentrant behavior. Thirdly, that the dominating interaction in the system determines the topology of the phase diagrams. Our model is in agreement with experimental observations of in vitro protein phase separation of pH-responsive intrinsically disordered proteins, as well as with observations of protein phase separation exhibited by many cytosolic proteins when the intracellular pH in yeast cells is brought close to the isoelectric point of such proteins. Moreover, this work analyses the physical mechanism behind the positioning of liquid-like organelles in the {\it{Caenorhabditis elegans}} organism known as P granules. In order to study this phenomenon, we first present firm experimental evidence showing that PGL-3 protein, a key component of P granules, forms liquid-like drops whose assembly can be modulated by RNA. We then present data showing that the RNA-binding affinity differs significantly between proteins relevant for the positioning of P granules, such as MEX-5 and the proteins forming the P granules, like the aforementioned PGL-3. This points to a possible mechanism of RNA-binding competition between P granule constituents and MEX-5 in order to spatially control the condensation and dissolution of P granules. Based on the experimental evidence, we propose a minimal model in which we couple phase separation of PGL-3 to a set of binding reactions involving the MEX-5 protein and RNA. We find that in order to explain the experimental data, the tendency for phase separation of the PGL-3 protein increases with the formation of complexes of PGL-3 bound to RNA. This therefore supports the idea that MEX-5 inhibits this protein phase separation by depleting the RNA available for PGL-3 to form such complexes. This simple mechanism is at the core of how P granules localize to the posterior side of the Caenorhabditis elegans embryo.

Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process