Graduate School of Life Sciences
Refine
Has Fulltext
- yes (22)
Is part of the Bibliography
- yes (22)
Document Type
- Doctoral Thesis (22)
Keywords
- Epigenetik (2)
- ADHD (1)
- Alzheimer's disease (1)
- Alzheimerkrankheit (1)
- Angeborene Immunität (1)
- Animal model (1)
- Anthropocene (1)
- Arbeitsteilung (1)
- Aspergillus fumigatus (1)
- Aussterbedynamik (1)
Institute
- Fakultät für Biologie (22) (remove)
Sonstige beteiligte Institutionen
Humans are continuously exposed to airborne spores of the saprophytic fungus Aspergillus fumigatus. In healthy individuals, local pulmonary host defence mechanisms can efficiently eliminate the fungus without any overt symptoms. In contrast, A. fumigatus causes devastating infections in immunocompromised patients. However, local host immune responses against A. fumigatus lung infections in immunocompromised conditions have remained largely elusive.
Given the dynamic changes in immune cell subsets within tissues upon immunosuppressive therapy, we dissected the spatiotemporal pulmonary immune response after A. fumigatus infection to reveal basic immunological events that fail to effectively control the invasive fungal disease. In different immunocompromised murine models, myeloid but not lymphoid cells were strongly recruited upon infection. Notably, neutrophils and macrophages were recruited to infected lungs in different immunosuppressed regimens. Other myeloid cells, particularly dendritic cells and monocytes were only recruited in the corticosteroid model after infection. Lymphoid cells, particularly CD4+ or CD8+ T-cells and NK cells were highly reduced upon immunosuppression and were not recruited after A. fumigatus infection. Importantly, adoptive CD11b+ myeloid cell transfer rescued immunosuppressed mice from lethal A. fumigatus infection. These findings illustrate that CD11b+ myeloid cells are critical for anti-A. fumigatus defence under immunocompromised conditions.
Despite improved antifungal agents, invasive A. fumigatus lung infections cause a high rate morbidity and mortality in neutropenic patients. Granulocyte transfusions have been tested as an alternative therapy for the management of high-risk neutropenic patients with invasive A. fumigatus infections. To increase the granulocyte yield for transfusion, donors are treated with corticosteroids. Yet, the efficacy of granulocyte transfusion and the functional defence mechanisms of granulocytes collected from corticosteroid treated donors remain largely elusive.
We aimed to assess the efficacy of granulocyte transfusion and functional defence mechanisms of corticosteroid treated granulocytes using mouse models.
In this thesis, we show that transfusion of granulocytes from corticosteroid treated mice did not protect cyclophosphamide immunosuppressed mice against lethal A. fumigatus infection in contrast to granulocytes from untreated mice. Upon infection, increased levels of inflammatory cytokines helped to recruit granulocytes to the lungs without any recruitment defects in corticosteroid treated and infected mice or in cyclophosphamide immunosuppressed and infected mice that have received the granulocytes from corticosteroid treated mice. However, corticosteroid treated human or mouse neutrophils failed to form neutrophil extracellular traps (NETs) in in vitro and in vivo conditions. Further, corticosteroid treated granulocytes exhibited impaired ROS production against A. fumigatus. Notably, corticosteroids impaired the β-glucan receptor Dectin-1 (CLEC7A) on mouse and human granulocytes to efficiently recognize and phagocytize A. fumigatus, which markedly impaired fungal killing. We conclude that corticosteroid treatment of granulocyte donors for increasing neutrophil yields or patients with ongoing corticosteroid treatment could result in deleterious effects on granulocyte antifungal functions, thereby limiting the benefit of granulocyte transfusion therapies against invasive fungal infections.
The resolution of fluorescence light microscopy was long believed to be limited by the diffraction limit of light of around 200-250 nm described in 1873 by Ernst Abbe. Within the last decade, several approaches, such as structured illumination microscopy (SIM), stimulated emission depletion STED and (direct) stochastic optical reconstruction microscopy (d)STORM have been established to bypass the diffraction limit. However, such super-resolution techniques enabling a resolution <100 nm require specialized and expensive setups as well as expert knowledge in order to avoid artifacts. They are therefore limited to specialized laboratories. Recently, Boyden and colleagues introduced an alternate approach, termed expansion microscopy (ExM). The latter offers the possibility to perform superresolution microscopy on conventional confocal microscopes by embedding the sample into a swellable hydrogel that is isotropically expanded. Since its introduction in 2015, expansion microscopy has developed rapidly offering protocols for 4x, 10x and 20x expansion of proteins and RNA in cells, tissues and human clinical specimens.
Mitochondria are double membrane-bound organelles and crucial to the cell by performing numerous tasks, from ATP production through oxidative phosphorylation, production of many important metabolites, cell signaling to the regulation of apoptosis. The inner mitochondrial membrane is strongly folded forming so-called cristae. Besides being the location of the oxidative phosphorylation and therefore energy conversion and ATP production, cristae have been of great interest because changes in morphology have been linked to a plethora of diseases from cancer, diabetes, neurodegenerative diseases, to aging and infection. However, cristae imaging remains challenging as the distance between two individual cristae is often below 100 nm. Within this work, we demonstrate that the mitochondrial creatine kinase MtCK linked to fluorescent protein GFP (MtCK-GFP) can be used as a cristae marker. Upon fourfold expansion, we illustrate that our novel marker enables visualization of cristae morphology and localization of mitochondrial proteins relative to cristae without the need for specialized setups. Furthermore, we show the applicability of expansion microscopy for several bacterial pathogens, such as Chlamydia trachomatis, Simkania negevensis, Neisseria gonorrhoeae and Staphylococcus aureus. Due to differences in bacterial cell walls, we reveal important aspects for the digestion of pathogens for isotropic expansion. We further show that expansion of the intracellular pathogens C. trachomatis and S. negevensis, enables the differentiation between the two distinct developmental forms, catabolic active reticulate bodies (RB) and infectious elementary bodies (EB), on a conventional confocal microscope. We demonstrate the possibility to precisely locate chlamydial effector proteins, such as CPAF or Cdu1, within and outside the chlamydial inclusion. Moreover, we show that expansion microscopy enables the investigation of bacteria, herein S. aureus, within LAMP1 and LC3-II vesicles. With the introduction of the unnatural α-NH2-ω-N3-C6-ceramide, we further present the first approach for the expansion of lipids that may also be suitable for far inaccessible molecule classes like carbohydrates. The efficient accumulation and high labeling density of our functionalized α-NH2-ω-N3-C6-ceramide in both cells and bacteria enables in combination with tenfold expansion nanoscale resolution (10-20 nm) of the interaction of proteins with the plasma membrane, membrane of organelles and bacteria. Ceramide is the central molecule of the sphingolipid metabolism, an important constituent of cellular membranes and regulates many important cellular processes such as differentiation, proliferation and apoptosis. Many studies report about the importance of sphingolipids during infection of various pathogens. While the transport of ceramide to Chlamydia has been reported earlier, one of the unanswered questions remaining was if ceramide forms parts of the outer or inner bacterial membrane. Expansion of α-NH2-ω-N3-C6-ceramide enabled the visualization of ceramide in the inner and outer membrane of C. trachomatis and their distance was determined to be 27.6 ± 7.7 nm.
The superfamiliy of bees, Apiformes, comprises more than 20,000 species. Within the group, the eusocial species like honeybees and bumblebees are receiving increased attention due to their outstanding importance for pollination of many crop and wild plants, their exceptional eusocial lifestyle and complex behavioral repertoire, which makes them an interesting invertebrate model to study mechanisms of sensory perception, learning and memory. In bees and most animals, vision is one of the major senses since almost every living organism and many biological processes depend on light energy. Bees show various forms of vision, e.g. color vision, achromatic vision or polarized vision in order to orientate in space, recognize mating partners, detect suitable nest sites and search for rewarding food sources. To catch photons and convert light energy into electric signals, bees possess compound eyes which consists of thousands of single ommatidia comprising a fixed number of photoreceptors; they are characterized by a specific opsin protein with distinct spectral sensitivity. Different visual demands, e.g. the detection of a single virgin queen by a drone, or the identification and discrimination of flowers during foraging bouts by workers, gave rise to the exceptional sex-specific morphology and physiology of male and female compound eyes in honeybees. Since Karl von Frisch first demonstrated color vision in honeybees more than 100 years ago, much effort has been devoted to gain insight into the molecular, morphological and physiological characteristics of (sex-specific) bee compound eyes and the corresponding photoreceptors. However, to date, almost nothing is known about the underlying mechanisms during pupal development which pattern the retina and give rise to the distinct photoreceptor distribution. Hence, in Chapter 2 and 3 I aimed to better understand the retinal development and photoreceptor determination in the honeybee eye. In a first step, the intrinsic temporal expression pattern of opsins within the retina was evaluated by quantifying opsin mRNA expression levels during the pupal phase of honeybee workers and drones. First results revealed that honeybee workers and drones express three different opsin genes, UVop, BLop and Lop1 during pupal development which give rise to an ultraviolet, blue, and green-light sensitive photoreceptor. Moreover, opsin expression patterns differed between both sexes and the onset of a particular opsin occurred at different time points during retinal development. Immunostainings of the developing honeybee retina in Chapter 2 showed that at the beginning of pupation the retina consist only of a thin hypodermis. However, at this stage all retinal structures are already present. From about mid of pupation, opsin expression levels increase and goes hand in hand with the differentiation of the rhabdoms, suggesting a two-step process in photoreceptor development and differentiation in the honeybee compound eye. In a first step the photoreceptor cells meet its fate during late pupation; in a second step, the quantity of opsin expression in each photoreceptor strongly increase up to the 25-fold shortly after eclosion. To date, the underlying mechanisms leading to different photoreceptor types have been intensively studied in the fruit fly, Drosophila melanogaster, and to some extend in butterflies. Interestingly, the molecular mechanisms seemed to be conserved within insects and e.g. the two transcription factors, spalt and spineless, which have been shown to be essential for photoreceptor determination in flies and butterflies, have been also identified in the honeybee. In chapter 3, I investigated the expression patterns of both transcription factors during pupal development of honeybee workers and showed that spalt is mainly expressed during the first few pupal stages which might correlate with the onset of BLop expression. Further, spineless showed a prominent peak at mid of pupation which might initiates the expression of Lop1. However, whether spalt and spineless are also essential for photoreceptor determination in the honeybee has still to be investigated, e.g. by a knockdown/out of the respective transcription factor during retinal development which leads to a spectral phenotype, e.g. a dichromatic eye. Such spectral phenotypes can then be tested in behavioral experiments in order to test the function of specific photoreceptors for color perception and the entrainment of the circadian clock. In order to evaluate the color discrimination capabilities of bees and the quality of color perception, a reliable behavioral experiment under controlled conditions is a prerequisite. Hence, in chapter 4, I aimed to establish the visual PER paradigm as a suitable method for behaviorally testing color vision in bees. Since PER color vision has considered to be difficult in bees and was not successful in Western honeybees without ablating the bee’s antennae or presenting color stimuli in combination with other cues for several decades, the experimental setup was first established in bumblebees which have been shown to be robust and reliable, e.g. during electrophysiological recordings. Workers and drones of the bufftailed bumblebee, Bombus terrestris were able to associate different monochromatic light stimuli with a sugar reward and succeeded in discriminating a rewarded color stimulus from an unrewarded color stimulus. They were also able to retrieve the learned stimulus after two hours, and workers successfully transferred the learned information to a new behavioral context. In the next step, the experimental setup was adapted to honeybees. In chapter 5, I tested the setup in two medium-sized honeybees, the Eastern honeybee, Apis cerana and the Western honeybee, Apis mellifera. Both honeybee species were able to associate and discriminate between two monochromatic light stimuli, blue and green light, with peak sensitivities of 435 nm and 528 nm. Eastern and Western honeybees also successfully retrieve the learned stimulus after two hours, similar to the bumblebees. Visual conditioning setups and training protocols in my study significantly differed from previous studies using PER conditioning. A crucial feature found to be important for a successful visual PER conditioning is the duration of the conditioned stimulus presentation. In chapter 6, I systematically tested different length of stimuli presentations, since visual PER conditioning in earlier studies tended to be only successful when the conditioned stimulus is presented for more than 10 seconds. In this thesis, intact honeybee workers could successfully discriminate two monochromatic lights when the stimulus was presented 10 s before reward was offered, but failed, when the duration of stimulus presentation was shorter than 4 s. In order to allow a more comparable conditioning, I developed a new setup which includes a shutter, driven by a PC based software program. The revised setup allows a more precise and automatized visual PER conditioning, facilitating performance levels comparable to olfactory conditioning and providing now an excellent method to evaluate visual perception and cognition of bees under constant and controlled conditions in future studies.
Attention-deficit/hyperactivity disorder (ADHD) is the most prevalent neurodevelopmental disorder described in psychiatry today. ADHD arises during early childhood and is characterized by an age-inappropriate level of inattention, hyperactivity, impulsivity, and partially emotional dysregulation. Besides, substantial psychiatric comorbidity further broadens the symptomatic spectrum. Despite advances in ADHD research by genetic- and imaging studies, the etiopathogenesis of ADHD remains largely unclear. Twin studies suggest a heritability of 70-80 % that, based on genome-wide investigations, is assumed to be polygenic and a mixed composite of small and large, common and rare genetic variants. In recent years the number of genetic risk candidates is continuously increased. However, for most, a biological link to neuropathology and symptomatology of the patient is still missing. Uncovering this link is vital for a better understanding of the disorder, the identification of new treatment targets, and therefore the development of a more targeted and possibly personalized therapy.
The present thesis addresses the issue for the ADHD risk candidates GRM8, FOXP2, and GAD1. By establishing loss of function zebrafish models, using CRISPR/Cas9 derived mutagenesis and antisense oligonucleotides, and studying them for morphological, functional, and behavioral alterations, it provides novel insights into the candidate's contribution to neuropathology and ADHD associated phenotypes. Using locomotor activity as behavioral read-out, the present work identified a genetic and functional implication of Grm8a, Grm8b, Foxp2, and Gad1b in ADHD associated hyperactivity. Further, it provides substantial evidence that the function of Grm8a, Grm8b, Foxp2, and Gad1b in activity regulation involves GABAergic signaling. Preliminary indications suggest that the three candidates interfere with GABAergic signaling in the ventral forebrain/striatum. However, according to present and previous data, via different biological mechanisms such as GABA synthesis, transmitter release regulation, synapse formation and/or transcriptional regulation of synaptic components. Intriguingly, this work further demonstrates that the activity regulating circuit, affected upon Foxp2 and Gad1b loss of function, is involved in the therapeutic effect mechanism of methylphenidate. Altogether, the present thesis identified altered GABAergic signaling in activity regulating circuits in, presumably, the ventral forebrain as neuropathological underpinning of ADHD associated hyperactivity. Further, it demonstrates altered GABAergic signaling as mechanistic link between the genetic disruption of Grm8a, Grm8b, Foxp2, and Gad1b and ADHD symptomatology like hyperactivity. Thus, this thesis highlights GABAergic signaling in activity regulating circuits and, in this context, Grm8a, Grm8b, Foxp2, and Gad1b as exciting targets for future investigations on ADHD etiopathogenesis and the development of novel therapeutic interventions for ADHD related hyperactivity. Additionally, thigmotaxis measurements suggest Grm8a, Grm8b, and Gad1b as interesting candidates for prospective studies on comorbid anxiety in ADHD. Furthermore, expression analysis in foxp2 mutants demonstrates Foxp2 as regulator of ADHD associated gene sets and neurodevelopmental disorder (NDD) overarching genetic and functional networks with possible implications for ADHD polygenicity and comorbidity. Finally, with the characterization of gene expression patterns and the generation and validation of genetic zebrafish models for Grm8a, Grm8b, Foxp2, and Gad1b, the present thesis laid the groundwork for future research efforts, for instance, the identification of the functional circuit(s) and biological mechanism(s) by which Grm8a, Grm8b, Foxp2, and Gad1b loss of function interfere with GABAergic signaling and ultimately induce hyperactivity.
Besides a growing tendency for delayed parenthood, sedentary lifestyle coupled with overnutrition has dramatically increased worldwide over the last few decades. Epigenetic mechanisms can help us understand the epidemics and heritability of complex traits like obesity to a significant extent. Majority of the research till now has focused on determining the impact of maternal factors on health and disease risk in the offspring(s).
This doctoral thesis is focused on deciphering the potential effects of male aging and obesity on sperm methylome, and consequences/transmission via germline to the next generation. In humans, this was assessed in a unique cohort of ~300 sperm samples, collected after in vitro fertilization/intracytoplasmic sperm injection, as well as in conceived fetal cord blood samples of the children. Furthermore, aging effect on sperm samples derived from a bovine cohort was analyzed.
The study identified that human male aging significantly increased the DNA methylation levels of the promoter, the upstream core element, the 18S, and the 28S regions of ribosomal DNA (rDNA) in sperm. Prediction models were developed to anticipate an individual’s age based on the methylation status of rDNA regions in his sperm. Hypermethylation of alpha satellite and LINE1 repeats in human sperm was also observed with aging. Epimutations, which are aberrantly methylated CpG sites, were significantly higher in sperm of older males compared to the younger ones. These effects on the male germline had a negative impact on embryo quality of the next generation. Consistent with these results, DNA methylation of rDNA regions, bovine alpha satellite, and testis satellite repeats displayed a significant positive correlation with aging sperm samples within the same individual and across different age-grouped bulls.
A positive association between human male obesity/body mass index (BMI) and DNA methylation of the imprinted MEG3 gene and the obesity-related HIF3A gene was detected in sperm. These BMI-induced sperm DNA methylation signatures were transmitted to next generation fetal cord blood (FCB) samples in a gender-specific manner. Males, but not female offsprings exhibited a significant positive correlation between father’s BMI and FCB DNA methylation in the two above-mentioned amplicons. Additionally, hypomethylation of IGF2 with increased paternal BMI was observed in female FCB samples. Parental allele-specific in-depth methylation analysis of imprinted genes using next generation sequencing technology also revealed significant correlations between paternal factors like age and BMI, and the corresponding father’s allele DNA methylation in FCB samples.
Deep bisulphite sequencing of imprinted genes in diploid somatic cord blood cells of offspring detected that the levels of DNA methylation signatures largely depended on the underlying genetic variant, i.e. sequence haplotypes. Allele-specific epimutations were observed in PEG1, PEG5, MEG3, H19, and IGF2 amplicons. For the former three genes, the non-imprinted unmethylated allele displayed more epimutations than the imprinted methylated allele. On the other hand, for the latter two genes, the imprinted allele exhibited higher epimutation rate than that of the non-imprinted allele.
In summary, the present study proved that male aging and obesity impacts the DNA methylome of repetitive elements and imprinted genes respectively in sperm, and also has considerable consequences on the next generation. Nevertheless, longitudinal follow-up studies are highly encouraged to elucidate if these effects can influence the risk of developing abnormal phenotype in the offspring during adulthood.
The research that is compiled in this thesis can be divided in two parts. The first part, consisting of four chapters, is centered around the role of epigenetic dysregulation in the etiopathophysiology of sporadic alzheimer's disease (sAD). In addition to providing insights into the most recent developments in neuroepigenomic studies of this disease, the first part of the thesis also touches upon remaining challenges, and provides a future outlook on possible developments in the field. The second part, which includes three more chapters, is focused on the application of induced pluripotent stem cell (iPSC)-based disease models for the study of AD, including but not limited to mechanistic studies on epigenetic dysregulation using this platform. Aside from outlining the research that has been conducted using iPSC-based models for sAD to date, the second part of the thesis also provides insights into the acquisition of disease-relevant neural cultures based on directed differentiation of iPSCs, and furthermore includes an experimental approach for the establishment of such a model system.
Desert ants of the genus Cataglyphis (Formicinae) are widely distributed in arid
areas of the palearctic ecozone. Their habitats range from relatively cluttered environments in the Mediterranean area to almost landmark free deserts. Due to their
sophisticated navigational toolkit, mainly based on the sky-compass, they were
studied extensively for the last 4 decades and are an exceptional model organism
for navigation. Cataglyphis ants exhibit a temporal polyethism: interior workers
stay inside the dark nest and serve as repletes for the first ∼2 weeks of their adult
life (interior I). They then switch to nursing and nest maintenance (interior II)
until they transition to become day-active outdoor foragers after ∼4 weeks. The
latter switch in tasks involves a transition phase of ∼2-3 days during which the
ants perform learning and orientation walks. Only after this last phase do the ants
start to scavenge for food as foragers.
In this present thesis I address two main questions using Cataglyphis desert ants
as a model organism:
1. What are the underlying mechanisms of temporal polyethism?
2. What is the neuronal basis of sky-compass based navigation in Cataglyphis
ants?
Neuropeptides are important regulators of insect physiology and behavior and as
such are promising candidates regarding the regulation of temporal polyethism in
Cataglyphis ants. Neuropeptides are processed from large precursor proteins and undergo substantial post-translational modifications. Therefore, it is crucial to biochemically identify annotated peptides. As hardly any peptide data are available
for ants and no relevant genomic data has been recorded for Cataglyphis, I started
out to identify the neuropeptidome of adult Camponotus floridanus (Formicinae)
workers (manuscript 1). This resulted in the first neuropeptidome described in an
ant species – 39 neuropeptides out of 18 peptide families. Employing a targeted
approach, I identified allatostatin A (AstA), allatotropin (AT), short neuropeptide
F (sNPF) and tachykinin (TK) using mass spectrometry and immunohistology to
investigate the distribution of AstA, AT and TK in the brain (manuscript 2). All
three peptides are localized in the central complex, a brain center for sensory integration and high-order control of locomotion behavior. In addition, AstA and
TK were also found in visual and olfactory input regions and in the mushroom
bodies, the centers for learning and memory formation. Comparing the TK immunostaining in the brain of 1, 7 and 14 days old dark kept animals revealed that
the distribution in the central complex changes, most prominently in the 14 day
old group. In the Drosophila central complex TK modulates locomotor activity
levels. I therefore hypothesize that TK is involved in the internal regulation of the
interior I–interior II transition which occurs after ∼2 weeks of age.
I designed a behavioral setup to test the effect of neuropeptides on the two traits:
’locomotor activity level’ and ’phototaxis’ (manuscript 3). The test showed that
interior I ants are less active than interior II ants, which again are less active
than foragers. Furthermore, interior ants are negatively phototactic compared to
a higher frequency of positive phototaxis in foragers. Testing the influence of AstA
and AT on the ants’ behavior revealed a stage-specific effect: while interior I behavior is not obviously influenced, foragers become positively phototactic and more
active after AT injection and less active after AstA injection. I further tested the
effect of light exposure on the two behavioral traits of interior workers and show that it rises locomotor activity and results in decreased negative phototaxis in
interior ants. However, both interior stages are still more negatively phototactic
than foragers and only the activity level of interior II ants is raised to the forager
level. These results support the hypothesis that neuropeptides and light influence
behavior in a stage-specific manner.
The second objective of this thesis was to investigate the neuronal basis of skycompass navigation in Cataglyphis (manuscript 4). Anatomical localization of the
sky-compass pathway revealed that its general organization is highly similar to
other insect species. I further focused on giant synapses in the lateral complex,
the last relay station before sky-compass information enters the central complex.
A comparison of their numbers between newly eclosed ants and foragers discloses
a rise in synapse numbers from indoor worker to forager, suggesting task-related
synaptic plasticity in the sky-compass pathway. Subsequently I compared synapse
numbers in light preexposed ants and in dark-kept, aged ants. This experiment
showed that light as opposed to age is necessary and sufficient to trigger this rise
in synapse number. The number of newly formed synapses further depends on the
spectral properties of the light to which the ants were exposed to.
Taken together, I described neuropeptides in C. floridanus and C. fortis, and provided first evidence that they influence temporal polyethism in Cataglyphis ants.
I further showed that the extent to which neuropeptides and light can influence
behavior depends on the animals’ state, suggesting that the system is only responsive under certain circumstances. These results provided first insight into the
neuronal regulation of temporal polyethism in Cataglyphis. Furthermore, I characterized the neuronal substrate for sky-compass navigation for the first time in
Cataglyphis. The high level of structural synaptic plasticity in this pathway linked
to the interior–forager transition might be particularly relevant for the initial calibration of the ants’ compass system.
Potential evolutionary responses to landscape heterogeneity and systematic environmental trends
(2020)
Over the course of the last century, humans have witnessed drastic levels of global environmental change that endangered both, the survival of single species as well as biodiversity itself. This includes climate change, in both environmental means and in variance and subsequently frequent extreme weather events, as well as land use change that species have to cope with.
With increasing urbanization, increasing agricultural area and increasing intensification, natural habitat is not only lost, but also changes its shape and distribution in the landscape. Both aspects can heavily influence an individual's fitness and therefore act as a selective force promoting evolutionary change.
This way climate change influences individuals' niches and dispersal. Local adaptation and dispersal are not independent of each other. Dispersal can have two opposite effects on local adaptation. It can oppose local adaptation, by promoting the immigration of maladapted indi-
viduals or favor local adaptation by introducing better adapted genotypes. Which of those effects of dispersal on local adaptation emerges in a population depends on the dispersal strategies and the spatial structure of the landscape. In principle an adaptive response can include adjustment of the niche optimum as well as habitat tolerance (niche width) or (instead) ecological tracking of adequate conditions by dispersal and range shifting. So
far, there has been no extensive modeling study of the evolution of the environmental niche optimum and tolerance along with dispersal probability in complex landscapes. Either only dispersal or (part of ) the environmental niche can evolve or the landscapes used are not realistic but rather a very abstract representation of spatial structures.
I want to try and disentangle those different effects of both local adaptation and dispersal during global change, as well as their interaction, especially considering the separation between the effects of increasing mean and increasing variance. For this, I implemented an individual based model (IBM), with escalating complexity.
I showed that both on a temporal as well as on a spatial scale, variation can be more influential then mean conditions.
Indeed, the actual spatial configuration of this heterogeneity and the relationship between spatial and temporal heterogeneity affect the evolution of the niche and of dispersal probability more than temporal or spatial mean conditions. I could show that in isolated populations, an increase of an environmental attribute's mean or variance can lead to extinction, under certain conditions. In particular, increasing variance cannot be tracked forever, since increasing tolerance has distinct limits of feasibility. Increasing mean conditions can also occur too fast to be tracked, especially from generalist individuals. When expanding the model to the metapopulation level without a temporal environmental trend, the degree of spatial vs.temporal heterogeneity influenced the evolution of random dispersal heavily. With increasing spatial heterogeneity, individuals from extreme and rare patches
evolve from being philopatric to dispersive, while individuals from average patches switch in the opposite direction.
With the last expansion to a different set of landscapes with varying degrees of edge density, I could show that edge effects are strong in pseudo-agricultural landscapes, while
in pseudo-natural habitats they were hardly found, regardless of emigration strategy. Sharp edges select against dispersal in the edge patches and could potentially further isolate populations in agricultural landscapes.
The work I present here can also be expanded further and I present several suggestions on what to do next. These expansions could help the realism of the model and eventually shed light on its bearing on ecological global change predictions. For example species distribution models or extinction risk models would be more precise, if they included both spatial and temporal variation. The current modeling practices might not be suffcient to
describe the possible outcomes of global change, because spatio-temporal heterogeneity and its influence on species' niches is too important to be ignored for longer.
Regulatory T cells (Tregs) are the masters of immune regulation controlling inflammation and tolerance, tissue repair and homeostasis. Multiple immunological diseases result from altered Treg frequencies and Treg dysfunction. We hypothesized that augmenting Treg function and numbers would prevent inflammatory disease whereas inhibiting or depleting Tregs would improve cancer immunotherapy.
In the first part of this thesis, we explored whether in vivo activation and expansion of Tregs would impair acute graft-versus-host disease (aGvHD). In this inflammatory disease, Tregs are highly pathophysiological relevant and their adoptive transfer proved beneficial on disease outcome in preclinical models and clinical studies. IL-2 has been recognized as a key cytokine for Treg function. Yet, attempts in translating Treg expansion via IL-2 have remained challenging, due to IL-2s extremely broad action on other cell types including effector T cells, NK cells, eosinophils and vascular leakage syndrome, and importantly, due to poor pharmacokinetics in vivo. We addressed the latter issue using an IL-2-IgG-fusion protein (irrIgG-IL-2) with improved serum retention and demonstrated profound Treg expansion in vivo in FoxP3-luciferase reporter mice. Further, we augmented Treg numbers and function via the selective-TNF based agonists of TNFR2 (STAR2). Subsequently, we tested a next-generation TNFR2 agonist, termed NewSTAR, which proved even more effective. TNFR2 stimulation augmented Treg numbers and function and was as good as or even superior to the IL-2 strategy. Finally, in a mouse model of aGvHD we proved the clinical relevance of Treg expansion and activation with irrIgG-IL-2, STAR2 and NewSTAR. Notably, the TNFR2 stimulating constructs were outstanding as we observed not the IL-2 prototypic effects on other cell populations and no severe side effects.
In the second part of this thesis, we explored Tregs in pancreatic ductal adenocarcinoma (PDAC) and developed targeting strategies. Among several tumor entities in which Tregs impact survival, preclinical and clinical data demonstrated their negative role on PDAC. In our studies we employed the orthotopic syngeneic Panc02 model in immunocompetent mice. Based on flow cytometric analysis of the tumor microenvironment we propose TIGIT and TNFRSF members as novel therapeutic targets. Surprisingly, we found that blocking TNFR2 did not interfere with intratumoral Treg accumulation. However, we decreased the highly abundant intratumoral Tregs when we disrupted the tumor extracellular matrix. In PDAC, Treg manipulation alone did not lead to tumor regression and we propose that an additional immune boost may be necessary for efficient tumor immune surveillance and cancer clearance. This contrasts with aGvHD, in which Treg manipulation alone was sufficient to improve disease outcome.
Conclusively, we demonstrated the enormous medical benefit of Treg manipulation. Our promising data obtained with our newly developed powerful tools highlight the potential to translate our findings into clinical practice to therapeutically target human Tregs in patients. With novel TNFR2 agonists (STAR2, NewSTAR) we augmented Treg numbers and function as (or even more) effectively than with IL-2, without causing adverse side effects. Importantly, exogenous in vivo Treg expansion protected mice from aGvHD. For the therapy of PDAC, we identified novel targets on Tregs, notably TIGIT and members of the TNFRSF. We demonstrated that altering the extracellular tumor matrix can efficiently disrupt the Treg abundance in tumors. These novel targeting strategies appear as attractive new treatment options and they may benefit patients suffering from inflammatory disease and cancer in the future.
The human-bacterial pathogen interaction is a complex process that results from
a prolonged evolutionary arms race in the struggle for survival. The pathogen employs
virulence strategies to achieve host colonization, and the latter counteracts using defense
programs. The encounter of both organisms results in drastic physiological changes
leading to stress, which is an ancient response accompanying infection. Recent evidence
suggests that the stress response in the host converges with the innate immune pathways
and influences the outcome of infection. However, the contribution of stress and the exact
mechanism(s) of its involvement in host defense remain to be elucidated. Using the model
bacterial pathogen Shigella flexneri, and comparing it with the closely related pathogen
Salmonella Typhimurium, this study investigated the role of host stress in the outcome of
infection.
Shigella infection is characterized by a pronounced pro-inflammatory response
that causes intense stress in host tissues, particularly the intestinal epithelium, which
constitutes the first barrier against Shigella colonization. In this study, inflammatory
stress was simulated in epithelial cells by inducing oxidative stress, hypoxia, and cytokine
stimulation. Shigella infection of epithelial cells exposed to such stresses was strongly
inhibited at the adhesion/binding stage. This resulted from the depletion of sphingolipidrafts
in the plasma membrane by the stress-activated sphingomyelinases. Interestingly,
Salmonella adhesion was not affected, by virtue of its flagellar motility, which allowed the
gathering of bacteria at remaining membrane rafts. Moreover, the intracellular replication
of Shigella lead to a similar sphingolipid-raft depletion in the membrane across adjacent
cells inhibiting extracellular bacterial invasion.
Additionally, this study shows that Shigella infection interferes with the host stress
granule-formation in response to stress. Interestingly, infected cells exhibited a nuclear
depletion of the global RNA-binding stress-granule associated proteins TIAR and TIA-1
and their accumulation in the cytoplasm.
Overall, this work investigated different aspects of the host stress-response in the
defense against bacterial infection. The findings shed light on the importance of the host
stress-pathways during infection, and improve the understanding of different strategies
in host-pathogen interaction.
Chlamydia trachomatis (Ct) is an obligate intracellular human pathogen. It causes blinding trachoma and sexually transmitted disease such as chlamydia, pelvic inflammatory disease and lymphogranuloma venereum. Ct has a unique biphasic development cycle and replicates in an intracellular vacuole called inclusion. Normally it has two forms: the infectious form, elementary body (EB); and the non-infectious form, reticulate body (RB). Ct is not easily amenable to genetic manipulation. Hence, to understand the infection process, it is crucial to study how the metabolic activity of Ct exactly evolves in the host cell and what roles of EB and RB play differentially in Ct metabolism during infection. In addition, Ct was found regularly coinfected with other pathogens in patients who got sexually transmitted diseases (STDs). A lack of powerful methods to culture Ct outside of the host cell makes the detailed molecular mechanisms of coinfection difficult to study.
In this work, a genome-scale metabolic model with 321 metabolites and 277 reactions was first reconstructed by me to study Ct metabolic adaptation in the host cell during infection. This model was calculated to yield 84 extreme pathways, and metabolic flux strength was then modelled regarding 20hpi, 40hpi and later based on a published proteomics dataset. Activities of key enzymes involved in target pathways were further validated by RT-qPCR in both HeLa229 and HUVEC cell lines. This study suggests that Ct's major active pathways involve glycolysis, gluconeogenesis, glycerolphospholipid biosynthesis and pentose phosphate pathway, while Ct's incomplete tricarboxylic acid cycle and fatty acid biosynthesis are less active. EB is more activated in almost all these carbohydrate pathways than RB. Result suggests the survival of Ct generally requires a lot of acetyl-CoA from the host. Besides, both EB and RB can utilize folate biosynthesis to generate NAD(P)H but may use different pathways depending on the demands of ATP. When more ATP is available from both host cell and Ct itself, RB is more activated by utilizing energy providing chemicals generated by enzymes associated in the nucleic acid metabolism. The forming of folate also suggests large glutamate consumption, which is supposed to be converted from glutamine by the glutamine-fructose-6-phosphate transaminase (glmS) and CTP synthase (pyrG).
Then, RNA sequencing (RNA-seq) data analysis was performed by me in a coinfection study. Metatranscriptome from patient RNA-seq data provides a realistic overview. Thirteen patient samples were collected and sequenced by our collaborators. Six male samples were obtained by urethral swab, and seven female samples were collected by cervicovaginal lavage. All the samples were Neisseria gonorrhoeae (GC) positive, and half of them had coinfection with Ct. HISAT2 and Stringtie were used for transcriptomic mapping and assembly respectively, and differential expression analysis by DESeq2, Ballgown and Cuffdiff2 are parallelly processed for comparison. Although the measured transcripts were not sufficient to assemble Ct's transcriptome, the differential expression of genes in both the host and GC were analyzed by comparing Ct positive group (Ct+) against Ct-uninfected group. The results show that in the Ct+ group, the host MHC class II immune response was highly induced. Ct infection is associated with the regulation of DNA methylation, DNA double-strand damage and ubiquitination. The analysis also shows Ct infection enhances host fatty acid beta oxidation, thereby inducing mROS, and the host responds to reduce ceramide production and glycolysis. The coinfection upregulates GC's own ion transporters and amino acid uptake, while it downregulates GC's restriction and modification systems. Meanwhile, GC has the nitrosative and oxidative stress response and also increases the ability for ferric uptake especially in the Ct+ group compared to Ct-uninfected group.
In conclusion, methods in bioinformatics were used here in analyzing the metabolism of Ct itself, and the responses of the host and GC respectively in a coinfection study with and without Ct. These methods provide metabolic and metatranscriptomic details to study Ct metabolism during infection and Ct associated coinfection in the human microbiota.
Neisseria gonorrhoeae (GC) is a human specific pathogenic bacterium. Currently, N. gonorrhoeae developed resistance to virtually all the available antibiotics used for treatment. N. gonorrhoeae starts infection by colonizing the cell surface, followed by invasion of the host cell, intracellular persistence, transcytosis and exit into the subepithelial space. Subepithelial bacteria can reach the bloodstream and disseminate to other tissues causing systemic infections, which leads to serious conditions such as arthritis and pneumonia. A number of studies have well established the host-pathogen interactions during the initial adherence and invasion steps. However, the mechanism of intracellular survival and traversal is poorly understood so far. Hence, identification of novel bacterial virulence factors and host factors involved in the host-pathogen interaction is a crucial step in understanding disease development and uncovering novel therapeutic approaches. Besides, most of the previous studies about N. gonorrhoeae were performed in the conventional cell culture. Although they have provided insights into host-pathogen interactions, much information about the native infection microenvironment, such as cell polarization and barrier function, is still missing.
This work focused on determining the function of novel bacterial virulence factor NGFG_01605 and host factor (FLCN) in gonococcal infection. NGFG_01605 was identified by Tn5 transposon library screening. It is a putative U32 protease. Unlike other proteins in this family, it is not secreted and has no ex vivo protease activity. NGFG_01605 knockout decreases gonococcal survival in the epithelial cell. 3D models based on T84 cell was developed for the bacterial transmigration assay. NGFG_01605 knockout does not affect gonococcal transmigration.
The novel host factor FLCN was identified by shRNA library screening in search for factors that affected gonococcal adherence and/or internalization. We discovered that FLCN did not affect N. gonorrhoeae adherence and invasion but was essential for bacterial survival. Since programmed cell death is a host defence mechanism against intracellular pathogens, we further explored apoptosis and autophagy upon gonococcal infection and determined that FLCN did not affect apoptosis but inhibited autophagy. Moreover, we found that FLCN inhibited the expression of E-cadherin. Knockdown of E- cadherin decreased the autophagy flux and supported N. gonorrhoeae survival. Both non-polarized and polarized cells are present in the cervix, and additionally, E-cadherin represents different polarization properties on these different cells. Therefore, we established 3-D models to better understand the functions of FLCN. We discovered that FLCN was critical for N. gonorrhoeae survival in the 3-D environment as well, but not through inhibiting autophagy. Furthermore, FLCN inhibits the E-cadherin expression and disturbs its polarization in the 3-D models. Since N. gonorrhoeae can cross the epithelial cell barriers through both cell-cell junctions and transcellular migration, we further explored the roles FLCN and E-cadherin played in transmigration. FLCN delayed N. gonorrhoeae transmigration, whereas the knockdown of E-cadherin increased N. gonorrhoeae transmigration.
In summary, we revealed roles of the NGFG_01605 and FLCN-E-cadherin axis play in N. gonorrhoeae infection, particularly in relation to intracellular survival and transmigration. This is also the first study that connects FLCN and human-specific pathogen infection.