@phdthesis{Imdahl2023,
  author    = {Imdahl, Fabian Dominik},
  title     = {Development of novel experimental approaches to decipher host-pathogen interaction at the single-cell level},
  doi       = {10.25972/OPUS-28943},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-289435},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Abstract: COVID-19 has impressively shown how quickly an emerging pathogen can have a massive impact on our entire lives and show how infectious diseases spread regardless of national borders and economic stability. We find ourselves in a post-antibiotic era and have rested too long on the laurels of past research, so today more and more people are dying from infections with multi-resistant germs. Infections are highly plastic and heterogeneous processes that are strongly dependent on the individual, whether on the host or pathogen side. Improving our understanding of the pathogenicity of microorganisms and finding potential targets for a completely new class of drugs is a declared goal of current basic research. To tackle this challenge, single-cell RNA sequencing (scRNA-seq) is our most accurate tool. In this thesis we implemented different state of the art scRNA-seq technologies to better understand infectious diseases. Furthermore, we developed a new method which is capable to resolve the transcriptome of a single bacterium. Applying a poly(A)-independent scRNA-seq protocol to three different, infection relevant growth conditions we can report the faithful detection of growth-dependent gene expression patterns in individual Salmonella Typhimurium and Pseudomonas aeruginosa bacteria. The data analysis shows that this method not only allows the differentiation of various culture conditions but can also capture transcripts across different RNA species. Furthermore, using state of the art imaging and single-cell RNA sequencing technologies, we comprehensively characterized a human intestinal tissue model which in further course of the project was used as a Salmonella enterica serovar Typhimurium infection model. While most infection studies are conducted in mice, lacking a human intestinal physiology, the in vitro human tissue model allows us to directly infer in vivo pathogenesis. Combining immunofluorescent imaging, deep single-cell RNA sequencing and HCR-FISH, applied in time course experiments, allows an unseen resolution for studying heterogeneity and the dynamics of Salmonella infection which reveals details of pathogenicity contrary to the general scientific opinion.},
  subject      = {Salmonella},
  language  = {en}
}
@phdthesis{Ranecky2023,
  author    = {Ranecky, Maria Helena},
  title     = {Experimentelle Charakterisierung intestinaler, GvHD-protektiver myeloider Empf{\"a}ngerzellen nach allogener Stammzelltransplantation},
  doi       = {10.25972/OPUS-31092},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-310924},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Die akute Graft-versus-Host Disease (GvHD) und speziell ihre intestinale Manifestation ist eine schwere Komplikation der allogenen Stammzelltransplantation mit erheblichem Einfluss auf Mortalit{\"a}t und Morbidit{\"a}t der Patienten. Pathophysiologisch stellt sie eine Immunreaktion von Spender-T-Zellen auf Empf{\"a}ngergewebestrukturen dar. In Versuchsm{\"a}usen ist die experimentelle Depletion CD11c+ Antigen-pr{\"a}sentierender Empf{\"a}ngerzellen in der fr{\"u}hen GvHD-Effektorphase assoziiert mit einem schlechteren klinischen Outcome, einer h{\"o}heren Dichte alloreaktiver T-Zellen und einer verst{\"a}rkten Entz{\"u}ndungsreaktion in der intestinalen Mukosa. Ziel der Studie war eine umfassende Charakterisierung und systematische Einordnung der folglich GvHD-protektiven intestinalen CD11c+ Empf{\"a}ngerzellen. Bez{\"u}glich ihrer Oberfl{\"a}chenproteinsignatur analysierten wir die myeloiden Zellen der intestinalen Mukosa am Tag 6 nach allogener Stammzelltransplantation. Mittels durchflusszytometrischer Analyse und Vergleich zwischen gesunden, allein bestrahlten und GvHD-M{\"a}usen ordneten wir die CD11c+ Empf{\"a}ngerzellen als Makrophagen ein und schlossen eine Identit{\"a}t als dendritische Zellen aus. In der Immunfluoreszenzmikroskopie wiesen wir ihre Kolokalisation mit allogenen T-Zellen nach und best{\"a}tigten darin eine PD-L1 Expression als m{\"o}glichen T-Zell-Suppressionsmechanismus. Bez{\"u}glich ihres Transkriptoms f{\"u}hrten wir eine Einzelzell-RNA-Sequenzierung intestinaler h{\"a}matopoetischer Empf{\"a}ngerzellen aus CD11c+ Zell-depletierten und nicht depletierten M{\"a}usen durch. Auf rein bioinformatischer Grundlage wurden die Einzelzellen kombiniert und anhand ihrer Transkriptomprofile in Cluster eingeteilt. Der Vergleich beider Versuchsgruppen offenbarte zwei unterschiedliche pr{\"a}sente bzw. depletierte und damit GvHD-protektive Zellcluster: Cluster 4 enthielt Zellen mit deutlicher Makrophagensignatur und gewebeprotektivem, antipathogenem Effektorprofil, welches in Kombination mit weiteren Genen ein Kontinuum der in Hom{\"o}ostase vorhandenen Makrophagen nahelegte. Cluster 10 dagegen enthielt Zellen mit immun- und spezifisch T-Zell-suppressivem Effektorprofil, weniger deutlicher Makrophagensignatur und {\"A}hnlichkeit zu myeloiden Suppressorzellen. Somit lieferte die Studie wichtige Hinweise auf einen Mechanismus der GvHD- bzw. T-Zell-Suppression und Gewebeprotektion in Form von physiologisch vorhandenen bzw. im Laufe der GvHD auftretenden Empf{\"a}ngermakrophagen.},
  subject      = {Makrophage},
  language  = {de}
}
@phdthesis{Fey2022,
  author    = {Fey, Christina},
  title     = {Establishment of an intestinal tissue model for pre-clinical screenings},
  doi       = {10.25972/OPUS-24410},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-244107},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {The small intestine represents a strong barrier separating the lumen from blood circulation thereby playing a major role in the absorption and the transport of pharmacological agents prior to their arrival on the respective target site. In order to gain more knowledge about specialized uptake mechanisms and risk assessment for the patient after oral admission of drugs, intestinal in vitro models demonstrating a close similarity to the in vivo situation are needed. In the past, cell line-based in vitro models composed of Caco-2 cells cultured on synthetic cell carriers represented the "gold standard" in the field of intestinal tissue engineering. Expressive advantages of these models are a reproducible, cost-efficient and standardized model set up, but cell function can be negatively influenced by the low porosity or unwanted molecular adhesion effects of the artificial scaffold material. Natural extracellular matrices (ECM) such as the porcine decellularized small intestinal submucosa (SIS) are used as alternative to overcome some common drawbacks; however, the fabrication of these scaffolds is time- and cost-intensive, less well standardized and the 3Rs (replacement, reduction, refinement) principle is not entirely fulfilled. Nowadays, biopolymer-based scaffolds such as the bacterial nanocellulose (BNC) suggest an interesting option of novel intestinal tissue engineered models, as the BNC shows comparable features to the native ECM regarding fiber arrangement and hydrophilic properties. Furthermore, the BNC is of non-animal origin and the manufacturing process is faster as well as well standardized at low costs. In this context, the first part of this thesis analyzed the BNC as alternative scaffold to derive standardized and functional organ models in vitro. Therefore, Caco-2 cells were cultured on two versions of BNC with respect to their surface topography, the unmodified BNC as rather smooth surface and the surface-structured BNC presenting an aligned fiber arrangement. As controls, Caco-2 in vitro models were set up on PET and SIS matrices. In this study, the BNC-based models demonstrated organ-specific properties comprising typical cellular morphologies, a characteristic tight junction protein expression profile, representative ultrastructural features and the formation of a tight epithelial barrier together with a corresponding transport activity. In summary, these results validated the high quality of the BNC-based Caco-2 models under cost-efficient conditions and their suitability for pre-clinical research purposes. However, the full functional diversity of the human intestine cannot be presented by Caco-2 cells due to their tumorigenic background and their exclusive representation of mature enterocytes. Next to the scaffold used for the setup of in vitro models, the cellular unit mainly drives functional performance, which demonstrates the crucial importance of mimicking the cellular diversity of the small intestine in vitro. In this context, intestinal primary organoids are of high interest, as they show a close similarity to the native epithelium regarding their cellular diversity comprising enterocytes, goblet cells, enteroendocrine cells, paneth cells, transit amplifying cells and stem cells. In general, such primary organoids grow in a 3D Matrigel® based environment and a medium formulation supplemented with a variety of growth factors to maintain stemness, to inhibit differentiation and to stimulate cell migration supporting long term in vitro culture. Intestinal primary spheroid/organoid cultures were set up as Transwell®-like models on both BNC variants, which resulted in a fragmentary cell layer and thereby unfavorable properties of these scaffold materials under the applied circumstances. As the BNC manufacturing process is highly flexible, surface properties could be adapted in future studies to enable a good cell adherence and barrier formation for primary intestinal cells, too. However, the application of these organoid cultures in pre-clinical research represents an enormous challenge, as the in vitro culture is complex and additionally time- and cost-intensive. With regard to the high potential of primary intestinal spheroids/organoids and the necessity of a simplified but predictive model in pre-clinical research purposes, the second part of this thesis addressed the establishment of a primary-derived immortalized intestinal cell line, which enables a standardized and cost-efficient culture (including in 2D), while maintaining the cellular diversity of the organoid in vitro cultures. In this study, immortalization of murine and human intestinal primary organoids was induced by ectopic expression of a 10- (murine) or 12 component (human) pool of genes regulating stemness and the cell cycle, which was performed in cooperation with the InSCREENeX GmbH in a 2D- and 3D-based transduction strategy. In first line, the established cell lines (cell clones) were investigated for their cell culture prerequisites to grow under simplified and cost-efficient conditions. While murine cell clones grew on uncoated plastic in a medium formulation supplemented with EGF, Noggin, Y-27632 and 10\% FCS, the human cell clones demonstrated the necessity of a Col I pre coating together with the need for a medium composition commonly used for primary human spheroid/organoid cultures. Furthermore, the preceding analyses resulted in only one human cell clone and three murine cell clones for ongoing characterization. Studies regarding the proliferative properties and the specific gene as well as protein expression profile of the remaining cell clones have shown, that it is likely that transient amplifying cells (TACs) were immortalized instead of the differentiated cell types localized in primary organoids, as 2D, 3D or Transwell®-based cultures resulted in slightly different gene expression profiles and in a dramatically reduced mRNA transcript level for the analyzed marker genes representative for the differentiated cell types of the native epithelium. Further, 3D cultures demonstrated the formation of spheroid-like structures; however without forming organoid-like structures due to prolonged culture, indicating that these cell populations have lost their ability to differentiate into specific intestinal cell types. The Transwell®-based models set up of each clone exhibit organ-specific properties comprising an epithelial-like morphology, a characteristic protein expression profile with an apical mucus-layer covering the villin-1 positive cell layer, thereby representing goblet cells and enterocytes, together with representative tight junction complexes indicating an integer epithelial barrier. The proof of a functional as well as tight epithelial barrier in TEER measurements and in vivo-like transport activities qualified the established cell clones as alternative cell sources for tissue engineered models representing the small intestine to some extent. Additionally, the easy handling and cell expansion under more cost-efficient conditions compared to primary organoid cultures favors the use of these newly generated cell clones in bioavailability studies. Altogether, this work demonstrated new components, structural and cellular, for the establishment of alternative in vitro models of the small intestinal epithelium, which could be used in pre-clinical screenings for reproducible drug delivery studies.},
  subject      = {D{\"u}nndarm},
  language  = {en}
}
@phdthesis{Schweinlin2016,
  author    = {Schweinlin, Matthias Oliver},
  title     = {Development of advanced human intestinal in vitro models},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142571},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {The main function of the small intestine is the absorption of essential nutrients, water and vitamins. Moreover, it constitutes a barrier protecting us from toxic xenobiotics and pathogens. For a better understanding of these processes, the development of intestinal in vitro models is of great interest to the study of pharmacological and pathological issues such as transport mechanisms and barrier function. Depending on the scientific questions, models of different complexity can be applied. In vitro Transwell® systems based on a porous PET-membrane enable the standardized study of transport mechanisms across the intestinal barrier as well as the investigation of the influence of target substances on barrier integrity. However, this artificial setup reflects only limited aspects of the physiology of the native small intestine and can pose an additional physical barrier. Hence, the applications of this model for tissue engineering are limited. Previously, tissue models based on a biological decellularized scaffold derived from porcine gut tissue were demonstrated to be a good alternative to the commonly used Transwell® system. This study showed that preserved biological extracellular matrix components like collagen and elastin provide a natural environment for the epithelial cells, promoting cell adhesion and growth. Intestinal epithelial cells such as Caco-2 cultured on such a scaffold showed a confluent, tight monolayer on the apical surface. Additionally, myofibroblasts were able to migrate into the scaffold supporting intestinal barrier formation. In this thesis, dendritic cells were additionally introduced to this model mimicking an important component of the immune system. This co-culture model was then successfully proven to be suitable for the screening of particle formulations developed as delivery system for cancer antigens in peroral vaccination studies. In particular, nanoparticles based on PLGA, PEG-PAGE-PLGA, Mannose-PEG-PAGE-PLGA and Chitosan were tested. Uptake studies revealed only slight differences in the transcellular transport rate among the different particles. Dendritic cells were shown to phagocytose the particles after they have passed the intestinal barrier. The particles demonstrated to be an effective carrier system to transport peptides across the intestinal barrier and therefore present a useful tool for the development of novel drugs. Furthermore, to mimic the complex structure and physiology of the gut including the presence of multiple different cell types, the Caco-2 cell line was replaced by primary intestinal cells to set up a de novo tissue model. To that end, intestinal crypts including undifferentiated stem cells and progenitor cells were isolated from human small intestinal tissue samples (jejunum) and expanded in vitro in organoid cultures. Cells were cultured on the decellularized porcine gut matrix in co-culture with intestinal myofibroblasts. These novel tissue models were maintained under either static or dynamic conditions. Primary intestinal epithelial cells formed a confluent monolayer including the major differentiated cell types positive for mucin (goblet cells), villin (enterocytes), chromogranin A (enteroendocrine cells) and lysozyme (paneth cells). Electron microscopy images depicted essential functional units of an intact epithelium, such as microvilli and tight junctions. FITC-dextran permeability and TEER measurements were used to assess tightness of the cell layer. Models showed characteristic transport activity for several reference substances. Mechanical stimulation of the cells by a dynamic culture system had a great impact on barrier integrity and transporter activity resulting in a tighter barrier and a higher efflux transporter activity. In Summary, the use of primary human intestinal cells combined with a biological decellularized scaffold offers a new and promising way to setup more physiological intestinal in vitro models. Maintenance of primary intestinal stem cells with their proliferation and differentiation potential together with adjusted culture protocols might help further improve the models. In particular, dynamic culture systems and co culture models proofed to be a first crucial steps towards a more physiological model. Such tissue models might be useful to improve the predictive power of in vitro models and in vitro in vivo correlation (IVIVC) studies. Moreover, these tissue models will be useful tools in preclinical studies to test pharmaceutical substances, probiotic active organisms, human pathogenic germs and could even be used to build up patient-specific tissue model for personalized medicine.},
  subject      = {Tissue Engineering},
  language  = {en}
}
@phdthesis{Srinivasan2013,
  author    = {Srinivasan, Aruna},
  title     = {RS1 protein dependent and independent short and long term regulation of sodium dependent glucose transporter -1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85665},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {The Na+-D-glucose cotransporter in small intestine is regulated in response to food composition. Short term regulation of SGLT1 occurs post-transcriptionally in response to changes in luminal glucose. Adaptation to dietary carbohydrate involves long term regulation at the transcriptional level. The intracellular protein RS1 (gene RSC1A1) is involved in transcriptional and post-transcriptional regulation of SGLT1. RS1 contains an N-terminal domain with many putative phosphorylation sites. By Expressing SGLT1 in oocytes of Xenopus laevis it was previously demonstrated that the post-transcriptional down-regulation of SGLT1 by RS1 was dependent on the intracellular glucose concentration and activated by protein kinase C (PKC). The role of RS1 for short term regulation of SGLT1 in mouse small intestine in response to glucose and PKC was investigated comparing effects in RS1-/- mice and wildtype mice. Effects on SGLT1 activity were determined by measuring phlorizin inhibited uptake of α-methylglucoside (AMG). The involvement of RS1 in glucose dependent short term regulation could not be elucidated for technical reasons. However, evidence for RS1 independent short-term downregulation of SGLT1 after stimulation of PKC could be provided. It was shown that this downregulation includes decrease in the amount and/or in turnover of SGLT1 in the brush-border membrane as well as an increase of substrate affinity for AMG transport. Trying to elucidate the role of RS1 in long term regulation of SGLT1 in small intestine in response to glucose and fat content of the diet, wildtype and RS1-/- mice were kept for 2 months on a normo-caloric standard diet with high glucose and low fat content (ND), on a hyper-caloric glucose-galactose reduced diet with high fat content (GGRD) or on a hyper-caloric diet with a high fat and high glucose content (HFHGD). Thereafter the animals were starved overnight and SGLT1 mediated AMG uptake was measured. Independent of diet AMG uptake in ileum was smaller compared to duodenum and jejunum. In jejunum of wildtype and RS1-/- mice kept on the fat rich diets (GGRD and HFHGH) transport activity of SGLT1 was lower compared to mice kept on ND with low fat content. This result suggests an RS1 independent downregulation due to fat content of diet. Different to RS1-/- mice, the duodenum of wildtype mice showed transport activity of SGLT1 smaller in mice kept on glucose galactose reduced diet (GGRD) compared to the glucose galactose rich diets (ND and HFHGG). These data indicate that RS1 is involved in glucose dependent long term regulation in duodenum.},
  subject      = {Glucosetransportproteine},
  language  = {en}
}