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Methods of murine brain 3D imaging focusing on tissue clearing
Novák, Jaromír ; Drbal, Karel (advisor) ; Němec, Pavel (referee)
1 ABSTRACT Many variants of microscopic techniques are the key methods for tissue structure examination in the research as well as in clinical practice. Since the vast majority of examined tissues are intrinsically opaque, it is difficult to reconstruct their 3D structure with light microscopy. However the spatial structure is inherently connected to the function of cells, tissues or whole organs. The most common approach is sample sectioning to the thin layers, which are subsequently examined or used for 3D structure reconstruction of the sample. A different approach is to use a series of chemical reagents able to clear the samples and make them accessible for imaging via microscopy without the need for physical sectioning. Although this approach was first used more than a century ago, the widespread use of these methods came in the last few years. Since the resurgence of tissue clearing method a lot of new principles how to clear the samples were discovered as well as many new chemical compounds can be used for this purpose.. Clearing methods are becoming more and more sophisticated: the volume of samples which can be cleared is continuously growing, new methods are becoming faster and automated, the quality of after-cleared tissues is improving and compatibility with many stains including antibodies is...
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Experimental verification of in silico predicted protein binder to FOXO4 transcription factor and transcriptome analysis of bladder cancer
Tauš, Petr ; Drbal, Karel (advisor) ; Převorovský, Martin (referee)
This diploma thesis includes an experimental and a bioinformatic part. The two parts are linked together through the subject of transcription factors of 'forkhead box O' (FOXO) family. FOXO transcription factors have a key role in many cellular processes including cell cycle regulation, apoptosis and metabolism. For a long time, they have been considered strictly as the tumor-suppressors yet a growing number of evidence is pointing out to their pro-tumorigenic role. In consequence FOXO transcription factors are studied intensively as potential therapeutic targets in cancer. In the past decade, in silico prediction of protein-protein interactions has become popular in basic research as well as in drug development. Nonetheless, the predicted structures are still far from fitting to the expected behavior of the respective biomolecules. In the experimental part of this thesis, I verified the interaction of four in silico predicted protein binders based on naturally occurring PDZ domain with FOXO4 using microscale thermophoresis. Non-invasive bladder tumors represent a heterogeneous disease where reliable prediction of tumor aggressiveness is still lacking despite an intensive research. In the bioinformatic part of this thesis, I described the cellular composition of the tumor microenvironment and demonstrated...
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Immunoscore in 3D tissue
Novák, Jaromír ; Drbal, Karel (advisor) ; Procházka, Jan (referee)
Solid tumors are complex structures comprising besides the cancer cells vasculature, extracellular matrix (ECM), soluble molecules and a plethora of various other cell types. These components form a so-called tumour microenvironment. From the numerous cell types that are part of tumor microenvironment, tumor infiltrating lymphocytes (TILs) play a major role in patient prognosis. Their presence is also of major importance with regard to new biological therapies based on immune checkpoint inhibitors. Crucial role of TILs is also reflected by the new approaches in cancer diagnostics namely by Immunoscore method (currently used in clinical settings). Immunoscore is based on localization and quantification of CD3+ and CD8+ TILs in thin histological sections of tumor tissue. The question remains to which extent the information obtained from 2D slices reflects the situation in tumor microenvironment considering its spatial heterogeneity. The development of new methodological approaches allowing evaluation of histological information in 3D is the key to answer this question. The theoretical part of this work first describes the heterogeneity of the tumor microenvironment and the role of immune cells within it. Then, the role of spatial heterogeneity and its possible influence on the histopathological...
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Antigenome defines a selection of mutated tumor peptides driving tumor-specific T-cell response
Hadlová, Petra ; Drbal, Karel (advisor) ; Dibus, Michal (referee)
T cells, as an essential part of the adaptive immune system, play crucial role in eradication of tumor growth. T cells target, interact with and eventually annihilate the tumor cells in antigen- specific (Ag) manner. T cells interact with tumor cells via short epitopes bound to the major histocompatibility complex (MHC) molecules on the tumor cell surface. Tumor specific neoepitopes arise from random somatic mutations and constitute a part of the tumor antigenome. Antigenome comprises of two classes of antigens, tumor specific antigens (TSA) and tumor associated antigens (TAA). TSA are neoantigens carrying neoepitopes unique to each tumor. TAA are self-antigens presented by both tumor cells and non-transformed cells. Each tumor cell is able to develop numerous ways to evade the immune system consisting of T cells, NK cells, macrophages and other mechanisms employed. Despite that immunotherapy has shown a great potential in personalized medicine. The stratification of responsive patients is essential for effective and durable management of therapy in clinical practice. Methods are employed, which study existing reactive T cell clones, somatic mutations present in each patient, role of somatic mutations in tumor development and present neoepitopes. All these patient- specific features facilitate...
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Immune response in mammalian species against progenitor cell types including induced pluripotent stem cells (iPSCs)
Kovandová, Barbora ; Drbal, Karel (advisor) ; Krulová, Magdaléna (referee)
Stem cells may be very useful tool for regenerative medicine. They are able to repair any tissue in a human body and cure any damage caused by injury, sickness or aging. But at first, we have to deal with problems, which are connected with their usage - especially their immunogenicity. This bachelor thesis is focused on immunogenicity of embryonal (ESC), induced pluripotent (iPSC) and adult stem cells (ASC). Tissues derived from ESC are in vivo described as strongly immunogenic, although they seem to be immunosuppressive in vitro. Another danger of their usage is their tumorigenic potential. There also exist ethical issues connected with their usage. iPSC were supposed to be a good replacement for ESC, because no immunological nor ethical problems were expected. Surprisingly, they were described as immunogenic, too, even in autologous environment. These cells were also described as tumorigenic; this is the main reason for now why they cannot be used for the replacement therapy. Immunogenicity, so as tumorigenicity of iPSC may be a consequence of their dedifferentiation from somatic back to stem cells. ASC are the only stem cells, which are already used for the replacement therapy (transplantation of bone marrow). Some of them are described as immunosuppressive or tumor-suppressive, other are...
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Změny střevního mikrobiomu u pacietů s idiotypickými střevními záněty léčenými pomocí anti-TNF-α
Damašková, Dagmar ; Mrázek, Jakub (advisor) ; Drbal, Karel (referee)
English Abstract Crohn's disease together with ulcerative colitis, is a type of inflammatory bowel disease (IBD) with increasing incidence and prevalence in developed countries. IBD is an immunologically mediated multifactorial disease and it's mechanism of action is still unknown. Current well- established treatment targets the inflammation with corticosteroids and immunosuppressive drugs. Apart from the intestinal inflammation, which is the primary target of the treatment, patients are characteristically afflicted with intestinal dysbiosis. Therefore, possible interventions might be an adjuvant or biological therapy. Adjuvant therapy directly aims the microbiota with probiotics, whereas the target of biological therapy is TNF-α, a pro- inflammatory cytokine excessively secreted by macrophages. The aim of this thesis is to evaluate intestinal microbiota composition changes in IBD patients with regard to courses of adjuvant and biological therapy. Bacterial diversity was analyzed using three different DNA extraction techniques. Rapid beat beating + column (RBB+C) was chosen for analyzing patient samples, as it showed the highest DNA yield and the highest DNA purity. Primarily the bacterial diversity was analyzed using degradation gradient gel electrophoresis (DGGE) with subsequent sequencing of bands of...
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Tumor microenvironment and the importance of anti-tumor immunity for clinical course of human cancers
Partlová, Simona ; Špíšek, Radek (advisor) ; Drbal, Karel (referee) ; Kovář, Marek (referee)
Cancer development and progression vary depending on tumor type, localization, invasion, immunogenicity and the ability of immune system to become activated. There are frequent interactions between tumor cells and immune cells, occuring locally at the site of primary tumor or distally through paracrine signalling of various mediators and cytokines. The main subject of this PhD thesis is to study key factors and aspects of immune response in cancer patients. In the first part, we analyzed immune cells infiltrating tumor tissues of ovarian cancer patients at different stages of disease. We focused on the dynamics of immune response, primarily on frequency of individual T lymphocyte populations in peripheral blood and tumor infiltrating T lymphocytes in tumors of early and advanced stages of ovarian cancer. We found that during disease progression there is a gradual decrease of proinflammatory Th17 and Th1 immune responses and a specific recruitment of regulatory T cells to the tumor site, which results in a significant immune suppression in the tumor microenvironment. In the second part, we demonstrated that the character of immune response in HPV-positive head and neck cancer patients is very different from the patients with tumors not associated with HPV infection. In HPV-positive patients, significantly...
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Molecular mechanisms and components controlling the Wnt signaling pathway output
Krausová, Michaela ; Kořínek, Vladimír (advisor) ; Drbal, Karel (referee) ; Bryja, Vítězslav (referee)
Beyond its essential roles in embryonic development, the Wnt-mediated signal transduction cascade is critically implicated in homeostasis of adult tissues. In the gastrointestinal epithelium, the threshold of active Wnt signaling is kept in a physiological range by a spectrum of regulatory networks and loops, thereby balancing the opposing processes of cell fate determination, proliferation and stem cell self-renewal. Furthermore, compelling evidence undoubtedly link an aberrant Wnt activity to the onset of bowel cancer. Understanding the principle causes and effects secondary to excessive Wnt signaling can provide valuable insights into the pathology of the malignant transformation of the colorectum. The proposed thesis attempts to focus on novel modes of the Wnt pathway modulation; both general and context-specific nuances of the Wnt level adjustment are thereby delineated. The results are presented in three distinct research publications and one review article. The first study examines the contribution of the distinct post-translational modifications, which the Wnt proteins undergo, to their proper processing, secretion and signaling activity. First, we investigated the sequential order and mutual interdependence of cysteine and serine-linked fatty acylation and N-linked glycosylation of murine...
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Regulatory mechanisms of CD47 surface expression
Jakubec, Martin ; Drbal, Karel (advisor) ; Dibus, Michal (referee)
CD47 glycoprotein can be found on the surface of all healthy cells in our body. The interaction of CD47 with inhibitory receptor SIRPα on the macrophage leads to the inhibition of phagocytosis. This makes CD47 irreplaceable for the safe recognition of own cells and removal of aged or apoptotic cells. Apart from this, CD47 plays a major role in several essential signalling pathways, such as cell adhesion and motility or calcium homeostasis. The level of CD47 expression and its presence on the cell membrane depends not only on the type of tissue, but also on the age of a cell. An increased expression of CD47 protein has also been observed in the cells undergoing tumorigenic transformation, allowing them to escape from tumour immunosurveillance. Spontaneous regulation of the CD47 gene expression is achieved via regulatory transcription factors, such as NF-κB or HIF-1. Another mechanism of CD47 regulation includes the 3'UTR of CD47 mRNA, which serves as a binding site for either regulatory proteins, such as HuR, or miRNAs. CD47 expression can thus be regulated on both transcriptional, as well as translational level. However, appropriate topological CD47 localization within the cell and on the cell surface has also an important effect of its physiological function. Our in depth understanding of key regulatory...
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