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Preclinical models of brain metastases
Smetana, Tadeáš Karel ; Výmolová, Barbora (advisor) ; Sedlák, František (referee)
Malignant diseases are the second most common cause of death in the Czech Republic. One of the serious complications of these diseases are brain metastases, the incidence of which is increasing due to the improvement of diagnostics and advances in the therapy of the primary tumors. However, the treatment of brain metastases is complicated by their localization and the presence of the blood-brain barrier, which affects the efficacy of many drugs. Preclinical models are essential for better understanding of the biological properties of metastasizing cells, their relationship to the unique microenvironment of brain tissue, and for testing new therapeutic approaches. This bachelor thesis focuses on in vitro and in vivo systems modelling key aspects of brain metastasis biology and their use in testing new therapeutic approaches.
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The role of cytochalasins in cancer cell migration and invasiveness
Brož, Alexandr ; Brábek, Jan (advisor) ; Bašta, Miroslav (referee)
While metastasis causes the majority of cancer related deaths, purely migrastatic drugs have been neglected in clinical research. This trend has been changing in recent years, with drugs capable of preventing metastasis, migrastatics, coming into focus. Cytochalasins are a large group of actin-directed fungal metabolites, often used for cytoskeletal and anticancer research. As the actin cytoskeleton plays a major role in tumour cell invasion and migration, processes integral in metastasis, it is possible that cytochalasins could have a future as migrastatics. The majority of cytochalasin-related research pertains to cytochalasin B and the more potent cytochalasin D, making both a large focus of this thesis, though the lesser researched cytochalasins A, E, H, Q and others are mentioned as well. Cytochalasins B and D have been shown to inhibit migration and invasion of cells with liposome encapsulation reducing side effects greatly, possibly enough to alleviate one of the main concerns of any cytochalasin therapy, toxicity. Though other cytochalasins have also been shown to inhibit cell motility, any conclusions as to their migrastatic translational potential are hard to draw due to the lack of research.
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Design, preparation and structural studies of biologically relevant protein variants of cancer-related Carbonic Anhydrase IX
Fejfarová, Adéla ; Maloy Řezáčová, Pavlína (advisor) ; Novotný, Marian (referee)
3 Abstract Carbonic anhydrase IX (CA IX) represents an attractive target for the development of anticancer drugs as it is overexpressed in various types of solid tumors. By its catalytic activity, CA IX assists the cancer cells to maintain the optimal intracellular pH and to acidify the extracellular milieu promoting tumor development. There are twelve enzymatically active carbonic anhydrases (CAs) present in human body, all sharing a high sequence identity and a typical β-sheet structural fold of the well-studied catalytic domain. Although, the activity of CAs is efficiently inhibited by sulfonamide-containing compounds, the design of inhibitor selective to the cancer-related CA IX has been hampered by the high sequence conservation. CA IX has several unique features compared to other members of the family, which investigation may help in the development of selective drug compounds. Namely, it is a type I transmembrane dimeric protein with unique N-terminal proteoglycan-like (PG) domain, extracellular catalytic domain, and short cytoplasmic C-terminal segment. The above denoted traits make CA IX subject of structure-based drug design efforts. However, the expression and purification in high yield as well as crystallization experiments has been challenging. Therefore, protein variant bearing six amino acid...
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Macrophages selectively sense mechanical cell death in CLASP-depleted melanoma cells to trigger CXCL10 response
Otruba, Matúš ; Labzin, Larisa (advisor) ; Filipp, Dominik (referee)
Melanoma represents a significant and often fatal form of cancer, with metastasis being a primary cause of cancer-related deaths. Immunotherapy aims to stimulate the immune system to eliminate tumors, but even when used together with traditional chemotherapy, still only has <50% success rate. Chemotherapeutic drugs induce tumor cell death, primarily through apoptosis, which is 'silent' and does not incite inflammation or immune cell infiltration into the tumor. During metastasis, tumor cells migrate through confined spaces. CLASP proteins protect organelles and cellular integrity during tumor cell metastasis; when CLASP proteins are depleted, tumor cells migrating through tissue die through a mechanical cell death. The immunological impact of CLASP depletion-induced cell death remains unknown. This study aims to explore whether macrophages, innate immune cells that sense neighboring dying cells, trigger inflammatory cytokine responses specifically to mechanical, as opposed to chemotherapeutic, melanoma cell death. To model mechanical cell death during metastatic migration, CLASP1, a microtubule stabilizing protein, was depleted, and cells were physically compressed to simulate forces encountered during metastasis. Chemotherapy was simulated using a B-Raf inhibitor and the apoptosis inducer...
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Context-dependent roles of cyclin-dependent kinase inhibitors (CDKi) in cancer
Doležalová, Šárka ; Janoštiak, Radoslav (advisor) ; Macůrek, Libor (referee)
Cell cycle progression is intricately regulated by many proteins. Among these proteins, cyclin- dependent kinase inhibitors (CKIs) play a key role, traditionally associated with cyclin- dependent kinase (CDK) inhibition and cell cycle arrest. However, recent research reveals that their function is much more complex in the context of cancer. CKI inhibitors are not mutated at all in many tumor types, and their expression is maintained or even increased, suggesting additional mechanisms by which they influence tumor pathogenesis. Post-translational modifications, especially phosphorylation, which affect their localization and stability, have a fundamental influence on their function. These modifications can then, for example, affect cell motility, apoptosis, or DNA repair. This can convert CKIs from tumor suppressors to tumor promoters or vice versa, strengthening their tumor suppressor properties. Key words: Cyclin-dependent kinases, inhibitors of cyclin-dependent kinases, cell cycle, cancer, post-translational modification
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Probing natural molecules with PPAR- to reveal potent agonist against Cancer
Špaková, Adriána ; Bhogal, Inderjeet (referee) ; Roy, Sudeep (advisor)
Práca sa zaoberá hľadaním prírodnej molekuly s potenciálnymi agonistickými vlastnosťami proti rakovine. Cieľom práce bolo predovšetkým pochopiť súvislosť medzi receptorom PPAR- a rakovinou. Následne boli molekuly zo šiestich databáz virtuálne skrínované a dokované k nukleárnemu receptoru PPAR- za využitia počítačom podporovaného dizajnu liečiv. Najlepšie molekuly podstúpili ďalšie preskúmanie, vrátane dynamickej simulácie a štúdie viazania voľnej energie. Overenie bezpečnosti najlepších molekúl bolo vykonané predikčnými modelmi ADMET. Dôležitou súčasťou práce bolo porovnanie novoobjavených molekúl disponujúcich agonistickými vlastnosťami proti rakovine s už známymi na trhu. Konkrétne Troglitazón a Rosiglitazón slúžili ako štandardy, ktoré sa vyznačujú vysokou afinitou k receptoru PPAR- a prejavili antineoplastické účinky v rôznych ľudských malígnych nádoroch, vrátane rakoviny prsníka, hrubého čreva a pankreasu. Na druhej strane, tieto dve syntetické molekuly čelia varovaniu zo strany FDA (Úrad pre potraviny a liečivá) v dôsledku ich nepriaznivých vedľajších účinkov. V rámci práce sa podarilo objaviť prírodné molekuly, ktoré vykázali lepšie vlastnosti ako aktuálne štandardy. Tieto sľubné výsledky si zaslúžia ďalšiu pozornosť. Jedna z molekúl by mohla potenciálne viesť k vývoju nového lieku.
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Methods for determination of tumor markers in the blood plasma and their clinical significance in diagnosing
Toman, Karel ; Márová, Ivana (referee) ; Čáslavský, Josef (advisor)
The thesis discusses the methods of determination of tumor markers and their clinical importance in medical diagnostics. The theoretical part describes clinically important tumor markers and also the chemiluminescent immunoassay methods used for their determination. The practical part of the thesis describes the introduction of new chemiluminescent methods for the determination of tumor markers in routine operation, evaluates its basic analytical parameters and compares it with the existing immunoturbidimetric method. The practical part also presents results of monitoring of cancer patients with various tumors, which is performed by evaluation of the values of tumor markers. Comparison of our method with other methods within the context of System of external quality control is also documented.
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Machine learning models for quantifying phenotypic signatures of cancer cells based on transcriptomic and epigenomic data
Koban, Martin ; PhD, Florian Halbritter, (referee) ; Mehnen, Lars (advisor)
S rozvojom techník pre efektívnu akvizíciu genomických dát sa jednou z kľúčových vedeckých výziev stala interpretácia výsledkov týchto experimentov v zmysluplnom biologickom kontexte. Táto práca sa zameriava na využitie informácií ukrytých v dobre charakterizovaných transkriptomických a epigenomických dátach z verejne dostupných zdrojov pre účely takejto interpretácie. Najskôr je vytvorený integrovaný súbor dát generovaných metódami DNase-seq a ATAC-seq, ktoré kvantifikujú chromatínovú dostupnosť. Tieto údaje sú doplnené verejne dostupnými výsledkami techniky RNA-seq pre kvantitatívne hodnotenie génovej expresie a vhodne predspracované pre ďalšiu analýzu. Pripravené dáta sú následne použité na trénovanie modelov strojového učenia (klasifikátorov) s dvomi základnými cieľmi. Po prvé za účelom augmentácie metadát prislúchajúcich k jednotlivým biologickým vzorkám v trénovacom dátovom súbore pomocou predikcie nedefinovaných anotácií. Po druhé pre anotáciu zle charakterizovaných testovacích dát (nepoužitých v trénovacej fáze) za účelom overenia generalizačnej schopnosti zostavených modelov. Dosiahnuté výsledky ukazujú, že natrénované klasifikátory sú schopné zachytiť biologicky relevantné informácie, zatiaľ čo vplyv technických artefaktov je minimalizovaný. Navrhnutý prístup je preto schopný prispieť k lepšiemu pochopeniu komplexných transkriptomických a epigenomických dát, predovšetkým v oblasti onkologického výskumu.
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Natural drugs in cancer treatment and their cytotoxicity
Hájková, Tereza ; Raudenská, Martina (referee) ; Provazník, Ivo (advisor)
The thesis deals with the natural substances in context with the cancer disease. The natural substances have a positive effect on the human organism and they are able to influence the viability and the growth of the cancer cells. The main mechanical device is to influence the mechanisms needed to start the apoptosis of the cancer cells and stopping further proliferation. The cancer cell lines utilization in the cancer disease is discussed in the thesis too. The thesis states common methods of determining the natural substances cytotoxicity. For the experimental part of the thesis it was chosen the MTT test method and the xCELLigence system for monitoring in real time. The mechanical device of the tested substance capsaicin in application on the prostate cell lines, tumorous PC3 and nontumorous PNT1A influence will be observed within the experimental part of the thesis.
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Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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