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Differential Gene expression using a negative binomial model
Janáková, Tereza ; Tkacz, Ewaryst (referee) ; Abo Khayal, Layal (advisor)
Hlavním cílem této diplomové práce je analýza diferenciální exprese genů na základě negativního binomického modelu. Úvodní část je věnována teoretickému základu, pojednává o sekvenování RNA, sekvenování nové generace, výhodách a možném využití, formátu fastQ aj. Následující část už se zabývá samotnou praktickou částí, zde byl vybrán vhodný set genů, které budou později analyzovány a příslušná data byla stažena. Tato data byla zarovnána k lidskému genomu verze 37 Burrowsovou-Wheelerovou transformací s využitím bowtie mapovače, byly tak vytvořeny soubory ve formátu SAM. Toto soubory dat byly později setříděny pomocí nástroje SAMtools. Následně byly v programovém prostředí Matlab (verze R2013b) vytvořeny anotované objekty genů s využitím služby Ensembl´s BioMart. Dále byla určena genová exprese a byly odhadnuty faktory velikosti knihovny. Na závěr byly odhadnuty parametry negativního binomického rozložení a byla vyhodnocena diferenciální exprese genů.
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Cancer Immunotherapy exploiting engineered antibody fragments against prostate-specific membrane antigen
Das, Gargi ; Bařinka, Cyril (advisor) ; Vaněk, Ondřej (referee) ; Ormsby, Tereza (referee)
Prostate cancer (PCa) remains a leading cause of male cancer-related mortality, necessitating thus the development of novel therapeutic approaches as conventional treatments have limited efficacy. Prostate-specific membrane antigen (PSMA) is an established biomarker for both imaging and therapy of PCa, as it is highly upregulated in neoplastic PCa tissues and metastatic castration- resistant prostate cancer. Consequently, immunological targeting of PSMA has gained significant attention as a therapeutic platform for the management of the disease. The thesis is focused on engineering of antibody fragments and fusion proteins derived from the high affinity anti-PSMA 5D3 monoclonal antibody that can be used as immune cell engagers to target and eliminate PSMA-positive cells. To this end, we engineered 5D3 single chain variable fragments (scFv) that were subsequently fused to anti-CD3 scFv and CP33 sequences, creating thus immune cell engagers targeting T-cells (BiTE) and monocytes (5D3-CP33), respectively. The engagers were expressed in insect cells, purified to homogeneity and their biophysical and functional characteristics evaluated using size exclusion chromatography, differential scanning fluorimetry, ELISA and flow cytometry. Ensuing cell-based assays revealed that both BiTE and 5D3-CP33 can...
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Theragnostics - new methods in nuclear medicine
PROCHÁZKOVÁ, Michaela
The main topic of the bachelor thesis is theragnostics - new methods in nuclear medicine. Theragnostics is a personalized treatment strategy that combines diagnostics with therapy and finds application primarily in the treatment of cancer. Theragnostics as a medical field is still evolving. The aim of this work was to map the practical use of current indications of theragnostic methods in nuclear medicine. The theoretical part of the thesis defines the concept of theragnostics and theragnostic methods containing nanoparticles and radionuclides. There is described the use of radionuclide theragnotics in clinical practice, especially in the treatment of thyroid gland, neuroendocrine tumors and prostate cancer. In this part of the thesis there are also clinical studies for theragnotic practice. Furthermore in the theoretical part of the thesis is maped the practical use of current indications of theragnotic methods, as well as possible future perspectives of theragnotic treatment. The theoretical part is processed from professional publications and articles. The practical part of the work focuses on the awareness of radiology assistants about this new treatment method. The respondents were radiology assistants across hospitals. There were 32 respondents involved to complete the research questions for the questionnaire survey. The evaluation from the collected data of the questionnaire survey is in the form of the percentage success of radiological assistants. The overall concept of this bachelor's thesis can serve as a study material for university students in the field of radiology assistant.
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Antibody derivatives for the detection of human glutamatecarboxypeptidase II
Bělousová, Nikola ; Bařinka, Cyril (advisor) ; Pavlíček, Jiří (referee)
Prostate cancer is one of the most common human malignancies and, consequently it is critical to develop appropriate diagnostic and therapeutic tools. Glutamate carboxypeptidase II (GCPII) is currently being considered one of the most important prostate cancer markers due to its tissue- specific expression. Whereas in healthy prostatic tissue the expression levels of GCPII are low, the transformation into the tumor is associated with the substantial increase of GCPII expression, with the highest levels observed in androgen-independent metastatic tumors. GCPII is thus considered a promising marker for early phase as well as advanced metastatic stages of prostate cancer. Current research is focused on the development of highly sensitive and specific reagents that allow detection of small amounts of GCPII, for example in early stages of cancer. Antibody derivatives are promising molecules for this purpose because they have high affinity and specificity and minimum negative side effects. Protein engineering is a prefered approach for preparation of various antibody molecules that differ in size, binding properties, stability, solubility, and production means. Different types of derivatives are being developed for medical needs such as in vitro diagnosis, therapy, and in vivo imagingSmall molecular...
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The use of immunochemical methods in the diagnostic of cancer and degenerative disease
Hanousková, Lenka ; Kotaška, Karel (advisor) ; Bronský, Jiří (referee) ; Štern, Petr (referee)
Introduction: Immunochemical methods have significant importance in biomedical research. The benefit of immunochemical methods is their high sensitivity and accuracy. The aim of the work was to use immunochemical methods in investigation of cancer biomarkers and degenerative diseases. A total of four studies were performed. Two studies were focused on the search for new biomarkers of prostate cancer, the third study was focused on evaluation of FGF23 in patients with hyperparathyroidism, and the fourth study looked at the assessment of hyaluronic acid in synovial fluid of patients with knee gonarthrosis. Methods and patients: Study 1: Concentrations of Chromogranin A, Endoglin, TIMP-1 and thymidine kinase 1 (TK1) in serum and Endoglin, SPINK-1, Annexin, TIMP-1 in urine were measured in 58 patients with the (mean age 68 years, range 45 - 82 years) with clinically diagnosed prostate cancer and in 30 healthy individuals with the (mean age 64 years, range: 55 - 78 years) without clinically relevant urological history and PSA values in the reference range. Subsequently, serum TK1 levels were measured in 169 patients (mean age 62 years, range 45- 82 years) with prostate cancer and in a control group of 39 healthy men (mean age 61 years, range 54-78 years). The TK1 assay was also used to determine the...
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Antibody derivatives for the detection of human glutamatecarboxypeptidase II
Bělousová, Nikola ; Bařinka, Cyril (advisor) ; Pavlíček, Jiří (referee)
Prostate cancer is one of the most common human malignancies and, consequently it is critical to develop appropriate diagnostic and therapeutic tools. Glutamate carboxypeptidase II (GCPII) is currently being considered one of the most important prostate cancer markers due to its tissue- specific expression. Whereas in healthy prostatic tissue the expression levels of GCPII are low, the transformation into the tumor is associated with the substantial increase of GCPII expression, with the highest levels observed in androgen-independent metastatic tumors. GCPII is thus considered a promising marker for early phase as well as advanced metastatic stages of prostate cancer. Current research is focused on the development of highly sensitive and specific reagents that allow detection of small amounts of GCPII, for example in early stages of cancer. Antibody derivatives are promising molecules for this purpose because they have high affinity and specificity and minimum negative side effects. Protein engineering is a prefered approach for preparation of various antibody molecules that differ in size, binding properties, stability, solubility, and production means. Different types of derivatives are being developed for medical needs such as in vitro diagnosis, therapy, and in vivo imagingSmall molecular...
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Comparing the effectiveness of selected methods of cancer treatment. Prostate cancer, breast cancer and lung cancer via survival analysis
Šimonková, Karolína ; Šimpach, Ondřej (advisor) ; Pechholdová, Markéta (referee)
This diploma thesis deals with various ways of treatment of selected oncological diseases and the effectiveness of treatment methods and evaluation of the influence of various factors influencing the survival of patients. The activity of individual healing processes is evaluated by survival analysis. The subjects of the study are patients with breast, lung and prostate cancer. The survival analysis considers the sex of the patient, the age and stage of his illness, and other factors to avoid distorted results. The aim of the work is to find out the effects of selected therapeutic procedures on patients' health and to identify factors that have a significant impact on the survival of patients. The data for the diploma thesis was provided by the Institute of Health Information and Statistics of the Czech Republic, the Statistical Office, the National Cancer Register (NOR), the US SEER database and the German Breast Cancer Study.
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Odpověď metastatických buněčných linií karcinomu prostaty na genotoxický stres
Imrichová, Terezie ; Hodný, Zdeněk (advisor) ; Rösel, Daniel (referee)
Prostate cancer is the fourth most frequent cause of cancer-related deaths in men worldwide. One of current successful approaches to treat prostate cancer is radical prostatectomy followed by radiotherapy. However, this treatment is not 100% successful, as 53% patients develop secondary tumors. Our hypothesis is, that ionizing radiation itself contributes to the development of metastases by inducing changes in cell phenotype, particularly in terms of epithelial-to-mesenchymal transition and stemness. To test this hypothesis, we irradiated the cells of metastatic prostate cancer cell line DU145 by fractionated radiation 2 x 10 Gy and we compared the expression of selected epithelial, mesenchymal and stem-cell markers prior to and after irradiation. Besides we focused on a subpopulation of so called floating cells which arise during irradiation. These cells can survive the radiation treatment and after some time they are able to reattach and give rise to readherent population. We wanted to asses what is the cell cycle profile of these cells and whether and how fast they proliferate. In this thesis we have shown that radiation causes only minor changes in epithelial/mesenchymal and stem-like character of adherent fraction of the DU145 cell line. However, we have also described that small population of...
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Differential Gene expression using a negative binomial model
Janáková, Tereza ; Tkacz, Ewaryst (referee) ; Abo Khayal, Layal (advisor)
Hlavním cílem této diplomové práce je analýza diferenciální exprese genů na základě negativního binomického modelu. Úvodní část je věnována teoretickému základu, pojednává o sekvenování RNA, sekvenování nové generace, výhodách a možném využití, formátu fastQ aj. Následující část už se zabývá samotnou praktickou částí, zde byl vybrán vhodný set genů, které budou později analyzovány a příslušná data byla stažena. Tato data byla zarovnána k lidskému genomu verze 37 Burrowsovou-Wheelerovou transformací s využitím bowtie mapovače, byly tak vytvořeny soubory ve formátu SAM. Toto soubory dat byly později setříděny pomocí nástroje SAMtools. Následně byly v programovém prostředí Matlab (verze R2013b) vytvořeny anotované objekty genů s využitím služby Ensembl´s BioMart. Dále byla určena genová exprese a byly odhadnuty faktory velikosti knihovny. Na závěr byly odhadnuty parametry negativního binomického rozložení a byla vyhodnocena diferenciální exprese genů.
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