National Repository of Grey Literature 23 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
Analysis of quantitative and qualitative genetic features in the pathogenesis of hereditary solid tumors.
Zemánková, Petra ; Kleibl, Zdeněk (advisor) ; Živný, Jan (referee) ; Tichý, Boris (referee)
Cancer the second most common causes of death in the Czech Republic. Carriers of mutations in genes predisposing to hereditary cancers represent a small but clinically significant group of high risk individuals. Today, dozens of predisposing genes for hereditary tumor syndromes are known and targeted next generation sequencing (NGS) has become a standard approach for their analysis. NGS allows rapid acceleration diagnostics of causal mutation in high-risk individuals. To identify mutations in genes predisposing to hereditary cancers, we designed a panel NGS analysis including subsequent bioinformatics analysis allowing a reliable identification of single nucleotide variants, insertions/deletions, and large intragenic rearrangements. The bioinformatics procedures described in this thesis were used for panel NGS validation, but also for identification of alterations associating with so far undescribed hereditary tumor types. Bioinformatics analyzes have become the basis for the unified processing of large datasets from the CZECANCA consortium and enable the construction of a population-specific database of genotypes that serve to improve clinical diagnostics of cancer predisposition in Czech patients. The versatility of NGS also allows its use for RNA (cDNA-based) analyzes of splicing variants in the...
Identification of hereditary alterations predisposing to breast cancer development using "next-gen" sequencing
Lhota, Filip ; Kleibl, Zdeněk (advisor) ; Zikán, Michal (referee) ; Mohelníková Duchoňová, Beatrice (referee)
Summary: Breast cancer (BC) is the most frequent cancer type in female population of Europe. Approximately 5 - 10 % accounts for its hereditary form which is characterized by high penetrance, early onset, risen recurrence risk and development of other cancers. Mutational analyses of high risk patients identify a predisposing mutation in one of the most studied genes (BRCA1, BRCA2, TP53, ATM, CHEK2, NBS1, PALB2) only in less than one third of tested breast cancer patients. Lately, with the use of new methods of next-generation sequencing, a number of other susceptibility or candidate genes were characterized, but the incidence of their pathogenic alteration is often geographically different. A notable proportion of high risk patients from families with hereditary BC can represent carriers of population-specific, or private mutations. Most of the to date identified BC susceptibility genes codes for proteins involved in DNA repair, especially repair of double strand break DNA repair. Nevertheless the mutation analysis was conducted only on a small fraction of these DNA repair genes. We can expect that in the group of yet nontested genes coding for DNA repair proteins a rare, but clinically important genetic alterations predisposing to BC in affected families can be discovered. This work describes a...
Model for study of transcription regulation of granulocytic genes MPO and MMP9 by different levels of PU.1 transcription factor
Chramostová, Kamila ; Pospíšil, Vít (advisor) ; Kleibl, Zdeněk (referee)
9 Abstract Enhancers are distal cis - regulatory DNA sequences that regulate (enhance) transcription of the respective gene driven by its promoter. Enhancers are found in non-coding DNA upstream or downstream of the gene coding sequence, or in introns or coding regions that are located up to hundreds kb away from the gene. Superenhancers are newly discovered clusters of multiple enhancers that play a vital role in activating tissue-specific genes, determining cell identity and regulating differentiation. PU.1 is the transcription factor (TF) that is necessary for normal haematopoiesis, specifically for the development of myeloid and lymphoid blood lineages. Distinct levels of PU.1 induce differentiation of hematopoietic cells into different cell lineages whereby disruption of PU.1 levels leads to leukemogenesis. High PU.1 levels stimulate macrophage development, while intermediate levels stimulate the development of granulocytes. This diploma thesis seeks to contribute to addressing the interesting biological question of what are the regulatory mechanisms to ensure that granulocytic genes are activated only at the intermediate concentration of PU.1, whereas macrophage genes are activated only at its high levels. The aim of this diploma thesis was to create a series of reporter vectors carrying regulatory...
Regulation of Gene Expression in Tumour Tissue
Kulda, Vlastimil ; Černý, Radim (advisor) ; Vachtenheim, Jiří (referee) ; Kleibl, Zdeněk (referee)
Deregulation of gene expression caused by genetic or epigenetic changes plays an important role in pathogenesis of cancer. The thesis is a commented collection of ten publications dealing with the molecular biology of tumours. The author has significantly contributed to all of them. All the articles contained in the thesis are linked to the topic of assessment of molecules involved in gene expression regulation (microRNAs) or DNA alterations that affect gene expression (promoter methylation, presence of a fusion gene). MicroRNAs are short single-stranded RNA molecules involved in posttranscriptional regulation of gene expression by triggering mRNA degradation or inhibiting translation. It is a basic mechanism with an impact on all cellular processes including the pathogenesis of various diseases. MicroRNAs can either act as oncogenes by decreasing the expression of tumour-suppressor genes or as tumour-suppressor genes by decreasing the expression of oncogenes. However, the network of microRNA - RNA interactions is much more complex. Our published results that are part of this thesis are focused on colorectal carcinoma (CRC), prostate cancer, head and neck squamous cell carcinoma (HNSCC), gastric cancer and non-small cell lung cancer (NSCLC). In patients with CRC, we demonstrated the prognostic...
Regulation of the DNA damage response by R2TP mediated MRN complex assembly and control of 53BP1 localisation.
Von Morgen, Patrick ; Hořejší, Zuzana (advisor) ; Bártová, Eva (referee) ; Kleibl, Zdeněk (referee)
DNA double strand breaks are the most dangerous type of DNA damage. The MRN complex and 53BP1 have essential functions in the repair of DNA double strand breaks and are therefore important for maintaining genomic stability and preventing cancer. DNA double strand breaks are repaired by two main mechanisms - homologous recombination and non- homologous end joining. The MRN complex senses DNA double strand breaks and activates a cascade of posttranslational modifications that activates and recruits other effector proteins. In addition MRN mediated resection is important for removing adducts in non-homologous end joining and creating single stranded DNA required for homologous recombination. 53BP1 is recruited to DNA double strand breaks by site specific ubiquitinations and inhibits DNA resection, thereby promoting non-homologous end joining at the expense of homologous recombination. In this thesis we show that MRE11 binds to the R2TP chaperone complex through a CK2 mediated phosphorylation. Knockdown of R2TP or mutating the MRE11 binding site leads to decreased MRE11 levels and impaired DNA repair. Similar phenotype has been observed in cells from patients with ataxia-telangiectasia-like disorder (ATLD), containing MRE11 deletion mutation which is missing the R2TP complex binding site. Based on R2TP...
Functional analysis of the population-specific checkpoint kinase gene CHEK2 sequence variants
Stolařová, Lenka ; Kleibl, Zdeněk (advisor) ; Živný, Jan (referee)
CHEK2 gene codes for serin/threonine kinase Chk2 (Checkpoint kinase 2). In response to genomic DNA damage, Chk2 phosphorylates its substrates (proteins Cdc25C, BRCA1 or p53), whose activation leads either to cell cycle arrest, DNA damage repair or induction of apoptosis. Germline mutations in CHEK2 gene increase risk of cancer development. Analysis of high risk breast cancer patients in Czech Republic reveals rare CHEK2 mutations (mainly missense) with yet unknown clinical significance. This work focuses on functional impact of these variants and analysis of kinase activity of variant isoforms of Chk2 kinase. For this purpose, recombinant constructs were expressed in bacterial cells of E. coli. Enzymatic activity of Chk2 kinase isoforms in crude cell lysates was measured by the phosphorylation of Chk2 arteficial substrate spectrophotometrically. Results of in vitro kinase assay were correlated to the results of in silico prediction software. The results show that from 15 analyzed mutations (together with one in frame deletion), kinase activity was abrogated in all variants affecting the kinase domain of Chk2, in concordance with in silico predictions. The same result has been found for a FHA domain variant p.R145Q. No significant changes in kinase activity were observed in case of two FHA domain variants...
Current methods of genome analysis and their use in identification of genetic determinants of human diseases
Stránecký, Viktor ; Kmoch, Stanislav (advisor) ; Kleibl, Zdeněk (referee) ; Pačes, Jan (referee)
The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.

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