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Genetic variability in sporadic colorectal cancer: Searching for novel risk, prognostic and predictive biomarkers.
Jirásková, Kateřina ; Vodička, Pavel (advisor) ; Machoň, Ondřej (referee) ; Eckschlager, Tomáš (referee)
Colorectal cancer (CRC) is a major public health problem worldwide. Despite improvements in the diagnostic process and advancement in the treatment methods, the prognosis remains poor. To improve survival rates, it is important to identify people with the predisposition for CRC and to detect the potentially curable early stage of the disease. Furthermore, identifying those who would have an adverse clinical outcome associated with a particular chemotherapy would help to avoid redundant chemotherapy burden in patients and contribute to enhanced therapeutic efficacy, while minimizing treatment-related toxicity. The aim of the Thesis was to search for novel promising diagnostic, prognostic and predictive DNA-based biomarkers of sporadic form of CRC. As each patient is genetically unique, these biomarkers would aid clinicians in better diagnosis and/or in the selection of an optimal type of therapy for an individual CRC patient based on their molecular profile. In order to explore this issue, we investigated several candidate genes in healthy individuals as well as in newly diagnosed cancer patients. The major outcomes of this PhD study, which were fully reported in seven publications included in the present Thesis, are 1) The observation of several candidate single nucleotide polymorphisms in microRNA...
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The role of DNA repair mechanisms in the pathogenesis of myelodysplastic syndrome.
Válka, Jan ; Čermák, Jaroslav (advisor) ; Pospíšilová, Dagmar (referee) ; Penka, Miroslav (referee)
Background: The high incidence of mutations and cytogenetic abnormalities in patients with myelodysplastic syndrome (MDS) suggests the involvement of DNA repair mechanism defects in the pathogenesis of this disorder. The first part of this work was focused on monitoring of gene expression of DNA repair genes in MDS patients and on their alterations during disease progression. In the second part, next generation sequencing was used to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with MDS development was evaluated. Methods: Expression profiling of 84 DNA repair genes was performed on bone marrow CD34+ cells of patients with MDS. Screening cohort consisted of 28 patients and expression of selected genes was further validated on larger cohort of 122 patients with all subtypes of MDS. Paired samples were used for monitoring of RAD51 and XRCC2 gene expression during disease progression. Immunohistochemical staining for RAD51 recombinase protein was done on samples acquired by trephine-biopsy. Targeted enrichment resequencing of exonic parts of 84 DNA repair genes was performed on the screening cohort of MDS patients. Real-time PCR was used for genotyping of selected SNPs in the population study. Results: RAD51 and XRCC2 genes showed...
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Role of yeast WSS1 protease in DNA repair.
Adámek, Michael ; Grantz Šašková, Klára (advisor) ; Čáp, Michal (referee)
Sustaining the integrity of DNA throughout the lifetime is critical for every living organism. Therefore organisms evolved numerous ways to detect and repair different types of DNA damage caused by various endogenous and exogenous factors resulting in replication stress. Defects in these repair mechanisms can lead to severe human diseases such as neurological disorders, familial cancers or developmental syndromes. In presented master thesis, we investigated the function of a yeast protein named Wss1, a metalloprotease that participates in a recently discovered DNA repair pathway that proteolytically removes DNA-protein crosslinks. Wss1 shows strong negative interaction with another DNA repair protease, Ddi1, in which case was discovered, that double-deleted yeast strain lacking WSS1 and DDI1 is hypersensitive to hydroxyurea. Hydroxurea is a ribonucleotide reductase inhibitor that, in the end, arrests cells in the S-phase of cell-cycle. Based on previous studies, we performed rescue experiments with various deletions and single-site mutants of Wss1p to assess the involvement of particular yeast Wss1p domains in the replication stress response to hudroxyurea.
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Structure and molecular mechanisms of DNA repair by Nei glycosylase
Landová, Barbora ; Šilhán, Jan (advisor) ; Lux, Vanda (referee)
Abasic sites (Ap site, from apurinic/apyrimidinic) are one of the most common lesions generated in DNA by spontaneous base loss or DNA repair processes. There are two equilibrating forms of an Ap site - ring-open aldehyde and cyclic hemiacetal. Ring- opened aldehydes are reactive electrophilic groups capable of formation covalent adduct with nucleophilic sites in DNA. DNA interstrand cross-link (ICL) resulting from the Ap sites is formed spontaneously as a covalent bond between ring-open aldehyde and amin group of adenin residue in the opposite strand of double stranded DNA. ICLs block DNA replication and transcription. The formation of Ap site derived ICL is relatively long process taking several hours. We assume that the ring-opening of an abasic site is the rate-limiting step in the formation of the thermodynamic ICL. However, formation, stability and DNA repair of Ap-ICL are still poorly understood processes. Here, I have set up mechanistic in vitro experiments to reveal and calculate the probability of Ap-ICl formation in vivo. In more detail, I study the rates of formation of Ap-ICLs in the sequence context of neighbouring nucleotides of freshly formed covalent bond of ICL. I focus on sequence preference, the influence of AT/ GC rich regions and the length of oligonucleotides. I have...
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The Role of DNA Repair in the Onset and Therapy of Ovarian Cancer
Tomášová, Kristýna ; Vodička, Pavel (advisor) ; Čáp, Michal (referee)
DNA repair and DNA damage response are very important biological systems, inevitable to maintain genomic stability and fidelity of the genetic information, for the onset of ovarian cancer. Further, DNA repair is also substantially involved in the response to the therapy, since many chemotherapeutics act as DNA damaging agents. This literary analysis is intended to survay the relevance of DNA repair to ovarian carcinogenesis. Special emphasis is placed on repair defects, as it is inextricably associated with the onset of cancer and treatment outcome. Apart from well-known alternations in ovarian cancer susceptibility genes, such as BRCA1 and BRCA2 involved in homologous recombination repair, ample space will be dedicated to less common gene mutations across different repair pathways. Research confirms that abnormalities in the proteins responsible for homologous recombination repair are the leading cause of ovarian cancer. The majority of authors also suggested that targeting DNA repair pathways, especially base excision repair, can improve chemotherapy efficiency in a synergic manner. The same applies to nucleotide excision repair, which repairs platinum-DNA adducts and thus contibutes to platinum drugs resistance emerging. By way of contrast, mismatch repair in ovarian cancer is rather poorly...
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L01 DNA damage formation and DNA repair following an intervention of colorectal cell lines with ganoderma lucidum
Vodička, Pavel ; Opattová, Alena ; Čumová, Andrea ; Slíva, D.
Colorectal cancer (CRC) is the third most common malignancy in the world and second most common cause of cancer related deaths in Europe. CRC is complex disease that develops as consequence of environmental and health risk factors with involvement of suboptimal DNA repair, resulting in an accumulation of DNA damage. Reactive oxygen species (ROS) are highly reactive molecules strictly controlled by cellular antioxidant system. Disturbance in the prooxidation–antioxidation homeostasis increases an extent of ROS and consequently an accumulation of DNA damage as well as apoptosis. \nMany natural compounds possess anti-cancer activities tentatively mediated by the generation of ROS. Cancer cells are more sensitive to oxidative DNA damage than non-malignant ones. Modulation of oxidative DNA damage and its repair by natural compounds may lead to selective cancer cell-death and further sensitization of cancer cells to the treatment. Ganoderma Lucidum (GLC) (Reishi, Ling-Zhi), a mushroom used in Chinese medicine for thousands of years, represents an example of a natural compound with empirically recorded anti-cancer as well as anti-proliferative effects. \nThe aim of our study is to define effect of Ganoderma lucidum (GLC) extract on DNA damage and DNA repair system in colorectal cell lines with different genetic backgrounds.\nOur results suggest that GLC extract decreases activity of the cellular antioxidant system which leads to oxidative DNA damage. GLC extract increases genotoxic burden in colorectal cancer cell lines, highlighted by the suppressed base excision repair capacity. These data indicate that specific oxidative DNA damage caused by natural compounds may become a potential tool for the improvement of specific anti-cancer treatment.\n
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Effects of natural substances on DNA damage and repair capacity in colorectal cell lines
Vodenková, Soňa ; Opattová, Alena ; Čumová, Andrea ; Slíva, D. ; Vodička, Pavel
Colorectal carcinoma)CRC) represents serious ilness with high incidence and mortality worldwide. Generaly, there is a lack of reliable predictive and prognostic biomarkers, implicated late diagnosis. The effectivity of treatment is rather low - about 50%. Main agent used in CRC treatment is 5 fluorouracil (5-FU), alone or in combination with other cytostatics. 5-FU is halogenated pyrimidine, which is or directly incorporated into DNA or disrupts thymidine synthesis in tumour cells. This damage is repaired by base excision repair (BBR) or mismatch repair. The aim of this study is to investigate the effect of 5FU together with extracts of Ganoderma lucidum (GL) and the role of BER in various lines of colorectal cancer cell lines. Results show increased oxidative damage after GL and 5FU+GL treatment and in the same time decrease of DNA repair in colorectal cell lines. This fact could contribute to improve of 5FU efficacy.
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Natural compounds and their effect on 5-fluorouracil in colorectal cancer cell lines
Čumová, Andrea ; Opattová, Alena ; Vodenková, Soňa ; Horák, Josef ; Slíva, D. ; Vodička, Pavel
Colorectal cancer (CRC) is the second most common type of cancer and the second most common cause of cancer related deaths in Europe. 5-Fluorouracil (5-FU) is widely used in treatment of various cancers including CRC, but apart from the cytotoxic effect on cancer cells may also cause adverse toxic side effects. 5-FU is an anti-metabolite with chemical structure similar to that of the pyrimidine molecules of DNA and RNA. However, response to chemotherapy is often limited by drug resistance. The p53 protein is one of the most widely studied tumour suppressors and mutations in TP53 gene are frequently detected in different types of tumours. \nGanoderma Lucidum (GLC) is a mushroom used in Traditional Eastern Medicine which exhibits anti-cancer and anti-proliferative effects in vitro\nThe aim of our study is to define the role of p53 in the interaction between 5-FU and GLC extract and their simultaneous effect on survival in CRC cell lines.\nOur results suggest that GLC extract significantly increases cytotoxicity and genotoxicity of 5-FU in CRC lines with different p53 status and may potentially modulate the response of p53 knock-out cells which are less sensitive to 5-FU treatment. Interaction of conventional chemotherapeutics with natural compounds introduces a novel aspect in cancer research and therapy.\n\n
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Posttranslational modification of the adapter protein DAXX in the cellular response to genotoxic stress
Bražina, Jan ; Anděra, Ladislav (advisor) ; Černý, Jan (referee) ; Vodička, Pavel (referee)
Maintaining the chromosome continuity and complete genetic information in human cells is crucial for cell survival and the whole organism. It prevents life-threatening pathologies and preserves genetic continuity. However, cellular DNA is exposed to both endogenous and exogenous stress damaging its content and integrity. This stress activates mechanisms involving detection and repair of these damaged sites (DDR). One of the most serious types of DNA damage double-stranded breaks (DSB) occuring when both strands are severed. DSBs trigger wave of PTMs that regulate protein interactions, nuclear localization and catalytic activity of hundreds of proteins. Such modifications include acetylation, methylation, SUMOylation, ubiquitinylation and especially phosphorylation. The most important kinases involved in DDR kinases are ATM, ATR and DNA-PK. These kinases are activated immediately after the detection of the damaged area. DAXX (Death-associated protein 6) is an adapter and predominantly nuclear protein, which is involved in chromatin remodeling, gene expression modulation, antiviral response and depositing histone H3.3 variants into chromatin or telomeres. Daxx is essential for murine embryogenesis, since the homozygous deletion is lethal in E9.5-10. In 2006 a study mapping the substrates of kinases...
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Mechanisms of DNA repair in the moss Physcomitrella patens
Holá, Marcela ; Angelis, Karel (advisor) ; Bříza, Jindřich (referee) ; Fajkus, Jiří (referee)
Over the course of an organism's life, its genome is exposed to endogenous and exogenous chemical, physical and biological agents - genotoxins. These genotoxins alter its basic structural components - sugar residues, phosphodiester bonds, and nitrogenous bases. Organisms have therefore evolved a plethora of different strategies to both repair DNA lesions and maintain genomic stability. These DNA repair pathways are linked with several other cell pathways, including chromatin remodelling, DNA replication, transcription, cell cycle control, apoptosis - programmed cell death (PCD), thereby providing a coordinated cellular response to DNA damage. Biochemical mechanisms of DNA repair are relatively well understood in yeast and mammals, however, far less so in plants. While these repair mechanisms are evolutionary conserved, significant differences still remain. Therefore, further investigation is required. This thesis summarises the introduction of a novel plant model - the moss, Physcomitrella patens (Physcomitrella). As a haploid gametophyte with unique characteristics of high frequency of homologous recombination (HR), and apical growth of filaments, it is an ideal organism to study DNA repair in plants. Previous research on Physcomitrella regarding mechanisms of DNA lesion repair induced by...
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