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Mutations in MLH1 gene and MSI status as molecular characteristics of sporadic colorectal cancer
Čaja, Fabián
Colorectal carcinoma (CRC) is one of the most prevalent malignancies in the Czech Republic. In general, there are two molecular pathways leading to CRC: one is characterized by chromosomal instability, the other by the deficiency in DNA mismatch repair (MMR) genes. MutL homologue 1 (MLH1) gene, a member of the MMR gene-family, represents a key component of the MMR system, responsible for recognition of nucleotide mismatches occurring during DNA replication, and for the recruitment of repair proteins to correct the replication errors. According to literature, somatic mutations in MMR genes, and MLH1 in particular, hallmark sporadic, MMR deficient, CRC cases. We aimed at analyzing somatic events in MLH1 gene and the determination of microsatellite instability (MSI) status in 99 DNA samples from 96 patients with sporadic CRC. Mutations were screened by high resolution melting (HRM) curve analysis. Positive cases in each run were subsequently verified by automated sequencing. Mainly gene variants were found in MLH1 gene: We discovered two new variants, one in exon 2 at position c. 204 C>G, p. Ile68Met (98 C/C, 1C/G) and the other in exon 11 at position c. 973 C>T, p. Arg325Trp (98 C/C, 1 C/T). Only the latter variant c. 973 C>T was identified as somatic mutation. All other variants found in MLH1 gene...
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Optimization of proces for detection of free tumor DNA in plasma and its clinical utility for colorectal cancer, lung cancer and pancreatic cancer patients
Belšánová, Barbora ; Benešová, Lucie (advisor) ; Tachezy, Ruth (referee)
In current days, examination of circulating tumor DNA (ctDNA) finds new use across different cancers. It is directed at tumor-derived short fragments of DNA present in peripheral blood of patiens (mainly in advanced stages). Due to its minimal invasivity, almost 100 % specificity and relatively high sensitivity in stage IV patients, this approch found its main potential clinical utility especially in early detection of disease relapse or progression after tumor resection (i.e. post-operative follow-up), prediction and monitoring of therapy response and estimation of prognosis. As a result of minute levels of ctDNA on a high background of other non-tumor DNA fragments present in plasma, a suitable method exhibiting highest sensitivity is the key for proper detection of this marker. The approach is predominantly based on initial identification of a mutation in tumor tissue and its subsequent detection in plasma. The present work is aimed at optimization of ctDNA isolation and method of its detection based on PCR amplification followed by heteroduplex analysis by denaturing capillary electrophoresis (DCE) to achieve highest sensitivity for detection of mutated fraction in plasma sample. I have applied the optimized protocol to examine ctDNA in three types of cancers, namely colorectal cancer (122...
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Utilisation of New Biomarkers for the Optimalization of Diagnostics and Therapy of Tumors of the Gastrointestinal Tract
Šafanda, Martin ; Kučera, Radek (advisor) ; Fínek, Jindřich (referee) ; Svobodová, Šárka (referee)
Utilisation of New Biomarkers for the Optimalization of Diagnostics and Therapy of Tumors of the Gastrointestinal Tract Introduction: Tumor markers are standard diagnostic tools. They are mainly used to monitor the course of the disease and to check the efficacy of the treatment. It is important to observe dynamics. Changing the level of the biomarker can prevent clinical manifestation and lead to early diagnosis of relapse, which in turn means improving the quality of life, including prolonging survival. Recently, we have encountered a number of diagnostic algorithms that suggest algorithms for estimating the risk of tumor presence or the risk of progression of cancer, using statistical methods. Objectives: The aim of this work is to verify new biomarkers for the diagnosis of gastric cancer and to develop an optimal algorithm for their use. Further, to evaluate the importance of cytokeratin markers - Tissue Polypeptide Antigen (TPA) and Tissue Polypeptide Specific Antigen (TPS) for the diagnosis of metastatic colorectal carcinoma in the liver. To carry out a pilot study of FGF23 levels in people with colorectal carcinoma and other gastrointestinal tumors. Methods and patients: Patient samples were analyzed using immunoradiometric, chemiluminescence and fluorescence assays. For each solved problem,...
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Characterization of tumor suppressor gene Hypermethylated in cancer 1 (Hic1) and its novel target genes in the intestinal epithelium and colorectal cancer
Baloghová, Nikol ; Janečková, Lucie (advisor) ; Doubravská, Lenka (referee)
Colorectal cancer is one of the most common cancer types worldwide. Both genetic and epigenetic alterations play a critical role in its initiation and progression. One of the genes frequently epigenetically silenced or lost in many types of human cancer is tumor suppressor gene Hypermethylated in Cancer 1 (HIC1). It encodes for transcriptional repressor regulating its target genes directly or indirectly. Twelve genes whose expression is repressed by HIC1 have been identified to date. These genes encode for transcription factors, cell cycle and apoptosis regulators or proteins involved in angiogenesis as well as cell migration and invasiveness. Employing mouse embryonic fibroblasts upon Hic1-conditional knockout we have revealed six novel genes potentially repressed by Hic1 including Toll-like receptor 2 (Tlr2). Here we show that Tlr2 is one of the Hic1 target genes and that Hic1 inactivation in the intestine leads to increased Tlr2 production. Moreover, enhanced inflammatory response upon chemical-induced colitis as well as increased tumor formation in ApcMin mice was observed in Hic1-deficient mice. Expression profiling in human fibroblast upon HIC1 knockdown revealed increased expression of another potential target gene, transcription factor E2F7. Our study describes a new relationship between HIC1 and...
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CIrcadian regulation of miRNA and clock-controlled genes in tumorigenesis
Balounová, Kateřina ; Pácha, Jiří (advisor) ; Bendová, Zdeňka (referee)
The circadian clock generates circadian rhythms, which participate on regulation of a number of signalling pathways. Disruption of the circadian regulatory mechanism is linked to a development and a progression of certain types of cancer including colorectal tumorigenesis. Progression of tumorigenesis depends on the cell cycle machinery related to cell proliferation and apoptosis. MiRNAs play a role in initiation and progression of tumorigenesis because they interfere in regulatory pathways associated with tumorigenesis. The aim of the thesis was to determinate existence of circadian rhytms in clock controlled genes (Tef, Dbp), miRNAs (miR-1-3p, miR-16-5p, miR-34a-5p, miR-155-5p, miR-192-3p) and genes of the cell cycle machinery (Ccnd1, Ccne1, Ccna1, Ccnb1) and apoptosis (Casp3, Bcl2, Bad). Further, to compare detected circadian rhythms during aging and neoplastic transformation of colon by quantitative RT-PCR. We have observed circadian expression of Tef, Dbp, Ccne1, Ccna1, Ccnb1, Casp3 and Bcl2 in young mice colon, Tef, Dbp, miR-1-3p, Ccne1, Ccna1 in old mice colon and Tef and Dbp in colorectal tumors. In summary, circadian expression of clock controlled genes varied but was maintained in mice colorectal tumors. In aging we demonstrated weakening of circadian rhythms of the genes of the cell...
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The effects of bacterial lysates on the gut barrier function and microbiota composition
Zákostelská, Zuzana ; Tlaskalová - Hogenová, Helena (advisor) ; Prokešová, Ludmila (referee) ; Rada, Vojtěch (referee)
Dynamic molecular interactions between the microbiota and the intestinal mucosa play an important role in the establishment and maintenance of mucosal homeostasis. Aberrant host- microbiota interaction could lead to many diseases such as inflammatory bowel disease. The aim of our study was to evaluate the commensal and probiotic bacteria activities and their ability to induce pathological or exert beneficial effects. The most important trigger for immune system development is an exposure to microbial components. Here, we show that there is a time window at about three weeks of age, which enables the artificial colonization of germ free mice by a single oral dose of cecal content. The delayed colonization by either inoculation or co-housing causes permanent changes in immune system reactivity, which may downgrade the results of experiments performed on first generation of colonized animals. In this thesis we report that even non-living commensal bacteria such as Parabacteroides distasonis (mPd) or well known probiotics such as L. casei DN-114 001 (Lc) possess anti-inflammatory effects in experimental model of colitis. The mechanisms that this effect is achieved by the lysate of L. casei DN-114 001 comprise: a) improvement in the gut barrier function, b) correction of the dysbiosis, and c) modulation of the...
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Mutations in MLH1 gene and MSI status as molecular characteristics of sporadic colorectal cancer
Čaja, Fabián ; Vodička, Pavel (advisor) ; Kadlecová, Jitka (referee)
Colorectal carcinoma (CRC) is one of the most prevalent malignancies in the Czech Republic. In general, there are two molecular pathways leading to CRC: one is characterized by chromosomal instability, the other by the deficiency in DNA mismatch repair (MMR) genes. MutL homologue 1 (MLH1) gene, a member of the MMR gene-family, represents a key component of the MMR system, responsible for recognition of nucleotide mismatches occurring during DNA replication, and for the recruitment of repair proteins to correct the replication errors. According to literature, somatic mutations in MMR genes, and MLH1 in particular, hallmark sporadic, MMR deficient, CRC cases. We aimed at analyzing somatic events in MLH1 gene and the determination of microsatellite instability (MSI) status in 99 DNA samples from 96 patients with sporadic CRC. Mutations were screened by high resolution melting (HRM) curve analysis. Positive cases in each run were subsequently verified by automated sequencing. Mainly gene variants were found in MLH1 gene: We discovered two new variants, one in exon 2 at position c. 204 C>G, p. Ile68Met (98 C/C, 1C/G) and the other in exon 11 at position c. 973 C>T, p. Arg325Trp (98 C/C, 1 C/T). Only the latter variant c. 973 C>T was identified as somatic mutation. All other variants found in MLH1 gene...
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Use of molecular-genetic methods for research of colorectal carcinoma
Janáková, Tereza ; Škutková, Helena (referee) ; Provazník, Ivo (advisor)
The aim of this bachelor work is to carry out statistical analysis of mutations in KRAS, BRAF and PIK3CA genes. Introductory part is focused on colorectal carcinoma in general. In following part of the work, we discuss genetics of tumors, description of KRAS, BRAF and PIK3CA genes, molecular-genetic analytical methods, widely used in genetics, especially PCR. Further detection of mutations is described. In the next part of the work, we propose a method for detection of mutations in KRAS, BRAF and PIK3CA genes, which consist in using PCR and commercial kits. The following chapter "Results of Analysis of mutations" contains detailed grafical presentation of mutations. Frequencies of mutations were compared with published data and with data from laboratories in Pilsen and Prague. In the end of the bachalor work, there is summary of results and their possible benefit.
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Primary and Secondary Prevention of Colorectal Carcinoma by People over 50
HORNÍKOVÁ, Kateřina
As the title reveals, the thesis deals with primary and secondary prevention of colorectal carcinoma among people over 50 years of age. Colorectal carcinoma, i.e. tumour disease of the colon or rectum, is a serious disease with increasing incidence. The Czech Republic has one of the highest incidence rates of this disease and is at the forefront of global statistics. Every year, about 8000 people are diagnosed with colorectal carcinoma in our country and about 4000 patients die of this disease every year. Almost four people out of ten have vicarious experience with colorectal carcinoma, claiming that someone in their immediate vicinity has developed this disease. Early detection of the disease is thus of crucial importance. Prevention and diagnostics play a major role because tumours detected at an early stage can be treated well. It is reported that lifestyle, the right regimen, plenty of physical activity, wholesome food with an appropriate proportion of fibre and vitamins have a 60 to 80 % impact on the development of carcinoma. The disease poses a threat mainly to people over fifty years of age and people with genetic predispositions. The thesis is divided into a theoretical and practical part. The theoretical part consists of several chapters. First of all, I will be dealing with the basic anatomy and physiology of the colon and rectum. Then I will be dealing with the colorectal carcinoma itself, its development, symptoms, incidence or epidemiological aspects of the disease in the Czech Republic. I will be dealing with the risk factors of colorectal carcinoma that include age, lifestyle, as well as hereditary predispositions. A large part of the thesis is dedicated to colorectal carcinoma prevention. I will be focusing on primary and secondary prevention, including the faecal occult blood test and colonoscopy. Finally, I will touch on diagnostics and treatment of colorectal carcinoma. The practical part makes use of the research data obtained through a quantitative interrogation method, a questionnaire. The questionnaire was anonymous and included 32 questions. The first group of the questions was focused on basic information about the respondents. The rest of the questions concerned respondents´ awareness of colorectal carcinoma, its risk factors and potential prevention. I explored the respondents´ attitudes to lifestyle, their concern for tumour diseases in general, as well as whether they regularly see their physician. A substantial part of the questionnaire was devoted to questions regarding the occult blood test and colorectal screening. The questionnaire was intended for people over 50 years of age. The purpose of the thesis was to map awareness of the risk factors of colorectal carcinoma, look into awareness of the options of secondary prevention of colorectal carcinoma and whether people attend regular screenings. I examined the importance of giving media publicity to the disease and thus related interest in this issue. I wished to know whether there is a gender difference in the interest in undergoing colorectal screening. Four hypotheses were established in the research. Hypothesis 1: People over the age of 50 are informed about the risk factors of colorectal carcinoma. This hypothesis was confirmed. Hypothesis 2: People over the age of 50 know the options of secondary prevention of colorectal carcinoma. This hypothesis was only partially confirmed. Hypothesis 3: The number of colorectal screenings undergone by women over the age of 50 is statistically more significant than that of man over 50 years of age. This hypothesis was not confirmed for the occult blood test. However, men underwent colonoscopy more often. Hypothesis 4: The interest in undergoing colorectal screening increases with the level of education attained. The actual proportion of those who underwent an occult blood test or colonoscopy does not differ depending on education, and therefore hypothesis number 4 was not confirmed.
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The role of general practitioner nurse in the prevention of the colorectal cancer in surgery.
TETÍKOVÁ, Hana
Current situation: The Czech Republic belongs to countries with high prevalence of colorectal carcinoma (CC). The theoretical part of this thesis includes basic information on carcinoma of the colon and the rectum. It also deals with its causes, symptoms and treatments. Primary, secondary and ternary prevention of CC is described in detail. Also the role of the nurse in general practitioner´s (GP) office in such prevention in adults is thoroughly investigated. Aims: Main aim of this work was to find the level of patient knowledge about the prevention program on CC and to map the role the nurse in GP office for adults has in this prevention. Methodology: Both qualitative and quantitative methods were chosen for this research. Obtained data was transferred into data matrix, evaluated using contingency tables and for statistical evaluation the one-sample and the two-sided t tests as well as the chi square test were used. The second method used was qualitative research in the form of structured interview. The interviews were transcribed into text. Through open coding analysis four categories were identified: The primary prevention of CC, The secondary prevention of CC, The immunochemical test for occult blood and The tertiary prevention of CC. Research group: The first research group consisted of patients aged 50 and above. The second research group consisted of five nurses working in the GP offices. Results: The first aim was to establish the level of knowledge in patients about CC. Four hypotheses were stated in order to fulfil the first aim. First hypothesis was: "Patients are informed about the prevention of CC". The level of significance for this hypothesis was calculated to 48.1 % and the hypothesis was therefore confirmed. However, reserves were discovered regarding the information on the primary prevention and first information about the secondary prevention is seen to dominate. This means that the research showed that patients that seldom visit the GP office fall through the CC screening. It is therefore very beneficial that a project has started from January 2014 with addressed invitations to the targeted population to such CC screenings. Second hypothesis presumes that "The knowledge of prevention of CC is gender indifferent". However, the reached level of significance at 2.2 % declines this hypothesis which means that the knowledge does differ based on gender. In fact the results show that women possess deeper knowledge on this subject. For example more women believe that smoking influences the prevalence of CC. The third hypothesis was supposed to either confirm or disprove that people are equally well informed about CC prevention in urban and rural areas. The level of significance of 1.2 % shows that this knowledge is better in urban areas. The last, fourth hypothesis asked whether patients have acquired their knowledge of CC prevention in the GP office. The level of significance for this hypothesis is 88.6 % and confirms the question. The second aim of this research was to map the role of the nurse in the GP office regarding the prevention of CC. The research question asked was" What role does the nurse have in CC prevention?" The research shows that her role is both irreplaceable and very significant.
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