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Sequence variants in metastatic colorectal cancer and their evolution during the disease course and treatment
Jandová, Eliška ; Boublíková, Ludmila (advisor) ; Vymetálková, Veronika (referee)
A deeper understanding of the molecular background of colorectal cancer (CRC) can help explain the development of the disease and its resistance to treatment, predict disease progression, and improve treatment prognosis. Some minimal molecular testing has been incorporated into standard clinical management to determine if a particular patient will benefit from a particular therapy, but more and more new genetic alterations are being discovered that appear to be associated with the development of resistance. Tissue biopsy of the tumor is the gold standard in terms of molecular testing, but there is an increasing demand for more non- invasive methods such as liquid biopsy. Using targeted next-generation sequencing, we analyzed sequence variants present in primary tumor, metastases, and cell-free tumor DNA - ctDNA of patients with metastatic CRC. The objectives were to analyze sequence variants of the primary tumor and identify possible pathogenic variants, to analyze differences between DNA of the primary tumor and metastases, to evaluate the use of ctDNA as a diagnostic tool, and to identify potential tumor-specific markers in ctDNA that can be used to monitor disease progression. Our results suggest the feasibility of using ctDNA for diagnostic purposes or even to monitor disease progression, but...
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Circulating biomarkers in colorectal cancer and their application in diagnosis and prognosis
Červená, Klára ; Vymetálková, Veronika (advisor) ; Boublíková, Ludmila (referee) ; Václavíková, Radka (referee)
Despite all the advances in the field of clinical and molecular oncology, the numbers related to the incidence and mortality of colorectal cancer (CRC) remain at unacceptable levels. In recent years, liquid biopsy consisting of circulating biomarkers has come to the forefront of research, offering many advantages over conventional biopsy, such as providing timely information on tumor heterogeneity and the ease of repeated sampling. This dissertation thesis aimed to identify novel candidate circulating biomarkers from microRNAs, long non-coding RNAs, and cell-free DNA that could be used for earlier diagnosis, better prognosis, or prediction of therapy response of CRC patients and thus further advance personalized medicine. The main results of this work are: 1) Circulating microRNAs in plasma (miR-122-5p and miR- 142-5p) can distinguish patients with rectal cancer and cancer-free individuals and could predict therapy response in patients (both in primary and metastatic CRC patients). 2) Gene amplification of the long non-coding RNA MALAT1 can represent an important step in the transition of healthy mucosa to adenoma tissue. Plasma MALAT1 is overexpressed in patients with colorectal adenomas and CRC patients compared to cancer-free individuals and has the potential as a predictive biomarker for CRC...
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The role of circulating microRNAs in the therapy response prediction in colorectal cancer patients.
Landecká, Aneta ; Vymetálková, Veronika (advisor) ; Hlaváč, Viktor (referee)
Colorectal cancer (CRC) is one of the most common cancers both in the world and in the Czech Republic. Predispositions for the development of CRC include genetic and epigenetic changes, as well as environmental and microenvironmental factors. These tumours often respond very well to treatment, especially in the early stages, but some patients experience early recurrence of the disease. As the incidence of CRC has not declined in recent years, this is a current problem requiring a new approach aimed at improving diagnosis, survival and quality of life of patients with CRC. For this reason, liquid biopsy, which is a minimally invasive approach to the patient and allows real-time monitoring of changes in the body, is increasingly gaining prominence. One of the biomarkers that can be detected by liquid biopsy are small non-coding RNA molecules - microRNAs (miRNAs). In this thesis, the gene expression of two miRNAs, namely miR-122-5p and miR-142-5p, was analyzed in plasma and tissues of CRC patients and in plasma of a control group of healthy blood donors. In our study, we identified significant changes in the expression levels of both miRNAs in CRC patients compared to healthy cancer- free subjects. Specifically, higher expression levels of both miRNAs were observed in CRC patients compared to the...
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Molecular aberrations in testicular germ cell tumors and their significance in tumor pathogenesis and clinical practice
Matoušková, Laura ; Boublíková, Ludmila (advisor) ; Vymetálková, Veronika (referee)
Testicular germ cell tumors (TGCT) are rare in general but they are also the most commonly occuring malignant tumors in adolescent and young males. Predispositions for the incidence of TGCT include genetic factors - a number of discovered DNA risk loci, epigenetic changes in DNA, alterations of various signaling pathways and also external environmental risk factors. These tumors usually respond to cisplatine therapy very well, nevertheless some patients develop a resistance to this cytostatic medicament. There is still relatively small amount of research dedicated to the cause of cisplatine resistance, as well as to bio-molecular characteristics of TGCT and their role in the pathogenesis. As a result, there is only a little development in TGCT therapy to this day and thus there is no targeted therapy available, which would be highly effective for treating patients with developed cisplatine resistance and/or poor prognosis of their disease. As a result of the fact that TGCT incidence is increasing in the recent decades, it can be considered an actual problem requiring urgent addressing in order to improve the survival rate and quality of life of patients with advanced TGCT. Theoretical part of this thesis deals with the main currently known molecular characteristics of TGCT as well as cisplatine...
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Genetic and epigenetic mechanisms (and their cooperation) in the leukemogenesis of acute myeloid leukemia in adults.
Šestáková, Šárka ; Šálek, Cyril (advisor) ; Vymetálková, Veronika (referee) ; Kubričanová Žaliová, Markéta (referee)
Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by great heterogeneity and clonal nature. In recent years, rapidly evolving next-generation sequencing methods provided a deep insight into the mutational background of AML. It was shown that ~ 44 % of AML patients harbor mutations in genes that regulate DNA methylation. So far, many researchers have tried to evaluate the prognostic significance of DNA methylation changes in AML, however, due to a great inconsistency in these studies, none of the reported markers were implemented into clinical practice. The aim of this work was to further investigate the DNA methylation changes in AML patients with specific mutations and their prognostic effect. Next, we wanted to develop a new approach for a complex evaluation of prognostically significant DNA methylation aberrations. In our first project, we assessed the overall DNA methylation, hydroxymethylation, and gene expression in AML patients with mutations in either DNMT3A or IDH1/2 or their combinations. We discovered that each genetic aberration is connected with a distinct pattern of DNA hydroxy-/methylation changes that are not entirely reflected in altered gene expression. Patients with mutations in both genes exhibited a mixed DNA methylation profile most similar to healthy...
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Small noncoding RNAs and their prognostic value in myelodysplastic syndromes
Hruštincová, Andrea ; Dostálová Merkerová, Michaela (advisor) ; Stopka, Tomáš (referee) ; Vymetálková, Veronika (referee)
Myelodysplastic syndromes (MDS) are a heterogeneous group of bone marrow (BM) disorders characterized by ineffective haematopoiesis, BM dysplasia, and peripheral blood cytopenia. In recent years, substantial progress has been made towards understanding the molecular pathogenesis of MDS that has brought new possibilities in MDS diagnostics, prognostics, and treatment. Small noncoding RNAs (sncRNAs), especially microRNAs (miRNAs), are in the field of scientific interest in terms of their expression, function, role in disease development, and potential utilization as disease biomarkers. Special attention has been focused on extracellular sncRNAs present in blood circulation, so called 'circulating' sncRNAs, which may become easily accessible biomarkers of disease state or risk of progression. We have conducted several studies on intracellular and extracellular sncRNA profiles of CD34+ BM cells and blood plasma, respectively, from MDS patients using microarrays or next generation sequencing (NGS). We aimed to identify specific sncRNA profiles associated with MDS and search for sncRNA biomarkers predictive of the patient prognosis and response to treatment with azacitidine (AZA). Another goal was to characterize and compare circulating sncRNA profiles of two different extracellular materials, total...
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From adenoma to colorectal cancer: The study of DNA methylation profiles
Fabianová, Ivana ; Vymetálková, Veronika (advisor) ; Šmahel, Michal (referee)
Colorectal cancer (CRC) is a major public health problem worldwide and is one of the most common types of cancer in advanced countries. Recent statistics still present that the Czech Republic has a high incidence of CRC worldwide, especially in Czech men. CRC is known to be a disease that is caused not only by genetic and chromosomal abnormalities but also by epigenetic changes with the best-known DNA methylation. Changes in DNA methylation are the most prominent mechanisms that alter gene expression. Loss of gene function by epigenetic silencing of critical genes plays a key role in the development and progression of sporadic human tumors, including CRC. CRC usually develops from a harmless protrusion, known as an adenoma. However, little is known about the exact timing of DNA methylation changes in the transition from a healthy colon, through an adenoma to a malignant state. This bachelor thesis aims to summarize in detail the aberrant changes in DNA methylation in people with adenoma and in patients with CRC and at the same time to summarize the currently used methods of DNA methylation detection. Keywords: colorectal cancer, DNA methylation, adenoma, CpG island methylation phenotype, hypermethylation, hypomethylation
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Genetic and epigenetic mechanisms (and their cooperation) in the leukemogenesis of acute myeloid leukemia in adults.
Šestáková, Šárka ; Šálek, Cyril (advisor) ; Vymetálková, Veronika (referee) ; Kubričanová Žaliová, Markéta (referee)
Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by great heterogeneity and clonal nature. In recent years, rapidly evolving next-generation sequencing methods provided a deep insight into the mutational background of AML. It was shown that ~ 44 % of AML patients harbor mutations in genes that regulate DNA methylation. So far, many researchers have tried to evaluate the prognostic significance of DNA methylation changes in AML, however, due to a great inconsistency in these studies, none of the reported markers were implemented into clinical practice. The aim of this work was to further investigate the DNA methylation changes in AML patients with specific mutations and their prognostic effect. Next, we wanted to develop a new approach for a complex evaluation of prognostically significant DNA methylation aberrations. In our first project, we assessed the overall DNA methylation, hydroxymethylation, and gene expression in AML patients with mutations in either DNMT3A or IDH1/2 or their combinations. We discovered that each genetic aberration is connected with a distinct pattern of DNA hydroxy-/methylation changes that are not entirely reflected in altered gene expression. Patients with mutations in both genes exhibited a mixed DNA methylation profile most similar to healthy...
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Molecular biomarkers of solid tumors and their use in prognosis and prevention of cancer
Elsnerová, Kateřina ; Václavíková, Radka (advisor) ; Fiala, Ondřej (referee) ; Vymetálková, Veronika (referee)
Molecular biomarkers of solid tumors and their use in prognosis and prevention of cancer Molekulární biomarkery solidních nádorů a jejich využití v prognóze a prevenci nádorových onemocnění Mgr. Kateřina Elsnerová Summary Malignant tumors of ovary and breast are among the most widespread cancers in women. Despite improvements in diagnostics and in therapy, mortality is still very high. An important tool for early cancer detection, as well as for monitoring prognosis and preventing progression, are molecular biomarkers; biomarkers were the topic of this work. The aim of this work was to find out (i) whether there are differences in gene expression between tumor and non-tumor tissues, and among controls (C), primary tumors (pT) and intraperitoneal metastases (iM), respectively; (ii) whether gene expression or genetic variants (single nucleotide polymorphisms, DNA methylation, germline mutations) associate with clinical data of patients, thus being potentially relevant for prognosis. In epithelial ovarian cancer (EOC), 50 of 94 genes were deregulated in controls compared to tumors. Fifteen of 66 genes were deregulated in intraperitoneal metastases compared to primary tumors. Gene expression of ABCA7, ABCB2, ABCC3, ESR2, NH1H4 and NR1I1 was deregulated either in comparison of primary tumors and metastases, or...
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IL 57 - Sporadic colorectal cancer: From genetic make-up to complex phenotypic measurement, from risk determination to prognostic markers
Vodička, Pavel ; Slyšková, Jana ; Pardini, B. ; Naccarati, A. ; Souček, P. ; Vodičková, Ludmila ; Vymetálková, Veronika ; Svoboda, Miroslav ; Foersti, A. ; Hemminki, K.
Colorectal carcinogenesis (CRC), is a complex process, resulting in both genomic and chromosomal instabilities. The valid theories of carcinogenesis accent either the role of somatic mutation or the surrounding microenvironment, however neither of them explains all features of cancer. Uncontrolled proliferation and genomic instability point to the DNA damage response and repair as to the key players. In the present study, we will overview several biomarkers in mapping heterogeneous complex CRC disease and providing prognostic information.\nVariants in genes involved in important pathways, such as DNA repair, cell cycle control, folate metabolism and methylation, insulin resistance and obesity, ABC transporters, selenoprotein genes, genes involved in inflammatory/immune response have shown various degree of association with CRC risk. We present also the data on mutations in high risk genes involved in colorectal carcinogenesis. Gene expression levels were determined in relevant pathways and complemented with other important parameters (epigenetic regulators of transcription by methylation). Additionally, the role of post-transcriptional regulation via miRNA or lncRNA was investigated in relation to the risk of CRC and the efficacy of chemotherapy. We have discovered several genetic and epigenetic markers affecting independently the prognosis of CRC. Functional DNA repair tests (complex phenotype) have been implemented as markers of individual susceptibility to sporadic CRC and its prognosis.\nAn application of the whole set of various biomarkers is inevitable to define the phenotypic landscape of the disease and to delineate the individual response to the therapy.\n
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