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Formation of complex chromosomal rearrangements in cancer cells and significance of these events
Rochlová, Kristina ; Zemanová, Zuzana (advisor) ; Rothová, Olga (referee)
Chromoanagenesis is a catch-all term of recently described catastrophic events that generate complex karyotypes. These events are divided according to the characteristic features and are termed chromothripsis, chromoplexis and chromoanasynthesis. Chromothripsis represents a disintegration of chromosomes or their parts into hundreds of small fragments. Those chromosome fragments are then incorrectly reassembled. Chromoplexis rearrangements are not very different from chromothripsis rearrangements. The main difference is a lower number of breakpoints and the distribution of aberrations in the whole genome. The erroneous replication processes occur during chromoanasynthesis. There are several mechanisms responsible for breakdowns of a DNA molecule. In the case of chromothripsis, micronucleus formation is probably the most important mechanism. During chromoplexis, transcriptional stress plays a major role. Replication stress is associated with chromoanasynthesis rearrangements. The result of all these processes are highly rearranged chromosomes with numerous losses or gains of genetic material. This work summarizes the current knowledge of the mechanisms that are mentioned above and the genesis of complex aberrations. At the same time, it represents the connection between complex karyotype and clonal...
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Frequency and significance of genetic changes in the genome of leukemia cells in children with T-ALL
Sládková, Lucie ; Zemanová, Zuzana (advisor) ; Březinová, Jana (referee)
T-ALL (T-cell acute lymphoblastic leukemia) is identified in 10-15 % cases of pediatric acute lymphoblastic leukemia and it is a clinically and genetically heterogeneous disease. About 50 % of patients have normal karyotype and although a number of cryptic recurrent chromosome aberrations have been reported their prognostic significance is not entirely clear. The aim of the study was to analyze bone marrow cells of children with T-ALL using cytogenomic methods to determine the frequency of cryptic aberrations and to assess their importance for disease prognosis. We examined diagnostic samples of 67 children with T-ALL (19 girls and 48 boys, median age 8 years). We analyzed the changes by G- banding, I-FISH (Dako, Abbott) and MLPA (MRC-Holland) methods. We detected cryptic aberrations in 60 children (91 %). The most frequent changes were deletions of the CDKN2A gene (48×) which were usually observed in combination with other changes and aberrations of loci for TCR genes (20×). TLX3 gene rearrangements were detected in 18 cases and were never associated with rearrangements of TCR loci. Complex karyotype was detected in 10 patients with recurrent breakpoints 5q35 and 10q24. 45 patients live in the first or second complete remission, relapse occurred in 14 children and 20 died. Statistical analysis of...
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MicroRNAs in AML pathogenesis
Koutová, Linda ; Korabečná, Marie (advisor) ; Zemanová, Zuzana (referee) ; Kotyza, Jaromír (referee)
Acute myeloid leukemia (AML) is a very heterogeneous disease associated with cytogenetic aberrations and genetic mutations. Many of these changes have been revealed and their detection became usual part of the diagnostic process today. However, changes of expression profiles of small, noncoding RNAs, so called microRNAs (miRNAs), are less known and not used for diagnostics yet. These RNAs, 19-24 nucleotides long, take part in the regulation of expression of different genes through complementary base pairing to the 3'non- translated region (3'UTR) of the target messenger RNA (mRNA). They can influence key processes of the cell, like differentiation, proliferation or apoptosis. The changes in expression of different miRNAs are known from different types of cancers. In solid tumors, they are usually detected from bioptic samples; but also plasma samples are now in the center of attention as so called liquid biopsies providing the information about molecular genetic events in the organism. Many studies have revealed deregulated miRNAs in the bone marrow, full blood or isolated progenitor cells (CD34+) of AML patients, only four of them have analyzed plasma samples. We focused on the plasma samples and we targeted on such miRNAs, which levels differ at AML diagnosis and after the chemotherapy. Out of...
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Assessment of asp reproductive population in Švihov Reservoir in 2017
Šmejkal, Marek ; Blabolil, Petr ; Bartoň, Daniel ; Kolařík, T. ; Soukalová, Kateřina ; Děd, Vilém ; Boborová, K. ; Michalička, P. ; Zemanová, Z. ; Kočvara, Luboš ; Duras, J. ; Kubečka, Jan
The aim of the contract was to capture reproducing asp by electrofishing and tag fish individually using individual marking technique (PIT-tags). Estimate of asp reproductive population in the Švihov Reservoir was performed on the basis of mark-recapture methods. Furthermore, the length and weight increments were computed for recaptured asp individuals. Tagged individuals were monitored using passive telemetry systems on the tributary of Švihov Reservoir.
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Molecular-cytogenetic diagnostics of marker chromosomes
Tesner, Pavel ; Kočárek, Eduard (advisor) ; Zemanová, Zuzana (referee) ; Šubrt, Ivan (referee)
Supernumerary marker chromosomes (sSMCs) are a relatively rare cytogenetic phenomenon. Their laboratory examination is often difficult, and the clinical interpretation is even more challenging. The main reason is that most sSMC carriers have no clinical manifestations. The chromosome origin and exact range of the aberration are very important, as well as the fact that sSMCs are often found in mosaics that can strongly influence both the phenotype and the interpretation of result. Prenatal sSMC finding is one of the most challenging situations in both clinical and laboratory genetics. This work deals with the investigation process of sSMC carriers using molecular cytogenetic techniques, especially fluorescence in situ hybridization (FISH). We investigated a total of 67 families collected both prospectively and retrospectively, and we found 70 unique sSMCs in a total of 74 individuals. Six cases were familial and in three cases two sSMCs were found in one individual. According to the initial karyotype finding, the cases were divided into two groups, sSMCs supernumerary to a normal karyotype (group A) and sSMCT s supernumerary to the Turner karyotype (group B). The chromosomal origin was successfully determined in 88,6 % sSMCs. In group A the most common findings were sSMCs derived from chromosome 15,...
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Molecular genetic analysis of selected cryptic rearrangements of human chromosomes
Šolc, Roman ; Hirschfeldová, Kateřina (advisor) ; Zemanová, Zuzana (referee) ; Kuglík, Petr (referee)
The presented dissertation summarizes the results of research focused on the study of cryptic rearrangements of human chromosomes. Specifically, it focuses on three core areas of research. The first area is the research of cryptic rearrangements identified as causal causes of mental retardation in patients with previously unknown aetiology. The most common are the so-called microdeletion syndromes. The large variability of the phenotype and often overlapping symptoms of microdeletion syndromes require a whole-genome approach. Within the research, 64 probands were investigated and in 10 (16%) cryptic rearrangements were found and further analyzed. The second area is the research of cryptic rearrangements associated with the pseudoautosomal region 1 (specifically with the SHOX gene region), which may be both natural components of population variability and the cause of the disease. Within the research, 98 patients with Léri-Weill dyschondrosteosis or idiopathic short stature were examined, with a causal mutation found in 68.8%, and 7.8% probands respectively. At the same time, the minor deletion (so-called L05101 deletion) was evaluated as a population polymorphism without an apparent phenotypic impact. Duplications with high pathogenic potential were identified by mean of comparative analysis of...
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Unbalanced changes in cancer cells genome and its role in cancer pathogenesis
Lhotská, Halka ; Zemanová, Zuzana (advisor) ; Jarošová, Marie (referee) ; Kuglík, Petr (referee)
Malignant transformation of cell is characterized by genomic instability that involves unbalanced changes besides other things. We analyzed genomic aberrations, promoter methylation and mutations of several clinically relevant genes using I-FISH, mFISH, mBAND, CGH array, SNP array, MLPA, MS-MLPA and MS-PCR methods. We focused on two groups of patients well known for frequent appearance of unbalanced changes - patients with malignant brain tumors (gliomas) and patients with myelodyspastic syndromes (MDS). In patients with low grade glioma (WHO grade I - II), the codeletion of 1p/19q (82,6% oligodendrogliomas and oligoastrocytomas), mutation of IDH1/IDH2 genes (87% WHO grade I-II gliomas), copy neutral loss of heterozygozyty of 17p (72,2% astrocytomas) and higher presence of unbalanced aberration in astrocytomas belongs to the most frequent findings. We described yet unpublished methylation of MLH3 gene promoter in 60,9% oligodendrogliomas and in 27,3% astrocytomas. We also observed clonal evolution in patients with recurrent tumors. We studied secondary rearrangements of deleted chromosome 5 in patients with MDS and complex karyotype and we described its most recurrent translocation partners and breakpoints. We observed chromothripsis in 49% of these patients and it was frequently associated with...
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Chromosomal aberrations in childhood acute leukemia.
Sládková, Lucie ; Zemanová, Zuzana (advisor) ; Šárová, Iveta (referee)
1 Abstract Leukemias are the most common cancer diseases in childhood. The majority of cases represent acute leukemias, the most common of which is acute lymphoblastic leukemia (ALL), the second most frequent subtype is acute myeloid leukemia (AML). One of the basic laboratory examinations at the time of diagnosis is the cytogenetic analysis of the karyotype of leukemic cells in which we are looking for the recurrent chromosomal aberrations. These changes in the structure or number of the chromosomes can be found in up to 90 % of patients and the exact prognostic significance is known for most of them. In ALL, the findings of high hyperdiploidy (>50 chromosomes) and translocation t(12;21)(p13;q22) are considered the most significant prognostic factor associated with good prognosis and translocations involving the KMT2A gene in the 11q23 region are associated with poor prognosis. In AML, the most frequent aberrations are t(8;21)(q22;q22), t(15;17)(q24;q21) and inv(16)(p13;q22) which are considered indicator of good prognosis. An important unfavourable prognostic finding in AML are the KMT2A gene rearrangements, the most common of which is the translocation t(9;11)(q23;p13.1). Nowadays, there are many ways to detect chromosomal aberrations in leukemic cells. G-banding is the most common method of classical...
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