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Morphological, immunohistochemical, and molecular analysis of leiomyocellular tumors of the female reproductive system
Gregová, Mária ; Dundr, Pavel (advisor) ; Mandys, Václav (referee) ; Škarda, Jozef (referee)
Introduction Leiomyoma with bizarre nuclei (LBN) and cellular leiomyoma (CL) are rare variants of uterine smooth muscle tumors. In diagnostic practice, LBN can be mistaken for leiomyosarcoma (LMS), while CL may mimic low grade endometrial stromal sarcoma (LG ESS). Careful evaluation of morphological features is necessary when making the diagnosis; in some borderline cases, immunohistochemical and molecular examinations may help. Literature data on molecular genetic alterations in LBN and CL is limited, but some of these tumors appear to share certain aberrations with classical leiomyomas (UL) and LMS. Aims The aim of the work is to expand the knowledge about smooth muscle tumors of the uterus, especially LBN and CL, and perform a complex morphological, immunohistochemical (IHC), and molecular evaluation of their features. The individual goals include: 1) confirmation of the hypothesized benign behaviour of LBN, 2) morphological analysis of LBN, 3) more detailed clarification of LBN tumorigenesis with a focus on the FH gene, 4) clarification of CL tumorigenesis, 5) the use of IHC FH antibody as a screening method to identify FH gene mutations, 6) the use of morphological evaluation and results of IHC examination to facilitate differential diagnostic balance between benign and malignant smooth muscle...
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Analysis of the spectrum of genetic variants associated with development of Parkinson's disease
Stočesová, Lucie ; Hirschfeldová, Kateřina (advisor) ; Fajkusová, Lenka (referee)
Parkinson's disease (PD) is one of the most common neurodegenerative disease in humans. It affects all age categories and the number of patients with this disease is still growing. However, the genetic cause of PD is not yet very clear and new and new candidate genes are constantly being discovered. The aim of the thesis is to perform a mutation analysis in a group of patients and controls from the Czech population and thus find possible genetic causes of parkinsonism in a cohort of researched patients. The second aim is to evaluate data correlation obtained by different methods. Next generation sequencing was used for this purpose. The results of this sequencing were verified with methods such as MLPA (Multiplex Ligation-Dependent Probe Amplification), analysis of short tandem repeats and Sanger sequencing. Using these methods, we obtained a wide range of possible genetic causes of parkinsonism in the studied group of patients. Patogenic or risk variants were found not only in classical candidate genes typical for PD (called PARK), but also in genes associated with other neurodegenerative diseases. For less than half of the patients (42,64 %), the genetic cause of parkinsonism was not found. Using several methods, we found that next generation sequencing is a very precise method, that can well...
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Genetic factors affecting course of selected forms of nephrotic syndrome
Šafaříková, Markéta ; Štekrová, Jitka (advisor) ; Král, Jiří (referee)
Nephrotic syndrome (NS) is characterized by proteinuria, hypalbuminemia and edemas. It occurs during first and second glomerulopathies. This disease can be divided into two groups: primary (idiopathic) and secondary. The heredity of the familial nephrotic syndrome is autosomal dominant and autosomal recessive. There are four most important genes that condition the formation of hereditary nephrotic syndrome in adult patienst. These genes are ACTN4, CD2AP, NPHS2 and TRPC6. The gene ACTN4, which encodes protein α-actinin 4, is responsible for the autosomal dominant form of focal segmental glomerulosclerosis (FSGS). FSGS is included in first glomerulopathies. α-Actinin 4 was also researched for some types of carcinomas. There was performed the mutational analysis of the gene ACTN4 on the set of 48 patients with nephrotic syndrome in this diploma thesis. High resolution melting (HRM) analysis and sequencing selected samples were used during this mutation detection. During this process many published and unpublished SNPs and one unpublished candidate mutation that could have causal associations with FSGS were found.
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The use of parallel sequencing methods in microbiology.
Pavlíková, Magdaléna ; Najmanová, Lucie (advisor) ; Vopálenský, Václav (referee)
The thesis describes the history of development of sequencing methods with special focus on the modern effective parallel sequencing methods and their application in microbiology. The development and improvements of sequencing systems lead to the acceleration of the process and considerable decrease of price, which consequently allow wider spectrum of applications. Each of the sequencing systems has its characteristic features including drawbacks stemming from the principle of the respective method. Not every method suitable for all the applications. In the thesis the sequencing methods are compared and examined with respect to their appropriateness for certain application fields in microbiology. The currently available sequencing methods are usually categorized into three "generations", distinguished by sets of typical features. First generation methods include the systems of Sanger and Maxam-Gilbert; "next generation" is represented by methods 454, Illumina, SOLiD and Helicos; and finally SMRT, Ion Torrent and the commercially not yet available nanopore sequencing are usually called "next-next generation". Now the sequencing becomes a standard technology of molecular biology, not only in the basic microbiological research, but it is also widely applied in medicine (quick identification of patogenes,...
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Molecular genetic analysis of chromosomal region 8q24 in patients with trichorhinophalangeal syndrome or isolated exostosis
Klugerová, Michaela ; Šolc, Roman (advisor) ; Křepelová, Anna (referee)
Trichorhinophalangeal syndrome is a malformation syndrome characterized by craniofacial and skeletal abnormalities and is inherited in an autosomal dominant manner. We distinguish free subtypes on clinical and molecular level - TRPS I, TRPS II, TRPS III. All TRPS patients have sparse hair, a pear-shaped nose, a long flat philtrum, a thin upper lip and protruding ears. Skeletal abnormalities include cone-shaped epiphyses at the phalanges, hip malformations and short stature are present. The subgroups TRPS I and TRPS III are result of the mutated TRPS1 gene, which is maped into the 8q24 region. This gene is situated proximal of the EXT1 gene, both genes are affected in a subgroup of patients with TRPS II. These patients suffer more from multiple (cartilaginous) exostoses and mental retardation. In this work we performed molecular genetic analysis of a sample of 16 patients, 8 probands showed a TRPS phenotype and 8 probands had only isolated exostoses. The peripheral venous blood of patients was used to gain purified DNA, which was subsequently used to investigate the chromosome 8q24 region using MLPA ("multiplex ligation-dependent probe amplification"). This analysis revealed a deletion in 1 TRPS patient and 1 patient with exostoses. Sequencing of the TRPS1 gene coding exons in remaining 7 TRPS...
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The comparison of morphology, expression, epigenetic changes and mutations of HNF1B in solid tumors and non-neoplastic lesions.
Bártů, Michaela ; Dundr, Pavel (advisor) ; Mandys, Václav (referee) ; Škarda, Jozef (referee)
Introduction HNF1B is a tissue-specific transcription factor, which plays a crucial role in the embryological development of a number of organs, especially kidneys, gastrointestinal system, pancreas and billiary system. While the significance of HNF1B in the development of urinary tract malformations has already been well described, its role in the pathogenesis of solid tumors has not yet been elucidated. Based on the current data it seems that depending on the type of individual tumor HNF1B can either act as an oncogene or a tumor suppressor. However, the precise mechanism of how it exerts its influence is still unclear. Aims: The thesis focuses on expanding the knowledge of the significance of HNF1B changes in selected solid tumors and non-neoplastic lesions. The individual goals include: 1) determining the role which HNF1B plays in the pathogenesis of these lesions, 2) evaluating the significance of HNF1B for differential diagnosis, 3) analysis of the prognostic and predictive meaning of HNF1B, 4) mutation analysis of the HNF1B gene in all the tumor and non-tumor tissues with the aim to identify novel pathogenic mutations, 5) methylation analysis of the HNF1B promoter. Material and methods: Immunohistochemical examination with the antibody against HNF1B was performed on 516 samples of tumor and...
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Spectrum of FGFR3 gene mutations in hypochondroplasia
Janoušková, Simona ; Křepelová, Anna (advisor) ; Baxová, Alice (referee)
Hypochondroplasia (MIM 146000) is a skeletal dysplasia characterized by disproportional dwarfism with rhizomelic or mesomelic shortening of the upper and lower extremities, with variable severity. Patients often have macrocephaly with normal facial features. Hypochondroplasia is a disease with autosomal dominant inheritance. In some patients it is caused by germline mutations in the FGFR3 gene, in others the cause of the disease remains unknown . The FGFR3 gene encodes a tyrosine kinase receptor. This receptor negatively regulates the conversion of cartilage to bone. FGFR3 gene mutations that cause hypochondroplasia lead to constitutive activation of the receptor and inhibit the growth of long bones. In this study, we analysed selected regions (exons) of the FGFR3 gene in 98 patients with disproportional dwarfism and clinical diagnosis of hypochondroplasia. Eighteen patients from 12 families had familial and 80 patients had sporadic form of the disease. All patients were previously tested negative for frequent germline mutations in exon 13 (codon 540) and exon 15 (codon 650). Genomic DNA was isolated from patient's peripheral blood leukocytes. The examination was conducted with the informed consent of the patient or his legal representative. We performed mutational analysis by direct sequencing of...
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Molecular genetic analysis of chromosomal region 8q24 in patients with trichorhinophalangeal syndrome or isolated exostosis
Klugerová, Michaela ; Šolc, Roman (advisor) ; Křepelová, Anna (referee)
Trichorhinophalangeal syndrome is a malformation syndrome characterized by craniofacial and skeletal abnormalities and is inherited in an autosomal dominant manner. We distinguish free subtypes on clinical and molecular level - TRPS I, TRPS II, TRPS III. All TRPS patients have sparse hair, a pear-shaped nose, a long flat philtrum, a thin upper lip and protruding ears. Skeletal abnormalities include cone-shaped epiphyses at the phalanges, hip malformations and short stature are present. The subgroups TRPS I and TRPS III are result of the mutated TRPS1 gene, which is maped into the 8q24 region. This gene is situated proximal of the EXT1 gene, both genes are affected in a subgroup of patients with TRPS II. These patients suffer more from multiple (cartilaginous) exostoses and mental retardation. In this work we performed molecular genetic analysis of a sample of 16 patients, 8 probands showed a TRPS phenotype and 8 probands had only isolated exostoses. The peripheral venous blood of patients was used to gain purified DNA, which was subsequently used to investigate the chromosome 8q24 region using MLPA ("multiplex ligation-dependent probe amplification"). This analysis revealed a deletion in 1 TRPS patient and 1 patient with exostoses. Sequencing of the TRPS1 gene coding exons in remaining 7 TRPS...
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The use of parallel sequencing methods in microbiology.
Pavlíková, Magdaléna ; Najmanová, Lucie (advisor) ; Vopálenský, Václav (referee)
The thesis describes the history of development of sequencing methods with special focus on the modern effective parallel sequencing methods and their application in microbiology. The development and improvements of sequencing systems lead to the acceleration of the process and considerable decrease of price, which consequently allow wider spectrum of applications. Each of the sequencing systems has its characteristic features including drawbacks stemming from the principle of the respective method. Not every method suitable for all the applications. In the thesis the sequencing methods are compared and examined with respect to their appropriateness for certain application fields in microbiology. The currently available sequencing methods are usually categorized into three "generations", distinguished by sets of typical features. First generation methods include the systems of Sanger and Maxam-Gilbert; "next generation" is represented by methods 454, Illumina, SOLiD and Helicos; and finally SMRT, Ion Torrent and the commercially not yet available nanopore sequencing are usually called "next-next generation". Now the sequencing becomes a standard technology of molecular biology, not only in the basic microbiological research, but it is also widely applied in medicine (quick identification of patogenes,...
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Genetic factors affecting course of selected forms of nephrotic syndrome
Šafaříková, Markéta ; Štekrová, Jitka (advisor) ; Král, Jiří (referee)
Nephrotic syndrome (NS) is characterized by proteinuria, hypalbuminemia and edemas. It occurs during first and second glomerulopathies. This disease can be divided into two groups: primary (idiopathic) and secondary. The heredity of the familial nephrotic syndrome is autosomal dominant and autosomal recessive. There are four most important genes that condition the formation of hereditary nephrotic syndrome in adult patienst. These genes are ACTN4, CD2AP, NPHS2 and TRPC6. The gene ACTN4, which encodes protein α-actinin 4, is responsible for the autosomal dominant form of focal segmental glomerulosclerosis (FSGS). FSGS is included in first glomerulopathies. α-Actinin 4 was also researched for some types of carcinomas. There was performed the mutational analysis of the gene ACTN4 on the set of 48 patients with nephrotic syndrome in this diploma thesis. High resolution melting (HRM) analysis and sequencing selected samples were used during this mutation detection. During this process many published and unpublished SNPs and one unpublished candidate mutation that could have causal associations with FSGS were found.
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