No description available.

Chromosomal rearrangements of the nucleoporin genes NUP214 and NUP98 are recurrent in aggressive cases of acute myeloid and lymphoid leukemias. NUP214 and NUP98 are components of the nuclear pore complex, a giant multiprotein structure that mediates nucleocytoplasmic shuttling. The two nucleoporins are enriched in phenylalanine-glycine (FG) repeats, which form the NPC permeability barrier and are essential for the interaction with nuclear transport receptors. NUP214 and NUP98 exhibit high affinity for the nuclear export receptor chromosomal region maintenance 1 (CRM1), which, alone, mediates the nuclear export of thousands of proteins and ribonucleoproteins. In the first part of this project, we report that the leukemogenic fusion proteins SET-NUP214 and DEK-NUP214 affect nucleocytoplasmic transport by perturbing the localization of essential nuclear transport factors, including endogenous nucleoporins and CRM1 nuclear export complexes. We further demonstrate that the two fusion proteins are sensitive to CRM1 inhibition and that targeted inhibition of nuclear export is sufficient to reduce the cell viability and proliferation of patient-derived cell lines with SET-NUP214 and DEK-NUP214 rearrangements. In the second part of the project, we used proximity-dependent biotin identification (BioID) to study the landscape of the NUP98-HOXA9 and SET-NUP214 environments. Though distinct endogenous binding partners have been documented for NUP214 and NUP98 chimeras, their total interactome has not been fully disclosed. Our results suggest that both fusion proteins interact with major regulators of RNA processing, with translation-associated proteins, and that both chimeras perturb the transcriptional program of the tumor suppressor p53. We further purpose that the two fusion proteins affect distinct cellular processes. According to our results, NUP98-HOXA9 likely perturbs Wnt, MAPK and estrogen receptor signaling pathways, as well as the cytoskeleton, the latter likely due to its interaction with the nuclear export receptor CRM1. Conversely, SET-NUP214 appears to affect cellular metabolism, likely due to the interaction with mitochondrial proteins and metabolic regulators. Overall, this research project provided new data supporting that CRM1 might be a possible therapeutic target in NUP214-related leukemia and revealed new clues on the mechanistic actions of nucleoporin fusion proteins. Hence, our findings might be of particular relevance in the search of new druggable targets for the treatment of nucleoporin-related leukemia. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Genomes of higher plants comprise a large proportion of repetitive DNAs, where one major class is satellite DNA. Satellite DNA is organized in tandem arrays of basic repeating units, which often occurs in heterochromatin of centromeric/pericentromeric and intercalary as well as subtelomeric regions. Besides these typical satellite repeats, there are also non-typical satellite DNAs, which are organized in short tandem arrays and integrated into a transposable element. The chromosomal localization of non-typical satellites is not in large regions of heterochromatin, but tend to be dispersed along chromosomes. This thesis describes the identification of the major repeat classes including major satellite content in six beet and related species. The focus was on identification and characterization of new satellite families in the beet genomes. In this study, the information regarding repetitive DNA as well as satellite families fraction in six beet and related species was gained based on graph-based clustering of next generation sequenced short sequence reads. The repeat proportion of the six analyzed species ranges from 34.4% in C. quinoa to 65.6% in B. lomatogona, in which the portion of nearly 50% belongs to B. vulgaris, B. nana, P. procumbens, and P. patellaris. Among all classes of repetitive DNAs, LTR retrotransposons are the most abundant repeat type in all analyzed genomes, which is a common feature of higher plant genomes. The other repeat sequences are DNA transposons, rDNA, and satellite DNA with variable portions in different species. A set of satellite families in each species was analyzed in detail and reflects the relationship between six species. The closely related relationship between B. lomatogona and B. nana as well as between P. procumbens and P. patellaris is affirmed by seven and 13 satellite families shared between two species, respectively. Similarly, the closer relationship between B. vulgaris and two species B. lomatogona and B. nana than between B. vulgaris and two species P. procumbens and P. patellaris from the sister-genus Patellifolia is also confirmed. C. quinoa is a distantly related species and this is reflected by vastly different satellite content. Therefore, satellite DNA analysis might be a useful tool to trace species evolution. In the B. lomatogona genome, by the application of RepeatExplorer tool, six novel tandemly repeated DNA sequences were identified and designated BlSat1-BlSat6. The three typical satellite families BlSat1, BlSat5, and BlSat6 are organized in tandem arrays in large heterochromatic blocks. BlSat1 is mainly localized in the pericentric region of the chromosome 3, 5, 6, and 9, while BlSat5 is amplified in the pericentromeric region of the chromosome 3, 5, and 7. BlSat6 is a chromosome-specific satellite and is located in the subtelomeric region on the south arm of the chromosome 8. The other three satellite families BlSat2, BlSat3, and BlSat4 are characterized as non-typical satellite DNA because of their dispersed distribution along chromosomes. BlSat2 and BlSat3 are identified as a tandem repeat domain in Ogre/Tat retrotransposons. The occurrence of one or several short tandem arrays in a transposable element is a common phenomenon in both animals and plants. These short repeats are considered to be continuously evolving and eventually amplifying to new satellite families. Furthermore, the distribution of the six new satellite families in beet and related species was confirmed by comparative PCR, comparative Southern hybridization, and mapping of sequence reads from referent species against each satellite sequence. The BlSat1 and BlSat6 satellite families are specific for the genus Beta, while BlSat5 is only amplified in two sections Corollinae and Nanae of the genus Beta. BlSat4 is an ancient satellite family which exists in all tested species belonging to the genera Beta, Patellifolia, Chenopodium, and Spinacia, whereas BlSat2 and BlSat3 might have evolved before the separation of the genus Beta and Patellifolia but their sequences have been lost or heavily diverged during the species radiation. Comparison of two wild beet genomes P. procumbens and P. patellaris was performed aiming to address the open question whether P. patellaris is auto- or allotetraploid. The high similarity between these two genomes indicates their close relationship. However, the genetic difference between two genomes, in particular the molecular characteristics as well as the chromosomal localization of two satellite families PproSat1 and PpatSat1, might support a hypothesis that P. patellaris is allotetraploid species with a half of its chromosome set derived from P. procumbens. The results obtained in this work might provide comprehensive information of the repetitive classes as well as satellite families in the genomes of beets and related species. The results can be used as the species-specific and chromosome-specific markers in beet genome studies.

Pediatric medulloblastoma (MB) is a cerebellar brain tumor namely characterized by its origination in early development, as early as embryogenesis. MB is thought to originate from the highly heterogeneous granular neuron precursor (GNP) cell population that resides within the rhombic lip of the dorsal hindbrain region, and is particularly susceptible to the effects of the oncogenic Sonic Hedgehog (SHH) signaling pathway. Patched 1 (Ptch1), typically a transmembrane SHH pathway tumor suppressor gene, is mutated in 20% of MB cases, otherwise known as SHH-group MBs. This mutation in MB presents as a loss of heterozygosity (LOH), where the wild type allele of Ptch 1 is deleted. Ptch 1 receptor silencing activates downstream target genes such as proto-oncogene Smoothened (Smo) and allows for the initiation of tumorigenesis. However, the molecular basis for Ptch1 LOH in MB remains elusive. We have discovered a cancer-testis antigen, Protamine 1 (Prm 1), that is present in the Ptch 1 locus in SHH-group MB tumors. By utilization of the RNAscope technique, we confirm mRNA expression of Prm 1 in cerebellar tumor tissue, predominantly from tumor cells, but not in stromal cells. These studies reveal that tumor cells highjack the promoter of Ptch 1 to express Prm 1, promoting tumor progression. These findings establish the mechanism for Ptch 1 LOH in SHH-group MB, and provide the rationale to define the cell of origin for SHH group MB based on Prm 1 expression. / Biomedical Sciences

No description available.

DNA encodes the genetic instructions for the development and function of organisms and hence maintaining genomic integrity is essential for the propagation of life. However, DNA molecules are under constant threat of metabolic and environmental insults resulting in DNA damages including DNA double strand breaks (DSB), which are considered as a serious threat to cell survival. The majority of these DSB are repaired by Non-homologous end joining (NHEJ). Unrepaired DSB can lead to genomic instability resulting in cell cycle arrest, apoptosis, and mutations. Thus, delineating this DNA repair process is important in understanding the molecular mechanisms of aging and malignant progression. B lymphocytes undergo physiological DNA breaks and NHEJ-mediated DNA repair during their bone marrow differentiation and peripheral class switch recombination (CSR), thus lending them as a good model system in which to delineate the DNA repair mechanisms. To determine the effect of aging on NHEJ, B lymphocytes from old mice were analyzed. The results showed compromised DNA repair in cells from old mice compared to cells from adult mice. These results suggest that NHEJ is compromised during aging and might play critical roles in the aging process and age-associated conditions. To delineate the role of a CT in regulating the immune system, transgenic mice expressing NUP98-HOXD13 (NHD13) were analyzed for B lymphocyte differentiation, peripheral development, CSR, and antibody production. The results showed impaired B cell development and antibody production, which worsened with antigenic stimulation, suggesting the role of NHD13 in immune regulation. These studies explored the possibility of altered NHEJ-mediated DNA repair as a contributing reason for aging process and age-associated conditions. Also, the results from NHD13 study suggested that a primary CT can result in impaired NHEJ and regulate immune cell development and function. Furthermore, the results pointed to the possibility that a primary CT may lead to secondary mutations through altered NHEJ. Thus, these studies shed insight into the molecular mechanisms of altered NHEJ and may help in developing preventive or therapeutic strategies against accumulation of DNA damage, aging process and secondary mutations. / Ph. D.

Die ALS ist eine fortschreitende neurodegenerative Erkrankung, deren Symptome durch den Untergang der Motoneuronen bedingt sind. Neueste zytogenetische Untersuchungen zeigen ein vermehrtes Auftreten konstitutioneller Chromosomenveränderunge bei ALS-Patienten. Dies lässt eine Verbindung zwischen dem Ausbruch der Erkrankung und der auffälligen Zytogenetik vermuten. Das Auftreten spontaner Chromosomenveränderungen als Zeichen einer chromosomalen Instabilität wurde in der vorliegenden Arbeit an ALS-Patienten untersucht. METHODE: Neben der Karyotypisierung, der Bestimmung der SCE-Rate und der Bruchrate nach Behandlung mit Bleomycin kam die Fluoreszenz in situ Hybridisierung zum Einsatz. Die Untersuchungen wurden an Patienten mit sporadischer ALS (45), an Kontrollpersonen (38) und Verwandten (9) durchgeführt. ERGEBNISSE: Die Karyotypisierung ergab bei den Patienten eine spontane Translokationsrate von 0,02 Translokationen/Zelle (t/Z), bei den Kontrollen 0,04 t/Z. Weitere numerische oder strukturelle Auffälligkeiten waren nicht signifikant verschieden. Es wurden keine konstitutionellen Chromosomenaberrationen gefunden. Die Häufigkeit der Schwesterchromatidaustausche (SCE-Rate) bewegte sich mit 7-8 SCE/Z in der Patientengruppe innerhalb der Normwerte. Durch die Zugabe von Bleomycin in die Zellkultur stieg die Zahl der Chromatidbrüche von 0,0 auf 0,8 Brüche/Z an. Dabei zeigten die untersuchten Gruppen ähnliche Progredienzen in den Bruchraten. Mit der Fluoreszenz in situ Hybridisierung werden quantitative Aussagen über spontane Translokationsraten gemacht. Sie betrug in der Kontroll-und Patientengruppe 0,03 bis 0,04 t/Z. DISKUSSION: Die vorliegenden Ergebnisse liefern keinen Anhalt für eine chromosomale Instabilität als Risikofaktor für die Entstehung der sporadischen ALS. Indizien für eine chromosomale Instabilität wie erhöhte Bruchraten und SCEs als auch vermehrtes Auftreten somatischer Aberrationen konnten bei den ALS-Patienten nicht nachgewiesen werden. Über mögliche Auffälligkeiten in den Motoneuronen lässt sich allerdings mit den Untersuchungen an Blutlymphozyten keine hinreichend sichere Aussage machen. / Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease which is characterized by the degeneration of motor neurons. Recently, a high rate of constitutional structural chromosomal rearrangements has been reported in apparently sporadic ALS patients. It remains questionable whether or not these genomic rearrangements are caused by a chromosomal instability involved in the pathogenesis of the disease. Therefore, we performed different cytogenetic studies on chromosomal instability. METHOD: We performed chromosome analyses from patients (N=45), control subjects (N=38), and relatives (N=9) after culturing blood lymphocytes. Conventional chromosome analysis after GTG-banding, chromosomal breakage test after Bleomycin treatment, the rate of sister chromatid exchange (SCE), and whole chromosome painting were used for these analyses. RESULTS: Neither karyotyping nor whole chromosome painting revealed higher levels of structural or numerical aberrations in lymphocytes of patients with sALS. After karyotyping we found 0.02 t/cell in patients and 0.04 t/cell in controls. Whole chromosome painting revealed 0.04 t/cell in patients and 0.03 t/cell in controls. The chromosomal breaks increased likewise after Bleomycin treatment in the control group and the patient group as well. Cell cultures without Bleomycin did not show any breaks while the highest Bleomycin concentration induced up to 0.08 breaks/cell. The SCE rate in patients which corresponds to the chromatid repair activity did not rise to a higher level than in the control individuals. Both groups were in the normal range of 7 to 8 SCE/cell. DISCUSSION: The pathomechanism of neurodegeneration in ALS patients is still unknown. We tried to find a cytogenetic correlative being a risk factor for the development of ALS. However, so far there is no clue for chromosomal instability being involved in the neurodegenerative process.

DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.

<p>Despite major advances in our understanding of the biology of childhood acute myeloid leukemia (AML) and the development of new cytotoxic drugs, the prognosis of long-term survival is still only 60-65 %.</p><p>In the present research, we studied the pharmacokinetics of drugs used in the induction therapy of childhood AML and performed in vitro drug sensitivity testing of leukemic cells from children with AML.</p><p>The aims of the studies were to correlate the results of the analysis to biological and clinical parameters and to identify subgroups of AML with specific drug sensitivity profiles in order to better understand why treatment fails in some patients and how therapy may be improved.</p><p>Blood samples were analysed to study the pharmacokinetics of doxorubicin (n=41), etoposide (n=45) and 6-thioguanine (n=50). Doxorubicin plasma concentration and total body clearance were correlated to the effect of induction therapy, and doxorubicin plasma concentration was an independent factor for complete remission, both in univariate and multivariate analysis including sex, age, and white blood cell count at diagnosis. For etoposide and 6-thioguanine no correlation was found between pharmacokinetics and clinical effect. Children with Down syndrome (DS) tended to reach higher blood concentrations of etoposide and thioguanine nucleotides, indicating that dose reduction may be reasonable to reach the same drug exposure as in children without DS.</p><p>Leukemic cells from 201 children with newly diagnosed AML, 15 of whom had DS, were successfully analysed for in vitro drug sensitivity by the fluorometric microculture cytotoxicity assay (FMCA). We found that samples from children with DS were highly sensitive to most drugs used in AML treatment. In non-DS children, the t(9;11) samples were significantly more sensitive to cytarabine (p=0.03) and doxorubicin (p=0.035) than other samples. The findings might explain the very favorable outcome reported in children with DS and t(9;11)-positive AML. A specific drug resistance profile was found for several other genetic subgroups as well. A detailed study of MLL-rearranged leukemia showed that cellular drug sensitivity is correlated both to partner genes and cell lineage, findings that support the strategy of contemporary protocols to include high-dose cytarabine in the treatment of patients with MLL-rearrangement, both in AML and acute lymphoblastic leukemia (ALL).</p><p>Our results indicate that drug resistance and pharmacokinetic studies may yield important information regarding drug response in different sub-groups of childhood AML, helping us to optimize future chemotherapy in childhood AML.</p>

8 Abstract Human Herpes Virus 6 (HHV-6) consists of two closely related DNA viruses: HHV-6A and HHV-6B. The primoinfection proceeds at an early childhood usually as sixth exanthem disease or without any clinical symptoms. Both HHV-6 viruses are able to integrate to human genome using recombinant mechanisms which is unique compared to other human herpesviruses. The aim of the thesis is to study Ci-HHV-6 in a group of patients with malign disease and in the healthy population. We analysed 812 patients with malign disease and 420 healthy subjects from general population. The Ci-HHV-6 was assessed by real-time PCR, the specific localization of Ci-HHV-6 was determined using fluorescent in situ hybridization (FISH). Using comparative study, we did not identify significant difference between frequency of Ci-HHV-6 in patients with malign disease (1.11%) and healthy subjects (0.95%) (P-value 0.8). Consequently, we proved the heritability of Ci-HHV-6 in affected families. We determined the localization of Ci-HHV-6 to telomeric regions of chromosomes 2 and 18. We studied the production of viral proteins in the subjects with Ci-HHV-6. In this work, we conducted the first epidemiological study of Ci-HHV-6 in the Czech Republic. We also introduced novel methods which contribute to better characterization of this phenomenom.