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 We described yet unpublished methylation of MLH3 gene promoter in 60,9% oligodendrogliomas and in 27,3% astrocytomas.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...

Myelodysplastic syndromes (MDS) represent a group of clonal stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenia, morphological dysplasia and the risk of transformation to acute myeloid leukemia (AML). MDS belongs to one of the most common hematological diseases in patients over 60 years old. MDS incidence is still increasing. Appropriate therapy of MDS remains challenging. There is no curative approach besides peripheral stem cells transplantation, which is regretfully appropriate only for a small group of patients due to a higher median age of the MDS population. This is why the search for therapeutic alternatives remains paramount. MDS treatment was rather frustrating until the recent introduction of two new therapeutic approaches: immunomodulation therapy with lenalidomide and epigenetic or demethylating therapy with 5-azacytidine. Both new drugs have significantly higher effect than standard therapy. However, the precise mechanism of this effect remains unknown. As a result, we decided to initiate several research projects while introducing this promising treatment to our patients. Our aim is to investigate the mechanism of both agents in relation to disease pathogenesis by examining changes of certain occurrences and factors prior to and during the course of...

Background: The high incidence of mutations and cytogenetic abnormalities in patients with myelodysplastic syndrome (MDS) suggests the involvement of DNA repair mechanism defects in the pathogenesis of this disorder. The first part of this work was focused on monitoring of gene expression of DNA repair genes in MDS patients and on their alterations during disease progression. In the second part, next generation sequencing was used to detect single nucleotide polymorphisms (SNPs) and mutations in DNA repair genes and their possible association with MDS development was evaluated. Methods: Expression profiling of 84 DNA repair genes was performed on bone marrow CD34+ cells of patients with MDS. Screening cohort consisted of 28 patients and expression of selected genes was further validated on larger cohort of 122 patients with all subtypes of MDS. Paired samples were used for monitoring of RAD51 and XRCC2 gene expression during disease progression. Immunohistochemical staining for RAD51 recombinase protein was done on samples acquired by trephine-biopsy. Targeted enrichment resequencing of exonic parts of 84 DNA repair genes was performed on the screening cohort of MDS patients. Real-time PCR was used for genotyping of selected SNPs in the population study. Results: RAD51 and XRCC2 genes showed...

Clonal evolution is a multistep process characterized by progression of the disease, adverse prognosis and shortening of overall survival. The aim of the dissertation was a detailed characterization of identified changes in patients with myelodysplastic syndromes (MDS) and clonal evolution and evaluation of their prognostic impact. We performed detail cytogenomic analyses in 36/469 (8%) patients with confirmed linear clonal evolution. We described 57 primary abnormalities (32% MDS-specific) at the time of diagnosis, the most frequent was deletion of long arm of chromosome 5. We proved 156 secondary aberrations (21% MDS-specific) during the course of the clonal evolution, the most frequent were trisomies/tetrasomies of chromosome 8. We identified acquired uniparental disomies (aUPD) in 19% of patients. In MDS-specific aUPDs 4q, 11q and 17p, we proved homozygous mutations of TET2, c-CBL and TP53 genes. We found a statistically significant difference in overall survival between the groups of patients divided according to their diagnostic cytogenomic findings. In patients with clonal evolution before treatment 54% of aberrations were gains of whole chromosomes, by contrast 44% of abnormalities identified in patients with clonal evolution after treatment were monosomies or deletions. The study of clonal...

Myelodysplastic syndromes (MDS) comprise a heterogeneous group of hematologic malignancies characterized by clonal hematopoiesis, one or more cytopenias such as anemia, neutropenia, or thrombocytopenia, abnormal cellular maturation, and a high risk of progression to acute myeloid leukemia. The bone marrow microenvironment (BMME) in general and mesenchymal stromal cells (MSCs) in particular contribute to both the initiation and progression of MDS. However, little is known about the role of MSC-derived extracellularmatrix (ECM) in this context. Therefore, we performed a comparative analysis of in vitro deposited MSC-derived ECM of different MDS subtypes and healthy controls. Atomic force microscopy analyses demonstrated that MDS ECM was significantly thicker and more compliant than those from healthy MSCs. Scanning electron microscopy showed a dense meshwork of fibrillar bundles connected by numerous smaller structures that span the distance between fibers in MDS ECM. Glycosaminoglycan (GAG) structures were detectable at high abundance in MDS ECM as white, sponge-like arrays on top of the fibrillar network. Quantification by Blyscan assay confirmed these observations, with higher concentrations of sulfated GAGs in MDS ECM. Fluorescent lectin staining with wheat germ agglutinin and peanut agglutinin demonstrated increased deposition of N-acetyl-glucosamine GAGs (hyaluronan (HA) and heparan sulfate) in low risk (LR) MDS ECM. Differential expression of Nacetyl- galactosamine GAGs (chondroitin sulfate, dermatan sulfate) was observed between LR- and high risk (HR)-MDS. Moreover, increased amounts of HA in the matrix of MSCs from LR-MDS patients were found to correlate with enhanced HA synthase 1 mRNA expression in these cells. Stimulation of mononuclear cells from healthy donors with low molecular weight HA resulted in an increased expression of various pro-inflammatory cytokines suggesting a contribution of the ECM to the inflammatory BMME typical of LR-MDS. CD34+ hematopoietic stem and progenitor cells (HSPCs) displayed an impaired differentiation potential after cultivation on MDS ECM and modified morphology accompanied by decreased integrin expression which mediate cell-matrix interaction. In summary, we provide evidence for structural alterations of the MSC-derived ECM in both LR- and HR-MDS. GAGs may play an important role in this remodeling processes during the malignant transformation which leads to the observed disturbance in the support of normal hematopoiesis.

No description available.

The myelodysplastic syndrome (MDS) is a group of hematopoietic clonal disorders resulting in the inefficient production of myeloid lineage blood cells, with the prevalence of patients older than 65 years. One of the possible treatment options for MDS is 5- azacytidine and 5-aza-2'-deoxycytidine therapy. These compounds have been shown to cause the induction of cell-cycle arrest, cell differentiation and/or apoptosis. The in vitro experiments with 5-aza-2'-deoxycytidine indicated that this compound causes the premature cellular senescence, a state of the irreversible cell-cycle arrest. We have asked, whether 5-azacytidine, as a molecule with similar structure, is capable of causing the same effect. This treatment strategy could be beneficial in case that the negative pro- inflammatory effect of senescent cells on their surroundings can be nullified. In this thesis we have shown that 5-azacytidine induces DNA damage response, which is described as a fundamental event for the onset of the cell senescence. We tested 5- azacytidine treated HeLa cells for several markers of the cell senescence - the increase of the β-galactosidase activity, the PML and PML nuclear bodies and the formation of persistent DNA damage signaling lesions - albeit all these markers were positive, it was the very low increase in...

Em nosso trabalho anterior mostramos que dentre as citocinas analisadas, os níveis do mRNA de LIF nas células estromais pediátricas, de SMD e de SMD-LMA foram maiores quando comparados às células estromais de crianças saudáveis. No presente estudo, observamos um aumento tempo dependente nos níveis da proteína LIF após adição de SFB em todas as células analisadas (células estromais de crianças saudáveis, de SMD e de SMD-LMA). O envolvimento de p38, ERK e JNK na expressão LIF nestas células foi determinado pelo uso de inibidores dos membros das proteínas quinase ativadas por mitógenos: ERK (PD98059), p38 (SB302580) e JNK (SP600125) os quais inibiram a produção de LIF nas células estromais de crianças saudáveis, após estas serem estimuladas por SFB. No entanto, os níveis da expressão de LIF-induzido por soro nas células estromais de SMD e de SMD-LMA tratadas com SB302580 (p38) foram significativamente diminuídos, em comparação com a inibição observada no tratamento com PD98059 e SP600125 (p <0001, teste ANOVA). Em adição analisamos as formas fosforiladas de p38 e ERK, após 48hs na ausência ou na presença de soro por diferentes tempos. Níveis de atividade de ERK e do p38 foram inicialmente elevados na ausência de soro. A atividade de p38 foi sustentada após tratamento com SFB, entretanto, ERK apresentou uma variação de atividade durante o tratamento. Sugerimos que a sinalização das MAPKs (p38, ERK e JNK), em resposta a fatores de crescimento presentes no soro, parece desempenhar um papel importante na expressão da LIF em células estromais de crianças saudáveis, mas a sinalização do p38 parece ser funcionalmente mais importante nas mielodisplasias ou naquelas associadas à LMA / Our previous report showed that among the cytokines analysed, LIF mRNA levels in stromal cells from pediatric MDS and MDS-AML were higher as compared to those found in healthy stromal cells. In the present study, we have observed an increased protein LIF levels in a time dependent manner after FCS stimulation in all stromal cells analysed (MDS, MDS-AML and healthy children) and the involvement of p38, ERK and JNK pathways in the LIF expression in these cells was determined. In stromal cells from two healthy children, LIF production was equally inhibited in a dose dependent manner after FCS stimulation by mitogen-activated protein kinase (MAPKs) members inhibitors: ERK (PD98059), p38 (SB302580) and JNK (SP600125). However, in MDS and MDS-AML stromal cells, the levels of LIF-induced by serum, were significantly decreased by SB302580, as compared with the inhibition observed by treatment with PD98059 and SP600125 (p <0,001, ANOVA test). In addition we have analysed the presence of p38 and ERK phosphorylated forms in stromal cells, after 48hs of serum starvation or in the presence of FCS for different times. Activated ERK and p38MAPK levels were initially elevated in the absence of serum. p38MAPK activation was sustained after treatment with FCS, whereas ERK presented a variation of the activated forms during treatment. We suggest that the signalling of the MAPKs (p38, ERK and JNK) in response to growth factors present in the serum, seems to play an important role in the LIF expression by stromal cells of healthy children, but p38 MAPK signalling appears to be functionally more important in MDS and MDS-AML

Les syndromes myélodysplasiques (SMD) forment un groupe de pathologies clonales de la cellule souche hématopoïétique (CSH) caractérisées par une hématopoïèse inefficace. La présence d’au moins une anomalie génétique (anomalie cytogénétique ou mutation somatique) est observée dans plus de 90% des cas. Ainsi, plusieurs clones moléculaires pouvaient coexister au moment du diagnostic de la maladie. Dans les SMD avec délétion du chromosome 5 (del(5q)), il a récemment été montré que les anomalies étaient présentes dès le stade de la CSH. Dans les SMD, la pénétrance des anomalies génétiques décrites est incomplète. De plus, peu de choses sont actuellement connues sur l’ordre d’apparition des mutations et leur impact fonctionnel sur les différents clones moléculaires dans le cas des SMD non-del(5q). Grâce au séquençage d’exome entier (WES) de patients ne présentant aucune mutation dans les gènes décrits dans les SMD, nous avons décrit l’existence de mutations dans les gènes BCOR et BCORL1, chez respectivement 4,2% et 0,8% des patients. Les mutations du gène BCOR arrivent tardivement au cours de l’évolution de la maladie et affectent le pronostic des patients. Des approches à l’échelle unicellulaire nous ont également permis d’observer que la majeure partie des mutations identifiées chez les patients sont retrouvées dès le stade CD34+CD38-. Chez les patients, plusieurs clones moléculaires coexistent à ce stade. De plus, les mutations des gènes de l’épissage et de la régulation épigénétique sont fréquemment acquises en premier dans les cellules hématopoïétiques les plus immatures des patients porteurs de SMD. Nous avons observé que certaines mutations, acquises secondairement, sont réparties inégalement dans les différents compartiments hématopoïétiques et peuvent avoir un impact sur la différenciation hématopoïétique. Enfin, nous montrons que la répartition des clones moléculaires évolue au cours du temps. En réponse au traitement par Lenalidomide, on observe également une évolution rapide de l’architecture clonale qui peut être liée au statut de réponse des patients. Ces résultats tendent à confirmer l’hétérogénéité génétique mais aussi fonctionnelle des SMD. Nous avons pu identifier de nouvelles mutations impliquées secondairement dans la physiopathologie des SMD. Il existe une dominance clonale précoce dans les SMD du fait de l’acquisition de toutes les mutations dans les cellules hématopoïétiques immatures. Cependant, les différentes populations hématopoïétiques peuvent présenter des génotypes différents. Enfin cette architecture est variable au cours de l’évolution de la maladie. / Myelodysplastic syndromes (MDS) are a group of clonal disorders of the hematopoietic stem cell (HSC) characterized by ineffective hematopoiesis. At least one genetic abnormality (cytogenetic abnormality or somatic mutation) is observed in more than 90% of cases. Thus, it has been observed several molecular clones which could coexist at diagnosis of the disease. In MDS with deletion of chromosome 5 (del (5q)), it has recently been shown that defects were present in the HSC. In MDS, the penetrance of genetic abnormalities described is incomplete. In addition, little is currently known about the order of appearance of mutations and their functional impact on different molecular clones in the case of non-del (5q) MDS. Through the whole exome sequencing (WES) of patients without mutation in the genes described in MDS, we described the existence of mutations in genes BCOR and BCORL1, in respectively 4.2% and 0.8% of patients. Mutations in the gene BCOR were acquired lately during the course of the disease and affect the prognosis of patients. Approaches at the single cell level have also allowed us to observe that most of the mutations identified in patients are found at the immature differentiation stage CD34+CD38-. In patients, several molecular clones could coexist at this stage. In addition, mutations in gene splicing and epigenetic regulation are frequently first acquired in the most immature hematopoietic cells of MDS patients. We found that certain mutations, acquired in a second time, are distributed unevenly in different hematopoietic compartment and may have an impact on hematopoietic differentiation. Finally, we showed that the distribution of molecular clones evolves over time. In response to treatment with Lenalidomide, it has also been observed a rapid evolution of clonal architecture that can be linked to patient response status. These results tend to confirm the genetic but also functional heterogeneity in MDS. We have identified new mutations involved in the pathogenesis of MDS. We observed an early clonal dominance in MDS because of the acquisition of all mutations in immature hematopoietic cells. However, different hematopoietic populations can have different genotype. Finally, the architecture of mutations could be modifying during the course of the disease.

Im Rahmen dieser Dissertation wurde retrospektiv die Minimale Resterkrankung von Patienten mit akuter myeloischer Leukämie und Myelodysplastischen Syndrom nach allogener Stammzelltransplantation mit minimaler Konditionierung untersucht. Hierfür wurden vier unterschiedliche Methoden zur Detektion der Minimalen Resterkrankung analysiert. Nach Etablierung einer quantitativen Real-Time PCR für das Wilms Tumor Gen 1 (WT1) im peripheren Blut wurden diese Ergebnisse mit bereits routinemäßig erhobenen Daten des Chimärismus im Gesamtknochenmark und in CD34+ Zellen sowie der Fluoreszenz-in-situ-Hybridisierung (FISH) krankheitsspezifischer chromosomaler Aberrationen von insgesamt 88 Patienten verglichen und statistisch ausgewertet. Es konnte gezeigt werden, dass die Genexpressionanalysen des WT1 sowie die Chimärismusanalysen ein Rezidiv im Gegensatz zu den FISH Analysen vier Wochen im Voraus detektieren können. In Reiceiver Operating Curve Analysen wurden eine WT1 Expression von > 24 WT1/10.000 ABL1 Kopien und der Abfall des CD34+ Spenderchimärismus von ≥ 5% als diagnostisch stärkste Methoden identifiziert. In uni- und multivariaten Analysen von insgesamt 20 Parametern wurden die beiden Methoden als unabhängige Variablen für ein frühes Rezidiv, progressionsfreies Überleben und Gesamtüberleben bestätigt. Kombiniert man beide Methoden, so kann bei jeweiligem negativen Testergebnis ein Rezidiv innerhalb der nächsten vier Wochen nahezu ausgeschlossen werden.