Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

Functional and molecular characterization of ethylene responsive factor genes involved in grape ripening

Grape berry is considered a non climacteric fruit, but there are some evidences that ethylene plays a role in the control of berry ripening. This PhD thesis aimed to give insights in the role of ethylene and ethylene-related genes in the regulation of grape berry ripening. During this study a small increase in ethylene concentration one week before véraison has been measured in Vitis vinifera L. ‘Pinot Noir’ grapes confirming previous findings in ‘Cabernet Sauvignon’. In addition, ethylene-related genes have been identified in the grapevine genome sequence. Similarly to other species, biosynthesis and ethylene receptor genes are present in grapevine as multi-gene families and their expression appeared tissue or developmental specific. All the other elements of the ethylene signal transduction cascade were also identified in the grape genome. Among them, there were ethylene response factors (ERF) which modulate the transcription of many effector genes in response to ethylene. In this study seven grapevine ERFs have been characterized and they showed tissue and berry development specific expression profiles. Two sequences, VvERF045 and VvERF063, seemed likely involved in berry ripening control due to their expression profiles and their sequence annotation. VvERF045 was induced before véraison and was specific of the ripe berry, by sequence similarity it was likely a transcription activator. VvERF063 displayed high sequence similarity to repressors of transcription and its expression, very high in green berries, was lowest at véraison and during ripening. To functionally characterize VvERF045 and VvERF063, a stable transformation strategy was chosen. Both sequences were cloned in vectors for over-expression and silencing and transferred in grape by Agrobacterium-mediated or biolistic-mediated gene transfer. In vitro, transgenic VvERF045 over-expressing plants displayed an epinastic phenotype whose extent was correlated to the transgene expression level. Four pathogen stress response genes were significantly induced in the transgenic plants, suggesting a putative function of VvERF045 in biotic stress defense during berry ripening. Further molecular analysis on the transgenic plants will help in identifying the actual VvERF045 target genes and together with the phenotypic characterization of the adult transgenic plants, will allow to extensively define the role of VvERF045 in berry ripening.

Identification of the N-Linked Glycosylation Sites of the Transcription Factor Rest and Effect of Glycosylation on DNA Binding and Transcriptional Activity

REST is a zinc-finger transcription factor implicated in several processes such as maintenance of embryonic stem cell pluripotency and regulation of mitotic fidelity in non-neuronal cells [Chong et al., 1995]. The gene encodes for a 116-kDa protein that acts as a molecular platform for co-repressors recruitment and promotes modifications of DNA and histones [Ballas, 2005]. REST showed different apparent molecular weights, consistent with the possible presence of post-translational modifications [Lee et al., 2000]. Among these the most common is glycosylation, the covalent attachment of carbohydrates during or after protein synthesis [Apweiler et al., 1999] My thesis has ascertained, for the first time, the presence of glycan chians in the transcription factor REST. Through enzymatic deglycosylation and MS, oligosaccharide composition of glycan chains was evaluated: a complex mixture of glycans, composed of N-acetylgalactosamine, galactose and mannose, was observed thus confirming the presence of O- and N-linked glycan chains. Glycosylation site mapping was done using a 18O-labeling method and MS/MS and twelve potential N-glycosylation sites were identified. The most probable glycosylation target residues were mutated through site-directed mutagenesis and REST mutants were expressed in different cell lines. Variations in the protein molecular weight and mutant REST ability to bind the RE-1 sequence were analyzed. Gene reporter assays showed that, altogether, removal of N-linked glycan chains causes loss of transcriptional repressor function, except for mutant N59 which showed a slight residual repressor activity in presence of IGF-I. Taken togheter these results demonstrate the presence of complex glycan chians in the transcription factor REST: I have depicted their composition, started defining their position on the protein backbone and identified their possible role in the transcription factor functioning. Considering the crucial role of glycosylation and transcription factors activity in the aetiology of many diseases, any further knowledge could find important and interesting pharmacological application.

DNA methylation, histone modification and the transcription factor dE2F1 in Drosophila

Drosophila melanogaster enthält eine geringe Menge an 5-methyl-Cytosin. Die von mir untersuchte männliche Keimbahn von Drosophila weist jedoch keine nachweisbaren Mengen an DNA-Methylierung auf. Eine künstliche Expression der murinen de novo Methyltransferasen, DNMT3A und DNMT3B1, in den Fliegenhoden, führte nicht zu der erwarteten Methylierungszunahme und hatte keinen Effekt auf die Fruchtbarkeit der Männchen. Auch die gewebespezifische Expression unter der Verwendung des UAS/GAL4-Systems zeigte keine phenotypischen Veränderungen. Hingegen fanden wir auf Protein-Ebene des Chromatins von D. melanogaster und D. hydei spezifische Modifikationsmuster der Histone H3 und H4 in der Keimbahn, wie auch in den somatischen Zellen des Hodenschlauches. Die Modifikationsmuster der beiden Zelltypen unterscheiden sich grundlegend und weichen zudem von dem für Eu- und Heterochromatin erwarteten ab, was auf eine größere Komplexität des „Histon-Codes“ als angenommen hindeutet. Folglich liegt die epigenetische Information in Drosophila wahrscheinlich anstatt auf DNA- auf Protein-Ebene, wodurch Genexpression über die Chromatinstruktur reguliert wird. Es wurde gezeigt, dass der Transkriptionsfaktor E2F, der eine Schlüsselfunktion im Zellzyklus hat, durch unterschiedliche Transkripte offenbar quantitativ reguliert wird. Unsere Nachforschungen ergaben, dass die drei E2F1 Genprodukte in Drosophila neben ihrer Zellspezifität auch in unterschiedlichen Expressionsniveaus auftreten, was die Annahme einer quantitativen Expression unterstützt. Die verschiedenen Funktionen der multiplen Gene in Säugern, könnten so funktionell kompensiert werden. Die durch die Expression dreier dE2F1-Transkripte vermutete Synthese verschiedener Proteine konnte nicht bewiesen werden.

Espressione del vascular endothelium growth factor (VEGF) nella micosi fungoide

La micosi fungoide (MF) è un linfoma a cellule T primitivo della cute usualmente indolente negli stadi iniziali, ma con prognosi decisamente peggiore nelle fasi avanzate, ove attualmente non sono presenti strategie terapeutiche tali da indurre remissioni durature. Recenti osservazioni indicano che alti livelli di espressione del vascular endothelial growth factor (VEGF) nelle cellule della MF sembrano correlare con una prognosi peggiore. Nel presente studio, sono state vagliate le eventuali differenze di espressione di VEGF nella MF e nei linfociti T normali. In primo luogo sono stati raffrontati 63 casi di MF con 20 campioni corrispondenti alle diverse sottopopolazioni di linfociti T normali, per stabilire quale fra questi esprimesse maggiori livelli di VEGF. Tale esperimento ha dimostrato che il gene è notevolmente più espresso nella MF. Si è provveduto a stabilire se tale dato sia da correlarsi ad un fenomeno patologico o fisiologico. Quindi sono state eseguite indagini di gene expression profiling (GEP) allo scopo di vagliare i livelli di VEGF nella popolazione linfocitaria T normale (CD4+, CD8+, HLA-DR+ e HLA-DR-): da ciò è risultato che i linfociti T attivati esprimono maggiormente VEGF e che il loro GEP è globalmente paragonabile a quello della MF. Pertanto, i linfociti T attivati sono stati considerati la controparte normale delle cellule della MF. Successivamente si è confrontata l’espressione quantitativa di VEGF nei linfociti T attivati e nelle cellule della MF, evidenziando come questa sia maggiore nella popolazione neoplastica indipendentemente dallo stadio della malattia. Le indagini immunoistochimiche condotte su 18 casi di MF, hanno confermato quanto evidenziato attraverso il GEP. Concludendo, la ricerca ha dimostrato per la prima volta l’espressione di VEGF negli elementi della MF. Ciò porta a supporre che la de-regolazione genica della via di VEGF sia correlata nella patogenesi della MF e che tale molecola possa considerarsi un potenziale bersaglio terapeutico.

Differential cell type-specific transcriptional regulation of the CYP1A1 gene

Cytochrome P450 1A1 (CYP1A1) monooxygenase plays an important role in the metabolism of environmental pollutants such as polycyclic aromatic hydrocarbons (PAHs) and halogenated polycyclic aromatic hydrocarbons (HAHs). Oxidation of these compounds converts them to the metabolites that subsequently can be conjugated to hydrophilic endogenous entities e.g. glutathione. Derivates generated in this way are water soluble and can be excreted in bile or urine, which is a defense mechanism. Besides detoxification, metabolism by CYP1A1 may lead to deleterious effects since the highly reactive intermediate metabolites are able to react with DNA and thus cause mutagenic effects, as it is in the case of benzo(a) pyrene (B[a]P). CYP1A1 is normally not expressed or expressed at a very low level in the cells but it is inducible by many PAHs and HAHs e.g. by B[a]P or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Transcriptional activation of the CYP1A1 gene is mediated by aryl hydrocarbon receptor (AHR), a basic-helix-loop-helix (bHLH) transcription factor. In the absence of a ligand AHR stays predominantly in the cytoplasm. Ligand binding causes translocation of AHR to the nuclear compartment, its heterodimerization with another bHLH protein, the aryl hydrocarbon nuclear translocator (ARNT) and binding of the AHR/ARNT heterodimer to a DNA motif designated dioxin responsive element (DRE). This process leads to the transcriptional activation of the responsive genes containing DREs in their regulatory regions, e.g. that coding for CYP1A1. TCDD is the most potent known agonist of AHR. Since it is not metabolized by the activated enzymes, exposure to this compound leads to a persisting activation of AHR resulting in diverse toxic effects in the organism. To enlighten the molecular mechanisms that mediate the toxicity of xenobiotics like TCDD and related compounds, the AHR-dependent regulation of the CYP1A1 gene was investigated in two cell lines: human cervix carcinoma (HeLa) and mouse hepatoma (Hepa). Study of AHR activation and its consequence concerning expression of the CYP1A1 enzyme confirmed the TCDD-dependent formation of the AHR/ARNT complex on DRE leading to an increase of the CYP1A1 transcription in Hepa cells. In contrast, in HeLa cells formation of the AHR/ARNT heterodimer and binding of a protein complex containing AHR and ARNT to DRE occurred naturally in the absence of TCDD. Moreover, treatment with TCDD did not affect the AHR/ARNT dimer formation and binding of these proteins to DRE in these cells. Even though the constitutive complex on DRE exists in HeLa, transcription of the CYP1A1 gene was not increased. Furthermore, the CYP1A1 level in HeLa cells remained unchanged in the presence of TCDD suggesting repressional mechanism of the AHR complex function which may hinder the TCDD-dependent mechanisms in these cells. Similar to the native, the mouse CYP1A1-driven reporter constructs containing different regulatory elements were not inducible by TCDD in HeLa cells, which supported a presence of cell type specific trans-acting factor in HeLa cells able to repress both the native CYP1A1 and CYP1A1-driven reporter genes rather than species specific differences between CYP1A1 genes of human and rodent origin. The different regulation of the AHR-mediated transcription of CYP1A1 gene in Hepa and HeLa cells was further explored in order to elucidate two aspects of the AHR function: (I) mechanism involved in the activation of AHR in the absence of exogenous ligand and (II) factor that repress function of the exogenous ligand-independent AHR/ARNT complex. Since preliminary studies revealed that the activation of PKA causes an activation of AHR in Hepa cells in the absence of TCDD, the PKA-dependent signalling pathway was the proposed endogenous mechanism leading to the TCDD-independent activation of AHR in HeLa cells. Activation of PKA by forskolin or db-cAMP as well as inhibition of the kinase by H89 in both HeLa and Hepa cells did not lead to alterations in the AHR interaction with ARNT in the absence of TCDD and had no effect on binding of these proteins to DRE. Moreover, the modulators of PKA did not influence the CYP1A1 activity in these cells in the presence and in the absence of TCDD. Thus, an involvement of PKA in the regulation of the CYP1A1 Gen in HeLa cells was not evaluated in the course of this study. Repression of genes by transcription factors bound to their responsive elements in the absence of ligands has been described for nuclear receptors. These receptors interact with protein complex containing histone deacetylase (HDAC), enzyme responsible for the repressional effect. Thus, a participation of histone deacetylase in the transcriptional modulation of CYP1A1 gene by the constitutively DNA-bound AHR/ARNT complex was supposed. Inhibition of the HDAC activity by trichostatin A (TSA) or sodium butyrate (NaBu) led to an increase of the CYP1A1 transcription in the presence but not in the absence of TCDD in Hepa and HeLa cells. Since amount of the AHR and ARNT proteins remained unchanged upon treatment of the cells with TSA or NaBu, the transcriptional upregulation of CYP1A1 gene was not due to an increased expression of the regulatory proteins. These findings strongly suggest an involvement of HDAC in the repression of the CYP1A1 gene. Similar to the native human CYP1A1 also the mouse CYP1A1-driven reporter gene transfected into HeLa cells was repressed by histone deacetylase since the presence of TSA or NaBu led to an increase in the reporter activity. Induction of reporter gene did not require a presence of the promoter or negative regulatory regions of the CYP1A1 gene. A promoter-distal fragment containing three DREs together with surrounding sequences was sufficient to mediate the effects of the HDAC inhibitors suggesting that the AHR/ARNT binding to its specific DNA recognition site may be important for the CYP1A1 repression. Histone deacetylase is recruited to the specific genes by corepressors, proteins that bind to the transcription factors and interact with other members of the HDAC complex. Western blot analyses revealed a presence of HDAC1 and the corepressors mSin3A (mammalian homolog of yeast Sin3) and SMRT (silencing mediator for retinoid and thyroid hormone receptor) in both cell types, while the corepressor NCoR (nuclear receptor corepressor) was expressed exclusively in HeLa cells. Thus the high inducibility of CYP1A1 in Hepa cells may be due to the absence of NCoR in these cells in contrast to the non-responsive HeLa cells, where the presence of NCoR would support repression of the gene by histone deacetylase. This hypothesis was verified in reporter gene experiments where expression constructs coding for the particular members of the HDAC complex were cotransfected in Hepa cells together with the TCDD-inducible reporter constructs containing the CYP1A1 regulatory sequences. An overexpression of NCoR however did not decrease but instead led to a slight increase of the reporter gene activity in the cells. The expected inhibition was observed solely in the case of SMRT that slightly reduced constitutive and TCDD-induced reporter gene activity. A simultaneous expression of NCoR and SMRT shown no further effects and coexpression of HDAC1 with the two corepressors did not alter this situation. Thus, additional factors that are likely involved in the repression of CYP1A1 gene by HDAC complex remained to be identified. Taking together, characterisation of an exogenous ligand independent AHR/ARNT complex on DRE in HeLa cells that repress transcription of the CYP1A1 gene creates a model system enabling investigation of endogenous processes involved in the regulation of AHR function. This study implicates HDAC-mediated repression of CYP1A1 gene that contributes to the xenobiotic-induced expression in a tissue specific manner. Elucidation of these processes gains an insight into mechanisms leading to deleterious effects of TCDD and related compounds.

Streptococcus agalactiae adapts to glucose stress conditions by modulating gene expression profile

Diabetes mellitus is considered a risk factor for Group B Streptococcus (GBS) infections. Typically, this pathology is associated to high glucose levels in the bloodstream. Although clinical evidences support this notion, the physiological mechanisms underlying GBS adaptation to such conditions are not yet defined. In the attempt to address this issue, we performed comparative global gene expression analysis of GBS grown under glucose-stress conditions and observed that a number of metabolic and virulence genes was differentially regulated. Of importance, we also demonstrated that by knocking-out the csrRS locus the transcription profile of GBS grown in high-glucose conditions was profoundly affected, with more than a third of glucose-dependent genes, including the virulence factor bibA, found to be controlled by this two-component system. Furthermore, in vitro molecular analysis showed that CsrR specifically binds to the bibA promoter and the phosphorilation increases the affinity of the regulator to this promoter region. Moreover, we demonstrated that CsrR acts as a repressor of bibA expression by binding to its promoter in vivo. In conclusion, this work by elucidating both the response of GBS to pathological glucose conditions and the underlined molecular mechanisms will set the basis for a better understanding of GBS pathogenesis.

Nukleation pflanzlicher Mikrotubuli: Expression relevanter Gene

Die wichtigsten Bestandteile des Cytoskeletts in pflanzlichen Zellen sind die Actinfilamente und die Mikrotubuli. Die Mikrotubuli spielen in der Organisation und der Morphogenese von pflanzlichen Zellen eine wichtige Rolle. Sie sind zusammen mit den Cellulosefibrillen an der Formgebung der Pflanzenzelle beteiligt. Sie bilden das Präprophaseband, das die Zellteilungsebene bestimmt und die Mitosespindel, die für die Trennung der Chromosomen sorgt, sowie den Phragmoplasten, der die Zellwand zwischen den Tochterzellen bildet. Weiterhin geben die Mikrotubuli durch Interaktion mit den Cellulose-Synthase-Komplexen die Richtung der Zellexpansion vor (GRANGER und CYR, 2001; LLOYD und CHAN, 2002; BASKIN, 2002). Die Mikrotubuli sind auch an der Stabilisierung der Zellform und an Transportprozessen beteiligt. Als Bestandteil der Mikrotubuli-organisierenden Zentren (MTOCs) wurde das γ-Tubulin identifiziert, das sehr wahrscheinlich an der Nukleation der Mikrotubuli beteiligt ist, indem es die Assemblierung der αβ-Tubulindimere zu Mikrotubuli einleitet. In tierischen Zellen ist durch intensive Forschung inzwischen relativ viel über die Funktion von γ-Tubulin, vor allem im Verlauf der Zellteilung bekannt, wie z. B. die Lokalisation in Centrosomen mit ihren paarweise angeordneten Centriolen, die die MTOCs darstellen. In pflanzlichen Zellen sind bisher nur wenige Funktionen des Proteins hinreichend geklärt. Die höheren Pflanzen besitzen keine Centriolen und keine Centrosomen. Über die Zellteilung hinaus gibt es kaum Anhaltspunkte über das Vorhandensein oder eventuelle Aufgaben von γ-Tubulin in expandierenden und voll expandierten Zellkulturen und Pflanzengeweben. In dieser Arbeit wurde die Expression über PCR und die Messung des Proteingehalts von cytoskelett-relevanten Proteinen in den Entwicklungsstadien der Zellsuspensionskultur (BY-2) und von Blattstadien der Tabakpflanze (SR1) von Nicotiana tabacum gemessen. Primäres Ziel war es eine Aussage zu erhalten, in welchem Ausmaß γ-Tubulin in expandierenden und voll expandierten Zellen noch exprimiert wird und ob bzw. wie eine Regulation (transkriptionell oder posttranskriptionell) des γ-Tubulins in der Pflanze stattfindet. Für den Nachweis des γ-Tubulins auf der Proteinebene wurde ein pflanzenspezifischer γ-Tubulin Antikörper zu entwickelt. Bei diesem Antikörper handelte es sich um einen polyklonalen Antikörper, der spezifisch gegen eine Sequenz in pflanzlichem γ-Tubulin gerichtet ist. Dabei zeigte der in der Arbeit entwickelte Antikörper gegen die pflanzliche JOSHI-Domäne spezifische Signale. Der erfolgte Nachweis von γ-Tubulin auf der Proteinebene und der Transkripte zeigte bis in die ältesten untersuchten Stadien der Zellsuspensionskultur (BY-2) und in Geweben der Blattstadien der Tabakpflanze (SR1) deutliche Signale für γ-Tubulin. Es war somit nicht nur in meristematisch aktiven Zellen und Geweben von Nicotiana tabacum, sondern auch in nichtmitotischen Zellen und Geweben vorhanden. Hierbei war über die Phasen der Zellteilung und der Zellformgebung hinweg auf beiden Ebenen eine parallele Entwicklung mit relativ konstanten starken Signalen zu beobachten. Nach dem Einstellen der Teilungsaktivität fiel der Gehalt an mRNA deutlich ab. Dabei nahm die Konzentration des Proteins im Vergleich zur mRNA zeitlich verzögert ab. Diese Ergebnisse bei der Zellsuspensionskultur (BY-2) und Tabakpflanze (SR1) gehen mit der möglichen Nukleationstätigkeit des Proteins konform. Es waren geringere aber doch deutlichen Signale bei Absterbenden Zellen der Zellkultur, bzw. bei expandierenden und voll expandierten und seneszenten Blättern der Tabakpflanze (SR1) nachzuweisen. Dies lässt die Folgerung zu, dass die nachgewiesene mRNA von γ-Tubulin nicht posttranskriptionell reguliert wird, sondern dass das γ-Tubulin auch eine wichtige Rolle außerhalb der Zellteilung in den postmitotischen Stadien, z. B. als organisierender Faktor bei der Umgestaltung oder Stabilisierung des Mikrotubuli-Cytoskeletts, spielt. Der γ-Tubulin-Gehalt in den Geweben der SR1-Pflanze zeigte über die Zellkultur hinaus, dass die Expression von α-Tubulin nach Einstellen der Teilungsaktivität kontinuierlich abnimmt. Dieses Ergebnis legt die Vermutung nahe, dass γ-Tubulin in älteren Blattgeweben zusätzliche Aufgaben übernehmen könnte, die nicht auf eine gleichzeitige Expression von α-Tubulin angewiesen sind. So kann beispielsweise eine Beteiligung von γ-Tubulin an der Stabilisierung der Mikrotubuli, und damit einhergehend eine Abnahme der dynamischen Instabilität dieser Filamente, eine denkbare Funktion des Proteins in expandierendem und voll expandiertem Gewebe sein. Die Aufgaben von γ-Tubulin in sehr altem Gewebe mit deutlichen Anzeichen der Seneszenz können allerdings nach dem derzeitigen Stand der Forschung nicht eindeutig beantwortet werden und bedürfen weitergehenden Untersuchungen, da dadurch ein die Komplexität und die Dynamik des pflanzlichen Cytoskeletts geklärt werden kann.

The KIT gene in familial mastocytosis

Familial cutaneous mastocytosis is an exceptional condition of unknown etiology. In this study we report the largest series of patients with familial cutaneous mastocytosis without other manifestations (18 affected subjects from seven unrelated families), and we investigate the role of germ-line KIT mutations in the pathogenesis of the disease. The mean age at onset was 5.4 years (range from birth to 22 years), and the clinical behavior was variable over a mean follow up period of 15.1 years (range 2-36): improvement in seven, stability in eight and worsening in the remaining three patients. The pattern of inheritance was compatible with an autosomal dominant trait with incomplete penetrance; a female preponderance (14 females vs 4 males, ratio 3.5:1) was noted; among the six women who have been pregnant at least once, three experienced important clinical changes during pregnancy. No germ-line mutation was found in the exons 10, 11, and 17 of the KIT proto-oncogene, which are the most commonly mutated exons in sporadic mastocytosis. However, in the majority of affected subjects we found the Met541Leu polymorphic variant of the KIT gene, which seems to confer a growth advantage to mast cells in vitro. This observation further suggests that the Met541Leu may be a predisposing factor of cutaneous mastocytosis, although it seems to be neither necessary nor sufficient for the development of the disease.

Airway Basal Cell Vascular Endothelial Growth Factor-mediated Cross-Talk Regulates Endothelial Cell Dependent Growth Support of Human Airway Basal Cells

The human airway epithelium is a pseudostratified heterogenous layer comprised of cili-ated, secretory, intermediate and basal cells. As the stem/progenitor population of the airway epi-thelium, airway basal cells differentiate into ciliated and secretory cells to replenish the airway epithelium during physiological turnover and repair. Transcriptome analysis of airway basal cells revealed high expression of vascular endothelial growth factor A (VEGFA), a gene not typically associated with the function of this cell type. Using cultures of primary human airway basal cells, we demonstrate that basal cells express all of the 3 major isoforms of VEGFA (121, 165 and 189) but lack functional expression of the classical VEGFA receptors VEGFR1 and VEGFR2. The VEGFA is actively secreted by basal cells and while it appears to have no direct autocrine function on basal cell growth and proliferation, it functions in a paracrine manner to activate MAPK signaling cascades in endothelium via VEGFR2 dependent signaling pathways. Using a cytokine- and serum-free co-culture system of primary human airway basal cells and human endothelial cells revealed that basal cell secreted VEGFA activated endothelium to ex-press mediators that, in turn, stimulate and support basal cell proliferation and growth. These data demonstrate novel VEGFA mediated cross-talk between airway basal cells and endothe-lium, the purpose of which is to modulate endothelial activation and in turn stimulate and sustain basal cell growth.

Gene expression analysis in ‘Candidatus Phytoplasma mali’-resistant and -susceptible Malus genotypes

Apple proliferation (AP) disease is the most important graft-transmissible and vector-borne disease of apple in Europe. ‘Candidatus Phytoplasma mali’ (Ca. P. mali) is the causal agent of AP. Apple (Malus x domestica) and other Malus species are the only known woody hosts. In European apple orchards, the cultivars are mainly grafted on one rootstock, M. x domestica cv. M9. M9 like all other M. x domestica cultivars is susceptible to ‘Ca. P. mali’. Resistance to AP was found in the wild genotype Malus sieboldii (MS) and in MS-derived hybrids but they were characterised by poor agronomic value. The breeding of a new rootstock carrying the resistant and the agronomic traits was the major aim of a project of which this work is a part. The objective was to shed light into the unknown resistance mechanism. The plant-phytoplasma interaction was studied by analysing differences between the ‘Ca. P. mali’-resistant and -susceptible genotypes related to constitutively expressed genes or to induced genes during infection. The cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) technique was employed in both approaches. Differences related to constitutively expressed genes were identified between two ‘Ca. P. mali’-resistant hybrid genotypes (4551 and H0909) and the ‘Ca. P. mali’-susceptible M9. 232 cDNA-AFLP bands present in the two resistant genotypes but absent in the susceptible one were isolated but several different products associated to each band were found. Therefore, two different macroarray hybridisation experiments were performed with the cDNA-AFLP fragments yielding 40 sequences encoding for genes of unknown function or a wide array of functions including plant defence. In the second approach, individuation and analysis of the induced genes was carried out exploiting an in vitro system in which healthy and ‘Ca. P. mali’-infected micropropagated plants were maintained under controlled conditions. Infection trials using in vitro grafting of ‘Ca. P. mali’ showed that the resistance phenotype could be reproduced in this system. In addition, ex vitro plants were generated as an independent control of the genes differentially expressed in the in vitro plants. The cDNA-AFLP analysis in in vitro plants yielded 63 bands characterised by over-expression in the infected state of both the H0909 and MS genotypes. The major part (37 %) of the associated sequences showed homology with products of unknown function. The other genes were involved in plant defence, energy transport/oxidative stress response, protein metabolism and cellular growth. Real-time qPCR analysis was employed to validate the differential expression of the genes individuated in the cDNA-AFLP analysis. Since no internal controls were available for the study of the gene expression in Malus, an analysis on housekeeping genes was performed. The most stably expressed genes were the elongation factor-1 α (EF1) and the eukaryotic translation initiation factor 4-A (eIF4A). Twelve out of 20 genes investigated through qPCR were significantly differentially expressed in at least one genotype either in in vitro plants or in ex vitro plants. Overall, about 20% of the genes confirmed their cDNA-AFLP expression pattern in M. sieboldii or H0909. On the contrary, 30 % of the genes showed down-regulation or were not differentially expressed. For the remaining 50 % of the genes a contrasting behaviour was observed. The qPCR data could be interpreted as follows: the phytoplasma infection unbalance photosynthetic activity and photorespiration down-regulating genes involved in photosynthesis and in the electron transfer chain. As result, and in contrast to M. x domestica genotypes, an up-regulation of genes of the general response against pathogens was found in MS. These genes involved the pathway of H2O2 and the production of secondary metabolites leading to the hypothesis that a response based on the accumulation of H2O2 in MS would be at the base of its resistance. This resembles a phenomenon known as “recovery” where the spontaneous remission of the symptoms is observed in old susceptible plants but occurring in a stochastic way while the resistance in MS is an inducible but stable feature. As additional product of this work three cDNA-AFLP-derived markers were developed which showed independent distribution among the seedlings of two breeding progenies and were associated to a genomic region characteristic of MS. These markers will contribute to the development of molecular markers for the resistance as well as to map the resistance on the Malus genome.

Role of the Transcription Factor Sox2 in the Osteogenic Lineage

The Sox2 transcription factor is modified by sumoylation at the K247 position although the addition of SUMO1 and Pias1 promotes the sumoylation of Sox2 at the additional K123 site. The role of sumoylation on Sox2 biological functions was analyzed by comparing the activity of WT and sumoylation mutants on the transcription of the FGF4 gene in HeLa cells and on the downregulation of the Wnt pathwayvin 293T cells. When SUMO1 and PIAS1 promote the sumoylation of WT Sox2, the transcriptional activity of the FGF4 promoter is inhibited showing that Sox2 sumoylation is necessary for the repression function. However, there is no effect of Sox2 sumoylation on β-Catenin activity. Since we were interested in osteoblast differentiation we set up an inducible system for Sox2 in primary osteoblasts. Following Sox2 doxycycline induction, 158 genes were differentially expressed: 120 up-regulated and 38 down-regulated. We annotated as direct Sox2 targets a number of genes involved in osteoblast biology and we further analyzed 3 of them involved in the BMP pathway. The results show that Sox2 regulates the BMP pathway without affecting SMAD phosphorylation, and that Sox2 sumoylation is not necessary for this function. We also found that genes involved in the Hippo pathway were direct Sox2 targets. As the Hippo pathway is activated by Sox2 and Sox2 interacts with the NF2 promoter, we checked the effect of Sox2 on the expression of NF2. We showed that Sox2 down-regulates the transcriptional activity of the NF2 promoter, allowing the transcription of the YAP/TEAD genes in osteoblasts, thus acting as an upstream regulator of the Hippo pathway. We conclude that Sox2 induction in osteoblasts triggers FGF dependent inhibition of the BMP, Wnt and Hippo pathways.

An interferon regulatory factor element controls the major immune modulator of murine cytomegalovirus

Immune modulation by herpesviruses, such as cytomegalovirus, is critical for the establishment of acute and persistent infection confronting a vigorous antiviral immune response of the host. Therefore, the action of immune-modulatory proteins has long been the subject of research, with the final goal to identify new strategies for antiviral therapy.rnIn the case of murine cytomegalovirus (mCMV), the viral m152 protein has been identified to play a major role in targeting components of both the innate and the adaptive immune system in terms of infected host-cell recognition in the effector phase of the antiviral immune response. On the one hand, it inhibits cell surface expression of RAE-1 and thereby prevents ligation of the activating natural killer (NK)-cell receptor NKG2D. On the other hand, it decreases cell surface expression of peptide-loaded MHC class I molecules thereby preventing antigen presentation to CD8 T cells. Ultimately, the outcome of CMV infection is determined by the interplay between viral and cellular factors.rnIn this context, the work presented here has revealed a novel and intriguing connection between viral m152 and cellular interferon (IFN), a key cytokine of the immune system: rnthe m152 promoter region contains an interferon regulatory factor element (IRFE) perfectly matching the consensus sequence of cellular IRFEs.rnThe biological relevance of this regulatory element was first suggested by sequence comparisons revealing its evolutionary conservation among various established laboratory strains of mCMV and more recent low-passage wild-derived virus isolates. Moreover, search of the mCMV genome revealed only three IRFE sites in the complete sequence. Importantly, the functionality of the IRFE in the m152 promoter was confirmed with the use of a mutant virus, representing a functional deletion of the IRFE, and its corresponding revertant virus. In particular, m152 gene expression was found to be inhibited in an IRFE-dependent manner in infected cells. Essentially, this inhibition proved to have a severe impact on the immune-modulatory function of m152, first demonstrated by a restored direct antigen presentation on infected cells for CD8 T-cell activation. Even more importantly, this effect of IRFE-mediated IFN signaling was validated in vivo by showing that the protective antiviral capacity of adoptively-transferred, antigen-specific CD8 T cells is also significantly restored by the IRFE-dependent inhibition of m152. Somewhat curious and surprising, the decrease in m152 protein simultaneously prevented an enhanced activation of NK cells in acute-infected mice, apparently independent of the RAE-1/NKG2D ligand/receptor interaction but rather due to reduced ‘missing-self’ recognition.rnTaken together, this work presents a so far unknown mechanism of IFN signaling to control mCMV immune modulation in acute infection.rnrn

Consequences of DNA damage for gene transcription : direct effects of modified nucleobases and the role of base excision repair = Folgen von DNA-Schäden für die Gentranskription

The presence of damaged nucleobases in DNA can negatively influence transcription of genes. One of the mechanisms by which DNA damage interferes with reading of genetic information is a direct blockage of the elongating RNA polymerase complexes – an effect well described for bulky adducts induced by several chemical substances and UV-irradiation. However, other mechanisms must exist as well because many of the endogenously occurring non-bulky DNA base modifications have transcription-inhibitory properties in cells, whilstrnnot constituting a roadblock for RNA polymerases under cell free conditions. The inhibition of transcription by non-blocking DNA damage was investigated in this work by employing the reporter gene-based assays. Comparison between various types of DNA damage (UV-induced pyrimidine photoproducts, oxidative purine modifications induced by photosensitisation, defined synthetic modified bases such as 8-oxoguanine and uracil, and sequence-specific single-strand breaks) showed that distinct mechanisms of inhibition of transcription can be engaged, and that DNA repair can influence transcription of the affectedrngenes in several different ways.rnQuantitative expression analyses of reporter genes damaged either by the exposure of cells to UV or delivered into cells by transient transfection supported the earlier evidence that transcription arrest at the damage sites is the major mechanism for the inhibition of transcription by this kind of DNA lesions and that recovery of transcription requires a functional nucleotide excision repair gene Csb (ERCC6) in mouse cells. In contrast, oxidisedrnpurines generated by photosensitisation do not cause transcriptional blockage by a direct mechanism, but rather lead to transcriptional repression of the damaged gene which is associated with altered histone acetylation in the promoter region. The whole chain of events leading to transcriptional silencing in response to DNA damage remains to be uncovered. Yet, the data presented here identify repair-induced single-strand breaks – which arise from excision of damaged bases by the DNA repair glycosylases or endonucleases – as arnputative initiatory factor in this process. Such an indirect mechanism was supported by requirement of the 8-oxoguanine DNA glycosylase (OGG1) for the inhibition of transcription by synthetic 8-oxodG incorporated into a reporter gene and by the delays observed for the inhibition of transcription caused by structurally unrelated base modifications (8-oxoguanine and uracil). It is thereby hypothesized that excision of the modified bases could be a generalrnmechanism for inhibition of transcription by DNA damage which is processed by the base excision repair (BER) pathway. Further gene expression analyses of plasmids containing single-strand breaks or abasic sites in the transcribed sequences revealed strong transcription inhibitory potentials of these lesions, in agreement with the presumption that BER intermediates are largely responsible for the observed effects. Experiments with synthetic base modifications positioned within the defined DNA sequences showed thatrninhibition of transcription did not require the localisation of the lesion in the transcribed DNA strand; therefore the damage sensing mechanism has to be different from the direct encounters of transcribing RNA polymerase complexes with DNA damage.rnAltogether, this work provides new evidence that processing of various DNA basernmodifications by BER can perturb transcription of damaged genes by triggering a gene silencing mechanism. As gene expression can be influenced even by a single DNA damage event, this mechanism could have relevance for the endogenous DNA damage induced in cells under normal physiological conditions, with a possible link to gene silencing in general.

Die Rolle von Chemokinrezeptor CXCR4 und Connective Tissue Growth Factor innerhalb der Tumor-Stroma-Interaktion in der akuten myeloischen Leukämie

Die akute myeloische Leukämie (AML) ist eine heterogene Erkrankung der hämatopoetischen Vorläuferzelle, die durch unkontrollierte Vermehrung und ein reduziertes Differenzierungsverhalten gekennzeichnet ist. Aufgrund von Therapieresistenzen und häufig vorkommenden Rückfällen ist die AML mit einer schlechten Langzeitprognose verbunden. Neue Studienergebnisse zeigen, dass leukämische Zellen einer hierarchischen Ordnung unterliegen, an deren Spitze die leukämische Stammzelle (LSC) steht, welche den Tumor speist und ähnliche Charakteristika besitzt wie die hämatopoetische Stammzelle. Die LSC nutzt den Kontakt zu Zellen der hämatopoetischen Nische des Knochenmarks, um die erste Therapie zu überdauern und Resistenzen zu erwerben. Neue Therapieansätze versuchen diese Interaktion zwischen leukämischen Zellen und supportiv wirkenden Stromazellen anzugreifen. rnrnIn dieser Arbeit sollte die Bedeutung des CXC-Motiv Chemokinrezeptors Typ 4 (CXCR4) und des Connective Tissue Growth Factors (CTGF) innerhalb der AML-Stroma-Interaktion untersucht werden. CXCR4, der in vivo dafür sorgt, dass AML-Zellen in der Nische gehalten und geschützt werden, wurde durch den neuwertigen humanen CXCR4-spezifischen Antikörper BMS-936564/MDX-1338 in AML-Zelllinien und Patientenzellen in Zellkulturversuchen blockiert. Dies induzierte Apoptose sowie Differenzierung und führte in Kokulturversuchen zu einer Aufhebung des Stroma-vermittelten Schutzes gegenüber der Chemotherapie. Für diese Effekte musste teilweise ein sekundärer Antikörper verwendet werden, der die CXCR4-Moleküle miteinander kreuzvernetzt.rnDie Auswertung eines quantitativen Real time PCR (qPCR)-Arrays ergab, dass CTGF in der AML-Zelllinie Molm-14 nach Kontakt zu Stromazellen hochreguliert wird. Diese Hochregulation konnte in insgesamt drei AML-Zelllinien sowie in drei Patientenproben in qPCR- und Western Blot-Versuchen bestätigt werden. Weitere Untersuchungen zeigten, dass diese Hochregulation (i) unabhängig von der Stromazelllinie ist, (ii) den direkten Kontakt zum Stroma benötigt und (iii) auch unter hypoxischen Bedingungen, wie sie innerhalb des Knochenmarks vorherrschen, stattfindet. Der durch Zell-Zell- oder Zell-Matrix-Kontakt gesteuerte Hippo-Signalweg konnte aus folgenden Gründen als möglicher upstream-Regulationsmechanismus identifiziert werden: (i) Dessen zentraler Transkriptions-Kofaktor TAZ wurde in kokultivierten Molm-14-Zellen stabilisiert, (ii) der shRNA-gesteuerte Knockdown von TAZ führte zu einer reduzierten CTGF-Hochregulation, (iii) CTGF wurde in Abhängigkeit von der Zelldichte reguliert, (iv) Cysteine-rich angiogenic inducer 61 (Cyr61), ein weiteres Zielgen von TAZ, wurde in kokultivierten AML-Zellen ebenfalls verstärkt exprimiert. Der Knockdown von CTGF führte in vitro zu einer partiellen Aufhebung der Stroma-vermittelten Resistenz und die Blockierung von CTGF durch den Antikörper FG-3019 wirkte im AML-Mausmodell lebensverlängernd. rn rnDie Rolle von CTGF in der AML ist bisher nicht untersucht. Die vorliegenden Ergebnisse zeigen, dass CTGF ein interessantes Therapieziel in der AML darstellt. Es bedarf weiterer Untersuchungen, um die Bedeutung von CTGF in der Tumor-Stroma-Interaktion näher zu charakterisieren und nachgeschaltete Signalwege zu identifizieren.