Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays

High density oligonucleotide expression arrays are a widely used tool for the measurement of gene expression on a large scale. Affymetrix GeneChip arrays appear to dominate this market. These arrays use short oligonucleotides to probe for genes in an RNA sample. Due to optical noise, non-specific hybridization, probe-specific effects, and measurement error, ad-hoc measures of expression, that summarize probe intensities, can lead to imprecise and inaccurate results. Various researchers have demonstrated that expression measures based on simple statistical models can provide great improvements over the ad-hoc procedure offered by Affymetrix. Recently, physical models based on molecular hybridization theory, have been proposed as useful tools for prediction of, for example, non-specific hybridization. These physical models show great potential in terms of improving existing expression measures. In this paper we demonstrate that the system producing the measured intensities is too complex to be fully described with these relatively simple physical models and we propose empirically motivated stochastic models that compliment the above mentioned molecular hybridization theory to provide a comprehensive description of the data. We discuss how the proposed model can be used to obtain improved measures of expression useful for the data analysts.

Experimental heart transplantation: effect of cyclosporine on expression and activity of metzincins

Metzincins, such as matrix metalloproteases (MMP), and extracellular matrix (ECM) proteins are differentially regulated in inflammation. We hypothesised that metzincins are also dysregulated in experimental acute cardiac allograft rejection. We investigated the Dark Agouti-to-Lewis (DA-to-Lew) rat model of acute cardiac allograft rejection. Cyclosporine (CsA) (7.5 mg/kg/d) was given from transplantation to sacrifice (day +5). At that time, mRNA levels were analysed by Affymetrix genechip and quantitative reverse transcription polymerase chain reaction (qRTPCR). MMP protein and activities were analysed by immunohistology, fluorometry, zymography and Western blots. In untreated rejected DA allografts, mRNA levels of MMP-2/-7/-9/-/12-/14, a disintegrin and metalloprotease (ADAM)-17, tissue inhibitor of metalloprotease (TIMP)-1/-3 were increased, whereas MMP-11/-16/-24 and TIMP-2/-4 were lowered compared to native DA hearts. With respect to these untreated allografts, CsA lowered mRNA levels of MMP-7, TIMP-1/-3 (TIMP-2/-4 remained relatively low) and ADAM17, but augmented mRNA levels of MMP-11/-16/-23 and of many ECM genes. Immunohistology showed increased staining of MMP-2 in acute rejection (AR). Overall MMP activity was augmented in both transplanted groups, but CsA reduced MMP-9 activity and MMP-14 production. Taken together, MMP and TIMP were upregulated during acute AR. CsA ameliorated histology of rejection but showed potential pro-fibrotic effects. Thus, MMP and TIMP may play a role in acute cardiac allograft rejection, and beneficial modification of the MMP-ECM balance requires interventions beyond CsA.

DYSREGULATION OF MEOX2 FOLLOWING WT1 MUTATION IN KIDNEY DEVELOPMENT AND WILMS TUMORIGENESIS

Wilms tumor (WT) is a childhood tumor of the kidney and a productive model for understanding the role of genetic alteration and interactions in tumorigenesis. The Wilms tumor gene 1 (WT1) is a transcriptional factor and one of the few genes known to have genetic alterations in WT and has been shown be inactivated in 20% of WTs. However, the mechanisms of how WT1 mutations lead to Wilms tumorigenesis and its influence on downstream genes are unknown. Since it has been established that WT1 is a transcriptional regulator, it has been hypothesized that the loss of WT1 leads to the dysregulation of downstream genes, in turn result in the formation of WTs. To identify the dysregulated downstream genes following WT1 mutations, an Affymetrix GeneChip Human Genome Array was previously conducted to assess the differentially expressed genes in the WT1-wildtype human and WT1-mutant human WTs. Approximately 700 genes were identified as being significantly dysregulated. These genes were further prioritized based on their statistical significance, fold change, chromosomal region, spatial pattern of gene expression and known or putative cellular functions. Mesenchyme homeobox 2 (MEOX2) was one of the most significantly upregulated genes in WT1-mutant WT. MEOX2 is known to play a role in cell proliferation, apoptosis, and differentiation. In addition to its biological roles, it is expressed during early kidney development in the condensed mesenchyme similar to WT1. Furthermore, the use of the Match® web-based tool from the BIOBASE Biological Data base identified a significant predicted WT1 binding site within the first intron of MEOX2. The similarity in spatial gene expression in the developing kidney and the significant predicted WT1 binding site found in the first intron of MEOX2 lead to the development of my hypothesis that MEOX2 is upregulated via a WT1-dependent manner. Here as a part of my master’s work, I have validated the Affymetrix GeneChip Human Genome Array data using an independent set of Wilms tumors. MEOX2 remained upregulated in the mutant WT1 Wilms tumor by 41-fold. Wt1 and Meox2 gene expression were assessed in murine newborn kidney; both Wt1 and Meox2 were expressed in the condensed, undifferentiated metanephric mesenchyme. I have shown that the in vivo ablation of Wt1 during embryonic development at embryonic day (E) 13.5 resulted in the slight increase of Meox2 gene expression by two fold. In order to functionally demonstrate the effect of the loss of Wt1 on Meox2 gene expression in undifferentiated metanephric mesenchyme, I have generated a kidney mesenchymal cell line to genetically ablate Wt1 in vitro by adenoviral infection. The ablation of Wt1 in the kidney mesenchymal cell line resulted in the upregulation of Meox2 by 61-fold. Moreover, the upregulation of Meox2 resulted in the significant induction of p21 and Itgb5. In addition to the dysregulation of these genes the ablation of Wt1 in the kidney mesenchymal cells resulted in decrease in cell growth and loss of cellular adherence. However, it is uncertain whether the upregulation of Meox2 caused this particular cellular phenotype. Overall, I have demonstrated that the upregulation of Meox2 is Wt1-dependent during early kidney development.

Transcriptional analysis of left-sided colitis, pancolitis, and ulcerative colitis-associated dysplasia.

BACKGROUND It is unknown why patients with extensive ulcerative colitis (UC) have a higher risk of colorectal cancer compared with patients with left-sided UC. This study characterizes the inflammatory processes in left-sided UC, pancolitis, and UC-associated dysplasia at the transcriptional level to identify potential biomarkers and transcripts of importance for the carcinogenic behavior of chronic inflammation. METHODS The Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied on colonic biopsies from UC patients with left-sided UC, pancolitis, dysplasia, and controls. Reverse transcription polymerase chain reaction and immunohistochemistry were performed for validating selected transcripts in the initial cohort and in 2 independent cohorts of patients with UC. Microarray data were analyzed by principal component analysis, and reverse transcription polymerase chain reaction and immunohistochemistry data by the Wilcoxon's rank-sum test. RESULTS The principal component analysis results revealed separate clusters for left-sided UC, pancolitis, dysplasia, and controls. Close clustering of dysplastic and pancolitic samples indicated similarities in gene expression. Indeed, 101 and 656 parallel upregulated and downregulated transcripts, respectively, were identified in specimens from dysplasia and pancolitis. Validation of selected transcripts hereof identified insulin receptor alpha (INSRA) and MAP kinase interacting serine/threonine kinase 2 (MKNK2) with an enhanced expression in dysplasia compared with left-sided UC and controls, whereas laminin γ2 (LAMC2) was found with a lower expression in dysplasia compared with the remaining 3 groups. CONCLUSIONS This study demonstrates pancolitis and left-sided UC as distinct inflammatory processes at the transcriptional level, and identifies INSRA, MKNK2, and LAMC2 as potential critical transcripts in the inflammation-driven preneoplastic process of UC.

Identification of diabetic retinopathy genes through a genome-wide association study among Mexican-Americans from Starr County, Texas

To identify genetic susceptibility loci for severe diabetic retinopathy, 286 Mexican-Americans with type 2 diabetes from Starr County, Texas completed detailed physical and ophthalmologic examinations including fundus photography for diabetic retinopathy grading. 103 individuals with moderate-to-severe non-proliferative diabetic retinopathy or proliferative diabetic retinopathy were defined as cases for this study. DNA samples extracted from study subjects were genotyped using the Affymetrix GeneChip® Human Mapping 100K Set, which includes 116,204 single nucleotide polymorphisms (SNPs) across the whole genome. Single-marker allelic tests and 2- to 8-SNP sliding-window Haplotype Trend Regression implemented in HelixTreeTM were first performed with these direct genotypes to identify genes/regions contributing to the risk of severe diabetic retinopathy. An additional 1,885,781 HapMap Phase II SNPs were imputed from the direct genotypes to expand the genomic coverage for a more detailed exploration of genetic susceptibility to diabetic retinopathy. The average estimated allelic dosage and imputed genotypes with the highest posterior probabilities were subsequently analyzed for associations using logistic regression and Fisher's Exact allelic tests, respectively. To move beyond these SNP-based approaches, 104,572 directly genotyped and 333,375 well-imputed SNPs were used to construct genetic distance matrices based on 262 retinopathy candidate genes and their 112 related biological pathways. Multivariate distance matrix regression was then used to test hypotheses with genes and pathways as the units of inference in the context of susceptibility to diabetic retinopathy. This study provides a framework for genome-wide association analyses, and implicated several genes involved in the regulation of oxidative stress, inflammatory processes, histidine metabolism, and pancreatic cancer pathways associated with severe diabetic retinopathy. Many of these loci have not previously been implicated in either diabetic retinopathy or diabetes. In summary, CDC73, IL12RB2, and SULF1 had the best evidence as candidates to influence diabetic retinopathy, possibly through novel biological mechanisms related to VEGF-mediated signaling pathway or inflammatory processes. While this study uncovered some genes for diabetic retinopathy, a comprehensive picture of the genetic architecture of diabetic retinopathy has not yet been achieved. Once fully understood, the genetics and biology of diabetic retinopathy will contribute to better strategies for diagnosis, treatment and prevention of this disease.^

Methionine adenosyltransferase 1A knockout mice are predisposed to liver injury and exhibit increased expression of genes involved in proliferation

Liver-specific and nonliver-specific methionine adenosyltransferases (MATs) are products of two genes, MAT1A and MAT2A, respectively, that catalyze the formation of S-adenosylmethionine (AdoMet), the principal biological methyl donor. Mature liver expresses MAT1A, whereas MAT2A is expressed in extrahepatic tissues and is induced during liver growth and dedifferentiation. To examine the influence of MAT1A on hepatic growth, we studied the effects of a targeted disruption of the murine MAT1A gene. MAT1A mRNA and protein levels were absent in homozygous knockout mice. At 3 months, plasma methionine level increased 776% in knockouts. Hepatic AdoMet and glutathione levels were reduced by 74 and 40%, respectively, whereas S-adenosylhomocysteine, methylthioadenosine, and global DNA methylation were unchanged. The body weight of 3-month-old knockout mice was unchanged from wild-type littermates, but the liver weight was increased 40%. The Affymetrix genechip system and Northern and Western blot analyses were used to analyze differential expression of genes. The expression of many acute phase-response and inflammatory markers, including orosomucoid, amyloid, metallothionein, Fas antigen, and growth-related genes, including early growth response 1 and proliferating cell nuclear antigen, is increased in the knockout animal. At 3 months, knockout mice are more susceptible to choline-deficient diet-induced fatty liver. At 8 months, knockout mice developed spontaneous macrovesicular steatosis and predominantly periportal mononuclear cell infiltration. Thus, absence of MAT1A resulted in a liver that is more susceptible to injury, expresses markers of an acute phase response, and displays increased proliferation.

Expression of HOXB2, a retinoic acid signaling target in pancreatic cancer and pancreatic intraepithelial neoplasia

Purpose: Despite significant progress in understanding the molecular pathology of pancreatic cancer and its precursor lesion: pancreatic intraepithelial neoplasia (PanIN), there remain no molecules with proven clinical utility as prognostic or therapeutic markers. Here, we used oligonucleotide microarrays to interrogate mRNA expression of pancreatic cancer tissue and normal pancreas to identify novel molecular pathways dysregulated in the development and progression of pancreatic cancer. Experimental Design: RNA was hybridized to Affymetrix Genechip HG-U133 oligonucleotide microarrays. A relational database integrating data from publicly available resources was created to identify candidate genes potentially relevant to pancreatic cancer. The protein expression of one candidate, homeobox B2 (HOXB2), in PanIN and pancreatic cancer was assessed using immunohistochemistry. Results: We identified aberrant expression of several components of the retinoic acid (RA) signaling pathway (RARa, MUC4, Id-1, MMP9, uPAR, HB-EGF, HOXB6, and HOXB2), many of which are known to be aberrantly expressed in pancreatic cancer and Pan IN. HOXB2, a downstream target of RA, was up-regulated 6.7-fold in pancreatic cancer compared with normal pancreas. Immunohistochemistry revealed ectopic expression of HOXB2 in 15% of early Pan IN lesions and 48 of 128 (38%) pancreatic cancer specimens. Expression of HOXB2 was associated with nonresectable tumors and was an independent predictor of poor survival in resected tumors. Conclusions: We identified aberrant expression of RA signaling components in pancreatic cancer, including HOXB2, which was expressed in a proportion of PanIN lesions. Ectopic expression of HOXB2 was associated with a poor prognosis for all patients with pancreatic cancer and was an independent predictor of survival in patients who underwent resection.

Microarray analysis of expression of cell death-associated genes in rat spinal cord cells exposed to cyclic tensile stresses in vitro

The application of mechanical insults to the spinal cord results in profound cellular and molecular changes, including the induction of neuronal cell death and altered gene expression profiles. Previous studies have described alterations in gene expression following spinal cord injury, but the specificity of this response to mechanical stimuli is difficult to investigate in vivo. Therefore, we have investigated the effect of cyclic tensile stresses on cultured spinal cord cells from E15 Sprague-Dawley rats, using the FX3000 Flexercell Strain Unit. We examined cell morphology and viability over a 72 hour time course. Microarray analysis of gene expression was performed using the Affymetrix GeneChip System, where categorization of identified genes was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) systems. Changes in expression of 12 genes were validated with quantitative real-time reverse transcription polymerase chain reaction (RT-PCR).

Identification and functional analysis of novel genes expressed in the Anterior Visceral Endoderm

During early vertebrate development, the correct establishment of the body axes is critical. The anterior pole of the mouse embryo is established when Distal Visceral Endoderm (DVE) cells migrate to form the Anterior Visceral Endoderm (AVE). Symmetrical expression of Lefty1, Cer1 and Dkk1 determines the direction of DVE migration and the future anterior side. In addition to the establishment of the Anterior-Posterior axis, the AVE has also been implicated in anterior neural specification. To better understand the role of the AVE in these processes, we have performed a differential screening using Affymetrix GeneChip technology with AVE cells isolated from cer1P-EGFP transgenic mouse embryos. We found 175 genes which were upregulated in the AVE and 36 genes in the Proximal-posterior sample. Using DAVID software, we characterized the AVE cell population regarding cellular component, molecular function and biological processes. Among the genes that were found to be upregulated in the AVE, several novel genes were identified. Four of these transcripts displaying high-fold change in the AVE were further characterized by in situ hybridization in early stages of development in order to validate the screening. From those four selected genes, one, denominated Adtk1, was chosen to be functionally characterized by targeted inactivation in ES cells. Adtk1 encodes for a serine/threonine kinase. Adtk1 null mutants are smaller and present short limbs due to decreased mineralization, suggesting a potential role in chondrogenesis during limb development. Taken together, these data point to the importance of reporting novel genes present in the AVE.

Identification of differentially expressed genes in the heart precursor cells of the chick embryo

Genetic evidence has implicated several genes as being critical for heart development. However, the inducers of these genes as well as their targets and pathways they are involved with, remain largely unknown. Previous studies in the avian embryo showed that at HH4 Cerberus (cCer) transcripts are detected in the anterior endomesoderm including the heart precursor cells and later in the left lateral plate mesoderm. We have identified a promoter element of chick cCer able to drive EGFP expression in a population of cells that consistently exit from the anterior primitive streak region, from as early as stage HH3+, and that later will populate the heart. Using this promoter element as a tool allowed us to identify novel genes previously not known to potentially play a role in heart development. In order to identify and study genes expressed and involved in the correct development and differentiation of the vertebrate heart precursor cell (HPC) lineages, a differential screening using Affymetrix GeneChip system technologies was performed. Remarkably, this screening led to the identification of more than 700 transcripts differentially expressed in the heart forming regions (HFR). Bioinformatic tools allowed us to filter the large amount of data generated from this approach and to select a few transcripts for in vivo validation. Whole-mount in situ hybridization and sectioning of selected genes showed heart and vascular expression patterns for these transcripts during early chick development. We have developed an effective strategy to specifically identify genes that are differentially expressed in the HPC lineages. Within this set we have identified several genes that are expressed in the heart, blood and vascular lineages, which are likely to play a role in their development. These genes are potential candidates for future functional studies on early embryonic patterning.

Hydrophobe und hydrophile Beladung polymerer Vesikel

Polymere Vesikel, gebildet durch Selbstorganisation des amphiphilen Blockcopolymers Polybutadien-b-Polyethylenoxid in Wasser, wurden in der vorliegenden Arbeit erfolgreich mit hydrophoben und hydrophilen Substraten beladen und detailliert charakterisiert. Über verschiedene Präparationsmethoden sind unilamellare PB130-PEO66-Vesikel unterschiedlicher Größen und Verteilungsbreiten zugänglich, die aber alle eine konstante hydrophobe Schalendicke von etwa 15nm aufweisen, wie aus TEM-Messungen hervorgeht. Die hydrophoben Farbstoffe Oil Red EGN, Oil Blue N, Nilrot sowie ein Perylen-Derivat wurden in diese hydrophobe Schale eingelagert. Durch Absorptions-, Emissions-, (cryo)TEM- und Fluoreszenzmikroskopie-Messungen konnte gezeigt werden, dass die selbstorganisierte Struktur durch die Einlagerung der hydrophoben Farbstoffe in die Schale nicht beeinflusst wird. Als zusätzliche hydrophobe Modell-Substrate wurden Halbleiter-Nanokristalle, sogenannte Quantum Dots (QDs, d=5.7nm), erfolgreich in die polymere Vesikelschale eingelagert und durch Fluoreszenz-Korrelations-Spektroskopie (FCS) in Kombination mit dynamischer Lichtstreuung (DLS) nachgewiesen. Die Position der QDs in der Mitte der polymeren Doppelmembran konnte durch cryogene TEM-Abbildungen aufgezeigt werden. Darüber hinaus wurde die hydrophile Beladung des Vesikelkerns mit dem wasserlöslichen Farbstoff Phloxin B erfolgreich realisiert.

Uptake mechanism, intracellular trafficking and endo-lysosomal pH monitoring of polystyrene nanoparticles

What is the intracellular fate of nanoparticles (NPs) taken up by the cells? This question has been investigated for polystyrene NPs of different sizes with a set of molecular biological and biophysical techniques.rnTwo sets of fluorescent NPs, cationic and non-ionic, were synthesized with three different polymerization techniques. Non-ionic particles (132 – 846 nm) were synthesized with dispersion polymerization in an ethanol/water solution. Cationic NPs with 120 nm were synthesized by miniemulsion polymerization Particles with 208, 267 and 603 nm were produced by seeding the 120 nm particle obtained by miniemulsion polymerization with drop-wise added monomer and polymerization of such. The colloidal characterization of all particles showed a comparable amount of the surface groups. In addition, particles were characterized with regard to their size, morphology, solid content, amount of incorporated fluorescent dye and zeta potential. The fluorescent intensities of all particles were measured by fluorescence spectroscopy for calibration in further cellular experiments. rnThe uptake of the NPs to HeLa cells after 1 – 24 h revealed a much higher uptake of cationic NPs in comparison to non-ionic NPs. If the same amount of NPs with different sizes is introduced to the cell, a different amount of particles is present in the cell medium, which complicates a comparison of the uptake. The same conclusion is valid for the particles’ overall surface area. Therefore, HeLa cells were incubated with the same concentration, amount and surface area of NPs. It was found that with the same concentration always the same polymer amount is taking up by cells. However, the amount of particles taken up decreases for the biggest. A correlation to the surface area could not be found. We conclude that particles are endocytosed by an excavator-shovel like mechanism, which does not distinguish between different sizes, but is only dependent on the volume that is taken up. For the decreased amount of large particles, an overload of this mechanism was assumed, which leads to a decrease in the uptake. rnThe participation of specific endocytotic processes has been determined by the use of pharmacological inhibitors, immunocytological staining and immunofluorescence. The uptake of NPs into the endo-lysosomal machinery is dominated by a caveolin-mediated endocytosis. Other pathways, which include macropinocytosis and a dynamin-dependent mechanism but exclude clathrin mediated endocytosis, also occur as competing processes. All particles can be found to some extent in early endosomes, but only bigger particles were proven to localize in late endosomes. No particles were found in lysosomes; at least not in lysosomes that are labeled with Lamp1 and cathepsin D. However, based on the character of the performed experiment, a localization of particles in lysosomes cannot be excluded.rnDuring their ripening process, vesicles undergo a gradual acidification from early over late endosomes to lysosomes. It is hypothesized that NPs in endo-lysosomal compartments experience the same change in pH value. To probe the environmental pH of NPs after endocytosis, the pH-sensitive dye SNARF-4F was grafted onto amino functionalized polystyrene NPs. The pH value is a ratio function of the two emission wavelengths of the protonated and deprotonated form of the dye and is hence independent of concentration changes. The particles were synthesized by the aforementioned miniemulsion polymerization with the addition of the amino functionalized copolymer AEMH. The immobilization of SNARF-4F was performed by an EDC-coupling reaction. The amount of physically adsorbed dye in comparison to covalently bonded dye was 15% as determined by precipitation of the NPs in methanol, which is a very good solvent for SNARF-4F. To determine influences of cellular proteins on the fluorescence properties, a intracellular calibration fit was established with platereader measurements and cLSM imaging by the cell-penetrable SNARF-4F AM ester. Ionophores equilibrated the extracellular and intracellular pH.rnSNARF-4F NPs were taken up well by HeLa cells and showed no toxic effects. The pH environment of SNARF-4F NPs has been qualitatively imaged as a movie over a time period up to 1 h in pseudo-colors by a self-written automated batch program. Quantification revealed an acidification process until pH value of 4.5 over 24 h, which is much slower than the transport of nutrients to lysosomes. NPs are present in early endosomes after min. 1 h, in late endosomes at approx. 8 h and end up in vesicles with a pH value typical for lysosomes after > 24 h. We therefore assume that NPs bear a unique endocytotic mechanism, at least with regards to the kinetic involvedrn

Untersuchungen über Wechselwirkungen zwischen Proteinen der Leber und dem großen Hüllprotein des Hepatitis-B-Virus

Zusammenfassung:Im Infektionszyklus des Hepatitis-B-Virus spielt das große L-Hüllprotein mit seiner einzigartigen PräS1-Domäne eine zentrale Rolle. Es vermittelt die Bindung und Aufnahme in die Leberzelle, die Verpackung der Nukleokapside in die Virushülle, die Regulation der cccDNA-Amplifikation und eine transkriptionelle Aktivierung in der Wirtszelle. Zur Erfüllung seiner vielfältigen Aufgaben benötigt das L-Protein Unterstützung durch Wirtzellfaktoren, von denen einige im Rahmen dieser Untersuchung durch Verwendung von PräS1-Konstrukten als Fängerproteine im Hefe-Zwei-Hybrid-System identifiziert wurden. Mehrere Klone, die im Hefe-Zwei-Hybrid-Test mit dem C-terminalen PräS1-Fängerprotein (Aminosäure 44-108) isoliert worden waren, enthielten Teile der cDNA von gamma2-Adaptin, einem mutmaßlichen Mitglied der Clathrin-Adaptor-Proteine. Diese sind für intrazelluläre Membrantransportprozesse mittels clathrinumhüllter Vesikel verantwortlich. Unter den interagierenden Klonen, die mit dem N-terminalen Konstrukt des L-Proteins (Aminosäure 1-70) isoliert worden waren, befand sich überproportional häufig eine cDNA, die der schweren Kette H4 der Inter-Alpha-Trypsin-Inhibitor-Familie homolog war. H4 besitzt vermutlich bei der 'Akute-Phase-Reaktion', die Entzündungen folgt, und bei der Stabilisierung der extrazellulären Matrix physiologische Bedeutung. Weitere Klone kodierten für die Serinprotease C1r. Diese ist Bestandteil des C1-Komplex, der ersten Komponente des klassischen Komplementsystems. Die Spezifität der Bindung zwischen den positiven Klonen und der PräS1-Domäne wurde in weiteren biochemischen Interaktionstests bestätigt, sodaß H4, C1r und gamma2-Adaptin als Wirtszellfaktoren in der Physiologie des Hepatitis-B-Virus wahrscheinlich eine Rolle spielen.Abstract:Little is known about host cell factors necessary for hepatitis B virus assembly and infectivity. Central to virogenesis is the large L envelope protein that mediates hepatocyte receptor binding, envelopment of viral capsids, regulation of supercoiled DNA amplification and transcriptional transactivation. To assess its multiple functions and host-protein assistance involved, we here initiated a yeast two-hybrid screen using the L-specific preS1 domain as bait to screen a human liver cDNA library for L-interacting proteins. One of the most prominent cDNAs interacting with aminoacid sequence 44-108 of L-protein encodes for gamma2-adaptin, a novel clathrin adaptor-related protein responsible for protein sorting and trafficking. Among the clones interacting with the N-terminal construct of L-protein (aminoacid sequence 1-70), a frequently isolated cDNA corresponds to the gene for inter-alpha-trypsin family heavy chain H4, likely to be involved in acute inflammatory phase response and stabilization of extracellular matrices. Some other interacting clones were found to carry the cDNA for the serine protease C1r, a subunit of the C1 complex which initiates the classical complement cascade. The specificity of the interaction between the positive clones and the preS1 domain was further confirmed in independent biochemical experiments. Taken together, the results suggest a role for H4, C1r and gamma2-adaptin as host-cell factors in L-mediated process of viral biogenesis and/or pathogenesis.

Charakterisierung des Rezeptors, des Aufnahmeweges und der Neutralisation humanpathogener Papillomviren

Im Rahmen dieser Arbeit wurden Pseudovirionen mit gfp als Reportergen generiert und zur Charakterisierung verschiedener Aspekte der HPV-Infektion verwendet. Es konnte gezeigt werden, daß Heparansulfatproteoglykane für die Infektion mit HPV16- und HPV33-Pseudovirionen essentiell sind, da: (i) Heparin, nicht aber Chondroitin- oder Dermatansulfat die Infektion inhibiert, (ii) Heparinase I oder chloratbehandelte Zellen vollständig bzw. teilweise resistent gegen eine Infektion sind, (iii) monoklonale Antikörper Pseudovirionen neutralisieren, indem sie die Bindung an Heparin verhindern. Ein intakter C-Terminus des L1-Proteins ist für die Heparinbindung nicht notwendig. Alpha-6 Integrin ist kein obligater HPV-Rezeptor. Die Neutralisation gebundener Pseudovirionen durch ein neutralisierendes Antiserum einerseits und durch Heparin andererseits demonstriert, daß die Aufnahme von Pseudovirionen sehr langsam verläuft und daß die Bindung von einem heparinsensitiven zu einem heparinresistenten Zustand übergeht, möglicherweise unter Beteiligung weiterer Rezeptoren. Die Wirkung von verschiedenen Inhibitoren auf die Pseudoinfektion lassen schließen, daß Pseudovirionen über eine mikrofilamentabhängige und energieabhängige Endozytose mit anschließender Penetration durch saure Vesikel aufgenommen werden. Caveolen sind an der Aufnahme nicht beteiligt. Untersuchungen zur Neutralisation von HPV16-, HPV18- und HPV33-Pseudovirionen durch Antiseren gegen HPV16, 18, 31, 33, 35, 39 und 45 zeigen eine Kreuzneutralisation zwischen HPV31 und HPV33 einerseits und zwischen HPV18 und HPV45 andererseits.

Signalling mechanisms affecting regulated neurotrophin secretion in hippocampal neurons

Die Neurotrophine aus Säugetiere BDNF und NT-3 sind von Neuronen sekretierte Wachstumsfaktoren. Ferner sind Neurotrophine in verschiedene Formen der aktivitätsabhängigen synaptische Plastizität involviert. Obwohl die Ausschüttung von Neurotrophine aus Synapsen beschrieben worden ist, sind die intrazellulären Signalkaskaden, die die synaptische Ausschüttung von Neurotrophine regulieren, bei weitem nicht verstanden. Deswegen ist die Analyse der Sekretion von Neurotrophine auf subzellulärer Ebene erforderlich, um die genaue Rolle von präsynaptische und postsynaptische NT-Sekretion in der synaptischen Plastizität aufzudecken. In der vorliegenden Arbeit wurden die Kulturen von dissoziierten hippocampalen Neuronen aus Ratten mit grün fluoreszierenden Protein-markierten Konstrukten von BDNF und NT-3 transfiziert und Neurotrophine-enthaltenden Vesikeln durch die Colokalisierung mit dem cotransfizierten postsynaptischen Marker PSD-95-DsRed an glutamatergen Synapsen identifiziert. Depolarisationsinduzierte Sekretion von BDNF und NT-3 wurde per Direktaufnahme am Fluoreszenzmikroskop beobachtet. Die unvermittelte postsynaptische Depolarisation mit erhöhtem Kalium, in Gegenwart von Inhibitoren der synaptischen Transmission, erlaubte die Untersuchung der Signalwege, die am postsynaptischen Sekretionsprozess der Neurotrophinvesikel beteiligt sind. Es konnte gezeigt werden, dass die depolarisationsinduzierte postsynaptische Ausschüttung der Neurotrophine durch Calcium-Einstrom ausgelöst wird, entweder über L-Typ-spannungsabhängige Calcium-Kanäle oder über NMDA-Rezeptoren. Eine anschließende Freisetzung von Calcium aus intrazellulären Speichern über Ryanodin-Rezeptoren ist für den Sekretionsprozess erforderlich. Die postsynaptische Neurotrophinausschüttung wird durch KN-62 und KN-93 gehemmt, was auf eine unmittelbare Abhängigkeit von aktiver alpha-Calcium-Calmodulin-abhängige Proteinkinase II (CaMKII) hinweist. Der Inhibitor der cAMP/Proteinkinase A (PKA), Rp-cAMP-S, sowie der NO-Donor, SNP, minderten die Neurotrophinausschüttung. Hingegen blieben die Erhöhung des intrazellulären cAMP und der NO-Synthase-Inhibitor L-NMMA ohne Wirkung. Mit dem Trk-Inhibitor K252a konnte gezeigt werden, dass autokrine Neurotrophin-induzierte Neurotrophinausschüttung nicht an der synaptischen Freisetzung der Neurotrophine beiträgt und, dass BDNF seine eigene postsynaptische Sekretion nicht auslöst. Freisetzungsexperimente mit dem Fluoreszenz-Quencher Bromphenolblau konnten den Nachweis erbringen, dass asynchrone und anhaltende Fusionsporenöffnung von Neurotrophinvesikeln während der Sekretion stattfindet. Wegen der im Vergleich zum komplexen Sekretionsprozess schnellen Fusionsporenöffnung, scheint die Freisetzungsgeschwindigkeit von Neurotrophine durch ihre Diffusion aus dem Vesikel begrenzt. Zusammenfassend zeigen diese Ergebnisse eine starke Abhängigkeit der aktivitätsabhängigen postsynaptischen Neurotrophinausschüttung vom Calcium-Einstrom, von der Freisetzung von Calcium aus internen Speichern, von der Aktivierung der CaMKII und einem intakten Funktion der PKA, während der Trk-Signalweg, die Aktivierung von Natrium-Kanäle und NO-Signale nicht erforderlich sind.