Proteins and their interactions are fundamental to cellular life. Disruption of protein-protein, protein-RNA, or protein-DNA interactions can lead to disease, by affecting the function of protein complexes or by affecting gene regulation. A better understanding of these interactions on the molecular level gives rise to new methods to predict protein interaction, and is critical for the rational design of new therapeutic agents that disrupt disease-causing interactions. This thesis consists of three parts that focus on various aspects of protein interactions and their prediction in the context of disease. In the first part of this thesis, we classify interfaces of protein-protein interactions. We do so by systematically computing all binding sites between protein domains in protein complex structures solved by X-ray crystallography. The result is SCOPPI, the Structural Classification of Protein Protein Interfaces. Clustering and classification of geometrically similar interfaces reveals interesting examples comprising viral mimicry of human interface binding sites, gene fusion events, conservation of interface residues, and diversity of interface localisations. We then develop a novel method to predict protein interactions which is based on these structural interface templates from SCOPPI. The method is applied in three use cases covering osteoclast differentiation, which is relevant for osteoporosis, the microtubule-associated network in meiosis, and proteins found deregulated in pancreatic cancer. As a result, we are able to reconstruct many interactions known to the expert molecular biologist, and predict novel high confidence interactions backed up by structural or experimental evidence. These predictions can facilitate the generation of hypotheses, and provide knowledge on binding sites of promising disease-relevant candidates for targeted drug development. In the second part, we present a novel algorithm to search for protein binding sites in RNA sequences. The algorithm combines RNA structure prediction with sequence motif scanning and evolutionary conservation to identify binding sites on candidate messenger RNAs. It is used to search for binding sites of the PTBP1 protein, an important regulator of glucose secretion in the pancreatic beta cell. First, applied to a benchmark set of mRNAs known to be regulated by PTBP1, the algorithm successfully finds significant binding sites in all benchmark mRNAs. Second, collaborators carried out a screen to identify changes in the proteome of beta cells upon glucose stimulation while inhibiting gene expression. Analysing this set of post-transcriptionally controlled candidate mRNAs for PTBP1 binding, the algorithm produced a ranked list of 11 high confident potential PTBP1 binding sites. Experimental validation of predicted targets is ongoing. Overall, identifying targets of PTBP1 and hence regulators of insulin secretion may contribute to the treatment of diabetes by providing novel protein drug targets or by aiding in the design of novel RNA-binding therapeutics. The third part of this thesis deals with gene regulation in disease. One of the great challenges in medicine is to correlate genotypic data, such as gene expression measurements, and other covariates, such as age or gender, to a variety of phenotypic data from the patient. Here, we address the problem of survival prediction based on microarray data in cancer patients. To this end, a computational approach was devised to find genes in human cancer tissue samples whose expression is predictive for the survival outcome of the patient. The central idea of the approach is the incorporation of background knowledge information in form of a network, and the use of an algorithm similar to Google s PageRank. Applied to pancreas cancer, it identifies a set of eight genes that allows to predict whether a patient has a poor or good prognosis. The approach shows an accuracy comparable to studies that were performed in breast cancer or lymphatic malignancies. Yet, no such study was done for pancreatic cancer. Regulatory networks contain information of transcription factors that bind to DNA in order to regulate genes. We find that including background knowledge in form of such regulatory networks gives highest improvement on prediction accuracy compared to including protein interaction or co-expression networks. Currently, our collaborators test the eight identified genes for their predictive power for survival in an independent group of 150 patients. Under a therapeutic perspective, reliable survival prediction greatly improves the correct choice of therapy. Whereas the live expectancy of some patients might benefit from extensive therapy such as surgery and chemotherapy, for other patients this may only be a burden. Instead, for this group, a less aggressive or different treatment could result in better quality of the remaining lifetime. Conclusively, this thesis contributes novel analytical tools that provide insight into disease-relevant interactions of proteins. Furthermore, this thesis work contributes a novel algorithm to deal with noisy microarray measurements, which allows to considerably improve prediction of survival of cancer patients from gene expression data.

In many European countries, migrants utilize cancer screening less often than non-migrants. In Germany, in contrast, higher rates of utilization among migrants as compared with non-migrants have been reported. The role of demographic and socioeconomic factors potentially confounding the association between migration status and participation in screening, however, could not be studied. The present study aims to investigate the utilization of cancer screening among migrant and nonmigrant women residing in Germany, adjusting for potential confounders. We used self-reported information from women surveyed on whether they have ever participated in screening for cancer (n = 11,709). The data was collected as part of a cross-sectional representative telephone survey conducted by the Robert Koch-Institute in 2010. We distinguished between three groups of women: (1) respondents of non-German nationality, those who had immigrated to Germany after their birth or those who have two foreign-born parents (“migrants with two-sided migration background”), (2) respondents who only have one foreign-born parent (“migrant with one-sided migration background”), and (3) all others (“non-migrants”). To account for confounders, logistic regression analysis was performed. Only individuals proficient in German were included in the survey, allowing to control for a bias arising from poor language proficiency. 84.9% of nonmigrant women, 82.1% of women with a one-sided, and 70.5% of women with a two-sided migration background had utilized screening for cancer at least once in their lifetime before the survey. The adjusted odds ratios (OR) as compared with nonmigrant women were 0.99 (95% confidence interval [95% CI]: 0.77–1.27) and 0.55 (95% CI: 0.47–0.64), respectively. The study shows that migrant women with a two-sided migration background residing in Germany utilize screening for cancer less often than nonmigrant women—independently of demographic and socioeconomic factors. This is in line with findings from other countries. Likely, barriers that migrant women encounter limit them from taking informed choices. These barriers need to be identified and appropriate measures aiming to enhance informed decision making must be implemented.

Our aim was to determine the characteristics, treatments and outcomes of patients with primary spinal glioblastomas (GB) or gliosarcomas (GS) reported in literature until March 2015. PubMed and Web of Science were searched for peer-reviewed articles pertaining to cases of glioblastomas / gliosarcomas with primary spinal origin, using predefined search terms. Furthermore we performed hand searches tracking the references from the selected papers. Eighty-two articles published between 1938 and March 2015 were eligible. They reported on 157 patients. Median age at diagnosis was 22 years. The proportion of patients who received adjuvant chemo- or radiotherapy clearly increased from the time before 1980 until present. Median overall survival from diagnosis was 8.0 ± 0.9 months. On univariate analysis age influenced overall survival, whereas tumor location, gender and the extent of initial resection did not. Outcomes did not differ between children (< 18 years) and adults. However, the patients who were treated after 1980 achieved longer survival times than the patients treated before. On multivariable analysis only age (< 60 years) and the time period of treatment (>1980) were confirmed as positive independent prognostic factors. In conclusion, primary spinal GB / GS mainly affect younger patients and are associated with a dismal prognosis. However, most likely due to the increasing use of adjuvant treatment, modest therapeutic progress has been achieved over recent decades. The characteristics and treatments of primary spinal glioblastomas should be entered into a central registry in order to gain more information about the ideal treatment approach in the future.

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. To improve the prognosis, novel molecular markers and targets for earlier diagnosis and adjuvant and/or neoadjuvant treatment are needed. Recent advances in human genome research and high-throughput molecular technologies make it possible to cope with the molecular complexity of malignant tumors. With DNA array technology, mRNA expression levels of thousand of genes can be measured simultaneously in a single assay. As several studies using microarrays in PDAC have already been published, this review attempts to compare the published data and therefore to validate the results. In addition, the applied techniques are discussed in the context of pancreatic malignancies. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Background: Tumor cells are highly dependent on glucose even in the presence of oxygen. This concept called the Warburg effect is a hallmark of cancer and strategies are considered to therapeutically exploit the phenomenon such as ketogenic diets. The success of such strategies is dependent on a profound understanding of tumor cell metabolism. With new techniques it is now possible to thoroughly analyze the metabolic responses to the withdrawal of substrates and their substitution by others. In the present study we used gas chromatography coupled to mass spectrometry (GC-MS) to analyze how glioblastoma brain tumor cells respond metabolically when glucose is withdrawn and substituted by pyruvate. Methods: Glioblastoma brain tumor cells were cultivated in medium with high (25 mM), medium (11 mM) or low (5.5 mM) glucose concentration or with pyruvate (5 mM). After 24 h GC-MS metabolite profiling was performed. Results: The abundances of most metabolites were dependent on the supply of glucose in tendency but not in a linear manner indicating saturation at high glucose. Noteworthy, a high level of sorbitol production and release was observed at high concentrations of glucose and high release of alanine, aspartate and citrate were observed when glucose was substituted by pyruvate. Intermediates of the TCA cycle were present under all nutritional conditions and evidence was found that cells may perform gluconeogenesis from pyruvate. Conclusions: Our experiments reveal a high plasticity of glioblastoma cells to changes in nutritional supply which has to be taken into account in clinical trials in which specific diets are considered for therapy.

Humane oder humanisierte monoklonale Antikörper haben sich in den letzten zehn Jahren als Arzneimittel etabliert. Sie sind hochspezifisch und zeigen in ihrer Anwendung im Vergleich zu konventionellen Therapeutika viel weniger Nebenwirkungen. In den 80er Jahren gelang es am Pathologischen Institut der Universität Würzburg eine Reihe von humanen Antikörpern aus Patienten zu isolieren, die hochspezifisch mit malignen Zellen reagieren und diese sowohl in vitro als auch im experimentellen Tiermodel selektiv durch Induktion von Apoptose töten. Um die Wirkungsweise von monoklonalen Antikörpern in der Krebstherapie zu erhöhen, werden die meisten in Kombination mit herkömmlichen Methoden, wie Chemotherapie, eingesetzt. Die ideale Therapieform sind hinsichtlich der Nebenwirkungen sog. Cocktails aus verschiedenen monoklonalen Antikörpern. Allerdings sind die Studien hierzu noch wenig fortgeschritten. Das Ziel dieser Arbeit war es, in präklinischen Versuchsreihen den Einsatz verschiedener tumorspezifischer humaner monoklonaler Antikörper als Cocktail und in Kombination mit Chemotherapie zu evaluieren. Hierzu wurden neun Antikörper in 32 verschiedenen Antikörperkombinationen hinsichtlich ihrer Auswirkungen auf die in vitro Proliferation einer Pankreaskarzinom-Zellinie untersucht. In Immunfluoreszenz-Aufnahmen ließ sich zeigen, dass kombinierte Antikörper an unterschiedlichen Stellen an der Zelle binden, was eindeutig auf verschiedene Zielstrukturen hinweist. Einige werden dabei endozytiert, während andere auf der Zellmembran bleiben. Interessanterweise ließen sich Kombinationen identifizieren, deren antiproliferative Wirkung sowohl additiv als auch synergistisch ist, das heißt größer als die Summe ihrer Einzelaktivitäten. Wurden Antikörper mit Zytostatika (5-Flurouracil) kombiniert, so ließen sich ebenfalls synergistische Effekte beobachten. In FACS-Analysen zeigt sich ein gesteigertes Bindungsverhalten der Antikörper, wenn die Zellen mit 5-FU vorinkubiert wurden. Zusammenfassend bestätigen die Ergebnisse dieser Arbeit die Beobachtung, dass die Wirkung humaner monoklonaler Antikörper in Kombination mit Chemotherapie erhöht werden kann. Für die Zukunft humaner Antikörper als Therapiemittel gegen maligne Erkrankungen mag allerdings noch wichtiger sein, dass Antiköper in Cocktails tatsächlich synergistische Wirkung zeigen können. / Cancer patients receiving antibodies as mono-therapy have benefited from these treatments. However, significant improvements could be made if the antibodies were used in combination with conventional chemotherapy. Having learned from the natural oligoclonal antibody response that cancer patients mount to their own tumours, we suppose that cocktails of monoclonal antibodies could be even more active in treating cancer. We have isolated a series of human monoclonal IgM antibodies from cancer patients, which bind to different tumor-specific surface receptors and induce apoptosis in vitro and in vivo. To study the antibody-mediated effects in cocktails, the antibodies were applied in different combinations to pancreas carcinoma cells and analyzed in cytotoxic assays. Depending on their target, it was found that some combinations showed a significant additive or synergistic killing effect, when compared to mono-therapy. We also investigated a combinatorial treatment with chemotherapy on pancreas and colon cancer cells and found that a pretreatment with 5-FU sensitizes the cancer cells to antibody treatment. Based on our own results and data from other laboratories, it is likely that the next phase of antibody immunotherapy will include cocktails of monoclonal antibodies.

Humane Antikörper sind aufgrund ihrer spezifischen, zielgerichteten Eigenschaften die idealen therapeutischen Waffen unserer modernen Medizin. Schon im ausgehenden letzen Jahrhundert gelang es dem pathologischen Institut der Universität Würzburg einige rein humane monoklonale Antikörper aus Geweben sowohl gesunder, als auch an einem Tumorleiden erkrankter Patienten zu isolieren. Zwei dieser Antikörper galt es im Rahmen dieser Arbeit näher zu untersuchen: LM-1 und PAM-1 , beides rein humane monoklonale IgM-Antikörper. Mithilfe immunhistochemischer Färbungen auf Paraffinschnitten von Adenocarcinomen des Colons, Carcinomen des Pancreas und Adeno- und Plattenepithelcarcinomen der Lunge ließ sich eindeutig demonstrieren, daß bei beiden Antikörpern eine tumorspezifische Reaktivität ohne Kreuzreaktion mit den umgebenden gesunden Geweben auf fast allen der ausgewählten Fälle der begutachteten Tumorarten vorlag. Daraus lässt sich eine zuverlässige und selektive Expression der jeweiligen Antigene auf den maligne entarteten Zellen folgern, die sich auch bei Betrachtung der Stadien der Tumoren und des Gradings der Zellen konstant zeigte. Damit scheint soweit keinen Zusammenhang zwischen der Entdifferenzierung der tumorösen Zellen, als auch der Größe und des Fortschreiten des Tumors erkennbar. Die hier demonstrierten Ergebnisse lassen sowohl PAM-1 als auch LM-1 als verlässliche Marker für multiple epitheliale Tumoren und deren Vorstufen erscheinen und können somit als wertvolles diagnostisches und wahrscheinlich auch therapeutisches Mittel eingestuft werden, doch muss die Diskussion dieser Aspekte weiterführenden Untersuchungen überlassen werden. / Human antibodies are ideal therapeutic agents in modern medicine because of their specific and determined abilities. In the end of the last century, the institute of Pathology at the University of Wuerzburg had been successful in isolating several fully human monoclonal antibodies from different tissues of cancer patients as well as from healthy human beings. In this piece of work, two of these had been looked at more closely: PAM-1 and LM-1, both completely human monoclonal IgM antibodies. Immunohistochemical stainings on paraffin sections of tissues of adenocarcinoma of the colon, carcinomas of the pancreas and adeno- and squamous cell carcinomas of the lung clearly demonstrated the tumor specific reactivity of both antibodies without interaction with healthy tissues surrounding the malignant cells in nearly all of the selected cases. We have seen a constant and exclusive expression of the corresponding antigens on the neoplastic cells that appears to be a steady characteristic on all malign cells, no matter which stadium the tumor already reached or which state of grading had been shown by the cells. So far there seems to be any correlation between the de-differentiation of the tumor cells as well as the size and the progression of the tumor. The demonstrated results show PAM-1 and LM-1 as reliable markers on multiple epithelial tumors and their precursor lesions. With their exclusive tumor specific affinity to their corresponding antigens and their ability of initiating ADCC and CDC as well as inducing apoptosis, these antibodies have to be measured as precious diagnostic agents and perhaps as cancer immunotherapeutics. But these aspects of possible future cancer therapy have to be postponed on further discussions and investigations.

Toutes les formes de vie assemblent et désassemblent continuellement des composés chimiques via un processus de consommation d'énergie appelé métabolisme. Le métabolisme est généralement modélisé en chimie et biologie par un cycle. Ce modèle dynamique traduit la transformation de composés de base en une cascade de produits appelés métabolites. Celui-ci est comparable à un ouragan à l’échelle moléculaire. De manière analogique et imagée un cyclone est constitué de deux éléments, l'air et l'eau, et transforme l’environnement qui l’entoure par un processus endothermique (consommateur d’énergie). Traditionnellement, la recherche chimique sur les origines de la vie est concentrée principalement sur la synthèse de composés chimiques sans suffisamment apprécier leur place dans la plus grande organisation biochimique de la vie. La vie construit toutes ses molécules à partir du dioxyde de carbone, pourtant elle manque étonnamment d'innovation à cet égard. Malgré presque 4 milliards d'années d'évolution, les organismes autotrophes utilisent seulement six voies différentes pour construire leurs molécules à partir du CO2. Parmi elles, deux voies – la voie de l’acétyle CoA (aussi appelée voie Wood-Ljungdahl) et le cycle du rTCA (également appelé le cycle de Krebs inverse) - sont considérées comme primitives, et contiennent les cinq molécules servant de précurseurs chimiques universels pour toute la biochimie. Comment et pourquoi les voies de l’acétyle CoA et du rTCA sont-elles apparues? Pour répondre à cette question, une recherche systématique a été effectuée afin de trouver des catalyseurs chimiques non-enzymatiques ou des minéraux simples, ainsi que des réactifs pouvant promouvoir les réactions d'anabolisme principal, particulièrement la voie de l’Acétyle CoA et le cycle de rTCA. A l’origine, pour créer les molécules organiques complexes comme les enzymes il a fallu que des molécules plus simples avec un moins grand nombre de carbone se forme sur terre et cela à partir du CO2. On peut donc supposer que les premiers produits à plusieurs carbones sont issus de synthèse totalement inorganique comme celles développer dans notre laboratoire, plutôt que d’une évolution chimique et organométallique simultanée, c’est-à-dire une interaction efficace entre une molécule carbonée et un ou plusieurs métaux à l’instar de certains enzymes. Après avoir trouvé autant de façons possible de promouvoir individuellement chaque étapes des cycles catalytiques étudiés, seules les conditions réactionnelles mutuellement compatibles (à savoir des conditions permettant de produire l’ensemble des métabolites dans le bon ordre) ont été retenu. / All life forms continuously build up and break down its constituent chemical building blocks, through an energy consuming process called metabolism. Just like a hurricane’s dynamic patterns and its building blocks (air and water) as being equally fundamental to its nature, so too should metabolism’s dynamic chemical patterns and chemical building blocks be viewed as equally characteristic. Traditionally, much chemical research on the origins of life is overly focused on the synthesis of chemical building blocks without sufficiently appreciating their place in life’s larger biochemical self-organization. Life ultimately builds all of its molecules from carbon dioxide, yet it is surprisingly lacking in innovation in this respect. Despite nearly 4 billion years of evolution, autotrophic organisms use only six pathways to build their molecules from CO2. Two of these pathways – the acetyl CoA pathway (also known as the Wood-Ljungdahl pathway) and rTCA cycle (also known as the reverse Krebs cycle) - are thought to be ancestral, with just five molecules within them serving as the universal chemical precursors for all of biochemistry. How and why did these pathways get their start? To answer this question, a systematic search was designed to find simple, non-enzymatic chemical or mineral catalysts and reagents, that can promote the reactions of core anabolism, particularly the acetyl CoA pathway and the rTCA cycle. After finding as many ways as possible to promote each reaction, they could be narrowed down to mutually compatible conditions where many reactions can occur in sequence. The more of core anabolism that can be achieved under a single set of purely chemical conditions, the more likely it is to have constituted early prebiotic chemistry rather than a later product of chemical and biological evolution.

In der vorliegenden Arbeit wurde das Expressionsverhalten fünf zellulärer Marker beim metastasierenden Plattenepithelkarzinom des Kopf- und Halsbereiches untersucht. Bei den getesteten Markern handelte es sich um einen MAGE-A, zwei verschiedenen VEGF, einen EGFR und einen C-Src-Tyrosinkinase Antikörper. Im Einzelnen sollte hinterfragt werden, ob ein Zusammenhang zwischen der Antikörperexpression und verschiedenen, klinischen und histopathologischen Parametern (pT-Stadium, pN-Stadium, histologisches Grading, Tumorverhornung, Patientenalter, Geschlecht des Patienten) besteht. Weiterhin war von Interesse, ob Parallelen zwischen dem Expressionsverhalten der verschiedenen Antikörper untereinander zu erkennen sind. Die Ergebnisse wurden anschließend mit Erkenntnissen aus anderen Studien und Literaturangaben verglichen. / This study aimed to evaluate the expression profiles of cellular marker in metastatic head and neck cancer in the primary tumor and in the metastases. The expression profiles of MAGE-A, VEGF-A, VEGF-C, EGFR and c-Src in 50 squamous cell carcinoma were characterised by immunhistochemical stainig.

No description available.