To determine the characteristics, treatments and outcomes of patients with glioblastoma multiforme (GBM) or gliosarcoma (GS) and metastases outside of the central nervous system (CNS).

Background: The naked mole-rat (NMR) is a long-lived and cancer resistant species. Identification of potential anti-cancer and age related mechanisms is of great interest and makes this species eminent to investigate anti-cancer strategies and understand aging mechanisms. Since it is known that the NMR expresses higher liver mRNA-levels of alpha 2-macroglobulin than mice, nothing is known about its structure, functionality or expression level in the NMR compared to the human A2M. Results: Here we show a comprehensive analysis of NMR- and human plasma-A2M, showing a different prediction in glycosylation of NMR-A2M, which results in a higher molecular weight compared to human A2M. Additionally, we found a higher concentration of A2M (8.3±0.44 mg/mL vs. and 4.4±0.20 mg/mL) and a lower total plasma protein content (38.7±1.79 mg/mL vs. 61.7±3.20 mg/mL) in NMR compared to human. NMR-A2M can be transformed by methylamine and trypsin resulting in a conformational change similar to human A2M. NMRA2M is detectable by a polyclonal antibody against human A2M. Determination of tryptic and anti-tryptic activity of NMR and human plasma revealed a higher anti-tryptic activity of the NMR plasma. On the other hand, less proteolytic activity was found in NMR plasma compared to human plasma.

The fundamental subject of this thesis is the development of tools for the analysis of DNA methylation data as well as their application on bisulfite sequencing data comprising a large number of samples. DNA methylation is one of the major epigenetic modifications. It affects the cytosines of the DNA and is essential for the normal development of cells and tissues. Unusual alterations are associated with a variety of diseases and, specially, in cancergeneous tissues global changes in the DNA methylation level have been detected. To sequence DNA methylation on single nucleotide resolution, the sequences are treated with sodium bisulfite before sequencing, whereby unmethylated cytosines are represented as thymines. Thus, specialized techniques are required to process and analyze these kind of data. Here, the bisulfite analysis toolkit BAT is introduced, that is designed to facilitate an quick analysis of bisulfite treated DNA methylation sequencing data. It covers all steps of processing raw sequencing data up to calling of differential DNA methylation. At the begin of analysis, sodium bisulfite treated sequence data are aligned and DNA methylation rates for each covered cytosine in the reference genome are called. Subsequently, BAT integrates annotation data and performs basic analysis, i. e., methylation rate distribution plots and hierarchical clustering of the samples. In addition, calling of differentially methylated regions is performed and statistics of called regions are automatically created. Finally, DNA methylation and gene expression data integration is covered by the calculation of correlating regions. Secondly, a novel algorithm, metilene, for the calculation of differentially methylated regions (DMRs) between two groups of samples is introduced. Existing methods are limited in terms of detection sensitivity as well as time and memory consumption. Our approach is based on a circular binary segmentation, using a scoring function to detect sub-regions that show a stronger difference between the mean methylation levels of two groups than the surrounding background. These sub-regions are tested using a two-dimensional Kolmogorov Smirnov test (2D-KS test) [Fasano 1987] for significant differences taking all samples of each group into account. The use of the non-parametric 2D-KS test allows to avoid assumptions about a background distribution. Furthermore, the two dimensions of the problem, i. e., (i) the detection of a region, such that (ii) the methylation rates of the samples in the groups are significantly different, are taken into account in a single test. The algorithm calls DMRs in sufficiently short time on single sample comparisons as well as on about 50 samples per group. Furthermore, it works on whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data and is able so estimate missing data points from the methylation rates of other samples in the group. Benchmarks on simulated and real data sets show that metilene outperforms other existing methods and is especially suitable for noisy datasets often found for example in cancer analysis. In the framework of this thesis, the previously introduced methods and algorithms are used to analyze a WGBS dataset of two different subtypes of germinal-center derived B-cell lymphomas and healthy controls. In both lymphoma subgroups genome-wide hypomethylation was found, with an exception for a specific type of promoter regions, i. e., poised promoters, that were frequently found to be hypermethylated. Using the previously presented algorithm, DMRs were called between the three entities. A strong enrichment of DMRs immediately downstream of the transcription start site was observed, indicating the regulatory relevance of this regions. The integration of gene expression data of the same samples, revealed that a considerable amount of the DMRs showed significant correlation between gene expression and DNA methylation. Finally, transcription factor binding sites and mutation data were combined with the methylation and expression data analysis. This identified strongly altered signaling pathways and cancer subtype specific genes. Furthermore, the data integration indicates that mutations and DNA methylation changes may act complementary to another. Finally, findings from the lymphoma study regarding the hypermethylation of poised promoters in cancer were extended to a huge data set comprising a variety of cancers. We could show that the relation of DNA methylation at a small set of frequently poised regions with respect to the background methylation level is sufficient to classify almost all samples based on DNA methylation data from 450k BeadChips into cancer or non-cancer probes. In addition, we found that the increase in methylation co-occurs with upregulated gene expression of several poised promoter regulated genes in almost all fresh cancer samples, implying a de-poising of poised regions. This upregulated gene expression is in contrast to the silencing of those genes in cancer cell lines, indicating that the upregulated gene expression might be a temporary status and possibly contributes to cancerogenesis.

Background: The Patient Health Questionnaire PHQ-9 is a widely used instrument to screen for depression in clinical research. The first aim of this study was to psychometrically test the PHQ-9 in a large sample of cancer patients. The second aim was to calculate unbiased estimates of the depression burden for several cancer groups taking into account age and gender distributions. Methods: A sample of 2,059 cancer patients with varying diagnoses were examined in this study six months after discharge from a rehabilitation clinic. A representative sample of 2,693 people from the general population served as controls. Expected PHQ-9 mean scores of the general population sample, regressed on age and gender, were calculated to enable a fair comparison of different groups of cancer patients. Results: While the reliability (Cronbach’s alpha) for the PHQ-9 scale was good (alpha ≥ 0.84), the CFA fit indices of the one-dimensional solution were unsatisfactory in the patients’ sample. The factorial analysis confirmed two factors. PHQ-9 mean scores for 15 types of cancer are given, ranging from 4.0 (prostate) to 8.2 (thyroid gland). Differences between expected mean scores (derived from the general population) and raw mean scores of the cancer subsamples are reported that provide a better estimate of the depression burden. Conclusions: The results confirmed that the PHQ-9 performs well in testing depression in cancer patients. Regression coefficients can be used for performing unbiased comparisons among cancer groups, not only for this study. The burden of patients with testis cancer and Hodgkin lymphoma is underestimated when age and gender are not taken into account.

Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest.

Single cell migration in artificial collagen gels as an in vitro model system in the context of cancer are studied. Cell and matrix mechanical properties are determined using atomic force microscopy and an advanced analysis method. Matrix pore-size is studied using a novel approach and analysis method. A novel, minimally invasive approach to determine the amount of displacement of the cell microenvironment due to force generation of single cells during migration in artificial 3D collagen gels is introduced. An automated analysis and user friendly software to analyze high-throughput cell invasion is introduced. These methods are used to study cell migration and mechanical properties of the breast cancer cell lines MDA-MB-231 and MCF-7 and the influence of cell nuclear elasticity is investigated. Using mouse embryonic fibroblasts, the role of focal adhesion kinase (FAK) during cell migration is studied using FAK deficient knock-out cell lines FAK-/- and control FAK+/+ as well as kinase-dead mutants FAKR454/R454 and control FAKWT/WT.:Abstract i Acknowledgements iii 1 Introduction 1 2 Background 5 2.1 Cancer — An ever-changing Disease 5 2.1.1 Carcinogenesis and Neoplasm 6 2.1.2 Hallmarks of Cancer 7 2.1.3 Metastasis— The malignant Progression of Cancer 7 2.1.4 Metastatic Cascade 9 2.2 The Cell— Where it begins 10 2.2.1 Actomyosin Complex 12 2.2.1.1 Actin Monomer 12 2.2.1.2 Polymerization 12 2.2.1.3 Structures 14 2.2.1.4 Actin Cortex 15 2.2.1.5 Filopodia 16 2.2.1.6 Lamellipodium 16 2.2.1.7 Invadopodium 17 2.2.1.8 Stress Fibers 17 2.2.1.9 Actin in Cancer and Metastasis 17 2.2.1.10 Myosin and Actin 18 2.2.2 Focal Adhesions 19 2.2.3 Microtubules 20 2.2.4 Intermediate Filaments 21 2.2.5 Cellular Stiffness 22 2.2.6 Nuclear Deformability 23 2.3 The Extracellular Matrix— Where it happens 24 2.3.1 Components and Structure 25 2.3.2 Collagen as a Model System 26 2.3.2.1 Collagen I Fibril Formation 27 2.3.2.2 The Rat/Bovine-Collagen-Mix Model System 28 2.4 Single Cell Migration— Why it spreads 29 3 Materials and Methods 31 3.1 Cell Culture 31 3.1.1 Cancer Cells 31 3.1.2 Mouse fibroblasts 32 3.1.3 Pharmacological treatment 34 3.2 Collagen matrices 34 3.3 Cell Elasticity 36 3.3.1 Atomic Force Microscopy 36 3.3.2 Preparation 37 3.3.3 Data Aquisition 38 3.3.4 Data Analysis 38 3.4 Matrix Stiffness 40 3.4.1 Preparation 40 3.4.2 Data Aquisition 41 3.4.3 Data Analysis 41 3.5 Invasion Assay 42 3.5.1 Preparation 42 3.5.2 Data aquisition 44 3.5.3 Data Analysis 44 3.6 Matrix Topology 48 3.6.1 Preparation 49 3.6.2 Data Acquisition 50 3.6.3 Data Analysis 51 3.6.3.1 Binarization 51 3.6.3.2 Pore-Size 53 3.6.3.3 Fiber Thickness 54 3.7 Fiber Displacement 55 3.7.1 Preparation 56 3.7.2 Data Aquisition 56 3.7.3 Data analysis 57 3.7.3.1 Fiber Displacement 59 3.7.3.2 Cell Segmentation 60 3.7.3.3 Shell Analysis 61 3.8 A toolset to understand Single Cell Migration and what influences it 62 4 Results 65 4.1 Cell Elasticity 65 4.1.1 Example Force-Distance Curves 66 4.1.2 Single Cell Elasticity 67 4.2 Matrix Stiffness 69 4.3 Invasion 71 4.4 Matrix Topology 75 4.5 Influence of Cell Nucleus on Cell Migration 79 4.5.1 Cellular Elasticity 79 4.5.2 Invasion 81 4.6 Fiber Displacement 89 4.7 Effect of FAK on Cell Invasion and Fiber Displacement 93 4.7.1 FAK Knock-Out 93 4.7.2 Kinase-dead FAK Mutant 96 5 Discussion 103 References 107 / Die Einzelzellmigration in künstlichen Kollagennetzwerken als ein in vitro Modellsystem im Kontext von Krebs wurde studiert. Mechanische Eigenschaften von Zellen und der verwendeten Kollagennetzwerke wurden mithilfe der Atomic Force Microscopy (AFM) und weiterentwickelten Analysemethoden bestimmt. Die Porengröße der verwendeten Kollagennetzwerke wurde mit einer neuentwickelten Auswertemethode analysiert. Eine neuartige, minimal-invasive Methode zur Bestimmung der Verformung der Mikroumgebung von Zellen während der Migration verursacht durch Kräftegenerierung der Zelle wird beschrieben. Die Analyse des Invasions-Assays wurde automatisiert und eine nutzerfreundliche Software entwickelt, mit der große Datenmengen ausgewertet werden können. Diese Methoden wurden verwendet, um mechanische Eigenschaften und Migration der humanen Brustkrebszellinien MDA-MB-231 und MCF-7 zu studieren. Die Rolle der focal adhesion kinase (FAK) wurde mithilfe von embryonalen Maus-Fibroblasten studiert. Sowohl eine FAK knock-out Zellinie FAK-/- und Kontrolle FAK+/+, als auch eine kinase-dead Mutante FAKR454/R454 und Kontrolle FAKWT/WT wurden hinsichtlich ihrer Invasion und Verformung der Mikroumgebung analysiert.:Abstract i Acknowledgements iii 1 Introduction 1 2 Background 5 2.1 Cancer — An ever-changing Disease 5 2.1.1 Carcinogenesis and Neoplasm 6 2.1.2 Hallmarks of Cancer 7 2.1.3 Metastasis— The malignant Progression of Cancer 7 2.1.4 Metastatic Cascade 9 2.2 The Cell— Where it begins 10 2.2.1 Actomyosin Complex 12 2.2.1.1 Actin Monomer 12 2.2.1.2 Polymerization 12 2.2.1.3 Structures 14 2.2.1.4 Actin Cortex 15 2.2.1.5 Filopodia 16 2.2.1.6 Lamellipodium 16 2.2.1.7 Invadopodium 17 2.2.1.8 Stress Fibers 17 2.2.1.9 Actin in Cancer and Metastasis 17 2.2.1.10 Myosin and Actin 18 2.2.2 Focal Adhesions 19 2.2.3 Microtubules 20 2.2.4 Intermediate Filaments 21 2.2.5 Cellular Stiffness 22 2.2.6 Nuclear Deformability 23 2.3 The Extracellular Matrix— Where it happens 24 2.3.1 Components and Structure 25 2.3.2 Collagen as a Model System 26 2.3.2.1 Collagen I Fibril Formation 27 2.3.2.2 The Rat/Bovine-Collagen-Mix Model System 28 2.4 Single Cell Migration— Why it spreads 29 3 Materials and Methods 31 3.1 Cell Culture 31 3.1.1 Cancer Cells 31 3.1.2 Mouse fibroblasts 32 3.1.3 Pharmacological treatment 34 3.2 Collagen matrices 34 3.3 Cell Elasticity 36 3.3.1 Atomic Force Microscopy 36 3.3.2 Preparation 37 3.3.3 Data Aquisition 38 3.3.4 Data Analysis 38 3.4 Matrix Stiffness 40 3.4.1 Preparation 40 3.4.2 Data Aquisition 41 3.4.3 Data Analysis 41 3.5 Invasion Assay 42 3.5.1 Preparation 42 3.5.2 Data aquisition 44 3.5.3 Data Analysis 44 3.6 Matrix Topology 48 3.6.1 Preparation 49 3.6.2 Data Acquisition 50 3.6.3 Data Analysis 51 3.6.3.1 Binarization 51 3.6.3.2 Pore-Size 53 3.6.3.3 Fiber Thickness 54 3.7 Fiber Displacement 55 3.7.1 Preparation 56 3.7.2 Data Aquisition 56 3.7.3 Data analysis 57 3.7.3.1 Fiber Displacement 59 3.7.3.2 Cell Segmentation 60 3.7.3.3 Shell Analysis 61 3.8 A toolset to understand Single Cell Migration and what influences it 62 4 Results 65 4.1 Cell Elasticity 65 4.1.1 Example Force-Distance Curves 66 4.1.2 Single Cell Elasticity 67 4.2 Matrix Stiffness 69 4.3 Invasion 71 4.4 Matrix Topology 75 4.5 Influence of Cell Nucleus on Cell Migration 79 4.5.1 Cellular Elasticity 79 4.5.2 Invasion 81 4.6 Fiber Displacement 89 4.7 Effect of FAK on Cell Invasion and Fiber Displacement 93 4.7.1 FAK Knock-Out 93 4.7.2 Kinase-dead FAK Mutant 96 5 Discussion 103 References 107

Conclusion: Surgery should be considered whenever possible. This means that the patient has to be in good clinical condition (Karnofsky performance score > 70), the extracerebral metastases should be stable, the number of cerebral lesions should not exceed more than 3 seedings, and the age of the patient should be below 70 years. Since brain metastases are usually well circumscribed, complete extirpation seems to be possible. Postoperative MRI should be demanded in order to confirm complete extirpation. Additional radiotherapy is indicated in case of subtotal resection of a single lesion and in multiple lesions. In single brain metastasis a prospective randomized trial is necessary to prove whether conventional radiotherapy is essential after surgery in the primary treatment of the tumors or can be delayed until cerebral lesions recur. Radiosurgery is an alternative to surgery in the treatment of metastasis. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

There is growing evidence that patients with type 2 diabetes mellitus have increased cancer risk. We examined the association between diabetes, cancer, and cancer-related mortality and hypothesized that insulin sensitizers lower cancer-related mortality. Participants in the Diabetes Cardiovascular Risk and Evaluation: Targets and Essential Data for Commitment of Treatment study, a nationwide cross-sectional and prospective epidemiological study, were recruited from German primary care practices. In the cross-sectional study, subjects with type 2 diabetes mellitus had a higher prevalence of malignancies (66/1308, 5.1%) compared to nondiabetic subjects (185/6211, 3.0%) (odds ratio, 1.64; 95% confidence interval, 1.12-2.41) before and after adjustment for age, sex, hemoglobin A1c, smoking status, and body mass index. Patients on metformin had a lower prevalence of malignancies, comparable with that among nondiabetic patients, whereas those on any other oral combination treatment had a 2-fold higher risk for malignancies even after adjusting for possible confounders; inclusion of metformin in these regimens decreased the prevalence of malignancies. In the prospective analyses, diabetic patients in general and diabetic patients treated with insulin (either as monotherapy or in combination with other treatments) had a 2- and 4-fold, respectively, higher mortality rate than nondiabetic patients, even after adjustment for potential confounders (incidence of cancer deaths in patients with type 2 diabetes mellitus [2.6%] vs the incidence of cancer deaths in patients without type 2 diabetes mellitus [1.2%]). Our results suggest that diabetes and medications for diabetes, with the exception of the insulin sensitizer metformin, increase cancer risk and mortality.

This study investigated several somatostatin analogues labeled with copper-64 for imaging and targeted therapy of SSTr positive cancer. Among three new cross-bridged bifunctional chelators coupled to Y3-TATE, 64Cu-CB-TE2A-Y3-TATE had the most favorable tumor targeting properties. The introduction of ionizable linker groups could not remedy the slow clearance from the kidney, and other modifications will be necessary to resolve this issue. The emerging idea of using the copper-64-labeled somatostatin antagonist 64Cu-CB-TE2A-sst2-ANT as a tumor targeting agent will require further experimentation. This radiopharmaceutical showed promising initial results in a biodistribution study in male Lewis rats, however, it should be compared to 111In-DOTA-sst2-ANT in the same model. Nuclear localization of copper-64 from two somatostatin analogues differing in their chelate stability strengthened the hypothesis of copper-64 dissociation from the bifunctional chelator prior to trafficking to the nucleus. However, the increased nuclear uptake of copper-64 from the less stable 64Cu-TETA-Y3-TATE did not result in a significant effect on cell killing of A427-7 cells. In experiments with [64Cu]copper acetate and the EGFR-antibody 64Cu-DOTA-cetuximab, the tumor suppressor protein p53 was identified as a mediator of the nuclear transport of copper. 64Cu-DOTA-cetuximab was also utilized in five cervical cancer cell lines with a wide range of EGFR expression. EGFR quantification by saturation receptor binding, and EGFR function as determined via internalization of 64Cu-DOTA-cetuximab closely followed the expression pattern of these cell lines found via EGFR mRNA profiling. This constitutes a first step in the evaluation of cetuximab for the treatment, and of 64Cu-DOTA-cetuximab for the imaging of advanced cervical cancer, as EGFR expression on the tumor cell surface clearly can be quantified and visualized with this experimental system. Copper-64 has been used in this study to probe the basic biochemical process of intracellular copper trafficking, and for the targeting of cell surface receptors via radiolabeled peptides and antibodies, providing an example of the powerful combination of radiopharmaceutical chemistry and cell biology.

Die Abschätzung der Prognose für Patienten, insbesondere Kinder mit onkologischen Erkrankungen stellt eine große Herausforderung an die behandelnden Ärzte dar. Vor Beginn einer Therapie werden daher viele Informationen gesammelt, um einen Patienten möglichst gut in eine vordefinierte Risikogruppe stratifizieren und dementsprechend eine mehr oder weniger intensive Therapie anbieten zu können. Diese Einteilungen sind allerdings für keinen Malignomtyp mit 100%-iger Sicherheit möglich. Das ist die Ursache dafür, dass auch in niedrige Risikogruppen eingeteilte Patienten nicht auf die Therapie ansprechen und einen unvorhergesehen schlechten Verlauf zeigen können. Auf der anderen Seite scheint es Patienten zu geben, die trotz initial schlecht eingeschätzter Prognose einen überaschend guten Verlauf nehmen, auf die Therapie gut ansprechen und letztlich geheilt werden können. Einen Beitrag zu leisten, um die Stratifizierung für Kinder, die an einem Neuroblastom erkrankt sind, zu verbessern und damit zu vermeiden, dass einige Patienten unter- oder andere Patienten übertherapiert werden müssen, ist das Ziel dieser Habilitationsarbeit. Zu diesem Zweck wurden differentielle, molekulare Marker in primären humanen Neuroblastomen identifiziert und deren prognostische Bedeutung dargestellt. Einzelne dieser Marker (differentiell expremierte mRNAs) wurden in Zellkultursystemen funktionell untersucht, um deren zellbiologische Funktion, die der jeweiligen prognostischen Bedeutung zugrunde liegen kann zu erklären. Desweiteren konnten genomische Merkmale des amplifizierten genomischen Abschnittes auf Chromosom 2p25 um MYCN beschrieben werden. Darauf basierend konnte eine patientenindividuelle und tumorzellspezifische PCR entwickelt werden (AFS-PCR), die sich als Marker für den Nachweis einer minimalen Resterkrankung eignet.