Molecular Characterization of the Mitochondrial Presequence Translocase

In this thesis, multiple pore-lining amino acid residues of the mitochondrial presequence translocation channel Tim23 were identified as constituents of the channel’s cation filter by combining single channel electrophysiology and site-directed mutagenesis. Unlike proposed before, the ion filter cannot be constituted by a localized constriction zone within the channel, but possibly by providing an energetically favorable or unfavorable surface pathway for ions, spanning the whole channel lumen. Using electrophysiology and yeast biochemistry, we showed that the cation preference is a key property in recognizing and especially translocating positively charged presequences in vitro and preproteins in organello. High-resolution analysis of electrophysiology data further indicates that the presequence-induced fast-gating state of Tim23 presumably corresponds to a translocating state with peptides in transit. Further, we investigated the domain origin for critical functions of the main receptor Tim50. We could show that both voltage regulation of, and presequence handover to Tim23 is independent of the essential presequence binding domain PBD but is localized in the soluble core domain of Tim50

Immune cell gene signatures for profiling the microenvironment of solid tumours

The immune composition of the tumor microenvironment regulates processes including angiogenesis, metastasis, and the response to drugs or immunotherapy. To facilitate the characterization of the immune component of tumors from transcriptomics data, a number of immune cell transcriptome signatures have been reported that are made up of lists of marker genes indicative of the presence a given immune cell population. The majority of these gene signatures have been defined through analysis of isolated blood cells. However, blood cells do not reflect the differentiation or activation state of similar cells within tissues, including tumors, and consequently markers derived from blood cells do not necessarily transfer well to tissues. To address this issue, we generated a set of immune gene signatures derived directly from tissue transcriptomics data using a network- based deconvolution approach. We define markers for seven immune cell types, collectively named ImSig, and demonstrate how these markers can be used for the quantitative estimation of the immune cell content of tumor and nontumor tissue samples. The utility of ImSig is demonstrated through the stratification of melanoma patients into subgroups of prognostic significance and the identification of immune cells with the use of single-cell RNA-sequencing data derived from tumors. Use of ImSig is facilitated by an R package (imsig)

Prognosefaktoren im Mammakarzinom und im Ovarialkarzinom unter besonderer Berücksichtigung der Cyclooxygenase-2

Zur Abschätzung der Prognose von Tumorerkrankungen und zur Therapieplanung können neben konventionellen klinischen Parametern auch molekulare Prognosemarker im Tumorgewebe bestimmt werden. In der vorliegenden Studie haben wir vier verschiedene potentielle molekulare Prognosefaktoren im Ovarialkarzinom und teilweise auch im Mammakarzinom untersucht: die Cyclooxygenase-2 (COX-2), das humane ELAV-ähnliche Protein HuR, das Oberflächenantigen CD24 und die Mitogen-aktivierte Protein Kinase Phosphatase-1 (MKP-1). Dabei lag der Schwerpunkt auf der Untersuchung der Cyclooxygenase-2 (COX-2), die sowohl in der Entzündungsreaktion als auch bei der Entstehung und Progression maligner Tumoren eine wichtige Rolle spielt. Wir konnten zeigen, dass eine erhöhte Expression der COX-2 beim Ovarialkarzinom und beim Mammakarzinom signifikant mit einer schlechteren Prognose assoziiert ist. In Zellkulturmodellen haben wir verschiedene Strategien zur Inhibition der COX-2 angewendet, nämlich die pharmakologische Inhibition durch NS-398 sowie die spezifische Inhibition durch RNA Interferenz. Dabei ergab sich, dass COX-2 Inhibitoren neben der Wirkung auf die COX-2 auch über anderen Zielproteine die Proliferation von Ovarialkarzinomzellen hemmen und zu einem Zellzyklusarrest führen. Bei weiteren Untersuchungen zur Regulation der COX-2 konnten wir zeigen, dass das RNA-stabilisierende Protein HuR mit der COX-2 Expression korreliert und ebenfalls ein Prognosefaktor für das Ovarialkarziom ist. Unsere Ergebnisse bilden eine Grundlage für klinische Studien zur Untersuchung des möglichen Effektes von COX-Inhibitoren in der Therapie maligner Tumoren.Molecular prognostic markers can be determined in tumor tissue and can be used - in addition to conventional clinicopathological parameters - to estimate patient prognosis and to plan the therapy of malignant tumors. In this study we have investigated the expression of four different molecular prognostic factors in ovarian carcinoma and partially in breast carcinoma: cyclooxygenase-2 (COX-2), the human ELAV-like protein HuR, the surface antigen CD24, as well as the mitogen-activated protein kinase phosphatase-1 (MKP-1). For further evaluation, we have focused on COX-2, which plays an important role in tumor biology and inflammation. Increased expression of COX-2 in tumor tissue was associated with poor prognosis in ovarian carcinoma and breast carcinoma. In cell culture models, we have used two different strategies for inhibition of COX-2: pharmacological inhibition and RNA interference. We found that COX-2 inhibitors act on other cellular targets in addition to COX-2 and inhibit proliferation of ovarian carcinoma cells by induction of cell cycle arrest. In further studies we could show that the RNA-stabilizing protein HuR is associated with increased COX-2 expression and is an prognostic factor in ovarian carcinoma, as well. These results provide a basis for further evaluation of COX-inhibitors in tumor therapy

Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data

Background: Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. Results: Ioncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR. Conclusions: Ioncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls

Cation selectivity of the presequence translocase channel Tim23 is crucial for efficient protein import.

Virtually all mitochondrial matrix proteins and a considerable number of inner membrane proteins carry a positively charged, N-terminal presequence and are imported by the TIM23 complex (presequence translocase) located in the inner mitochondrial membrane. The voltage-regulated Tim23 channel constitutes the actual protein-import pore wide enough to allow the passage of polypeptides with a secondary structure. In this study, we identify amino acids important for the cation selectivity of Tim23. Structure based mutants show that selectivity is provided by highly conserved, pore-lining amino acids. Mutations of these amino acid residues lead to reduced selectivity properties, reduced protein import capacity and they render the Tim23 channel insensitive to substrates. We thus show that the cation selectivity of the Tim23 channel is a key feature for substrate recognition and efficient protein import

Dynamics of the intratumoral immune response during progression of high-grade serous ovarian cancer

PURPOSE: Tumor-infiltrating lymphocytes (TILs) have an established impact on the prognosis of high-grade serous ovarian carcinoma (HGSOC), however, their role in recurrent ovarian cancer is largely unknown. We therefore systematically investigated TIL densities and MHC class I and II (MHC1, 2) expression in the progression of HGSOC. EXPERIMENTAL DESIGN: CD3+, CD4+, CD8+ TILs and MHC1, 2 expression were evaluated by immunohistochemistry on tissue microarrays in 113 paired primary and recurrent HGSOC. TILs were quantified by image analysis. All patients had been included to the EU-funded OCTIPS FP7 project. RESULTS: CD3+, CD4+, CD8+ TILs and MHC1 and MHC2 expression showed significant correlations between primary and recurrent tumor levels (Spearman rho 0.427, 0.533, 0.361, 0.456, 0.526 respectively; P<.0001 each). Paired testing revealed higher CD4+ densities and MHC1 expression in recurrent tumors (Wilcoxon P=.034 and P=.018). There was also a shift towards higher CD3+ TILs levels in recurrent carcinomas when analyzing platinum-sensitive tumors only (Wilcoxon P=.026) and in pairs with recurrent tumor tissue from first relapse only (Wilcoxon P=.031). High MHC2 expression was the only parameter to be significantly linked to prolonged progression-free survival after first relapse (PFS2, log-rank P=.012). CONCLUSIONS: This is the first study that analyzed the development of TILs density and MHC expression in paired primary and recurrent HGSOC. The level of the antitumoral immune response in recurrent tumors was clearly dependent on the one in the primary tumor. Our data contribute to the understanding of temporal heterogeneity of HGSOC immune microenvironment and have implications for selection of samples for biomarker testing in the setting of immune-targeting therapeutics

Neutrophil gelatinase-associated lipocalin (NGAL) predicts response to neoadjuvant chemotherapy and clinical outcome in primary human breast cancer

In our previous work we showed that NGAL, a protein involved in the regulation of proliferation and differentiation, is overexpressed in human breast cancer (BC) and predicts poor prognosis. In neoadjuvant chemotherapy (NACT) pathological complete response (pCR) is a predictor for outcome. The aim of this study was to evaluate NGAL as a predictor of response to NACT and to validate NGAL as a prognostic factor for clinical outcome in patients with primary BC. Immunohistochemistry was performed on tissue microarrays from 652 core biopsies from BC patients, who underwent NACT in the GeparTrio trial. NGAL expression and intensity was evaluated separately. NGAL was detected in 42.2% of the breast carcinomas in the cytoplasm. NGAL expression correlated with negative hormone receptor (HR) status, but not with other baseline parameters. NGAL expression did not correlate with pCR in the full population, however, NGAL expression and staining intensity were significantly associated with higher pCR rates in patients with positive HR status. In addition, strong NGAL expression correlated with higher pCR rates in node negative patients, patients with histological grade 1 or 2 tumors and a tumor size <40 mm. In univariate survival analysis, positive NGAL expression and strong staining intensity correlated with decreased disease-free survival (DFS) in the entire cohort and different subgroups, including HR positive patients. Similar correlations were found for intense staining and decreased overall survival (OS). In multivariate analysis, NGAL expression remained an independent prognostic factor for DFS. The results show that in low-risk subgroups, NGAL was found to be a predictive marker for pCR after NACT. Furthermore, NGAL could be validated as an independent prognostic factor for decreased DFS in primary human BC