Systems biology has emerged over the last decade. Driven by the advances in sophisticated measurement technology the research community generated huge molecular biology data sets. These comprise rather static data on the interplay of biological entities, for instance protein-protein interaction network data, as well as quite dynamic data collected for studying the behavior of individual cells or tissues in accordance with changing environmental conditions, such as DNA microarrays or RNA sequencing. Here we bring the two different data types together in order to gain higher level knowledge. We introduce a significantly improved version of the KeyPathwayMiner software framework. Given a biological network modelled as a graph and a set of expression studies, KeyPathwayMiner efficiently finds and visualizes connected sub-networks where most components are expressed in most cases. It finds all maximal connected sub-networks where all nodes but k exceptions are expressed in all experimental studies but at most l exceptions. We demonstrate the power of the new approach by comparing it to similar approaches with gene expression data previously used to study Huntington's disease. In addition, we demonstrate KeyPathwayMiner's flexibility and applicability to non-array data by analyzing genome-scale DNA methylation profiles from colorectal tumor cancer patients. KeyPathwayMiner release 2 is available as a Cytoscape plugin and online at http://keypathwayminer.mpi-inf.mpg.de.
VEGFR-2 is expressed on tumor vasculature and a target for anti-angiogenic intervention. VXM01 is a first in kind orally applied tumor vaccine based on live, attenuated Salmonella bacteria carrying an expression plasmid, encoding VEGFR-2. We here studied the safety, tolerability, T effector (Teff), T regulatory (Treg) and humoral responses to VEGFR2 and anti-angiogenic effects in advanced pancreatic cancer patients in a randomized, dose escalation phase I clinical trial. Results of the first 3 mo observation period are reported. Locally advanced or metastatic, pancreatic cancer patients were enrolled. In five escalating dose groups, 30 patients received VXM01 and 15 placebo on days 1, 3, 5, and 7. Treatment was well tolerated at all dose levels. No dose-limiting toxicities were observed. Salmonella excretion and salmonella-specific humoral immune responses occurred in the two highest dose groups. VEGFR2 specific Teff, but not Treg responses were overall increased in vaccinated patients. We furthermore observed a significant reduction of tumor perfusion after 38 d in vaccinated patients together with increased levels of serum biomarkers indicative of anti-angiogenic activity, VEGF-A, and collagen IV. Vaccine specific Teff responses significantly correlated with reductions of tumor perfusion and high levels of preexisting VEGFR2-specific Teff while those showing no antiangiogenic activity had low levels of preexisting VEGFR2 specific Teff, showed a transient early increase of VEGFR2-specific Treg and reduced levels of VEGFR2-specific Teff at later time points - pointing to the possibility that early anti-angiogenic activity might be based at least in part on specific reactivation of preexisting memory T cells.
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