Development and investigation of a novel model system representing all three subtypes of pancreatic ductal adenocarcinoma reveals novel biomarkers and distinct drug sensitivities

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with dismal prognosis. Despite the discovery of several promising drug candidates, recent trials with targeted therapies have shown limited or no benefit. For a number of cancers, subclasses have been uncovered that allow the use of therapies that target specific molecular alterations present in only a subset of patients. Recently three distinct subtypes of PDAC have been identified based on gene expression profiles derived from laser-microdissected human tumor tissue. This raised the possibility that differences between such subclasses could be exploited to stratify patients and develop novel targeted therapies. However, a major bottleneck for subtype-specific drug discovery was the lack of pre-clinical models that faithfully recapitulate the full heterogeneity of human pancreatic cancer. The aim of this thesis was the development and verification of such models, analysis of subtype-specific differences and the subsequent discovery of novel treatment options for human PDAC. Our newly developed culture, termed PACO, preserves the molecular features of the corresponding primary tumors, and describes the first models of the exocrine-like subtype. Moreover, orthotopic transplantation of PACO cells re-initiates patient similar tumors that recapitulate these features in vivo, including the characteristic histopathology of the primary tumor specimens. The PACO-cells thus provide a consistent platform for subtype specific in vitro discovery and subsequent in vivo verification. The power of our system is demonstrated by the identification of a novel set of biomarkers that can be easily integrated into routine pathology. Application of this marker set on a tissue microarray representing a cohort of >200 patients revealed that the three subtypes significantly differ in frequency and overall survival. A combined approach of in silico predictions coupled with biochemical and immunohistochemical verification demonstrated that the three subtypes differ in activation of important oncogenic pathways. Moreover we could show that the three PDAC subtypes vastly differ in their response to cytotoxic and targeted therapy. Taken together our data demonstrate the need for stratification of PDAC-patients to individualize and improve treatment. Our study introduces novel patient-specific pre-clinical models for pancreatic cancer. Importantly these models are phenotypically consistent from the in vitro to the in vivo application, providing major improvements in pre-clinical drug studies. The PACO model thus enables stratification of individual patients and concomitant personalized treatment according the specific subtypes of human PDAC

På vej mod 8 timers arbejdsdag 1900-1914

På vej mod 8 timers arbejdsdag 1900-191

Efterskrift

Efterskrif

Beretning for 2009

Beretning for 200

Indledning

Indlednin

Ice core and stratigraphic constraints on modelling dynamic Antarctic outlet systems

Model reconstruction of past ice dynamic changes are essential for our understanding of future ice sheet responses to climate change. However, paleo ice sheet model studies are poorly constrained as spatiotemporal coverage of proxy reconstructions are sparse. Previously, we showed, that it is possible to identify or exclude past ice sheet instabilities by using the isotopic record and age structure of a deep ice core in vicinity to dynamic outlet sectors as a constraint for flow parameterizations in an ice sheet model. Here, we highlight key Antarctic ice sheet domains in which deep ice cores in concert with radar observations of the ice sheet’s stratigraphy hold great potential to provide an even more rigid observational tuning target for ice flow models. In some of these regions dated deep ice cores are already available, often including coverage of internal reflection horizons potentially connecting the ice core age structure with faster flowing outlet sectors. In other regions either an ice core providing age constraints or radar observations are not yet available. We discuss the potential of ice core/stratigraphically calibrated ice flow modelling of dynamic Antarctic drainage systems. Furthermore, we present first model estimates of the age structure in these regions and identify promising sites for future ice coring expeditions or ice penetrating radar missions

Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel–D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections