Pancreatic adenocarcinoma is the deadliest solid cancer and currently the fourth most frequent cause for cancer related deaths. Over the past decades, there has hardly been any substantial therapeutic progress regarding clinical endpoints. New hope has now been generated by the re-emerging cancer stem cell (CSC) concept. We have identified and characterized pancreatic CSC in the context of tumour growth, metastasis, and resistance to chemotherapy. To eventually be able to develop a targeted therapy for eliminating CSCs as the root of the tumour, we will perform comparative functional and genomic analyses of the identified, highly purified human CSC populations, their more differentiated progenies, normal tissue resident stem cells, and hematopoietic stem cells. For these analyses, we are also focusing on their demonstrated resistance of CSC to chemotherapy as well as their invasive properties and tumour-initiating capacity as demonstrated in our orthotopic mouse models. Subsequent functional characterization of newly identified genes regarding their biological function for tumour angiogenesis, invasiveness, and metastasis will be carried out. Moreover, it is similarly important to investigate in parallel the origin of CSCs, which may aid us to develop new therapeutic strategies to prevent transformation of tissue-resident stem cells. The role of risk factors that have been associated with the development of pancreatic cancer, namely smoking and chronic pancreatitis will be investigated in this context. Together, the above experiments will generate important clues how CSCs circumvent the physiological regulatory elements of stem cell functionality and, even more importantly, how these cells escape the response to standard cancer therapy. Eventually, these new insights may allow us to develop novel targeted and multimodal treatment modalities for the successful elimination of these cells as the previously unrecognized root of the tumour.