Identification of biomarkers from circulating tumor cells

Cancer represents a tremendous health and economical problem. Despite overall improvements in many cancer therapies, our understanding of why individual patients respond to therapy and others do not and why some patients relapse, remains poor. Indeed, current prognostication based on clinicopathological staging usually provides little information about response to treatment of individual patients. Therefore, there is a tremendous search for protein and genetic markers, which may refine prognostic information and predict the benefit derived from systemic treatment. Although some important genetic biomarkers with predictive and prognostic information have recently been identified, the question remains how serial monitoring of tumor genotypes, which are prone to changes under selection pressure, can be performed. To this end, non-invasive means by the analysis of circulating tumor cells (CTCs) appear to be especially attractive. Their routine analysis is, however, hampered by substantial questions, such as how to extract a maximum of information from these cells. Here we want to apply our high-resolution single-cell technologies to CTCs. We will employ a spectrum of cutting-edge technologies, including whole- genome amplification, array-technologies, next-generation sequencing and bioinformatics for an in-depth characterization of the CTC-genome. We will test our strategies in samples derived from patients with metastatic prostate and colorectal cancer. As result we expect the establishment of a reliable strategy for CTC analysis, which may pave the way to use CTCs as prognostic and predictive biomarkers.

Cancer represents a tremendous health and economical problem. Despite overall improvements in many cancer therapies our understanding of why individual patients respond to therapy and others do not and why some patients relapse remains poor. Indeed, current prognostication based on clinicopathological staging usually provides little information about response to treatment of individual patients. Therefore there is a tremendous search for protein and genetic markers which may refine prognostic information and predict the benefit derived from systemic treatment. Although some important genetic biomarkers with predictive and prognostic information have recently been identified, the question how serial monitoring of tumor genotypes, which are prone to changes under selection pressure, can be performed remains. To this end, non-invasive means by the analysis of circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA) in the peripheral blood of patients with cancer appear to be especially attractive. Both CTCs and ctDNA represent proxies for the tumor genome and as they can be obtained with a blood collection they are frequently referred to as liquid biopsies. Their routine analysis is, however, hampered by substantial questions such as how to extract a maximum of information from these liquid biopsies. In our project entitled Identification of biomarkers from circulating tumor cells (CTCs) we developed high- resolution methods for the detailed analysis of single CTCs. Isolated CTCs were subjected to a spectrum of cutting-edge technologies, including whole-genome amplification, array- technologies, next-generation sequencing, and bioinformatics for an in-depth characterization of the CTC-genome. In parallel we also applied this spectrum of technologies to the other source of tumor derived material in the peripheral blood, i.e. ctDNA. As a result we have now tools allowing the detailed characterization of CTCs and ctDNA with unprecedented resolution. During the course of the project we used these techniques to confirm that even a malignant disease such as glioblastoma multiforme (GBM), the most frequent and aggressive brain tumor in adults, which was thought to spread only within the brain, can spread hematogenously, which has changed current concepts about the biology of this disease. Furthermore, we demonstrated that CTCs have a significant heterogeneity, but that the majority of CTC-specific changes can be found in the respective primary tumor at subclonal level. Together with our ctDNA efforts we also showed that liquid biopsies are capable of detecting resistance markers against targeted therapies, often even before appropriate clinical signs evolved. In summary, we established reliable strategies for liquid biopsy analyses, which may pave the way to using them as prognostic and predictive biomarkers in individuals with cancer.