Core Facilities Berlin
Several core facilities centralize expertise and equipment in Berlin to support translational cancer research. Facilities are set up for amplicon panel analysis, metabolomics, mass cytometry (CyTOF2), small animal imaging and biobanking. DKTK researchers also have access to further facilities at the Charité, Max-Delbrück Centrum (MDC) and Berlin Institute of Health (BIH), which include Genomics, Proteomics, Bioinformatics, IT, Chemical Biology, Stem Cells and Transgenics Cores
4C-PMU Unit (Cancer Center Unit for personalized medicine)
The 4C-PMU is a joint cancer sequencing initiative of the Charité Comprehensive Cancer Center (CCCC), DKTK, and the Laboratory of Molecular Tumor Pathology (MTP), and the molecular pathology unit at the Institute of Pathology. The sequencing unit houses two Ion Torrent PGM systems, one Ion Chef and one Illumina MiSeq system (Fig. 1). Sequencing approaches are focused on customized and commercially available gene panels permitting in-depth analysis of heterogeneous cancer samples. Specific gene panels were developed for the following cancer entities: colon cancer, head and neck carcinoma, lymphoma, neuroendocrine carcinomas, breast cancer and leukemia. Panels for ovarian cancer, pediatric tumors, and melanoma and are still under development. Two Droplet Digital PCR systems and two StepOnePlus Real-Time PCR systems were installed for the validation of the sequencing data. The analysis of liquid biopsy samples is currently being developed for head and neck cancer. The 4C-PMU performs on request companion diagnostics based on NGS analysis within clinical trials organized at the CCCC.
Bioinformatics analysis is done as a community effort conducted mainly by local DKTK groups, and supported by the Computational Modeling Group at IRI (Humboldt University) and the informatics unit (CUBI) at the Berlin Institute of Health (BIH).
Dr Ingeborg Tinhofer-Keilholz (MiSeq)
Prof. Dr. Christine Sers (PGM Ion Torrent)
Cancer Metabolomics Platform
The metabolome reflects the current functional status of the cell. Metabolomic changes play a central role in the pathogenesis and therapy of malignant diseases. The at the DKTK partner site Berlin established gas chromatography, coupled with high resolution mass spectrometry (GC-MS), is a sensitive and robust platform for the analysis of metabolites of the primary metabolism (amino acids, sugars, nucleic acids) (Fig. 2). This technique offers a broad applicability in tumor biology and interdisciplinary problems. The MS technology (APCI Q-TOF) allows quantitative statements and is particularly suitable for the elucidation of the structure of unknown analytes and for the analysis of very small samples volumes. Metabolic flux analysis is currently under establishment. As increasingly important extension of other, in Berlin reproached omics platforms, the cancer metabolomics platform enables functional, systems biology insights into the tumor metabolism and contributes to the identification of novel therapeutic principles.
Dr. Jan Lisec
Biobank – ZeBanC
For innovative biomedical research scientists need high-quality biomaterials such as blood, urine and tissue samples and treatment data. The biobank service not only includes all steps of the processing chain from surgery to storage but also includes services covering many aspects of tissues such as histology, immunphenotyping, RNA/DNA extraction and all steps of quality control. A major focus is the handling and storage of fresh tumor tissues. The Charité Biobank ZeBanC provides a total number of 2.5 Mill FFPE samples (10,000 cancer patients/per year = 100,000 FFPE samples per year) and 100,000 fresh frozen samples.
With the joint biobank, in which Charité and BIH invest a total of 3.9 million euros, better conditions for successful, independent and internationally competitive translational research will be provided. The new biobank building will be located at the Charité Campus and completed by April 2016.
Charité is also the host for the BMBF-funded German Biobank Node (GBN) and acts via BBMRI as a hub for the European biobank infrastructure BBMRI-ERIC.
Notably, the Charité also hosts specialized collections of tumor specimens including the Tumor bank Ovarian Carcinoma (TOC), the German Breast Group Biobank and biobanks for pediatric relapsed ALL, central nervous system lymphomas and brain tumors.
Berlin Experimental Radionuclide Imaging Center (BERIC)
The BERIC offers as a core facility of the Charité all modalities of modern hybrid small animal imaging with radiopharmaceuticals.
The multidisciplinary team is using its expertise and the latest state-of-the-art equipment (SPECT / CT, PET / MR; Angiography/PET, Fig. 2) available to users. The service offered includes all steps from consulting to study design, the tracer selection, tracer production, keeping of radioactive animals, conduction of the animal experiments, including image and data analysis and data storage as well as post mortem biodistribution experiments. The BERIC also offers services such as radiolabeling of ligands, in vitro evaluation of tracers and the generation of (genetically modified) cell lines and animal models (orthotopic, subcutaneous and metastatic tumor, stroke and myocarditis models etc.). Own research interests within the BERIC concentrate on the development and characterization of new radiotracers and theranostics for various tumor entities, as well as the development of new quantitative multi-parametric imaging approaches.