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Tumorzentrum Freiburg - CCCF

DKTK Program

Molecular Diagnostics, Early Detection, and Biomarker Development (MDEB)


Activities Partner Site Freiburg

The potential of whole exome sequencing for entity-specific and entity-independent stratification of cancer patients  is of increasing interest for cancer diagnosis and treatment as these studies are expected to result in a good chance for the development of a prognostic tumor assessment. Assigning patients to individual treatment options is another strong argument to put effort in such diagnostic and prognostic cancer research. The contributing departments in Freiburg (Dpt. Clinical Pathology, Dpt. Pedatric Hematolgy and Oncology Dpt. Hematology, Oncology and Stem Cell Transplantation and Dpt. Urology) are supported by Dr. Dr. Melanie Börries with regard to bioinformatics and whole genome sequencing.

 

Topic: Molecular Analysis of Pediatric Neoplasms

Department of Pediatric Hematology and Oncology
Prof. Dr. Charlotte Niemeyer
Dr. Marcin Wlodarski

This research topic is worked on by a cooperation of the consortium sites Freiburg, Berlin, Essen/Düsseldorf, Frankfurt/Mainz, Heidelberg, München and Tübingen.  As this topic is planned as a cross-entity comparison in genetically “clean” pediatric tumors each site is examining a selection of entities to identify disease relevant targets.  At the site Freiburg Prof. Dr. Charlotte Niemeyer (leading medical director of the Department of Pediatric Hematology and Oncology) and her group are working on the selected diseases Childhood Myelodysplastic Syndromes (MDS) and Juvenile Myelomonocytic Leukemia (JMML).  The clinic for pediatric hematology and oncology Freiburg aims to recruit a sufficient number of samples for these entities to perform specific analyses. One of the main objective of this analysis is to prove the hypothesis that underlying predisposition to Childhood MDS and JMML, clinically rather sporadic tumors is much higher than expected.

Next-generation sequencing (NGS) technologies have paved the way towards more individualized diagnostic and treatment concepts and whole exome sequencing has become affordable and robust enough to apply it in a regular diagnostic setting. With this project we aim to establish the largest network of pediatric oncology centers that commit to routinely sequence tumor and germline from all patients being treated at the respective sites who give their informed consent. First sequencing studies in childhood cancers have uniformly yielded a fairly low number of (mostly) driver mutations per tumor. We expect to learn a lot from these overall rare cancers that is also centrally important for adult cancers, which often are dominated by the "genetic noise" of hundreds of passenger mutations per tumor, which renders the prioritization of functional testing a lot harder. Furthermore, common themes such as mutations in genes involved in chromatin modifications and embryonic pathways have been identified across pediatric entities making these particularly attractive targets for therapeutic interference. Finally, it becomes evident, that predisposing germline events in childhood cancers are much more frequent than previously anticipated, thus requiring novel concepts for early detection of these syndromes in the first individual of an affected family. Surveillance programs have demonstrated that early detection of cancers in these families dramatically increases the chances of cure with less intense therapies.

In concordance with the overall aims of the program “molecular diagnostics of childhood malignancies” within the DKTK consortium the project network (Fig. 1) pursues the following aims:

  • Cross-entity comparison (common database) in genetically “clean” pediatric tumors (much higher proportion of driver mutations than in adult malignancies) will allow for the identification of druggable hits of broad interest.
  • The consortium approach will allow for the recruitment of a sufficient number of samples per entity to perform entity-specific analyses on these overall rare tumors. This will be conducted by members of the consortium with entity-specific expertise in close cooperation with the central database and analysis pipeline in Heidelberg.
  • Based on early results from NGS studies in childhood malignancies, assessing the true frequency of hereditary cancer predisposition in childhood malignancies in an unbiased approach will be an important goal following the hypothesis that the existence of underlying predisposition in clinically sporadic tumors is much higher than expected.


Topic: Development and Validation of Biomarkers

Development and validation of biomarkers for metastasis (focus on GI-Cancer)

Institute for Surgical Pathology
Prof. Martin Werner
Prof. Silke Laßmann (Bsc., PhD)
Contributing:
Prof. Dr. Dr. Melanie Börries

Targeted therapies are integrated into clinical care for gastrointestinal tract cancers in the metastasized setting (e.g. EGFR-targted therapy in colorectal cancers since 2004/2006, or Her2-targeted therapy for gastric and gastric-esophageal junction carcinomas since 2010). Associated predictive marker analyses are however still limited to RAS and HER2-status evaluation and do not fully foresee potential resistance arising during treatment. Thus, there is still a need for better understanding development of resistance during targeted treatment/in the disease course and to define spatio-temporal biomarkers for the metastatic processes and the specific metastatic sites. Therefore, this project shall define a comprehensive spatio-temporal map of biomarkers associated with the disease courses of colorectal cancer (CRC) and in part esophageal cancer patients in distinct settings: a) neoadjuvant radio-/chemotherapy, b) adjuvant chemotherapy and c) adjuvant targeted therapy. A specific focus will be on analyses of case-matched synchronous and metachronous metastatic sites (liver, lung) of CRC patients. Moreover, since there is increasing evidence of specific molecular CRC subclasses, including those regulated by epigenetic alterations, this project shall further define the effect and mechanisms of CIN, MSI and CIMP-type CRCs on treatment responses and metastasis formation. Whether or not these epigenetic alterations are based on mutations in epigenetic modifiers (e.g. HDACs) and whether or not they may represent synergistic targets to current chemo- and or targeted therapies will be studied in vitro and in situ. Finally, established and novel biomarkers as well as the advanced and innovative tools for their detection will be brought forward to the clinico-pathological routine setting and will be integrated into analyses of other gastrointestinal cancers.

miRNA and proteomic profiling as prognosticators and predictors of treatment response in breast and ovarian cancer

Institute for Surgical Pathology
Prof. Martin Werner

Preventative screening diagnostics, especially in breast cancer, are playing an integral role in cancer early detection and prevention. This development leads to two challenges in cancer diagnostics and research. Firstly, the actual cancer specimens are becoming smaller. Secondly, minimal invasive biopsies (e.g. liquid biopsy) are increasingly used. Therefore, sensitive and material sparing isolation and amplification techniques are needed. Based on innovative techniques (Ahmad-Nejad et al., 2015; Bronsert et al., 2014; Erbes et al., 2015, Sigloch et al., 2015,  Jaeger et al. in prep (Appendix)) that were developed and established in the years 2010 – 2015, this project focuses on the synchronous analysis of formalin fixed-paraffin-embedded (FFPE) specimens for combined miRNA and proteomic analysis and on liquid biopsies (blood and urine) for further miRNA profiling. Considering the high diversity of breast cancer, this project aims at the deep molecular (microRNA, proteomics) and clinico-pathological profiling of triple-negative breast cancers (TNBCs), which often represent particularly poor prognosis. We will investigate independent, well characterized patient cohorts of the Comprehensive Cancer Center Freiburg (CCCF), the collaborating DKTK partner site Heidelberg and the AGO/GBG Intergroup GAIN trail. In cooperation with the German Breast Group (GBG) and the DKTK partner site Charité as well as the CCP-Biobank the clinico-pathological data of GAIN trail cohort will be fully evaluated in a fully integrated manner. The outcome of the “multi-omics” approach should enable a fine-tuned TNBC classification as well as yielding prognostic markers and actionable (e.g. drugable) targets for therapeutic intervention. Furthermore, the application of the microRNA detection method aims to detect circulating microRNAs in liquid biopsies (blood and urine) in prospective studies to monitor treatment response to neoadjuvant therapy as well as to detect early recurrence. The proposed project applies innovations of the first DKTK funding period and addresses unmet clinical and pathological needs for breast and ovarian cancer in a collaborative manner involving multiple DKTK sites.

Dpt. of Hematology, Oncology and Stem Cell Transplantation

Prof. Michael Lübbert
Collaboration with:
Prof. Justus Duyster
Prof. Roland Schüle
Dr. Cornelius Miething

DKTK Investigator Prof. Lübbert is coordinating a clinical phase II trial using the HMA Decitabine for firstline treatment of older, non-fit AML patients (DECIDER). Within the framework of this trial,  It is of great interest to better define the epigenetic mechanisms of resistance development since it occurs invariably with continued HMA treatment, and represents a highly unmet clinical need. Therefore methylome comparisons  between the pre-therapeutic and resistance timepoints will be conducted, in order to define signatures of HMA resistance. In addition, acquired genetic alterations associated with HMA resistance will be determined by use of SNP arrays and whole-exome sequencing (to be extended to whole-genome sequencing for selected patients). For these studies primary AML blasts, isolated and purified both at diagnosis and at time of resistance to  Decitabine patients with available matched blast samples from both timepoints will be used. The infrastructure including bioinformatic analysis of the data is fully established, within the  ongoing collaboration between the Freiburg center and DKFZ. It is planned to build on the results  by treatment with different HMAs and other drugs, in order to define second-line treatments which may be active in patients resistant treatment with decitabine.


Topic: New Techniques for Molecular Diagnostics

Prof. Nikolas von Bubnoff
Prof. Silke Laßmann
in collaboration with:
Prof. Dr. Dr. Melanie Börries

The main goal of this topic is to advance molecular and molecular pathology-based approaches in cancer care beyond current standardized therapy to complement patient care by precision medicine to novel predictive biomarkers and treatment strategies. The CCC Freiburg Molecular Tumorboard integrates key competences of clinicians, routine and advanced diagnostic facilities as well as clinical and translational scientists to guide individualized treatment of cancer patients. As an interdisciplinary platform it translates molecular findings in specific cancer types to research projects and recommends treatment options beyond standard guidelines for the rare tumors discussed, including clinical trials. This concept allows both individualized patient care and translational as well as clinical research with a focus on therapy-refractory tumors and/or rare types of tumors.  Within the setting of the DKTK this provides a unique opportunity for sharing knowledge of special tumor cases within a molecular tumor board and to develop new biomarkers and treatment strategies, which may lead to novel investigator initiated trials within the DKTK.

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Prof. Dr. Christoph Peters
Tumorzentrum Freiburg CCCF
Phone: +49-761-270-71500
Hugstetter Str. 49
79106 Freiburg

and

Institute of Molecular Medicine and Cell Research
University of Freiburg
Stefan-Meier-Str. 17
79104 Freiburg
Phone: +49-761-203-9600/9601
christoph.peters@mol-med.uni-freiburg.de​​

Dr. Anja Hernández
Deutsches Krebsforschungszentrum (DKFZ)
Im Neuheimer Feld 280
69120 Heidelberg
++49 (0)761 270 22810
anja.hernandez@dkfz-heidelberg.de

Dr. Anna Dost
Deutsches Krebsforschungszentrum (DKFZ)
Im Neuheimer Feld 280
69120 Heidelberg
+49 (0)761 270 77121
a.dost@dkfz-heidelberg.de