Research Group Molecular Tumor Pathology
The Laboratory of Molecular Tumor Pathology is located in the heart of Berlin at the Institute of Pathology of the Charité – Universitätsmedizin Berlin.
On the following pages you can find information on the group, its projects and publications.
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Laboratory of Molecular Tumor Pathology
Following up on early studies on the molecular identification and functional characterization of cellular oncogenes and their antagonists, the tumor suppressor genes, our current research focuses on systems-oriented tumor biology, particularly on signal transduction systems in cancer cells. The objectives of research projects are aiming at a detailed understanding of the organization, regulation and biological features of signalling systems in order to integrate basic cancer research, molecular tumor diagnostics and predictive oncology.
The laboratory of molecular tumor pathology, founded in 1996, was supported by grants from the German Cancer Aid, including a Mildred Scheel Professorship.
Main Research Focus – Prof. Sers
The main focus of the research lab is tumor-specific onogenic signal transduction.
The international team organizes and participates in different research consortia studying mechanisms how to suppress oncogene-induced tumor growth and therapy resistance:
- DKTK - German Cancer Consortium
- BMBF Consortia
- EU Consortia
Team members are recruited from international study courses including Charité Masters’ Molecular Medicine and Graduate Schools like BSIO at Charité.
ColoNET – A systems biology approach for integrating molecular diagnostics and targeted therapy in colorectal cancer
The major objective of the project is to accomplish an in silico network of genetic, epigenetic and signaling processes to tailor diagnostics with predictive information for therapies targeting receptor tyrosine kinases (e.g. EGFR) in colorectal cancer. The network model is expected to provide diagnostic guidance for the improvement of therapy response prediction by achieving an in-depth functional understanding of receptor-mediated signaling and downstream processes. The core model will consist of a “static” colon-specific signaling network model that serves as a framework for integrating detailed kinetic models of MAPK and Wnt pathways, existing genetic/epigenetic information, high-throughput data, knowledge on predictive markers obtained by literature mining, and physiologically relevant data. The dynamics of MAPK and Wnt pathways, which are crucial for targeted therapies, will be subjected to detailed mathematical modeling based on results from focused experimental measurements. Once detailed models of pathways, key signaling nodes, feed-back loops and marker combinations are established, we will turn the static network into a dynamic model in an iterative process. Finally, this approach should generate a tool for the in silico evaluation of novel markers or combinations of them for an improved therapy prediction. We expect that our models will also be useful for other types of cancer and related predictive diagnostics.
Christine Sers, Charité
Hanspeter Herzel, HU/Charité
Nils Blüthgen, Charité
Reinhold Schäfer, Charité
Manfred Dietel, Charité
Peter-Michael Schlag, Charité
Ulf Leser, HU
Edda Klipp, HU
Joachim Selbig, University Potsdam
Christoph Röcken, University Kiel,
Jörn Walter, University Saarland
Barbara Seliger, University Halle
Holger Sültmann, DKFZ
Iduna Fichtner EPO, MDC
05/2009 – 12/2012
OncoPATH – The ColoNET Follow-up: Dissecting and Modelling Vulnerabilities of Oncogenic Pathways and Metabolism in Solid Cancers
The overall aim of the OncoPATH Consortium is to analyze the qualitative and quantitative impact of frequent genetic and epigenetic alterations on the signaling pathways and metabolic networks in colorectal cancer cells. The changes in the metabolic networks and in signal transduction will be integrated into a mathematical model and functionally analyzed. Thereby, the theoretical model will be successively adapted and improved resembling single experimental models (e.g. a cell line) or even individual patients. The model can then be used to simulate therapeutic interference and propose new therapeutic options.
Prof. Nils Blüthgen, Charité–Universitätsmedizin Berlin
Prof. Christine Sers, Charité – Universitätsmedizin
- Reinhold Schäfer, Charité – Universitätsmedizin
- Markus Morkel, Charité – Universitätsmedizin
- Ulf Leser, Humboldt Universität zu Berlin
- Edda Klipp, Humboldt Universität zu Berlin
- Tilmann Brummer, Institute of Molecular Medicine and Cell Research, University of Freiburg
- Stefan Legewie, Institute of Molecular Biology, Mainz
- Stefan Kempa, Max Delbrück Center for Molecular Medicine
- Iduna Fichtner, EPO GmbH, Berlin
SFB618: Modelling of signalling cascades – the impact of RAS signal transduction on transcription
Within the Collaborative Reserch Center for Theoretical Biology: Robustness, Modularity and Evolutionary Design of Living Systems (SFB 618) the mechanisms of gene regulation through activated MEK/ERK signaling cascades were investigated in the reserach area "Molecular Systems" (subproject A1, jointly with Martin Vingron).
The execution of the oncogenic program is significantly influenced by large scale transcriptional alteration downstream of the RAS oncogene. Therefore we assessed some of the most frequently altered/deregulated transcription factors in detail and used a combination of experimental and theoretical approach to gain further insight into the molecular consequences of RAS activation.
Fra1 is the only AP1 member showing significantly increased levels upon comparison of HRASv12-transformed human embryonic kidney cells (HA1ER) to their immortal counterpart, HA1EB cells. From both cells, we generated genome-wide expression profiles after Fra1-siRNA-mediated knock-down by microarray expression analysis and observed large differences in the Fra1-regulated genes between the immortal and RAS-transformed cells. Functional enrichment analysis identified transcriptional regulators as a major group of Fra1-regulated genes only in the RAS-transformed cells. We confirmed Fra1-binding to regulatory regions of several of these genes by ChIP and verified HMGA1, HMGA2, AEBP1, NPAS2 and TCFL5 to be directly regulated by Fra1. Our results suggest novel regulatory feed-back mechanisms stabilizing mitogenic signalling and AP1/Fra1-dependent transcription in transformed cells thus strongly favouring a role for Fra1 as a master transcriptional regulator in tumors.
DFG (SFB 618)
05/2009 – 06/2013
Main Research Focus – Prof. Schäfer
Many external signals for growth, survival and differentiation converge on RAS proteins through membrane-based receptors. RAS proteins act as essential molecular switches that integrate extracellular stimuli with the genetic program via highly complex signal transduction systems. Adapter proteins, small GTP-binding proteins, signalling kinases and transcription factors contribute to signalling output.
Due to the high intrinsic complexity of signal transduction pathways, different biological read-outs can be generated. Ras mutations or receptor amplification result in permanent oncogenic activation of the signalling system, deregulate the genetic program and mediate malignant transformation. Our group has systematically catalogued the effects of activated RAS signalling on the transcriptome and identified numerous deregulated target genes. Ras pathway-responsive genes are either up-regulated, expressed de novo or down-regulated. Often, tumor suppressors or anti-proliferative genes are repressed. Currently, we investigate the transcriptional network responsible for target gene deregulation and try to understand the underlying principles affecting multiple genes.
We employ RNA interference approaches for the functional characterization of regulators and targets, establish genome-wide mRNA and micro-RNA expression response profiles to determine their contribution to the network and quantitate the biological consequences using cell cultures and animal models.
ColoNet – A systems biology approach for integrating molecular diagnostics and targeted therapy in colorectal cancermore information about ColoNet
The major objective of the project is to accomplish an in silico network of genetic, epigenetic and signaling processes to tailor diagnostics with predictive information for therapies targeting receptor tyrosine kinases (e.g. EGFR) in colorectal cancer. The network model is expected to provide diagnostic guidance for the improvement of therapy response prediction by achieving an in-depth functional understanding of receptor-mediated signaling and downstream processes. The core model will consist of a “static” colon-specific signaling network model that serves as a framework for integrating detailed kinetic models of MAPK and Wnt pathways, existing genetic/epigenetic information, high-throughput data, knowledge on predictive markers obtained by literature mining, and physiologically relevant data. The dynamics of MAPK and Wnt pathways, which are crucial for targeted therapies, will be subjected to detailed mathematical modeling based on results from focused experimental measurements. Once detailed models of pathways, key signaling nodes, feed-back loops and marker combinations are established, we will turn the static network into a dynamic model in an iterative process. Finally, this approach should generate a tool for the in silico evaluation of novel markers or combinations of them for an improved therapy prediction. We expect that our model will also be useful for other types of cancer and related predictive diagnostics.
Subproject: Molecular characterization of experimental models
Key features of the project are experimental models extensively characterized for para-meters known or expected to be involved in therapy efficacy. A significant proportion of information is available from the partners’ previous work and through public databases, while the generation of missing information will produce a high experimental standardization and ensure maximal clinical relevance.
Subproject: Assessing the dynamics of key pathways following specific intervention
This project will focus on two paradigmatic oncogenic pathways: the receptor-MAPK and the Wnt signaling systems, directly relevant for prediction and therapy and including the functionally associated receptors and underlying genetic and epigenetic alterations. For dynamic modeling at the systems level, multi-level data harboring functional and quantitative information will be gathered after defined perturbation of potential predictive markers. The focus will be on direct pathways intervention effects, the dynamics of such processes and effects on potentially associated “tumor” markers, e.g. transcriptional and DNA-methylation markers.
Supported by: BMBF, MedSYS
Systems biology of genetic diseases - Mutanom
Subproject: Effects of cancer gene mutations on the intracellular signalling network and transformed phenotype more information about Mutanom
The objective of this subproject is to analyze novel mutated cancer genes a) known to occur in solid human tumors, b) to be involved in cancer-related developmental disorders and c) identified/nominated by the consortium for their contribution to transformed phenotypes and for their impact on the signalling network. The experimental strategy depends on the nature of the mutations (deletion, duplication, insertion, nonsense, splice site alteration) and on the assignment of the affected gene to a functional group based on Gene Ontology (GO)-based molecular function or biochemical process groups. Depending on the previous characterization of the mutations, functional tests are chosen to either interrogate transforming or tumor-suppressing activities. More detailed investigations that exceed the proof of transforming or transformation-suppressing activity are done in collaboration with the partners. In view of already known common mechanisms of cancer initiation and progression, it is desirable to study the impact of mutated cancer genes, regardless of their putative tumor-promoting or -limiting function, on the handful of signalling pathways with oncogenic potential. Understanding how the perturbation of the signalling network ultimately determines the malignant features of cancer cells is a prerequisite for identifying the rate-limiting steps in cancer growth and to design rational therapies.
Supported by BMBF, NGFN Plus
Modelling of signalling cascades – the impact of RAS signal transduction on transcription
Special Collaborative Reserch Center (SFB 618), Theoretical Biology: Robustness, Modularity and Evolutionary Design of Living Systems, subproject A3 (jointly with Nils Blüthgen) more information about SFB618
Recently, the RAS pathway hit the headlines of translational cancer research again due to the finding that KRAS mutations have an impact on the clinical response toward receptor-targeted cancer therapies. Mutational activation of KRAS is primarily associated with therapy resistance, while wild-type KRAS activity is associated with a therapeutic benefit, however, only in a subset of cancer patients. At present, therapy responders and non-responders cannot be distinguished in molecular terms. Treatment allocation based on detailed knowledge of the molecular mechanisms is not possible. Therefore, signalling processes downstream of the RAS molecular switch are among the prime candidate mechanisms to be screened for clinically relevant alterations. Particularly, studying stimulus-response characteristics, dynamics and feedback regulation of the RAS/MAPK pathway and of other RAS-dependent pathways as well as assessing the integration of pathway activation with the transcriptional program are of utmost importance for defining functionally relevant nodes for therapeutic intervention and for identifying prognostic parameters.
During the past funding period, we have addressed several themes related to RAS/MAPK pathway dynamics. Using mathematical models, we investigated ultrasensitivity, bistability and feedback regulation in MAPK signaling. The models were experimentally tested in cell populations and in single cells stimulated by growth factors or by expression of conditional RAS genes. By expression profiling and the development of a new algorithm, which predicts biological functions regulated by a combinatorial interaction of transcription factors, we identified dual specificity phosphatases (DUSPs) as MAPK-dependent target genes involved in negative feedback regulation. Mathematical models were fitted to experimental time-series of MAPK activation and phosphatase expression. By mining microarray data and results from the literature we also confirmed that transcriptional negative feedback is a general design pattern in PI3K, cAMP, SMAD and STAT signalling pathways.
During the current funding period (until 2013), we (1) aim to investigate the noise/reliability in the expression of MAPK targets and downstream transcriptional networks identified before, to refine our predictions and to further underpin them with experimental data. Specific questions are as follows: How homogeneously do direct target genes respond, how does the noise in gene expression transmit into downstream transcriptional networks and does it rise in magnitude? (2) We have identified about 50 differentially regulated transcription factors in RAS-transformed epithelial cells compared to normal precursor cells. Seven factors have been selected for a series of RNAi-based pertubation experiments. Modular response analysis (MRA), a reverse engineering approach, is used to deduce transcription factor interactions. We plan to extend MRA and other computational methods to the entire set of transcription factors. Phenotypic read-outs of pertubation experiments established in the previous period will be used to study the biological consequences of network interference with respect to proliferation and neoplastic transformation. (3) The RAL pathway is gaining increased importance as the third major pathway downstream of RAS, particularly in model systems based on human cells as well as in tumours. Our previous expression profiling studies have identified functionally relevant target genes, grouped in a KRAS-dependent transcriptional module that responds neither to MAPK nor to PI3K pathway signals. We plan to investigate the role of the Ral pathway in the transcriptional and phenotypic response, using approaches developed for the MAPK pathway.
Supported by DFG/SFB 618
Ovarian Carcinoma Project
Ovarian carcinoma – Molecular and functional characterization of a KRAS oncogene-driven tumor model
We have established an ovarian cancer model based on ovarian epithelial cells. To mimick oncogenic pathway activation, which often is mediated by membrane-based receptors in the clinical setting, we introduced and expressed a mutated KRAS gene in those cells. Transfected cells exhibit the typical features of transformation in vitro such as anchorage-independence, epithelial-mesenchymal transition (EMT) and motility. Progressively growing tumors are formed in nude mice following subcutaneous or intraperitoneal injection of cells. The malignant phenotype is associated with numerous alterations of gene expression. To understand the causal role of these alterations and the mechanisms of gene deregulation, we perform functional studies. For example, we investigate the role of the HMGA2 protein, an architectural transcription factor, in KRAS-transformed ovarian epithelial cells. HMGA2 expression is silenced by RNA interference and the effects on proliferation, EMT and anchorage independence are determined. For comparison, an HMAG2 expression vector is introduced into normal ovarian epithelial cells to find out, if HMGA2 may act as a oncogene itself. We measure the transcription of KRAS-responsive target genes by interrogating a customized oligonucleotide microarray (RASTA, RAS target array), which represents approx. 300 validated deregulated genes. Moreover, we search for transcription factor binding sites in the regulatory regions of HMGA2-regulated targets. This will help to elucidate the network of HMGA2, acting a as a potential master regulator, and interacting specific transcription factors driving malignancy in the ovarian epithelium.
Supported by: Berlin Cancer Society
Additional Collaborative Projects
Collaboration with the Hungarian Academy of Science and Semmelweis University Budapest
Meta-analysis of gene signatures relevant for cancer prognosis and functional analysis of therapy resistance in solid tumors
The international collaborative project TREAT 1000 (Tumor Research and Treatment) was launched in 2009. The objective of the project partners at the Charité Comprehensive Cancer Center, the Max-Planck-Institute for Molecular Genetics and the Genome Center, Harvard Medical School, is to fully sequence 1000 tumor genomes and to correlate mutation patterns, expression profiles and other characteristics with clinical parameters. As a result, a comprehensive assessment of all active signalling pathways and regulatory circuits will be generated for each tumor. The integrated information is used to deduce therapy recommendations based on available inhibitors. In this way, TREAT 1000 is the necessary step in pursuing the concept of personalized cancer medicine. more information about TREAT1000
Laboratory of Functional Genomics (LFGC) – a Charité core facility
Profs. R. Schäfer and Christian Hagemeier, Laboratory of Pediatric Molecular Biology, jointly coordinate the Charité Core Facility LFGC. The lab specializes in microarray technologies and offers full service, including bioinformatics, to all Charité groups. Very recently, the technical portfolio has been enlarged substantially. Besides Affymetrix technology, several other microarray platforms are available, e.g. for the detection of miRNA. In collaboration with Prof. Achim Kramer, Laboratory of Chronobiology, LFGC provides access to a lentiviral shRNA library for functional studies. For more information on LFGC organization and services click here.
Studies and Education
- The group's teaching activities comprise education in molecular pathology as part of the regular pathology curriculum and the "International Master's Program Molecular Medicine". The lab provides an on-going platform for experimental thesis work in medicine, cellular and molecular biology as well as in cancer systems biology.
- In Addition the group coordinates the elective module "Clinical and Molecular Tumor Pathology" (M24) within the New Revised Medical Curriculum of the Charité - Universitätsmedizin Berlin. This module is building a bridge between pre-clinical tumor research and clinical application. Contact person: PD Dr. Markus Morkel
- To the Internet Portal for students and teachers in medicine at the Charité "CampusNet".