Project Consortium Map

 

 

Project Coordinator

STICHTING VUMC, Netherlands

Prof. Dr. Tom Würdinger

 

 

 

 

 

STICHTING VUMC, Netherlands

Dr. Danijela Koppers-Lalic

 

 

Project Participants

 

 

University Medical Center Hamburg-Eppendorf (UKE)

Prof. Dr. Klaus Pantel

Director of the Institute of Tumor Biology

www.uke.de/institutes/tumor-biology

The Institute of Tumor Biology (ITB) headed by Prof. Klaus Pantel is part of the University Cancer Centre Hamburg (UCCH). The ITB was founded in 2002 to bridge between basic research and the clinic. Our research combines state-of-the art liquid biopsy analysis tools with cutting-edge genomics technologies to investigate cancer metastasis. Translational research conducted in our laboratory aims at a better understanding of the molecular mechanisms underlying cancer development and progression, improved cancer diagnostics and also treatment of cancer patients, with a particular emphasis on so called ‘targeted therapies’. The pioneer work of Prof. Pantel in the field of cancer micro-metastasis and circulating tumor cells is reflected by more than 450 publications in excellent high ranking biomedical and scientific journals (incl. NEJM, Lancet, Nature Journals, PNAS, JCO, JNCI, Cancer Research and Cancer Discovery).

 

 

Catalan Institute of Oncology
Germans Trias i Pujol Health Sciences Institute and Hospital, Barcelona, Spain

Dr. Rafael Rosell

 

http://www.germanstrias.org/research/cancer/3/cancer-biology-and-precision-medicine

Dr. Rosell’s group was among the first to perform large scale screening for epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma patients. We currently focus on demonstrating that compensatory signaling pathways are immediately activated once a tumor driver genetic alteration is blocked by a specific targeted therapy, making the tumor independent of the initial driver oncogene, causing resistance to monotherapy.

We execute in vitro assays to determine the efficacy, mechanisms of action and mechanisms of resistance of targeted therapies. We work to elucidate the effectiveness of upfront combinatorial therapies for oncogene driven tumors and investigate quantitative assays and biomarkers to help patient stratification in clinical trials. The aim of our translational research is to integrate advancements in molecular biology with clinical trials, taking research from “bench-to-bedside”.

Since 1998, we’ve worked with circulating-free DNA in non-small cell lung cancer (NSCLC) patients and continue to work on the development of liquid biopsy based tools for cancer screening, diagnosis and prediction of treatment, response and resistance. Our goal is to implement liquid biopsy in the clinical practice, facilitating its access to all our patients.

 

 

Champalimaud Research, Lisbon, Portugal

Dr. Bruno Costa-Silva

Head of Systems Oncology Group

http://neuro.fchampalimaud.org/en/research/investigators/research-groups/group/Costa-Silva/

Our general interest is to understand how non-tumor cells contribute to tumor initiation, growth and metastasis. More than focusing on specific tumor types, we investigate the biological systems that support oncologic disease. For instance, by releasing soluble factors and/or extracellular vesicles, tumor cells can induce phenotypic modifications of stromal cells locally and at future sites of tumor dissemination (also known as pre-metastatic niches), which support tumor growth and metastasis. Extracellular vesicles isolated from liquid biopsies (such as plasma and other body fluids) are emerging as a powerful non-invasive and abundant source of information not only about tumor cells, but also potentially about how non-tumor cells respond/interact with malignant cells. By using animal models of tumor initiation, progression and metastasis, in combination with thorough analysis of extracellular vesicle composition isolated from patients with diverse clinical profiles, we intend to characterize novel cellular and molecular determinants of cancers.

 

 

University Medical Center of Montpellier, France

Dr.Catherine Alix-Panabières

http://www.chu-montpellier.fr for the hospital
http://www.chu-montpellier.fr/fr/chercheurs/plateformes/les-plateformes-recherche/lccrh/

The LCCRH is a laboratory specialized in enrichment, detection and characterization of circulating tumor cells (CTCs) in solid cancers. Our main expertise is detecting and analyzing viable CTCs using a functional assay based on an in vitro short-term cell culture, EPISPOT. This original assay has been recently developed and patented at the single cell level (EPIDROP).
The LCCRH has also an expertise on the (i) CellSearch® system (Menarini), the only technology that has been cleared FDA-USA; (ii) DEPArray® System (Menarini), which enables isolation of individual cells for further in-depth characterization; (iii) PARSORTIX system (Angle) for enriching CTCs based on their size/deformability, (iv) CellCollector® (GILUPI) for in vivo capturing CTCs in the patient’s vein.
This expertise gave a considerable advance to the LCCRH for using CTCs in diagnostic and monitoring cancer. The group has authored >60 publications in this field and is currently involved in different national and international projects.

 

 

University of Plovdiv, Plovdiv, Bulgaria

Dr. Vesselin Baev

bio.uni-plovdiv.bg

Faculty of Biology, Bioinformatics and Gene Regulation Group

 

Development of new methods, algorithms and computational software for exploring and interpreting genomic data in a framework of automated sequence analysis. Our current emphasis is on the small RNAs (microRNAs and small interfering RNAs) in plants and animals. Analysis of small RNA and transcriptome libraries from deep-sequencing data, expression regulation profiling, discover, and annotation novel miRNA genes, as well as identification of stress-related small RNAs.

 

 

 

University of Granada, Granada, Spain

Dr. Michael Hackenberg

Associate Professor at the Genetics Department

Computational Epigenomics Lab

bioinfo2.ugr.es

Over the last years, our main research lines were on DNA methylation and small RNAs, developing tools like miRanalyzer (PubMed) , sRNAbench/sRNAtoolbox (PubMed), MethylExtract (PubMed) and NGSmethDB (PubMed) for the analysis of high-throughput sequencing data and its storage into integrated databases.  We are involved in teaching both, genetics (classical and molecular genetics in the Biology Degree) and subjects related to bioinformatics both at degree (Biochemistry Degree) and master level (Genetics and Evolution, and Biotechnology Master Programs).

 

 

University of Granada, Granada, Spain

Dr. Alberto Fernandez

Department of Computer Science and Artificial Intelligence

http://decsai.ugr.es

The Soft Computing and Intelligent Information Systems (sci2s) research group is focused on the development of intelligent systems and Data Science algorithms. In this sense, it comprises a complete workflow that includes processes to collect, prepare, analyze, visualize and model data to generate useful knowledge to understand complex problems and assist in decision-making. On many occasions, these are large volumes of data that due to their complexity and diversity require innovative architectures and techniques to extract relevant knowledge: it is the well-known Big Data.

Artificial Intelligence is at the heart of Data Science. The use of intelligent data analysis techniques has led to the development of technologies that are being successfully applied for knowledge extraction and, together with the availability of massive data, have made Big Data and Data Science a very important part of the fundamental technologies of digital transformation that are accelerating the transformation of the knowledge-based economy and society.

In our research group, the more important areas of development are Fuzzy Rule Based Systems, Evolutionary Fuzzy Systems, Preprocessing techniques, Subgroup discovery, Learning with imbalanced datasets, Extracting association rules, Ensemble learning algorithms, and many other methodologies and areas of Artificial Intelligence and Machine Learning that are aimed to solve problems in the field of Data Science.

 

 

Pangaea Biotech Sl, Barcelona, Spain

Dr. Niki Karachaliou

Director, Translational Research Program, Pangaea Oncology, Dexeus University Hospital, Quirónsalud Group, Barcelona, Spain
Head, Medical Oncology Service, Dr. Rosell Oncology Institute, Sagrat Cor University Hospital, Quirónsalud Group, Barcelona, Spain

www.panoncology.com

Founded in Barcelona in 2007, Pangaea Oncology is a medical services company focused on precision oncology: personalized medicine based on genetic analyses to improve survival and quality of life for cancer patients. The company has two main areas of activity: (i) its clinical care division, the Dr. Rosell Oncology Institute (IOR). Based on the concept of personalized medicine, IOR delivers medical oncology services and related activities at four of the largest hospitals of the Quirónsalud Group in Catalonia; (ii) its Diagnostic and R&D services division, providing diagnostic and in-vitro services to IOR patients and Pangaea’s portfolio of pharmaceutical clients, including over 15 multinationals. Pangaea is highly invested in technology, focusing on the development of innovative, proprietary diagnostic techniques (its main commercialized asset is Liquid Biopsy), and development of targeted drugs. The synergy between these areas forms the foundation of Pangaea’s future growth strategy.

Exosomics Siena Spa, Italy

 

List of partner organizations

University of Twente
Netherlands

University of Sofia “St. Kliment Ohridski”
Bulgaria

University of Padova
Italy

IZON Science Limited
United Kingdom

GILUPI GMBH
Germany

TATAA Biocenter ab
Sweden

GenomeScan B.V.
Netherlands

European Cancer Patient Coalition
Belgium