HERCULES brings together ten research groups and one company from eight different organization across Europe with expertise in first-hand clinical care of ovarian cancer patients, tumour cell biology, systems medicine, drug response modelling, single-cell sequencing methodologies, biological network modelling, and development and sale of diagnostic systems for professional use. Bioinformatics and data analysis are an integral part of the project, and participation of multiple strong computer science and mathematical partners ensures that the large amounts of data generated in the project can be interpreted productively.
Sampsa Hautaniemi, DTech, Principal Investigator at the Research Programs Unit and Professor of Systems Biology at the Faculty of Medicine, University of Helsinki, is the coordinator of the HERCULES project. In addition to coordination and management, the System Biology lab led by Professor Hautaniemi is responsible for quality control and analysis of mass cytometry data and processing whole-genome and transcriptomics deep sequencing data. They will also construct and maintain a database for sharing the data generated in the project. The Hautaniemi lab has developed several data integration tools and an efficient infrastructure for processing and analysing large amounts of biomedical data. Website
Tero Aittokallio, PhD, is an EMBL Group Leader at Institute of Molecular Medicine Finland (FIMM), with a professorship in Applied Mathematics and Statistics at the University of Turku. Professor Aittokallio’s Computational Systems Medicine group has expertise in system-level modelling of how cancer survival pathways can be targeted by synergistic and synthetic lethal interactions through multi–targeted perturbations. The group develops computational, mathematical and statistical modelling tools to combine the functional information obtained from high-throughput drug screening with information from personal genomic profiling to provide a more comprehensive network view of clinically actionable molecular targets in ovarian cancer and other complex diseases. Website
Krister Wennerberg, PhD, is a Group Leader and head of the High Throughput Biomedicine Unit at FIMM. Wennerberg’s Cancer Chemical Systems Biology group is focused on gaining fundamental novel understanding of cancers and their phenotypes using a chemical systems biology approach by discovery and validation of novel oncology drug targets through the development of molecular probes and by using collections of defined bioactive compounds, approved and investigational drugs on cancer cells. Together, these approaches allow us to discover novel personalized therapeutic strategies and to define and understand the molecular mechanisms driving the cancers, their drug responses and mechanisms of resistance. In HERCULES, Wennerberg’s lab uses these approaches to study drug responses in the high-grade serous ovarian cancer cells.
Anna Vähärautio, PhD, is establishing her own research group as an independent researcher in Medicum, focusing on single-cell studies. She has expertise in molecule counting and method development of RNA-sequencing as well as development of other sequencing-based methodologies. In HERCULES, she will be involved in the sample preparation, including single-cell capture and sequencing library preparation, for single-cell whole genome and transcriptome sequencing of high-grade serous ovarian cancer primary and interval tumour subpopulations. Website
Seija Grénman, MD, PhD, is Professor and Head of the Department of Obstetrics and Gynecology, at the University of Turku and Turku University Central Hospital (TUCH), which belongs to the Hospital District of Southwest Finland. Professor Grénman has a strong background in performing translational and clinical research and extensive experience from clinical work as gynecologic oncologists. The prospective patient samples for the project are collected at TUCH. Annually around 80 new cases of ovarian cancer are operated on at the Department of Obstetrics and Gynecology at TUCH, and the surgical team at the department is trained to take systematically the needed specimens for research protocols, ensure the logistics of the samples and collaborate with other research teams.
Olli Carpén, MD, PhD, is a senior scientist and affiliated professor at the University of Turku and (from 1.10.2015) professor of pathology at the University of Helsinki. Professor Carpén has a strong background and expertise in translational cancer research and in pathology oriented biomarker discovery. He is also the scientific director of Helsinki Biobank and affiliated with Turku based Auria biobank, where we previously worked as professor of biobank research. In HERCULES his research group at Turku focuses on ovarian cancer samples, cell lines and pre-clinical models, and his role is essential in the biomarker validation of the project results.
Serena Bonin graduated in Chemistry at the University of Trieste and obtained the PhD in life sciences at the Open University of London. Since 1997 she has been assistant professor at the Department of Medical Sciences of the University of Trieste. She has also been involved in teaching in courses and since 2003 she's been member of the teaching board of the School of Doctorate of Nanotechnology. Her main research activities are focused on the study and application of molecular analyses in biomolecules from formalin fixed paraffin embedded tissues, in particular RNA. She is part as an expert in the Biobanking and Biomolecular Resources Research European Infrastructure (BBMRI-ERIC). She is co-chair of Working Group 2 (FFPE tissues) in the BBMRI- ERIC program on quality management, aiming to harmonise CEN Standards for European biobanks. She is the author of more that 100 scientific publications on international journals, book chapters and conference proceedings.
Giorgio Stanta, Professor of Pathology in the University of Trieste, is in charge of the Molecular Histopathology Lab of the Medical Sciences Department of the University of Trieste. His laboratory has been the first one to develop molecular analysis in fixed and paraffin-embedded tissues and it has been the first one to extract and quantify RNA from this kind of tissues. The laboratory is involved in the European Working Groups of the European Society of Pathology (ESP), the Organisation of European Cancer Institutes (OECI) and the Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-ERIC) about pre-analytical conditions of tissues, standardization in molecular methods, standardization of tumour heterogeneity in diagnostics and clinical research, verification and validation of biomarkers, and organisation of archive tissue biobanking. Professor Stanta has an important role especially in the validation of biomarkers from FFPE samples.
Mauro Biffoni, MD, is a Research Director at the Hematology, Oncology and Molecular Medicine (EOMM) Department of Istituto Superiore di Sanità. Biffoni’s research group has a consolidated experience focused on identification and characterization of tumor initiating cells in colorectal cancer and functional characterization of stem-like cells in glioblastoma, colon and lung cancer. He is responsible of the flow cytometry and mass cytometry section at the institute. In HERCULES, Dr Biffoni is in charge of selection of a panel of biomarkers for high-grade serous ovarian cancer by MC analysis.
Luca Pasquini, PhD, is a Contract Researcher at the Istituto Superiore di Sanità. Dr. Pasquini has expertise in cell chemoresistance, isolation and characterization of stem cell-likeness and identification of critical signatures responsible for high heterogeneity in ovarian cancer and several other neoplasms. He has developed high competence in multiparametric analysis through Flow- and Mass- Cytometry technologies in ISS. Dr Pasquini will contribute to the project by setting up the MC procedure and analysis of high-grade serous ovarian cancer samples
Benno Schwikowski, PhD, leads the Systems Biology Lab at Institut Pasteur. He has pioneered the analysis of large-scale protein interaction networks, and the Cytoscape software for the integrated analysis and visualization of such networks. In collaboration with groups from US and Canada, Dr. Schwikowski has been developing Cytoscape into the world-leading software platform for data-driven network analysis. His group continues the development of statistical and computational tools to analyse large-scale, high- throughput data, in particular, in network contexts. Recent work includes novel approaches to the analysis of flow cytometry data. In HERCULES, Dr Schwikowski is leading the network modelling effort, which aims at connecting the molecular-level measurements of individual subpopulations with predicted drug combination effects. Website
Dino Paladin, PhD, is the founder and Research and Development Director of AB Analitica, an Italian innovation-driven small-medium enterprise focusing on the design, development, production and trade of in vitro medical-diagnostic devices (IVD). The company has a track-record of successfully implementing and commercializing diagnostic methods that quantitatively and qualitatively detect disease-related genetic mutations, risk alleles for multifactorial diseases and cancer chromosomal rearrangements using reverse-line blot and Real-Time PCR. Dr Paladin in charge of the general coordination for developing and commercializing a test for the prediction of ovarian cancer patients’ response to chemotherapy drugs in HERCULES.
Jussi Taipale is a Principal Investigator and Herschel Smith Professor of Biochemistry at the Department of Biochemistry in University of Cambridge. Professor Taipale has extensive experience in methods for regulatory genomics, systems biology and genome-scale technologies. His laboratory includes both experimental biologists and computer scientists. The main strength of the group is in systems biology/genomics and molecular biology of signal transduction and growth control. They have expertise in high-throughput screening using cDNA and RNA interference, computational and experimental methods to identify causative regulatory mutations in non-protein coding DNA and to analyse genetic networks, as well as method development in quantitative RNA-sequencing. In HERCULES, the Taipale lab is responsible for the gene regulation and expression studies on sub-populations of high-grade serous ovarian cancer cells.
University of Cambridge has replaced Karolinska Institutet as a partner in the project due to Jussi Taipale's relocation.