Periodic Report Summary 1 - SYSTEMS MICROSCOPY (Systems microscopy - a key enabling methodology for next-generation systems biology) Project context and objectives: The mission: Single cells in four-dimensional (4D) imaging The SYSTEMS MICROSCOPY Network of Excellence (NoE) is developing a technological platform that will enable the studies of single cells in the 3D space and time at the systems level. This is an important analysis capacity in cases where spatiotemporal events in cellular subpopulations play a critical role, such as in cancer development, progression and metastasis. Advanced light microscopy forms the technological basis for the project as it is the only technology that can deliver sufficient sensitivity, as well as spatial and temporal resolution in single living cells. When employed quantitatively and with high throughput, microscopy allows for the acquisition of complex and rich data sets at the systems level. Efforts to increase the speed and the confidence with which high content data from microscopic images can be produced, will strengthen the emerging methodology referred to as systems microscopy and will establish it as a corner stone in the systems biology analysis of the living cell. As a paradigm to enable systems biology at the cellular scale of biological organisation, the network addresses, as its core biological theme, two major mechanisms underlying cancer progression and metastasis: cell division and cell migration. The network joins world authorities in the fields of microscopy, systems biology, bioinformatics, mathematical statistics and modelling, as well as in cell migration and cell division and provides a unique opportunity for Europe to acquire global lead in systems microscopy. Project objectives The overall objective of the SYSTEMS MICROSCOPY NoE is to develop systems microscopy into a powerful enabling platform for next-generation systems biology. It will be achieved through the following sub-objectives: - to develop a novel pan-European systems microscopy infrastructure for systems biology, including new imaging platforms and image extraction software, new tailored methods for statistics, bioinformatics, and modelling, and standards, as well as a database for SYSTEMS MICROSCOPY; - by using cell division and migration as our core subjects; - to gain a systems-level understanding of two basic mechanisms underlying cancer, and identify novel pathways for translational research; - to perform translational research using results and methodology from our systems microscopy research; - to disseminate our results to the research community, industry and other interested parties; - to train the next generation of scientists in systems microscopy; - to make our network, as well as its results and structures durable beyond the European Commission (EC) financing period. Project results: Improving throughput The throughput of high-resolution and high-information-content imaging assays can be increased by the use of software that was released in the first period by network members. The publically available software, Micropilot, provides a machine learning-based module to control microscope tasks in the absence of previously required manual efforts (Work package (WP) three). Maximising content Available high-throughput image analysis software offer efficient algorithms for analysis of single time-point assays while the analysis of cellular dynamics in multi-dimensional large-scale imaging is very limited with existing tools. To enable systems biology analyses of the cell division and cell migration, the network is currently developing an image analysis tool (WP4) aimed at increasing the data content that can be extracted in parallel through microscopy. The requirements for an ambitious software platform were presented in M9. Data processing and modelling Large, multi-dimensional image-based data sets pose high demands on the tools used for statistical analysis. Network members have continued to improve software (WP5) that performs primary statistical analysis of complex data along with quality assessment and significance analysis. The software image High-throughput screening (HTS) and associated methodology was tested and successfully applied on numerous high content screens. A new release of the software was made in M11 and is available as open-source through http://www.bioconductor.org The network has developed a model that represents the temporal evolution of perturbed cell populations from the mitosis screening project Mitocheck (WP6). The model allows clustering and classification of cell division movies based on similarity of the underlying dynamic process, while largely eliminating time-lag and amplitude effects. In efforts towards building models of phenotypic landscapes, genetic modules and genetic interactions, data has been collected from lung cancer cell populations. Methods to determine the genetic variants underlying the cellular phenotypic heterogeneity observed in the lung cancer cells were established in the first period. Standardisation measures A central task for this NoE is the development of standards that will enable exchange, interoperability and integration of data from different laboratories. The consortium has agreed on the Hierarchical data format five (HDF5) as common data format to report and exchange data sets (WP8). A prototype database for systems microscopy data is developed (WP9) that further will facilitate standardisation efforts. By storing, organising and providing access to data, it will constitute a central resource for data sharing that will serve as a prototype for a long-term, production-scale systems microscopy public data base. In the first period, a first draft of a Cellular phenotype ontology (CPO) that will be integrated into the database was developed. The biological systems Systems microscopy is an essential approach to gain the understanding of cell division and cell migration needed to further the field of cancer biology. The studies of these complex biological processes form the basis for the activities in WPs 1,2. In the first project period, the WPs established several tools, including software and model systems, for the quantitative analysis of cell division and cell migration. Systems wide screens with perturbing agents were performed in the selected model systems. The initial steps to translate the findings of genes influencing mitosis and migration obtained from screening in WPs 1,2, respectively were taken in period 1. The analysis of basal breast cancer samples identified deregulation of a set of mitosis-related genes, genes originally identified through WP1 activities (WP7). Potential impact: The area of systems microscopy is just emerging, but has already proven its impact in being able to powerfully combine systems biology with detailed visual analysis of cellular processes. This NoE aims to enable systems biology of complex cellular processes. This aim will be fulfilled by the development and provision of common technical and computational tools for systems microscopy, as well as experimental and theoretical resources to carry out systems experiments and model their results. A generic approach for next-generation systems biology will be offered to the research community. The joint research programme will generate data and models that are expected to further our systems-level understanding of cell division and migration, both of which are crucially involved in the development and progression of cancer, thereby providing new avenues for the translation of basic research into applied research. Novel testing systems for drug sensitivities and gene dependencies in primary cultures of cancer patients will be developed, tests that are expected to help guide future cancer diagnosis and therapy choices thereby paving the way for personalised medicine for the benefit of European citizens. New technologies are developed in an area with significant future potential for innovation in biology and medicine, including translation to industry. We believe that at the end of this programme, we will have developed significant tools, including software, screening systems and more, for translational applications that will provide opportunity for industrial collaborations to promote the NoE science and technology, thus strengthening European competitiveness. The results obtained in this project on cell division and migration, particularly in relation to cancer, may highlight and illuminate numerous opportunities for translational research breakthroughs, and consequent industrial benefits, such as novel drug targets, as well as mechanisms of drug action. Furthermore, it is likely that systems microscopy will become an indispensable tool to monitor drug effects in cellular systems in vitro, thereby playing a crucial role towards the development of future diagnostic applications. We will execute a multidisciplinary training programme, providing European research institutions with well-trained scientists to further develop this emerging area. The training programmes will create a large user base, as well as contribute to the creation of future experts in this field across Europe. The power of the technology, the dissemination of knowledge and infrastructure will together serve as guarantor for the durability of the systems microscopy strategy. Project website: http://systemsmicroscopy.eu/ Other report summaries Periodic Report Summary 4 - SYSTEMS MICROSCOPY (Systems microscopy – a key enabling methodology for next-generation systems biology) Periodic Report Summary 3 - SYSTEMS MICROSCOPY (Systems microscopy – a key enabling methodology for next-generation systems biology) Periodic Report Summary 2 - SYSTEMS MICROSCOPY (Systems microscopy - A key enabling methodology for next-generation systems biology)