Project development P1 (2011)

Improving throughput

Modern microscopy allows for the imaging of live cells for long periods of time. The microscope does however need human assistance to select the cells to be studied, a bottle neck that has hampered automation procedures. A piece of software, Micropilot, that pro­vides a machine learning-based module to control microscope tasks in the absence of previously required manual efforts was released by network members (WP3) early in the period and has proven to increase the throughput of high-resolution and high-information-content imaging assays tremendously.

Maximizing 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 designed to execute the broadest type of multiparametric image analyses of dynamic systems has been developed as part of the joint programme and a report outlining the requirements was delivered in M9. In agreement with the resulting specification, software for the platform is now being developed by several NoE partners.

Data processing and modeling

The large, multi-dimensional image-based data sets that are generated from systems microscopy studies 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 imageHTS and associated methodology was tested and successfully applied on more than a dozen high content screens. A new release of the software was made in M11 and it is now available to the community as open-source through www.bioconductor.org.

Data derived from a number of different experimental set-ups have been used to commence bold modeling projects that will ultimately serve to describe the dynamic processes of cell migration and division. Close collaboration between experimental and modeling partners, which are actively exchanging modelling methodology and know-how, has generated extremely promising initial results (WP6). The network has developed a model that represents the temporal evolution of perturbed cell populations from the mitosis screening project Mitocheck. 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. Work on adapting this approach to cell migration assays is on-going.

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.

In another project relevant to cancer, the motility phenotype of cancer cells was correlated to protein dynamics. The natural variability in more than 700 proteins, and the natural variability in motility in the same cells, was measured in order to decipher in an unperturbed manner, which proteins relate to motility.

Standardization measures

Systems biology aims to produce comprehensive models of biological systems, requiring integration of multiple experimental techniques, analytical methods and modelling approaches. A central task for this NoE is therefore the development of standards that enable exchange, interoperability and integration of data from different laboratories. To this end, the consortium has agreed on the HDF5 format as common data format to report and exchange data sets (WP8). The NoE is further developing nomenclature of the quantitative parameters extracted from cellular images, interfaces enabling the communication between different software, standardized protocols for statistical analysis and standards for database depositions.

A prototype database for systems microscopy data is being developed (WP9) that further will facilitate standardization efforts. By storing, organizing and providing access to data, the database will constitute a central resource to the network that will enable data sharing among the network partners and serve as a prototype for a long-term, production-scale systems microscopy public data base. In the first period, the major needs and requirements for this repository have been defined. In line with this, a first draft of a cellular phenotype ontology (CPO) was developed. The ontology will be integrated into the database after feedback from the network.

The biological systems

The characteristics of cancer biology and its clinical consequences render a strong case for studying cell division and migration at the systems level. Cell division and cell migration are dynamic processes, in which the dramatic spatiotemporal dynamics of cells, sub-cellular machineries and molecules completely controls the outcome. Therefore, systems microscopy is an essential approach to gain understanding of cell division and cell migration. The molecular complexity of these biological processes and their deregulation in cancer cells, need to be addressed by powerful imaging tools combined with systems-scale perturbation experiments. The study of cell division and cell migration form the basis for the activities in WP1 and WP2 respectively. In the first project period, the work packages 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 consortium is also dedicated to leverage the powerful systems microscopy tools developed within the project in specific translational applications, such as exploration and diagnosis of the dependency of cancer on specific targets, or reactivity towards specific drugs (WP7). The in vivo relevance of the systems biological models and findings obtained will also be validated using pre-clinical mouse models and clinical cancer data. The initial steps to translate the findings of genes influencing mitosis and migration obtained from screening in WPs 1 and 2, respectively were taken in period 1. The analysis of basal breast cancer samples identified deregulation of a set of 29 mitosis-related genes, genes that originally had been found through WP1 activities. These findings will be used for our follow-up studies, including validation on tissue microarrays (TMAs) and studies on whether these genes are suitable predictors of cancer cell responsiveness to drug treatment in vitro and whether RNAi knockdown of these genes has an impact in animal models in vivo.

Training the next generation

The network was pleased to welcome a high number of junior participants to its kick-off meeting which offered plenty of opportunities to discuss and present research, opportunities that were well received by this active participant category.The first course supported by the NoE was organized in P1 and was attended by both NoE external and NoE associated participants, thus providing training in systems microscopy methodology within as well as outside of the network. In training the next generation of scientists, both events contributed to the durability objective of the training work package (WP10).  A large number of postdocs and students have further been enrolled within the NoE and started their training by research, which constitutes the main training method applied in this NoE.

Dissemination

A symposium to spread knowledge about the emerging field of systems microscopy was organized in the first period and was attended by over 100 participants of which 2/3 were from outside the network.

Structures for internal as well as external communication (WP11) have been set up and a plan for dissemination has been established. The project web site was released as planned and will constitute a core tool for dissemination and knowledge management. Events organized by the network have attracted a wide audience of research professionals, students and industry representatives.

Seventh Framework Programme

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