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3D image analysis tool development for high-content screening

Final Report Summary - 3D HCS IMAGING (3D image analysis tool development for high-content screening)

EU funds large scale 3D cell quantification

The Marie Curie International Reintegration Grant was instrumental in providing the funding to establish an independent line of research. It was an enormous help in the most critical moment of my scientific career. The research work that I started as a career development fellow (Postdoctoral Fellow) was recognized by a promotion to be a permanent investigator scientist. The grant effectively contributed to be able to establish my independent Bioinformatics Image Core (BIONIC) facility in the Laboratory for Molecular Cell Biology at University College of London (UCL).

High-content screening is a powerful state of the art tool for gene and compound selection. The results can be used to study and alternate cellular behaviour and potentially cure diseases. The enormous amount of genes and chemicals require automatic microscopes and computational algorithms to process this huge image data.

The aim of this proposal was to develop a high-content analytical cellular imaging workflow, where the cells and subcellular organelles were quantified by 3D segmentation. As a result, a software system was expected to be developed that is able to process confocal microscopic image stacks of high-throughput biological data such from RNAi or small molecule screens. The software was aimed to process 3D images, extract multidimensional information and generate a statistically valid gene list or compound hit list as an answer to a biological hypothesis.

My professional reintegration was based on the development of 3D imaging and quantification, which is a new tool for numerous European research groups working with high-content data in cell and developmental biology. I established a collaboration with director Dr. Hiroyuki Osada from RIKEN Advanced Science Institute, studying the effect of microorganism-derived NPDepo natural product compounds on human autophagy. My results are leading to several high-profile scientific publications.

I developed a volumetric 3D HCS image processing pipeline, that was used to analyze hypertrophy of human pluripotent stem cell-derived cardiomyocytes. My morphologic analysis of the endothelial-specific secretory granule Weibel-Palade bodies, demonstrated that engineering an organelle’s size provides a novel approach to reprogram its function. I developed a HCS workflow that quantitatively demonstrated that in epithelial cells the intracellular bacterial pathogen Salmonella enterica Typhimurium can activate endoplasmic reticulum stress responses in the absence of Toll-like receptor signalling interactions during replication within intracellular vacuoles. Furthermore, the high-content workflow can be used in studying non-conventional type of secretion.

I was invited to chair a session and present my results at SMi 9th Imaging in Cancer Drug Development, presented my results at the 16th Academic Screening Group Meeting (17/11/2011, Sutton, UK) “From image processing to hits: a high-content analysis pipeline using free software”, at the SLAS2012 Society for Laboratory Automation & Screening Conference, (4-8/2/2012, USA) and Cambridge Healthtech Institute’s 9th annual High-Content Analysis conference “Single-Cell Volume Determination for 3D Segmentation of Human Cancer and Nontumourigenic Cells to Identify Autophagic Phenotypes in High-Content Screening”, and at the Company of Biologists Imaging in Cell Biology Workshop (14-17/10/2012, UK).

I supervised a master student from the UCL MSc Drug Design program and two students in the frame of UCL Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX) program.

The Marie Curie grant successfully lead to my reintegration to the European research community and the establishment of the Bioinformatics Image Core facility in the LMCB headed by me. My results strengthened the European scientific community in a novel area of research that has the potential to become a very prominent field of investigation. I have brought to Europe my knowledge of the theoretical and practical aspects of this original and very promising project, as well as new technological developments, that I worked out at the A-STAR Bioinformatics Institute, Singapore and earlier at Kyoto University in Japan.

The main part of my work, the development of a 3D high-content screening analysis software for large-scale drug screening, is currently in preparation for publication. In fact, this has been successfully used in a small molecule drug screen to identify regulators of autophagy, a cellular process involved in the pathogenesis of neurodegenerative disorders. Some of the compounds identified promise to be good hit candidates for drug discovery lead development and I am engaged with MRC-Technology to assess the possibility to patent some of my findings. I was successfully awarded a UCL Confidence in Concept grant as a co-applicant in order to build on the research results of this project.

Overall, the Marie-Curie Reintegration grant has been extremely helpful to realize my long-term career aspirations. Not only has it given me the support to perform high-level research within a very stimulating research environment. It has also provided me with the financial basis in order to establish myself as a leading expert in image analysis that is recognized by the research community, as evidenced by multiple invitations as a speaker at international conferences. Furthermore, during this phase, I have been promoted to become a group leader and enabled to build my own bioinformatic core facility at the LMCB.