Periodic Reporting for period 1 - OrganVision (OrganVision: Technology for real-time visualizing and modelling of fundamental process in living organoids towards new insights into organ-specific health, disease, and recovery)
Période du rapport: 2021-07-01 au 2022-06-30
Problem statement: OrganVision envisions to shift the paradigm for organoids from disease or drug-screening models to observable tissue micro-bio-environment for unravelling key physiological and pathological processes in humans. We aspire to enable the exploitation of the most important feature of organoids – life, health, disease, and death unfolding in real-time at sub-cellular and inter-cellular scales in cells and tissues, respectively. Our ambition is to (a) overcome the central obstacle that prevents realization of the vision, namely lack of real-time high-resolution label-free imaging technology suitable for organoids, and (b) create new opportunities for organoid research and exploit them.
Importance to society: Cardiovascular disease (CVD) causes over 1.8 million deaths in EU each year (~37% of all deaths in the EU) and is estimated to cost the EU economy €210 billion a year . It is the leading cause of human deaths globally, and a high priority in the UN’s sustainable development goal no. 3 (good health and well-being). Understanding the mechanisms of CVDs and regenerative and repair potential definitely has a direct impact on the global cardiovascular health, potentially leading to better prevention, treatment, and cure of CVD. The technology platform will also be tested on cancer spheroids, therefore readying it for a big impact in the future. The technologies developed will serve the society and the globe by advancing understanding and resolving other diseases as well. Lastly, with better exploitation of organoids, the number of primary cells and tissues harvested from animals for biological studies will reduce. This will contribute to animal welfare.
The broad objectives of OrganVision are:
• Create a ground-breaking comprehensive science & technology platform that alters state-of-the-art across multiple disciplines by leaps, and thereby infusing new and promising R&D streams in each of them
• Redefine the possibilities for organoid research and its impact on finding new age solutions for diseases and supporting new knowledge discovery
• Create a lasting impact on global cardiovascular health
• Build a strong consortium of young research leaders
The scientific objectives of OrganVision are:
1. To develop a novel multi-scale imaging technology for real-time living tissue imaging
2. To develop a novel artificial intelligence engine that is able to model collective dynamics of life processes in organoid
3. To undertake biological studies for understanding cardiac toxicity, cell-cell interaction mechanisms and their impact on post-injury cardiac health, and changes in mitochondrial transfer and turnover in a cardiac injury setting
Importance to society: Cardiovascular disease (CVD) causes over 1.8 million deaths in EU each year (~37% of all deaths in the EU) and is estimated to cost the EU economy €210 billion a year . It is the leading cause of human deaths globally, and a high priority in the UN’s sustainable development goal no. 3 (good health and well-being). Understanding the mechanisms of CVDs and regenerative and repair potential definitely has a direct impact on the global cardiovascular health, potentially leading to better prevention, treatment, and cure of CVD. The technology platform will also be tested on cancer spheroids, therefore readying it for a big impact in the future. The technologies developed will serve the society and the globe by advancing understanding and resolving other diseases as well. Lastly, with better exploitation of organoids, the number of primary cells and tissues harvested from animals for biological studies will reduce. This will contribute to animal welfare.
The broad objectives of OrganVision are:
• Create a ground-breaking comprehensive science & technology platform that alters state-of-the-art across multiple disciplines by leaps, and thereby infusing new and promising R&D streams in each of them
• Redefine the possibilities for organoid research and its impact on finding new age solutions for diseases and supporting new knowledge discovery
• Create a lasting impact on global cardiovascular health
• Build a strong consortium of young research leaders
The scientific objectives of OrganVision are:
1. To develop a novel multi-scale imaging technology for real-time living tissue imaging
2. To develop a novel artificial intelligence engine that is able to model collective dynamics of life processes in organoid
3. To undertake biological studies for understanding cardiac toxicity, cell-cell interaction mechanisms and their impact on post-injury cardiac health, and changes in mitochondrial transfer and turnover in a cardiac injury setting
Work was done on five WPs, namely, WP1, WP2, WP5, WP6 and WP7. The main results achieved by the first reporting period are being presented here.
Progress in WP1: The central idea of our envisioned microscope is the illumination of the sample with rapidly varying customized light patterns. So far, we have worked on the generation of such customized light patterns. We have made progress on two different fronts. First, we selected and purchased all the components required for rapidly creating tunable two-dimensional (2D) light patterns. We have integrated them into a commercial optical microscope, aligned the resulting system, and started characterizing its optical performance. Secondly, we have worked on the high-speed control of light along the optical axis (z-axis) to extract quantitative phase information from non-fluorescent samples.
Progress on WP2: The first step in developing computational microscopy solutions is to model the physics of light behavior in the sample and through the microscope. This is referred to as developing forward models or forward solvers. In OrganVision, we need to develop forward solvers based on electromagnetic elastic scattering, fluorescence, and radiative transfer equation of light dispersion. So, far we have developed forward electromagnetic scattering solver and forward fluorescence microscope solver. These solvers have been developed for small samples, and the work needs to be extended for thick and large samples. The work on developing forward solver for the radiative transfer equation in underway. Furthermore, it is important to verify that the solver emulates a practical microscopy image well. While benchmark samples exist for small scales such as already achieved, benchmark samples for thick tissue situations are scarce. Therefore, we have developed thick benchmark samples for the purpose of verifying the solvers and calibrating the microscopes.
Progress on WP5: This work package was not supposed to start until later. However, it has been started in year 1 itself as we have recognized the need of performing a variety of preliminary tasks that will facilitate the other work packages as well as eventually this WP. We have started developing calibration samples of different thickness and density for calibrating the instrument in WP1 and the solvers in WP2. We have started acquiring the first correlative label-free and fluorescence images of EHTs to identify the right paradigms for generating correlative datasets for WP3.
Progress on WP6: So far we have generated three different fluorescently labeled human induced pluripotent stem cell (hiPSC) lines. Fluorochrome expression was confirmed by flow cytometry and fluorescence microscopy. Master and working cell banks have been generated from these cells. It has been demonstrated that cardiac differentiation can be performed. We have generated the first engineered heart tissues (EHTs) from fluorescently labeled cardiomyocytes. Further, hiPSCs with fluorescent mitochondria were produced. These were successfully differentiated into cardiomyocytes and used for production of beating engineered heart tissue.
Progress on WP7: An architecture has been developed for collective dynamics modeling framework. Further models to assign identities to certain set of sub-cellular entities and track them have been developed. 3D shape simulators are essential for developing simulated microscopy datasets in order to provide ground truth for collective dynamics modeling engine. Preliminary versions of 3d shape simulator for mitochondria and vesicles, and 2D shape simulators of sarcomeres have been developed. Segmentation models for sarcomeres, mitochondria and vesicles have been developed.
Progress in WP1: The central idea of our envisioned microscope is the illumination of the sample with rapidly varying customized light patterns. So far, we have worked on the generation of such customized light patterns. We have made progress on two different fronts. First, we selected and purchased all the components required for rapidly creating tunable two-dimensional (2D) light patterns. We have integrated them into a commercial optical microscope, aligned the resulting system, and started characterizing its optical performance. Secondly, we have worked on the high-speed control of light along the optical axis (z-axis) to extract quantitative phase information from non-fluorescent samples.
Progress on WP2: The first step in developing computational microscopy solutions is to model the physics of light behavior in the sample and through the microscope. This is referred to as developing forward models or forward solvers. In OrganVision, we need to develop forward solvers based on electromagnetic elastic scattering, fluorescence, and radiative transfer equation of light dispersion. So, far we have developed forward electromagnetic scattering solver and forward fluorescence microscope solver. These solvers have been developed for small samples, and the work needs to be extended for thick and large samples. The work on developing forward solver for the radiative transfer equation in underway. Furthermore, it is important to verify that the solver emulates a practical microscopy image well. While benchmark samples exist for small scales such as already achieved, benchmark samples for thick tissue situations are scarce. Therefore, we have developed thick benchmark samples for the purpose of verifying the solvers and calibrating the microscopes.
Progress on WP5: This work package was not supposed to start until later. However, it has been started in year 1 itself as we have recognized the need of performing a variety of preliminary tasks that will facilitate the other work packages as well as eventually this WP. We have started developing calibration samples of different thickness and density for calibrating the instrument in WP1 and the solvers in WP2. We have started acquiring the first correlative label-free and fluorescence images of EHTs to identify the right paradigms for generating correlative datasets for WP3.
Progress on WP6: So far we have generated three different fluorescently labeled human induced pluripotent stem cell (hiPSC) lines. Fluorochrome expression was confirmed by flow cytometry and fluorescence microscopy. Master and working cell banks have been generated from these cells. It has been demonstrated that cardiac differentiation can be performed. We have generated the first engineered heart tissues (EHTs) from fluorescently labeled cardiomyocytes. Further, hiPSCs with fluorescent mitochondria were produced. These were successfully differentiated into cardiomyocytes and used for production of beating engineered heart tissue.
Progress on WP7: An architecture has been developed for collective dynamics modeling framework. Further models to assign identities to certain set of sub-cellular entities and track them have been developed. 3D shape simulators are essential for developing simulated microscopy datasets in order to provide ground truth for collective dynamics modeling engine. Preliminary versions of 3d shape simulator for mitochondria and vesicles, and 2D shape simulators of sarcomeres have been developed. Segmentation models for sarcomeres, mitochondria and vesicles have been developed.
The speed at which the 2D light patterns are generated exceeds the current state-of-the-art. We have also retrieved quantitative phase information from samples at rates beyond those reported in the literature. These are promising steps toward the development of the envisioned microscope in Organvision.
Full-field 3D electromagnetic scattering forward solver for label-free microscopes is beyond the state-of-the-art.
Full-field 3D electromagnetic scattering forward solver for label-free microscopes is beyond the state-of-the-art.