Periodic Reporting for period 2 - BRAINTIME (Molecular atlas of the brain across the human lifespan)
Periodo di rendicontazione: 2021-01-01 al 2022-06-30
BRAINTIME brought together six laboratories that are international leaders in the field of single- cell genomics with the aim to apply their knowledge and expertise to understand the human brain: Karolinska Institute (Sweden), Weizmann Institute (Israel), ETH Zürich (Switzerland), Cartana/10x Genomics (Sweden) and Allen Institute for Brain Research (USA). The goals of BRAINTIME were to:
• Perform a comprehensive multi-omic analysis of the developing human midbrain and hindbrain and generate an atlas of key monoaminergic cell populations in healthy adulthood, ageing and neurodegenerative disease;
• Embed our new cell type maps into 3D contexts and temporal developmental models by integrating new approaches for computational modelling, cell fate tracking, spatial analysis and capturing cell-cell interactions;
• Establish single-cell genomics-empowered ex-vivo protocols and standardized ex-vivo/in-vivo projection algorithms to allow flexible model testing and perturbation analysis on midbrain and hindbrain tissues
• Establish an effective and sustainable technological and analytical pipeline for the analysis of brain tissue at the single-cell level that can be used by the community to probe other brain regions or states and be extended to other human tissues.
Key results at the conclusion of the project include:
• A comprehensive multiomic atlas of the whole developing human brain, with emphasis on the midbrain and hindbrain and identifying key monoaminergic populations
• Multiomic single-cell survey of adult, ageing and diseased human brains again focusing on the brainstem and monoaminergic populations
• Single-cell multiomic atlas of midbrain organoid development
• Spatial multisection (pseudo-3D) atlas of midbrain development using highly multiplexed RNA detection (EEL FISH)
• Integration of in vivo human midbrain atlas with ex vivo (midbrain organoid) to reveal differences and similarities, and validate the fidelity of the ex vivo model system
• Development of tools for lineage tracing, lineage inference and simulation
• Data, visualization tools, and other resources for the commmunity to explore
• Perform a comprehensive multi-omic analysis of the developing human midbrain and hindbrain and generate an atlas of key monoaminergic cell populations in healthy adulthood, ageing and neurodegenerative disease;
• Embed our new cell type maps into 3D contexts and temporal developmental models by integrating new approaches for computational modelling, cell fate tracking, spatial analysis and capturing cell-cell interactions;
• Establish single-cell genomics-empowered ex-vivo protocols and standardized ex-vivo/in-vivo projection algorithms to allow flexible model testing and perturbation analysis on midbrain and hindbrain tissues
• Establish an effective and sustainable technological and analytical pipeline for the analysis of brain tissue at the single-cell level that can be used by the community to probe other brain regions or states and be extended to other human tissues.
Key results at the conclusion of the project include:
• A comprehensive multiomic atlas of the whole developing human brain, with emphasis on the midbrain and hindbrain and identifying key monoaminergic populations
• Multiomic single-cell survey of adult, ageing and diseased human brains again focusing on the brainstem and monoaminergic populations
• Single-cell multiomic atlas of midbrain organoid development
• Spatial multisection (pseudo-3D) atlas of midbrain development using highly multiplexed RNA detection (EEL FISH)
• Integration of in vivo human midbrain atlas with ex vivo (midbrain organoid) to reveal differences and similarities, and validate the fidelity of the ex vivo model system
• Development of tools for lineage tracing, lineage inference and simulation
• Data, visualization tools, and other resources for the commmunity to explore
During the first year, work was severely disrupted by the COVID pandemic. Nevertheless, the project has made good progress. In WP3, Linnarsson group has generated large datasets from human fetal brain, both single-cell RNA-seq and ATAC-seq (250k cells). We have also now begun to generate Multiome data, combining RNA and ATAC, which will aid integration across modalities. In WP4, the Lein group focused on experiments to optimize tissue handling and nuclei isolation from human brain tissues derived from aged and Alzheimer’s disease human tissue donors. In WP5, the Amit and Treutlein groups have developed and calibrated advanced experimental models of human microglia in different organoid model systems. We are currently comparing these models to data we collected from human microglia in different stages of development with an aiming of using the most relevant model for perturbation experiments. In WP6, the Tanay group worked toward parametric manifold models and implementation of spatio temporal data analysis schemes over them. Application of Metaman and the network flows approach to data on gastrulation and initial deployment of the new tools for understanding Braintime data demonstrate the remarkable potential of these approach, in particular given very large scale data.
In the final period, the project completed data acquisition for both fetal, adult, diseased and ageing human brain, as well as organoids, and the preparation of several manuscripts for submission. We completed the atlas of the developing brain comprising more than 1.6 million (RNA) and 500,000 (ATAC, Multiome) cells. A first manuscript is currently in revision. Similarly, we completed a single-cell survey of adult, ageing and disease human brains. We performed spatial RNA detection using a greatly improved method (EEL FISH) capable of detecting up to 440 genes in large tissue sections (WP3). We developed and optimized methods for computational modelling of cellular manifolds (WP6) and corresponding methods for genetic lineage tracing (e.g. iTracer, WP5), as well as applying methods for cell-cell interaction analysis (PIC-seq, WP5). We further developed new and improved strategy for mapping query scRNA-seq on atlases, and we developed a scalable and interactive browser enabling thew community to explore our datasets.
Overall, these results meant that the key objectives were achieved.No exploitable intellectual property was generated during the project. Tools, data and results were shared without restriction (beyond what was required for protecting the privacy of donors). Dissemination activities included a large number of attended conferences, including some co-organized by partners; preprints submitted to bioRxiv; scientific publications; scoail media and web presence.
In the final period, the project completed data acquisition for both fetal, adult, diseased and ageing human brain, as well as organoids, and the preparation of several manuscripts for submission. We completed the atlas of the developing brain comprising more than 1.6 million (RNA) and 500,000 (ATAC, Multiome) cells. A first manuscript is currently in revision. Similarly, we completed a single-cell survey of adult, ageing and disease human brains. We performed spatial RNA detection using a greatly improved method (EEL FISH) capable of detecting up to 440 genes in large tissue sections (WP3). We developed and optimized methods for computational modelling of cellular manifolds (WP6) and corresponding methods for genetic lineage tracing (e.g. iTracer, WP5), as well as applying methods for cell-cell interaction analysis (PIC-seq, WP5). We further developed new and improved strategy for mapping query scRNA-seq on atlases, and we developed a scalable and interactive browser enabling thew community to explore our datasets.
Overall, these results meant that the key objectives were achieved.No exploitable intellectual property was generated during the project. Tools, data and results were shared without restriction (beyond what was required for protecting the privacy of donors). Dissemination activities included a large number of attended conferences, including some co-organized by partners; preprints submitted to bioRxiv; scientific publications; scoail media and web presence.
BRAINTIME has significantly expanded the basic understanding of cellular and molecular mechanisms and functions of the brain during development in adulthood and ageing. Our research strengthens the understanding of cellular interactions in the brain by establishing baseline reference atlas of cell states in the developing and the adult brain. Knowledge gained in this project will advance basic science across diverse fields, including developmental biology, regeneration, stem cell biology, RNA biology, epigenetics, signalling, neurobiology and metabolism.
With the first single-cell transcriptomic census of the entire human brain in normal development, and targeted analysis of the human brain in adulthood, and ageing, we provide a resource for understanding the molecular diversity of the human brain in health and disease. The synthesis of 21st century biology and data sciences in BRAINTIME can stimulate new developments in the healthcare sector, providing benefits to the EU economy. Insights acquired using the baseline reference and the calibrated organoid systems of a healthy brain at a single-cell resolution can serve as a basis for the development of targeted medicines for neurological disorders. The implementation of innovative technologies in neurological studies and brain modelling, and better understanding and improvement of stem cell technology used in research and development of novel therapies for neurodegenerative diseases, will lead to substantial savings in the cost of drug development for the pharmaceutical industry in Europe.
BRAINTIME also enabled the development of several advanced analytical tools, combining cutting-edge computational, single-cell and organoid development methods, which can support various advanced basic and translational science breakthroughs.
With the first single-cell transcriptomic census of the entire human brain in normal development, and targeted analysis of the human brain in adulthood, and ageing, we provide a resource for understanding the molecular diversity of the human brain in health and disease. The synthesis of 21st century biology and data sciences in BRAINTIME can stimulate new developments in the healthcare sector, providing benefits to the EU economy. Insights acquired using the baseline reference and the calibrated organoid systems of a healthy brain at a single-cell resolution can serve as a basis for the development of targeted medicines for neurological disorders. The implementation of innovative technologies in neurological studies and brain modelling, and better understanding and improvement of stem cell technology used in research and development of novel therapies for neurodegenerative diseases, will lead to substantial savings in the cost of drug development for the pharmaceutical industry in Europe.
BRAINTIME also enabled the development of several advanced analytical tools, combining cutting-edge computational, single-cell and organoid development methods, which can support various advanced basic and translational science breakthroughs.