discovAIR: discovering the Cellular Landscape of the Airways and Lung Tissue
Lung diseases, such as COPD (Chronic Obstructive Pulmonary Disease) and to a lesser extent asthma, are a leading cause of death, with increasing incidence and lack of curative treatments. The development of novel therapeutic treatments is hampered by our incomplete knowledge of the cellular complexity of the lung. To get a better grip on this, we need knowledge about the different types of cells in the lung, what their specific characteristics are and how they communicate with each other in healthy and diseased individuals. To achieve this, discovAIR will create an Atlas of the Human Lung.
This Atlas of the Human Lung will be a 3D reconstruction of lung tissue architecture and contain detailed information on the state of cells under healthy and disease conditions. Tissue from different lung patients and healthy individuals will be used to identify the specific properties of different cell types and how their properties change from a healthy to a diseased state. In addition, a spatial map of these different cell types and states will be generated. Novel computational methods will be developed and used to combine all this information and create the first draft of the human lung cell atlas.
The Human Lung Cell Atlas
The discovAIR results shall be shared with scientists, clinical experts, diagnostic and pharmaceutical industries through an open-access online data visualization and exploration platform. The information in this platform will enable progress in regenerative and precision medicine and identify new candidates for precision diagnostics and curing treatments in lung disease, thereby contributing to healthy ageing and active living in Europe.
Martijn is molecular cell biologists, geneticist and immunologist with an interest in functional genetics of chronic airway diseases such as asthma and COPD. He has developed single-cell approaches for translational research in respiratory disease and plays a leading role in the Lung working group of the Human Cell Atlas. He will be the discovAIR programme coordinator and leader of WP5 and WP6.
Kerstin is interested in the cellular landscape of the lung over the life span, charting the lung in embryogenesis and childhood, and examining changes associated with infection and inflammatory disease in the adult. Within discovAIR, she is the lead for WP1, carrying out multi-modal profiling of dissociated cells in multiple locations of the lung in 5 individuals and coordinating tissue distribution for the spatial analysis of gene expression in these samples.
Fabian Theis is head of the Institute of Computational Biology and the Helmholtz AI unit, full professor at the Technical University of Munich and associate faculty at the Wellcome Trust Sanger Institute in Hinxton, UK. The focus of his lab is biomedical AI and machine learning, in particular in the context of single-cell biology. In discovAIR, he will be involved in the development of machine learning methods and computational tools for automated image analysis and integration of single cell and imaging data.
Michael von Papen
Michael is a data science consultant in the Life Science team at Comma Soft and coordinates the academic projects. He is an expert in the statistical analysis and inference of coupling and causality in complex systems. He did his PhD in Space Physics at the University of Cologne with application in plasma turbulence and then moved to the field of Neuroscience, where he focused on dynamical resting state networks in the brain. He will be team coordinator for contributions of Comma Soft within discovAIR.
Kourosh is a Clinical Lecturer in the Department of Surgery, University of Cambridge and was appointed as University Lecturer and Honorary Consultant Transplant Surgeon in 2012. In 2015, he founded CBTM which has since facilitated >55 research projects by >30 PIs in regenerative medicine, infection and immunity, cellular and molecular medicine, cancer, systems medicine and Human Cell Atlas as well as enabling submission of >35 applications for funding. Kourosh also leads an academic research group focused on regenerative cellular therapies, cancer immunotherapies and transplant related ischaemia reperfusion injury. He will provide lung tissue to the discovAIR consortium.
Ugis leads the Functional Genomics Software Development team. We build and run the BioStudies database, a database for aggregating all biomedical data linked to a publication, and contribute to the development of the BioImage Archive. In discovAIR we will ensure that image data generated in the project flows into the BioImage Archive and is usable for further analysis when the data is released to the general scientific community. He will ensure that image data generated in discovAIR flows into the BioImage Archive and is usable for further analysis when the data is released to the general scientific community (FAIR data).
Valérie is ERS Scientific Activities Project Leader. She will together with her colleague Alessandra Marguerat coordinate the contribution of the ERS in the WP4 “Dissemination, exploitation and outreach”. It includes the organization of the kick-off Research Seminar and user-group meeting in March 2020, featuring discovAIR at the ERS International Congresses 2020 and the organization of a symposium at the ERS International Congress 2021 to launch the platform. She will ensure a broad dissemination of discovAIR’s outcomes toward the ERS community.
The CartaNA AB team leader, Malte (main founder, EVP and Head of R&D), has a PhD in molecular medicine. He has extensive experience in nucleic acid analysis and RCA-based assays. He received his PhD degree from Uppsala University in Sweden. During his PhD, Malte focused on developing sensitive nucleic acid detection methods for infectious disease diagnostics and configuring them into easy-to-access format, e.g. using a mobile phone as read-out. He will manage the contributions of CartaNA AB to discovAIR
Herbert is an independent research group leader at the Helmholtz Zentrum München and the German Center for Lung Research, focusing on experimental systems biomedicine of lung diseases. He combines expertise in quantitative proteomics and single cell genomics to identify fundamental principles of regulation of cell plasticity in health, regeneration, and disease. In the discovAIR project he will lead efforts at Helmholtz Zentrum München to dive into transcriptional changes in endstage lung disease patients, and human ex vivo lung tissue slice cultures exposed to defined perturbations, to characterize and dissect lung cell plasticity through the lens of single cell genomics.
Pascal has investigated epithelial function, including respiratory tissues, in the context of several human pathologies. He was directly associated to the development of state-of-the-art technologies and resources to facilitate the use by academics of DNA microarrays then high throughput sequencing, contributing to the creation of France Génomique, a national infrastructure for high throughput sequencing. In discovAIR, he will coordinate the tasks at CNRS and will be involved in data analysis.
Joachim central expertise is at the interphase of immunoregulation and genomics, with a focus on transcriptional and epigenetic control of cell activation and immunoregulation, particularly in macrophages and monocytes. He works as professor and became head of Genomics and Immunoregulation at the University of Bonn. He will be responsible for the scientific supervision of those parts of discovAIR that will be carried out at the University of Bonn.
Peter leads the Biological Image Analysis and Machine learning group in the Synthetic and Systems Biology at the Biological Research Center (BRC; Szeged, Hungary). In addition, he is the Director of the Institute of Biochemistry at the BRC. In discovAIR, he will be responsible for LCM-based scRNA-seq testing and data analysis and the development of computational methods.
Sylvie has degrees in pulmonology, thoracic oncology, immuno-allergology and rare lung diseases (Lille University France). In 2010, she was recruited by the Nice University Hospital to develop the outpatient clinic for pulmonary diseases, including an cystic fibrosis referral centre, a referral centre for rare lung disease and a referral centre for severe allergies. She also was a key player in the development of clinical research at the Nice University Hospital. In discovAIR she will draft the clinical protocol, setting up procedures in accordance with European and French regulations, recruit patients and follow up.
Pippa has headed up the European Lung Foundation (ELF) since 2005 and has worked together with the Chairs to develop and grow the organisation. More recently, she has focused on information for patients, working with the press and media to ensuring accurate reporting of respiratory science and awareness campaigns for the general public. Pippa has championed the role of the patient within science and has been working with professionals to find best practice for patient and public input into healthcare. She will manage and guide on ELFs input into discovAIR.