A system view of lung fibrogenesis using spatial transcriptomics – Lustra

Pulmonary fibrosis is a deadly disease for which the only therapeutic option is lung transplantation. Pulmonary fibrosis is a chronic and progressive disease characterized by the destruction of the alveoli and its replacement by a fibrotic scar. Alveolar gas exchanges are therefore disrupted thus leading to organ failure and patient's death. The etiology of pulmonary fibrosis is complex. It may be associated with genetic predisposition (e.g. associated to mutations in RTEL1) or it may occur as a complication of thoracic radiotherapy (RIPF, Radiation Induced Pulmonary Fibrosis). Its physiopathology remains poorly characterized although fibroblasts transformation, chronic pro-inflammatory microenvironment as well as senescence are proposed to play a key role in disease progression.
In this project, we will study, in a mouse model of radiation induced pulmonary fibrosis as well as in human lungs after radiotherapy (Pancoast tumor), the molecular and cellular consequences of radiation injury in the alveolar compartment, the functional unit of the lung. For this aim, we will:
• Characterize the transcriptomic profiles of human and mouse lung cells by single cell RNAseq (scRNAseq) in order to identify the markers for each cell type and determine the molecular alterations induced by radiation in the distinct cell types forming the alveoli. This information will be used to infer potential intercellular functional interactions.
• Map the cellular interactions between the alveolar cell types and their spatial rearrangement after irradiation (i.e. from acute pneumonitis to pulmonary fibrosis) by spatial transcriptomic. For this, we will apply a high throughput smFISH strategy that will allow us to visualize dozens of probes simultaneously to unambiguously identify each cell type of the alveolar compartment. High quality images will be acquired in an automated way and will be analyzed using deep learning methods to create a reference map for the alveolus. This physical map will be compared to the functional map.
• With this approach, we will be able to create a model of the alveolar architecture under physiological conditions and determine how these interactions evolve during pneumonitis and fibrogenesis.
Our preliminary results provide a proof of principle for our spatial transcriptomics approach. First analyses of scRNAseq in mouse and human lung as well as spatial transcriptomics, indicate that endothelial cells enter senescence in response to irradiation. Experimentally, we will thus focus primarily on the role of endothelial cells, their transcriptomic profiles and their interaction with other cell types like AT2 cells and macrophages that are known to play a key role in repair, regeneration and fibrosis in the lung. Comparisons between mouse and human data should allow us to identify common molecular signatures specific of pulmonary fibrogenesis. This work has the potential to identify key physiopathogenic pathways that could be therapeutically targeted to prevent pulmonary fibrosis, a disease with very limited therapeutic intervention.