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Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung

ABSTRACT: Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.

ORGANISM(S): Mus musculus

PROVIDER: GSE223816 | GEO | 2024/01/16

REPOSITORIES: GEO

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Project description:Injury of the lung epithelium is one of the initial events driving acute lung diseases such as acute lung injury and acute respiratory distress syndrome. Repeated epithelial injury followed by aberrant repair leads to fibroblast activation and extracellular matrix deposition and is therefore considered as the major cause of chronic pulmonary diseases, such as idiopathic pulmonary fibrosis. In vitro models as well as in vivo animal models are necessary to investigate early disease mechanisms and altered signalling pathways of epithelial cells. One way to target specific cells is the diphtheria toxin receptor/diphtheria toxin (DTR/DT) system. The human DTR (hDTR) is sensitive to DT, thereby inducing cell death by blocking protein synthesis, while the murine DTR is at least 10^5 times more resistant to DT. Consequently, expression of the hDTR and application of DT lead to targeted cell depletion. Therefore, a novel and flexible DTR/DT model of acute epithelial lung injury was established and described recently, which is driven by adeno-associated virus (AAV) variant 6.2 mediated hDTR expression. The AAV6.2 vector transduces specifically into bronchial epithelial and alveolar epithelial type II cells leading to their depletion after DT administration. In this study we analysed the bulk lung proteome of the recently established AAV-DTR/DT mouse model of acute epithelial lung injury, providing a detailed insight into proteomic changes upon injury. Frozen pulverized lung tissue samples (~10 mg per sample) from AAV-stuffer control (1 E11 viral genome, n=7) and AAV-hDTR (0.3 E11 viral genome, n=7) treated mice 24 h after intratracheal application of 100 ng DT were analysed in a TMTpro-based workflow. TMTpro-labelled peptides were fractionated into 24 fractions using off-line high pH reversed phase chromatography. Fractions were analysed on an Orbitrap Eclipse Tribrid mass spectrometer in combination with the FAIMS Pro Interface (Thermo Scientific) using a SPS-MS3 based method including real-time search.

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Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung

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