Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts

• Main Authors: Alexandra B. Ysasi, Robert D. Bennett, Willi Wagner, Cristian D. Valenzuela, Andrew B. Servais, Akira Tsuda, Saumyadipta Pyne, Shuqiang Li, Jonna Grimsby, Prapti Pokharel, Kenneth J. Livak, Maximilian Ackermann, Paul C. Blainey, Steven J. Mentzer
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-04-01
• Series: Frontiers in Medicine
• Subjects: warburg effect; glucose metabolism; aerobic glycolysis; metabolic reprogramming; cholangiocarcinoma
• Online Access: https://www.frontiersin.org/article/10.3389/fmed.2020.00112/full

Lung regeneration occurs in a variety of adult mammals after surgical removal of one lung (pneumonectomy). Previous studies of murine post-pneumonectomy lung growth have identified regenerative “hotspots” in subpleural alveolar ducts; however, the cell-types participating in this process remain unclear. To identify the single cells participating in post-pneumonectomy lung growth, we used laser microdissection, enzymatic digestion and microfluidic isolation. Single-cell transcriptional analysis of the murine alveolar duct cells was performed using the C1 integrated fluidic circuit (Fluidigm) and a custom PCR panel designed for lung growth and repair genes. The multi-dimensional data set was analyzed using visualization software based on the tSNE algorithm. The analysis identified 6 cell clusters; 1 cell cluster was present only after pneumonectomy. This post-pneumonectomy cluster was significantly less transcriptionally active than 3 other clusters and may represent a transitional cell population. A provisional cluster identity for 4 of the 6 cell clusters was obtained by embedding bulk transcriptional data into the tSNE analysis. The transcriptional pattern of the 6 clusters was further analyzed for genes associated with lung repair, matrix production, and angiogenesis. The data demonstrated that multiple cell-types (clusters) transcribed genes linked to these basic functions. We conclude that the coordinated gene expression across multiple cell clusters is likely a response to a shared regenerative microenvironment within the subpleural alveolar ducts.