Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts
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 uncl...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmed.2020.00112/full |
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| author | 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 Paul C. Blainey Steven J. Mentzer |
| author_facet | 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 Paul C. Blainey Steven J. Mentzer |
| author_sort | Alexandra B. Ysasi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T14:12:31Z |
| format | Article |
| id | doaj.art-1d3219b82a0046cf97d080489744ae17 |
| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-11T14:12:31Z |
| publishDate | 2020-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-1d3219b82a0046cf97d080489744ae172022-12-22T01:03:21ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2020-04-01710.3389/fmed.2020.00112460382Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar DuctsAlexandra B. Ysasi0Robert D. Bennett1Willi Wagner2Cristian D. Valenzuela3Andrew B. Servais4Akira Tsuda5Saumyadipta Pyne6Shuqiang Li7Jonna Grimsby8Prapti Pokharel9Kenneth J. Livak10Maximilian Ackermann11Paul C. Blainey12Paul C. Blainey13Steven J. Mentzer14Laboratory of Adaptive and Regenerative Biology, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, United StatesLaboratory of Adaptive and Regenerative Biology, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, United StatesInstitute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University, Mainz, GermanyLaboratory of Adaptive and Regenerative Biology, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, United StatesLaboratory of Adaptive and Regenerative Biology, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, United StatesMolecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA, United StatesPublic Health Dynamics Laboratory, University of Pittsburgh, Pittsburgh, PA, United StatesFluidigm Corporation, South San Francisco, CA, United StatesBroad Institute of Harvard and MIT, Cambridge, MA, United StatesBroad Institute of Harvard and MIT, Cambridge, MA, United StatesFluidigm Corporation, South San Francisco, CA, United StatesInstitute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University, Mainz, GermanyBroad Institute of Harvard and MIT, Cambridge, MA, United StatesDepartment of Biological Engineering, MIT, Cambridge, MA, United StatesLaboratory of Adaptive and Regenerative Biology, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, United StatesLung 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.https://www.frontiersin.org/article/10.3389/fmed.2020.00112/fullwarburg effectglucose metabolismaerobic glycolysismetabolic reprogrammingcholangiocarcinoma |
| spellingShingle | 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 Paul C. Blainey Steven J. Mentzer Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts Frontiers in Medicine warburg effect glucose metabolism aerobic glycolysis metabolic reprogramming cholangiocarcinoma |
| title | Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts |
| title_full | Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts |
| title_fullStr | Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts |
| title_full_unstemmed | Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts |
| title_short | Single-Cell Transcriptional Profiling of Cells Derived From Regenerating Alveolar Ducts |
| title_sort | single cell transcriptional profiling of cells derived from regenerating alveolar ducts |
| topic | warburg effect glucose metabolism aerobic glycolysis metabolic reprogramming cholangiocarcinoma |
| url | https://www.frontiersin.org/article/10.3389/fmed.2020.00112/full |
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