Novel approach for pancreas transcriptomics reveals the cellular landscape in homeostasis and acute pancreatitis Journal Article
| Authors: | Aney, K. J.; Jeong, W. J.; Vallejo, A. F.; Burdziak, C.; Chen, E.; Wang, A.; Koak, P.; Wise, K.; Jensen, K.; Pe'er, D.; Dougan, S. K.; Martelotto, L.; Nissim, S. |
| Article Title: | Novel approach for pancreas transcriptomics reveals the cellular landscape in homeostasis and acute pancreatitis |
| Abstract: | Background & Aims: Acinar cells produce digestive enzymes that impede transcriptomic characterization of the exocrine pancreas. Thus, single-cell RNA-sequencing studies of the pancreas underrepresent acinar cells relative to histological expectations, and a robust approach to capture pancreatic cell responses in disease states is needed. We sought to innovate a method that overcomes these challenges to accelerate study of the pancreas in health and disease. Methods: We leverage FixNCut, a single-cell RNA-sequencing approach in which tissue is reversibly fixed with dithiobis(succinimidyl propionate) before dissociation and single-cell preparation. We apply FixNCut to an established mouse model of acute pancreatitis, validate findings using GeoMx whole transcriptome atlas profiling, and integrate our data with prior studies to compare our method in both mouse and human pancreas datasets. Results: FixNCut achieves unprecedented definition of challenging pancreatic cells, including acinar and immune populations in homeostasis and acute pancreatitis, and identifies changes in all major cell types during injury and recovery. We define the acinar transcriptome during homeostasis and acinar-to-ductal metaplasia and establish a unique gene set to measure deviation from normal acinar identity. We characterize pancreatic immune cells, and analysis of T-cell subsets reveals a polarization of the homeostatic pancreas toward type-2 immunity. We report immune responses during acute pancreatitis and recovery, including early neutrophil infiltration, expansion of dendritic cell subsets, and a substantial shift in the transcriptome of macrophages due to both resident macrophage activation and monocyte infiltration. Conclusions: FixNCut preserves pancreatic transcriptomes to uncover novel cell states during homeostasis and following pancreatitis, establishing a broadly applicable approach and reference atlas for study of pancreas biology and disease. © 2024 AGA Institute |
| Keywords: | adult; controlled study; metaplasia; genetics; nonhuman; pancreas; animal cell; mouse; animal; metabolism; animals; mice; animal tissue; gene expression profiling; cell infiltration; dendritic cell; animal experiment; animal model; pathology; transcriptomics; mice, inbred c57bl; c57bl mouse; disease model; th2 cell; cellular immunity; immune response; transcription regulation; neutrophil; pancreatitis; fibroblast; monocyte; disease models, animal; macrophage; macrophages; homeostasis; cell metabolism; transcriptome; cell expansion; t lymphocyte subpopulation; immunocompetent cell; acinar cell; acute disease; single cell analysis; single-cell analysis; macrophage activation; pancreas cell; rna-seq; procedures; acute pancreatitis; pancreas, exocrine; humans; human; male; article; rna sequencing; acinar-to-ductal metaplasia; exocrine pancreas; single cell rna seq; whole transcriptome sequencing; acinar cells; dithiobis(succinimidyl propionate); fixncut; pancreas single-cell rna-sequencing; 3,3' dithiobis(succinimidyl propionate) |
| Journal Title: | Gastroenterology |
| Volume: | 166 |
| Issue: | 6 |
| ISSN: | 0016-5085 |
| Publisher: | Elsevier Inc. |
| Date Published: | 2024-06-01 |
| Start Page: | 1100 |
| End Page: | 1113 |
| Language: | English |
| DOI: | 10.1053/j.gastro.2024.01.043 |
| PUBMED: | 38325760 |
| PROVIDER: | scopus |
| PMCID: | PMC11102849 |
| DOI/URL: | |
| Notes: | Article -- Source: Scopus |
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