Novel Approach for Pancreas Transcriptomics Reveals the Cellular Landscape in Homeostasis and Acute Pancreatitis

Area of Science:

• Pancreatology
• Single-cell genomics
• Immunology

Background:

• Acinar cells in the exocrine pancreas pose challenges for transcriptomic studies due to digestive enzyme production.
• Current single-cell RNA-sequencing (scRNA-seq) methods underrepresent pancreatic acinar cells.
• A need exists for improved methods to study pancreatic cell responses in disease.

Purpose of the Study:

• To develop an innovative method for overcoming transcriptomic characterization challenges in pancreatic acinar cells.
• To accelerate the study of the pancreas in both healthy and diseased states.
• To provide a robust approach for capturing pancreatic cell responses during acute pancreatitis.

Main Methods:

• Utilized FixNCut, a reversible tissue fixation technique prior to single-cell preparation.
• Applied FixNCut to a mouse model of acute pancreatitis.
• Validated findings with GeoMx whole transcriptome atlas profiling and integrated human and mouse datasets.

Main Results:

• Achieved unprecedented definition of pancreatic acinar and immune cell populations in homeostasis and acute pancreatitis.
• Identified transcriptomic changes across major cell types during pancreatic injury and recovery.
• Characterized immune cell responses, including neutrophil infiltration and macrophage transcriptome shifts, and T-cell polarization towards type-2 immunity.

Conclusions:

• FixNCut effectively preserves pancreatic transcriptomes, enabling the discovery of novel cell states.
• The method provides a broadly applicable approach for studying pancreas biology and disease.
• Established a reference atlas for pancreas research, aiding in understanding homeostasis and pancreatitis.