The cellular heterogeneity of the human pancreas has not been previously characterized due to the presence of extreme digestive enzymatic activities, causing rapid degradation of cells and RNA upon resection. Therefore, previous cellular mapping studies based on gene expression were focused on pancreatic islets, leading to a vast underrepresentation of the exocrine compartment. By profiling the transcriptome of more than 110,000 cells from human donors, we created the first comprehensive pancreas cell atlas including all the tissue components. We unveiled the existence of four different acinar cell states and suggest a division of labor for enzyme production within the healthy exocrine pancreas, which has so far been considered a homogeneous tissue. This work provides a novel and rich resource for future investigations of the healthy and diseased pancreas.
Main textSingle-cell RNA sequencing (scRNA-seq) has tremendously expanded our understanding of heterogeneous human tissues and made the identification of novel functional cell types in the lung, brain and liver possible 1-5 . The development of single-nucleus RNA-seq (sNuc-seq) has further broadened its application to tissues which are difficult to dissociate or already archived, such as clinical samples 6 . Pancreatic exocrine tissues contain among the highest level of digestive enzymatic activities in the human body 7 , hindering the preparation of undegraded RNA from this organ. Therefore, previous scRNA-seq studies of the human pancreas have been restricted to the islets of Langerhans (the endocrine part of the organ) in order to remove the exocrine compartment, namely the acinar and ductal cells responsible for the production and transport of digestive enzymes. Following their isolation, the endocrine islets were cultured in vitro, enzymatically dissociated and processed on microfluidics devices before next-generation sequencing [8][9][10][11][12][13][14] . While this strategy proved to be successful in generating a draft of the endocrine human pancreas cell atlas, it has distinct disadvantages. For example, only a very small number of exocrine cells have been captured and their numbers are largely underrepresented relative to homeostatic physiological conditions (approximately 5% rather than 95%). Moreover, in vitro culture and dissociation steps are known to introduce technical artefacts in gene expression measurements 15 . In this work we opted to use flash-frozen tissue biopsies isolated from pancreata of six human donors followed by sNuc-seq ( Fig. 1a), avoiding in vitro expansion and dissociation procedures, aiming to obtain an unbiased sampling of the organ.