Single-nucleus and in situ RNA-sequencing reveal cell topographies in the human pancreas
Open accessPublished version of a preprint
Abstract
Background & aims Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been yet established because of the local concentration and cascade of hydrolytic enzymes that can rapidly degrade cells and RNA upon pancreatic resection. We sought to better understand the heterogeneity and cellular composition of the pancreas in neonates and adults in healthy and diseased conditions using single-cell sequencing approaches. Methods We innovated single-nucleus RNA-sequencing protocols and profiled more than 120,000 cells from pancreata of adult and neonatal human donors. We validated the single-nucleus findings using RNA fluorescence in situ hybridization, in situ sequencing, and computational approaches. Results We created the first comprehensive atlas of human pancreas cells including epithelial and nonepithelial constituents, and uncovered 3 distinct acinar cell types, with possible implications for homeostatic and inflammatory processes of the pancreas. The comparison with neonatal single-nucleus sequencing data showed a different cellular composition of the endocrine tissue, highlighting the tissue dynamics occurring during development. By applying spatial cartography, involving cell proximity mapping through in situ sequencing, we found evidence of specific cell type neighborhoods, dynamic topographies in the endocrine and exocrine pancreas, and principles of morphologic organization of the organ. Furthermore, similar analyses in chronic pancreatitis b…
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Recently, a few protocols have been introduced to enhance RNA quality by employing VRC or acidic buffers during nucleus isolation for snRNA-seq, particularly for kidney and pancreas samples.
“Recently, we encountered a few protocols that have been introduced to enhance RNA quality by employing VRC or acidic buffers during nucleus isolation for snRNA-seq, particularly for kidney (Soccio et al., 2014) and pancreas (Tosti et al., 2021) samples.”
From Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity (2025) · cites this paper as Tosti et al., 2021
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- Authors
- Tosti, L., Hang, Y., Debnath, O., Tiesmeyer, S., Trefzer, T., Steiger, K., Ten, F. W., Lukassen, S., Ballke, S., Kühl, A. A., Spieckermann, S., Bottino, R., Ishaque, N., Weichert, W., Kim, S. K., Eils, R., & Conrad, C.
- Affiliations
- Humboldt-Universität zu Berlin (DE)
- Stanford Medicine (US)
- Technical University of Munich (DE)
- Allegheny Health Network (US)
- Heidelberg University (DE)
- Corresponding author
- Kim, Seung K.
- Eils, Roland
- Conrad, Christian
- ORCID
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 160
- Issue
- 4
- Pages
- 1330-1344.e11
- ISSN
- 0016-5085 (ISSN-L)
- OpenAlex
- W3106000943
- Cited by
- 228
- References
- 12
- Citations by year
- 2026: 37 · 2025: 36 · 2024: 42 · 2023: 43 · 2022: 36 · 2021: 28 · 2020: 6
- FWCI
- 9.16
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Gastroenterology (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- mediaTUM (Technical University of Munich) (submittedVersion)
- Funders
- Chan Zuckerberg Initiative
- European Commission
- H2020 Marie Skłodowska-Curie Actions
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Surgery › Pancreatic function and diabetes
- Health Sciences › Medicine › Oncology › Pancreatic and Hepatic Oncology Research
- Keywords
- human pancreas, single-nucleus RNA sequencing, in situ sequencing, spatial transcriptomics, pancreatic development, neonatal pancreas, chronic pancreatitis, tuft cells, macrophages, cell topography
- MeSH terms
- RNA-Seq, Adolescent, Adult, Age Factors, Aged, Animals, Cell Fractionation, Cell Nucleus, Child, Child, Preschool, Female, Humans, Infant, Male, Middle Aged, Swine, In Situ Hybridization, Fluorescence, Models, Animal, Pancreas, Exocrine, Young Adult, Single-Cell Analysis
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