Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
- Author
- Martin Guilliams (UGent) , Johnny Bonnardel (UGent) , Birthe Haest (UGent) , Bart Vanderborght (UGent) , Camille Wagner (UGent) , Anneleen Remmerie, Anna Bujko (UGent) , Liesbet Martens (UGent) , Tinne Thoné (UGent) , Robin Browaeys (UGent) , Federico Francesco De Ponti (UGent) , Bavo Vanneste (UGent) , Christian Zwicker (UGent) , Freya Svedberg (UGent) , Tineke Vanhalewyn (UGent) , Amanda Gonçalves (UGent) , Saskia Lippens (UGent) , Bert Devriendt (UGent) , Eric Cox (UGent) , Giuliano Ferrero, Valerie Wittamer, Andy Willaert (UGent) , Suzanne J.F. Kaptein, Johan Neyts, Kai Dallmeier, Peter Geldhof (UGent) , Stijn Casaert (UGent) , Bart Deplancke, Peter ten Dijke, Anne Hoorens (UGent) , Aude Vanlander, Frederik Berrevoet (UGent) , Yves Van Nieuwenhove (UGent) , Yvan Saeys (UGent) , Wouter Saelens (UGent) , Hans Van Vlierberghe (UGent) , Lindsey Devisscher (UGent) and Charlotte Scott (UGent)
- Organization
-
- Department of Biomedical molecular biology
- VIB
- Department of Internal Medicine and Pediatrics
- Department of Applied mathematics, computer science and statistics
- Department of Biology
- Department of Translational Physiology, Infectiology and Public Health
- Department of Biomolecular Medicine
- Department of Diagnostic Sciences
- Ghent University Hospital
- Department of Human Structure and Repair
- Department of Basic and Applied Medical Sciences
- Project
-
- Unravelling cellular heterogeneity and dynamics in normal and malignant hematopoiesis using singlecell bioinformatics
- Study of the origins and functions of distinct hepatic macrophage subsets in the pathogenesis of acute liver failure.
- Investigating the role of ZEB transcription factors in cDC biology
- iPSC-based parenchymal and sinusoidal liver cell mimics for DILI and NAFLD studies (iPSC-LiMic)
- Unraveling the cell-cell interactions driving liver regeneration
- Modelling intercellular signaling events during cellular differentiation from single-cell transcriptomics data
- Investigating the function and development of ‘lipid-associated macrophages’ (LAMs) in liver fibrosis across species.
- Abstract
- The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITEseq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multiomic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells, including a population of lipid-associated macrophages (LAMs) at the bile ducts. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and LAMs. We also uncover the respective spatially resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that LAMs are induced by local lipid exposure, leading to their induction in steatotic regions of the murine and human liver, while Kupffer cell development crucially depends on their cross-talk with hepatic stellate cells via the evolutionarily conserved ALK1-BMP9/10 axis.
- Keywords
- General Biochemistry, Genetics and Molecular Biology, hepatic cells, KUPFFER CELLS, SINGLE, STEATOHEPATITIS, VISUALIZATION, ENDOTHELIUM, FEATURES, LIGANDS, NETWORK, IMAGE
Downloads
-
published.pdf
- full text (Published version)
- |
- open access
- |
- |
- 22.26 MB
Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-8738275
- MLA
- Guilliams, Martin, et al. “Spatial Proteogenomics Reveals Distinct and Evolutionarily Conserved Hepatic Macrophage Niches.” CELL, vol. 185, no. 2, 2022, pp. 379–96, doi:10.1016/j.cell.2021.12.018.
- APA
- Guilliams, M., Bonnardel, J., Haest, B., Vanderborght, B., Wagner, C., Remmerie, A., … Scott, C. (2022). Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. CELL, 185(2), 379–396. https://doi.org/10.1016/j.cell.2021.12.018
- Chicago author-date
- Guilliams, Martin, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Camille Wagner, Anneleen Remmerie, Anna Bujko, et al. 2022. “Spatial Proteogenomics Reveals Distinct and Evolutionarily Conserved Hepatic Macrophage Niches.” CELL 185 (2): 379–96. https://doi.org/10.1016/j.cell.2021.12.018.
- Chicago author-date (all authors)
- Guilliams, Martin, Johnny Bonnardel, Birthe Haest, Bart Vanderborght, Camille Wagner, Anneleen Remmerie, Anna Bujko, Liesbet Martens, Tinne Thoné, Robin Browaeys, Federico Francesco De Ponti, Bavo Vanneste, Christian Zwicker, Freya Svedberg, Tineke Vanhalewyn, Amanda Gonçalves, Saskia Lippens, Bert Devriendt, Eric Cox, Giuliano Ferrero, Valerie Wittamer, Andy Willaert, Suzanne J.F. Kaptein, Johan Neyts, Kai Dallmeier, Peter Geldhof, Stijn Casaert, Bart Deplancke, Peter ten Dijke, Anne Hoorens, Aude Vanlander, Frederik Berrevoet, Yves Van Nieuwenhove, Yvan Saeys, Wouter Saelens, Hans Van Vlierberghe, Lindsey Devisscher, and Charlotte Scott. 2022. “Spatial Proteogenomics Reveals Distinct and Evolutionarily Conserved Hepatic Macrophage Niches.” CELL 185 (2): 379–396. doi:10.1016/j.cell.2021.12.018.
- Vancouver
- 1.Guilliams M, Bonnardel J, Haest B, Vanderborght B, Wagner C, Remmerie A, et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. CELL. 2022;185(2):379–96.
- IEEE
- [1]M. Guilliams et al., “Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches,” CELL, vol. 185, no. 2, pp. 379–396, 2022.
@article{8738275,
abstract = {{The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITEseq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multiomic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells, including a population of lipid-associated macrophages (LAMs) at the bile ducts. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and LAMs. We also uncover the respective spatially resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that LAMs are induced by local lipid exposure, leading to their induction in steatotic regions of the murine and human liver, while Kupffer cell development crucially depends on their cross-talk with hepatic stellate cells via the evolutionarily conserved ALK1-BMP9/10 axis.}},
author = {{Guilliams, Martin and Bonnardel, Johnny and Haest, Birthe and Vanderborght, Bart and Wagner, Camille and Remmerie, Anneleen and Bujko, Anna and Martens, Liesbet and Thoné, Tinne and Browaeys, Robin and De Ponti, Federico Francesco and Vanneste, Bavo and Zwicker, Christian and Svedberg, Freya and Vanhalewyn, Tineke and Gonçalves, Amanda and Lippens, Saskia and Devriendt, Bert and Cox, Eric and Ferrero, Giuliano and Wittamer, Valerie and Willaert, Andy and Kaptein, Suzanne J.F. and Neyts, Johan and Dallmeier, Kai and Geldhof, Peter and Casaert, Stijn and Deplancke, Bart and ten Dijke, Peter and Hoorens, Anne and Vanlander, Aude and Berrevoet, Frederik and Van Nieuwenhove, Yves and Saeys, Yvan and Saelens, Wouter and Van Vlierberghe, Hans and Devisscher, Lindsey and Scott, Charlotte}},
issn = {{0092-8674}},
journal = {{CELL}},
keywords = {{General Biochemistry,Genetics and Molecular Biology,hepatic cells,KUPFFER CELLS,SINGLE,STEATOHEPATITIS,VISUALIZATION,ENDOTHELIUM,FEATURES,LIGANDS,NETWORK,IMAGE}},
language = {{eng}},
number = {{2}},
pages = {{379--396}},
title = {{Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches}},
url = {{http://doi.org/10.1016/j.cell.2021.12.018}},
volume = {{185}},
year = {{2022}},
}
- Altmetric
- View in Altmetric
- Web of Science
- Times cited: