Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Martin Guilliams ,Bavo Vanneste ,Johan Neyts ,Yves Van Nieuwenhove ,Kai Dallmeier ,Wouter Saelens ,Peter Ten Dijke ,Yvan Saeys ,Robin Browaeys ,Lindsey Devisscher ,C Zwicker ,Valérie Wittamer ,Johnny Bonnardel ,Giuliano Ferrero ,Birthe Haest ,Amanda Gonçalves ,Saskia Lippens ,Suzanne Kaptein ,Anne Hoorens ,Anna Bujko ,Bart Deplancke ,Peter Geldhof ,Aude Vanlander ,Federico Ponti ,Tineke Vanhalewyn ,Freya R Svedberg ,Camille Wagner ,Stijn Casaert ,Liesbet Martens ,Bart Vanderborght ,Eric Cox ,Frederik Berrevoet ,Andy Willaert ,Anneleen Remmerie ,Hans Van Vlierberghe ,Bert Devriendt ,Tinne Thoné ,Charlotte Scott

doi:10.1016/j.cell.2021.12.018

Abstract

SummaryThe 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 CITE-seq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multi-omic 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.

Highlights

The immense advances in single-cell transcriptomics have enabled a better understanding of the cellular composition of different organs across species
A practical proteogenomic atlas of the murine liver To generate a proteogenomic atlas of the liver, we first examined the optimal method for retrieving all hepatic cells
As we sought to generate a proteogenomic atlas of all hepatic cells, we opted to use a combination of all protocols

Summary

Introduction

The immense advances in single-cell transcriptomics have enabled a better understanding of the cellular composition of different organs across species. While the spatial organization of hepatocytes within the liver is understood (Halpern et al, 2017), that of nonparenchymal liver cells remains unclear. This is the case for the mouse liver, but even more so for the human liver, where the identity and the precise localization of most hepatic cells is unknown. The link between the transcriptome and the proteome has not been studied, resulting in a lack of reliable surface markers to identify these cells by flow cytometry and confocal microscopy. We used proteogenomic techniques including cellular indexing of transcriptomes and epitomes by sequencing (CITE-seq) and spatial approaches to identify all cells and their specific locations within the healthy and obese livers of mice and humans. Demonstrating the usefulness of this approach, we identify the evolutionary conserved and spatially restricted signals driving the distinct hepatic macrophage phenotypes

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Results

Discussion

Conclusion