Dissecting differentiation and diversification of gut macrophages

Macrophages reside in virtually all organs and play a key role in host defense and tissue homeostasis. Tissue macrophages are particularly important in the gut where they defend the body against a wide variety of pathogens and toxic substances.
However, gut macrophages also contribute to pathology. Aberrant activation of macrophages plays an important role in disorders such as inflammatory bowel disease (IBD; ulcerative colitis and Crohn’s disease), necrotizing enterocolitis in infants and mobility dysfunctions. Importantly also, tumor-associated macrophages in colorectal cancer can promote cancer growth.
Although gut macrophages are instrumental in both host defense and pathology, knowledge about their origin, heterogeneity and functional properties is scarce. To increase our understanding of macrophages in the intestine we recently performed transcriptional, phenotypical and functional profiling of tissue macrophages in the human small intestine. We found that macrophages consist of several transcriptional states and by examining gut macrophages in a unique organ transplantation setting we found that blood monocytes emigrated into duodenal transplants and differentiated, through short-lived intermediates, into mature macrophages that survive for months.
To get a deeper understanding of macrophage diversity and functions we have applied single cell RNA sequencing to analyze macrophages isolated from the intestinal mucosa and the underlying smooth muscle layers (muscularis propria). We find that there is an unexpected macrophage heterogeneity within both compartments and between the compartments. Our findings raise several questions we will address in this project: What are the microenvironmental signals that imprint macrophage identity and diversity? Since macrophages are so diverse, is it possible to reprogram macrophages? And do they all originate from the same precursor cells?
We will apply an integrated approach combining high throughput single-cell technologies with unique clinical material and 3D organ cultures. Computational integration of the data will provide a spatiotemporal reconstruction of how monocyte-to-macrophage differentiation and diversification in the human gut is regulated and reveal functional properties.

Immunofluorescence image of macrophages (CD68/CD163, green) in mucosa and submucosa of colon. Lyve1+ macrophages (yellow) are only found in submucosa.
UMAP clustering (A), dot plot (B) and UMAP (C) of selected genes, and pseudotime trajectory (D) of macrophages derived from colonic mucosa
Spatial Trancriptomics visualizing S100A8/A9+ (left) and HLA class II high macrophages (right) in colon.