Macrophage and neutrophil heterogeneity at single-cell spatial resolution in inflammatory bowel disease

Ulcerative colitis (UC) and Crohn’s disease (CD) are chronic inflammatory intestinal diseases that show a perplexing heterogeneity in manifestations and response to treatment. The molecular basis for this heterogeneity remains uncharacterized. We applied single-cell RNA sequencing and CosMx™ Spatial Molecular Imaging to human colon and found the highest diversity in cellular composition in the myeloid compartment of UC and CD patients. Besides resident macrophage subsets (M0 and M2), patients showed a variety of activated macrophages including classical (M1 CXCL5 and M1 ACOD1) and new inflammation-dependent alternative (IDA) macrophages. In addition, we captured intestinal neutrophils in three transcriptional states. Subepithelial IDA macrophages expressed NRG1 , which promotes epithelial differentiation. In contrast, NRG1 low IDA macrophages were expanded within the submucosa and in granulomas, in proximity to abundant inflammatory fibroblasts, which we suggest may promote macrophage activation. We conclude that macrophages sense and respond to unique tissue microenvironments, potentially contributing to patient-to-patient heterogeneity. ### Competing Interest Statement H.H. is co-founder of Omniscope and a scientific advisory board member of MiRXES. A.S. is the recipient of research grants from Roche-Genentech, Abbvie, GSK, Scipher Medicine, Pfizer, Alimentiv, Inc, Boehringer Ingelheim and Agomab; receives consulting fees from Genentech, GSK, Pfizer, HotSpot Therapeutics, Alimentiv, Origo Biopharma, Deep Track Capital, Great Point Partners and Boxer Capital; and is on the advisory boards of BioMAdvanced Diagnostics, Goodgut and Orikine. M.E. has received support for conference attendance and research support from Abbvie, Biogen, Faes Farma, Ferring, Jannsen, MSD, Pfizer, Takeda, and Tillotts. J.P. received financial support for research from AbbVie and Pfizer; consultancy fees/honorarium from AbbVie, Arena, Athos, Atomwise, Boehringer Ingelheim, Celgene, Celltrion, Ferring, Galapagos, Genentech/Roche, GlaxoSmithKline, Janssen, Mirum, Morphic, Nestle, Origo, Pandion, Pfizer, Progenity, Protagonist, Revolo, Robarts, Takeda, Theravance and Wasserman; reports payment for lectures including service on speaker bureau from Abbott, Ferring, Janssen, Pfizer and Takeda; and reports payment for development of educational presentations from Abbott, Janssen, Pfizer Roche and Takeda. A.M.C has received financial support for conference attendance, educational activities, and research support from Abbvie, Biogen, Ferring, Jannsen, MSD, Takeda, Dr. Falk Pharma and Tillotts. E.K, Y.K, and M.L. are current/former employees and shareholders of NanoString Technologies. S.V. is a current employee of Boehringer-Ingelheim Pharmaceuticals.