Dear reviewer, this GitHub repository is the deposit of source codes for the bioinformatic analyses in the manuscript:

Domien Vanneste^1,2, Wen Peng^1,2, Zhuangzhuang Liu^3,4, Malik Hamaïdia⁵, Raphaël La Rocca^1,2, Joan Abinet^1,2, Alexis Balthazar^2,6, Fabienne Perin⁷, Alexandre Hego⁸, Didier Cataldo⁷, Fabrice Bureau^2,9, Philippe Compère^10,11, Bénédicte Machiels^2,6, Charlotte L. Scott^3,4, Coraline Radermecker^1,2 & Thomas Marichal^1,2,12,13

¹Laboratory of Immunophysiology, GIGA Institute, University of Liège, Liège, Belgium
²Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
³Laboratory of Myeloid Cell Biology in Tissue Damage and Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
⁴Department of Biomedical Molecular Biology, Faculty of Science, Ghent University, Ghent, Belgium
⁵Laboratory of Cellular and Molecular Epigenetics, GIGA Institute, University of Liège, Liège, Belgium
⁶Laboratory of Immunology-Vaccinology, FARAH Institute, University of Liège, Liège, Belgium
⁷Laboratory of Tumour and Development Biology, GIGA Institute, University of Liège, Liège, Belgium
⁸In Vitro Imaging Platform, GIGA Institute, University of Liège, Liège, Belgium
⁹Laboratory of Cellular and Molecular Immunology, GIGA Institute, University of Liège, Liège, Belgium
¹⁰Laboratory of Functional and Evolutionary Morphology, FOCUS Research Unit, Department of Biology, Ecology and Evolution, University of Liège, Liège, Belgium
¹¹Center for Applied Research and Education in Microscopy (CAREM) and Biomaterials Interfaculty Center (CEIB), University of Liège, Liège, Belgium
¹²Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
¹³Lead contact
Correspondence: [email protected] (T.M.) and [email protected] (D.V.)

Homeostatic resident tissue macrophages (RTMs) are characterized by a remarkable diversity but also share common features that are thought to be driven by conserved transcriptional programs. While the transcription factor MafB is highly expressed in the macrophage lineage, little is known about its role in establishing RTM identity and functions. Here, we found that MafB expression gradually increased during macrophage development and was required for the full development of bone-marrow-derived macrophages (BMDMs) and most RTM populations in vivo. The absence of MafB retained RTM in a CD52^high immature stage associated with a disruption of global and tissue-specific RTM identities and functions across organs, impairing phagocytosis, splenic iron recycling, lung, kidney and gut physiology. Mechanistically, epigenetic profiling of MafB binding sites revealed that MafB directly regulated expression of key RTM differentiation and identity genes in mouse and humans, including Csf1r, Mertk, Fcgr1, Cd163 and Zeb2. Finally, in silico analyses showed that MafB binding sites were highly conserved across vertebrates. Our findings demonstrate the crucial and evolutionarily conserved role of MafB as regulator of RTM development and functional identity, connecting MafB-dependent transcriptional programs with unique defining features of RTMs and tissue homeostasis.