Tissue signatures of human macrophages during homeostasis and activation

Human macrophages (MΦs) reside in tissues and develop tissue-specific identities. While studies in mice have identified molecular signatures for site-specific MΦ differentiation, less is known about the transcriptional profiles of human MΦs in distinct sites, including mucosal tissues and lymphoid organs during homeostasis and activation. Here, we use multimodal single-cell sequencing and ex vivo stimulation assays to define tissue signatures for populations of human MΦs isolated from lungs, small intestine, spleen, bone marrow, and lymph nodes obtained from individual organ donors. Our results reveal distinct tissue-adapted gene and protein profiles of metabolic, adhesion, and immune interaction pathways, which are specific to MΦs and not monocytes isolated from the same sites and exhibit homology to murine MΦs from the same sites. Tissue-adapted MΦs remained responsive to polarizing cytokine stimuli ex vivo, with upregulation of expected transcripts and secreted proteins, while retaining tissue-specific profiles. Patterns of chromatin accessibility in tissue MΦs identified from single-nucleus assay for transposase-accessible chromatin by sequencing reflected gene expression signatures and indicate that differential utilization of transcription factors may drive stable tissue-adapted profiles. Together, our findings show how human MΦ identity is coupled to their site of residence for mucosal and lymphoid organs and is intrinsically maintained during activation and polarization.