Identification of human macrophage tissue signatures at homeostasis and during polarization

Human macrophages (MΦs) reside in tissues and develop tissue-specific identities. Murine studies have dissected molecular signatures of tissue MΦ differentiation, but the translatability of these findings to human systems and the maintenance of these identities during MΦ activation is relatively unexplored. Here, we use multimodal single-cell sequencing and ex vivo stimulation to uncover MΦ tissue signatures in human lung, small intestine, spleen, bone marrow, and lymph nodes. Tissue-adapted gene and protein profiles were specific to MΦs, not monocytes isolated from the same sites, and biased populations to distinct metabolomic, adhesion, and immune profiles which were concordant with previous murine signatures. Tissue-adapted MΦs remained responsive to distinct cytokine polarization ex vivo, upregulating gene signatures and producing cytokines consistent with monocyte polarization. Despite this plasticity, MΦs maintain their tissue-specific phenotypes ex vivo, demonstrating memory and persistence of their tissue-specific programs in the absence of continuous external signaling. CITE-seq of human macrophages and monocytes isolated from different human organ donor tissues and cultured for 12 hours in media, or stimulated with LPS+IFNγ or IL-4