{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T20:56:10Z","timestamp":1793134570533,"version":"4.5.0"},"reference-count":99,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T00:00:00Z","timestamp":1765497600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Seed Networks for the Human Cell Atlas"},{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"publisher","award":["CZF2019-002452"],"award-info":[{"award-number":["CZF2019-002452"]}],"id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Aging Biology Foundation","award":["CU19-2301"],"award-info":[{"award-number":["CU19-2301"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["AI106697"],"award-info":[{"award-number":["AI106697"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["AI057266"],"award-info":[{"award-number":["AI057266"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Columbia University Graduate Training Program in Microbiology and Immunology","award":["T32AI106711"],"award-info":[{"award-number":["T32AI106711"]}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Columbia Stem Cell Initiative Flow Cytometry Core"},{"name":"Columbia Center for Translational Immunology Flow Cytometry Core"},{"name":"Herbert Irving Comprehensive Cancer Center Flow Cytometry Shared Resources"},{"name":"Sulzberger Columbia Genome Center"},{"name":"Columbia Single Cell Analysis Core","award":["P30CA013696"],"award-info":[{"award-number":["P30CA013696"]}]},{"name":"Columbia Single Cell Analysis Core","award":["P30DK132710"],"award-info":[{"award-number":["P30DK132710"]}]},{"name":"Columbia Single Cell Analysis Core","award":["S10OD030282"],"award-info":[{"award-number":["S10OD030282"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Human macrophages (M\u03a6s) reside in tissues and develop tissue-specific identities. While studies in mice have identified molecular signatures for site-specific M\u03a6 differentiation, less is known about the transcriptional profiles of human M\u03a6s 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 M\u03a6s 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 M\u03a6s and not monocytes isolated from the same sites and exhibit homology to murine M\u03a6s from the same sites. Tissue-adapted M\u03a6s 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 M\u03a6s 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 M\u03a6 identity is coupled to their site of residence for mucosal and lymphoid organs and is intrinsically maintained during activation and polarization.<\/jats:p>","DOI":"10.1093\/jimmun\/vkaf317","type":"journal-article","created":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T15:08:46Z","timestamp":1765552126000},"source":"Crossref","is-referenced-by-count":3,"title":["Tissue signatures of human macrophages during homeostasis and activation"],"prefix":"10.1093","volume":"215","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1500-8713","authenticated-orcid":false,"given":"Daniel P","family":"Caron","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9198-7743","authenticated-orcid":false,"given":"William L","family":"Specht","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddhi","family":"Nargund","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9710-1857","authenticated-orcid":false,"given":"David","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5428-0683","authenticated-orcid":false,"given":"Steven 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A","family":"Sims","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]},{"name":"Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center , New York, NY,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8236-9183","authenticated-orcid":false,"given":"Donna L","family":"Farber","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Columbia University Irving Medical Center , New York, NY,","place":["United States"]},{"name":"Department of Surgery, Columbia University Irving Medical Center , New York, NY,","place":["United 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