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Using integrated single-cell analysis of mouse and human atherosclerosis, we here aimed to refine the nomenclature of mononuclear phagocytes in atherosclerotic vessels and to compare their transcriptomic profiles in mouse and human disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods and results<\/jats:title>\n                    <jats:p>We integrated 12 single-cell RNA-sequencing (scRNA-seq) datasets of immune cells isolated from healthy or atherosclerotic mouse aortas, and data from 11 patients (n = 4 coronary vessels, n = 7 carotid endarterectomy specimens) from two studies. Integration of mouse data identified subpopulations with discrete transcriptomic signatures within previously described populations of aortic resident (Lyve1), inflammatory (Il1b), as well as foamy (Trem2hi) macrophages. We identified unique transcriptomic features distinguishing aortic intimal resident macrophages from atherosclerosis-associated Trem2hi macrophages. Also, populations of Xcr1+ Type 1 classical DCs (cDC1), Cd209a+ cDC2, and mature DCs (Ccr7, Fscn1) with a \u2018mreg-DC\u2019 signature were detected. In humans, we uncovered macrophage and DC populations with gene expression patterns similar to those observed in mice. In particular, core transcripts of the foamy\/Trem2hi signature (TREM2, SPP1, GPNMB, CD9) mapped to a specific population of macrophages in human lesions. Comparison of mouse and human data and direct cross-species data integration suggested transcriptionally similar macrophage and DC populations in mice and humans.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We refined the nomenclature of mononuclear phagocytes in mouse atherosclerotic vessels, and show conserved transcriptomic features of macrophages and DCs in atherosclerosis in mice and humans, emphasizing the relevance of mouse models to study mononuclear phagocytes in atherosclerosis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/cvr\/cvac161","type":"journal-article","created":{"date-parts":[[2022,9,30]],"date-time":"2022-09-30T16:19:30Z","timestamp":1664554770000},"page":"1676-1689","source":"Crossref","is-referenced-by-count":196,"title":["Integrated single-cell analysis-based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis"],"prefix":"10.1093","volume":"119","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8551-4729","authenticated-orcid":false,"given":"Alma","family":"Zernecke","sequence":"first","affiliation":[{"name":"Institute of Experimental Biomedicine, University Hospital W\u00fcrzburg , Josef Schneider Str. 2, 97080 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3574-6983","authenticated-orcid":false,"given":"Florian","family":"Erhard","sequence":"additional","affiliation":[{"name":"Institute for Virology and Immunobiology, Julius-Maximilians-University W\u00fcrzburg , Versbacher Stra\u00dfe 7, 97078 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0024-020X","authenticated-orcid":false,"given":"Tobias","family":"Weinberger","sequence":"additional","affiliation":[{"name":"Medizinische Klinik und Poliklinik I, Klinikum der Universit\u00e4t, Ludwig-Maximilians-Universit\u00e4t , Campus Gro\u00dfhadern Marchioninistra\u00dfe 15, 81377 Munich , Germany"},{"name":"DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance , Munich , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Schulz","sequence":"additional","affiliation":[{"name":"Medizinische Klinik und Poliklinik I, Klinikum der Universit\u00e4t, Ludwig-Maximilians-Universit\u00e4t , Campus Gro\u00dfhadern Marchioninistra\u00dfe 15, 81377 Munich , Germany"},{"name":"DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance , Munich , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9339-3672","authenticated-orcid":false,"given":"Klaus","family":"Ley","sequence":"additional","affiliation":[{"name":"La Jolla Institute for Immunology , 9420 Athena Circle La Jolla, CA 92037 , USA"},{"name":"Department of Bioengineering, University of California , San Diego, La Jolla, CA 92093 , USA"},{"name":"Immunology Center of Georgia, Augusta University , Augusta, GA 30912 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8539-2784","authenticated-orcid":false,"given":"Antoine-Emmanuel","family":"Saliba","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI) , Josef Schneider Str. 2, 97080 W\u00fcrzburg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0340-1745","authenticated-orcid":false,"given":"Cl\u00e9ment","family":"Cochain","sequence":"additional","affiliation":[{"name":"Institute of Experimental Biomedicine, University Hospital W\u00fcrzburg , Josef Schneider Str. 2, 97080 W\u00fcrzburg , Germany"},{"name":"Comprehensive Heart Failure Center W\u00fcrzburg, University Hospital 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