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Distinct endothelial phenotypes and transcriptional programs are linked to vessel size and anatomical location, but it remains unclear how this intrinsic heterogeneity is organized within a particular niche. We performed compartment-specific single-cell profiling of human pulmonary artery (PA) ECs from healthy donors and from patients with two clinically divergent forms of pulmonary hypertension (PH): pulmonary arterial hypertension (PAH) and pulmonary hypertension associated with pulmonary fibrosis (PH-PF). We identified and localized three major EC subsets in healthy and remodeled PAs termed immuno-, vascular tone- and vascular plasticity modulatory, reflecting their enrichment for distinct biological processes. Expression signatures defining each subset were shared with other arterial beds, including the aorta and\u00a0coronary arteries, and murine PA. Both PAH and PH-PF altered PAEC subset compositions, with increased immunomodulatory and decreased vascular plasticity modulatory PAECs. PH-PF PAECs were generally defined by dysregulated angiogenesis and antigen presentation, whereas PAH PAECs exhibited lipid metabolic dysfunction and enhanced vasoregulatory signaling. By uncovering endothelial heterogeneity and pathology-specific transcriptional programs in PAs, this study underscores the need of disease-specific therapeutic targeting.<\/jats:p>","DOI":"10.1038\/s42003-026-10204-0","type":"journal-article","created":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T15:10:21Z","timestamp":1778512221000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptional landscape of pulmonary artery endothelium reveals subpopulation- and disease-specific remodeling signatures"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-1494-8471","authenticated-orcid":false,"given":"Thomas","family":"Lins","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Valzano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Flie\u00dfer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2527-6199","authenticated-orcid":false,"given":"Izabela","family":"Borek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0820-3318","authenticated-orcid":false,"given":"Slaven","family":"Crnkovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Morley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4716-1285","authenticated-orcid":false,"given":"Maria C.","family":"Basil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Katzen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Cantu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7714-8076","authenticated-orcid":false,"given":"Jonas C.","family":"Schupp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolaus","family":"Kneidinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00f6rg","family":"Lindenmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7787-991X","authenticated-orcid":false,"given":"Clemens","family":"Aigner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3549-4720","authenticated-orcid":false,"given":"Alberto","family":"Benazzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward E.","family":"Morrisey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6872-9082","authenticated-orcid":false,"given":"Marek","family":"Bartkuhn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1754-9249","authenticated-orcid":false,"given":"Leigh M.","family":"Marsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8358-8377","authenticated-orcid":false,"given":"Anna","family":"Birnhuber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grazyna","family":"Kwapiszewska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,11]]},"reference":[{"key":"10204_CR1","doi-asserted-by":"publisher","first-page":"2003957","DOI":"10.1183\/13993003.03957-2020","volume":"58","author":"CE Evans","year":"2021","unstructured":"Evans, C. 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