{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T12:50:15Z","timestamp":1782996615127,"version":"3.54.5"},"posted":{"date-parts":[[2026,6,29]]},"reference-count":116,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T00:00:00Z","timestamp":1782691200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["R01HD107841"],"award-info":[{"award-number":["R01HD107841"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["R01AR071435"],"award-info":[{"award-number":["R01AR071435"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["R01AR066703"],"award-info":[{"award-number":["R01AR066703"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["5T32AR060710"],"award-info":[{"award-number":["5T32AR060710"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["P30AR075049"],"award-info":[{"award-number":["P30AR075049"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100015326","name":"NIH Common Fund","doi-asserted-by":"crossref","award":["1F31AR085379-01"],"award-info":[{"award-number":["1F31AR085379-01"]}],"id":[{"id":"10.13039\/100015326","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100001582","name":"Dermatology Foundation","doi-asserted-by":"crossref","award":["Physician-Scientist Career Development Award"],"award-info":[{"award-number":["Physician-Scientist Career Development Award"]}],"id":[{"id":"10.13039\/100001582","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Human scalp hair has an extraordinary ability to grow continuously for years while maintaining structural and functional integrity. However, the cell states and lineage organization that enable this capacity and how they are disrupted in inflammatory hair loss disorders remain poorly defined in humans. Here we establish a high-resolution, multimodal atlas of human scalp by integrating deep-coverage spatial transcriptomics with single-cell RNA-seq and multiomics data. This reference resolves spatially organized epithelial and mesenchymal states and links\n                  <jats:italic>in situ<\/jats:italic>\n                  transcriptional programs to chromatin accessibility dynamics and lineage trajectories at single-cell resolution, revealing human-specific principles of tissue organization and previously unrecognized features of hair follicle architecture and lineage progression. We validate key aspects of matrix cell organization and cell activities using live imaging, connecting molecularly defined cell states to dynamic cell behaviors and lineage progression in the matrix. Leveraging the atlas as a spatial reference, we project patient scRNA-seq profiles from alopecia areata and lichen planopilaris onto defined cell compartments, resolving disease-specific perturbations in fibroblasts, epithelial and immune populations. This comparison delineates distinct cellular programs associated with non-scarring versus scarring hair loss and highlights compartment- and state-specific pathways with diagnostic and therapeutic potential. Together, this work provides a foundational resource for human hair biology and establishes a generalizable framework for spatially resolved, multimodal interrogation of tissue organization and disease in complex human tissues.\n                <\/jats:p>","DOI":"10.64898\/2026.06.29.735239","type":"posted-content","created":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T22:05:12Z","timestamp":1782770712000},"source":"Crossref","is-referenced-by-count":0,"title":["Multimodal Human Scalp Atlas Defines Cell Landscape and Lineage Architecture In Situ"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7352-7642","authenticated-orcid":false,"given":"Edward B.","family":"Li","sequence":"first","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Hair-Alopecia Innovation and Research Program, Northwestern Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher M.","family":"Stephens","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meredith","family":"Klay","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian","family":"Carcamo","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jimin","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor L.","family":"Quan","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Hair-Alopecia Innovation and Research Program, Northwestern Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria L.","family":"Colavincenzo","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Hair-Alopecia Innovation and Research Program, Northwestern Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross L.","family":"Pearlman","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon S.","family":"Yoo","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Hair-Alopecia Innovation and Research Program, Northwestern Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Tissot","sequence":"additional","affiliation":[{"name":"L\u2019Or\u00e9al Research and Innovation, Aulnay-sous-Bois, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Bornschl\u00f6gl","sequence":"additional","affiliation":[{"name":"L\u2019Or\u00e9al Research and Innovation, Aulnay-sous-Bois, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In\u00eas","family":"Sequeira","sequence":"additional","affiliation":[{"name":"Centre for Oral Immunobiology and Regenerative Medicine, Barts Centre for Squamous Cancer, Institute of Dentistry, Queen Mary University of London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Hair-Alopecia Innovation and Research Program, Northwestern Medicine; Chicago, IL 60611, USA"},{"name":"Department of Pathology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA"},{"name":"Robert H. 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