{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:27:43Z","timestamp":1785403663050,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,16]]},"group-title":"Immunology","reference-count":58,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"award":["ZIA DE000747"],"award-info":[{"award-number":["ZIA DE000747"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Chronic graft-versus-host disease (cGVHD) frequently follows allogeneic hematopoietic stem cell transplantation and impacts the mucosa. This atlas study highlights the role of exhausted-like effector CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cells (T\n                  <jats:sub>EXEF<\/jats:sub>\n                  ) in oral mucosal cGVHD pathogenesis. Biopsies from the oral mucosa were collected at oral cGVHD onset or at six months post-transplant and analyzed using single-cell RNA sequencing and other modalities. At cGVHD onset, in addition to changes in the myeloid compartment, two distinct populations of CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cells with a T\n                  <jats:sub>EXEF<\/jats:sub>\n                  phenotype were prevalent: an inflammatory CD8T cell cluster (CD8T_4) expressing\n                  <jats:italic>CCL4<\/jats:italic>\n                  ,\n                  <jats:italic>CD69<\/jats:italic>\n                  , and\n                  <jats:italic>TNFSF9<\/jats:italic>\n                  , and an exhausted CD8T cell cluster (CD8T_5) characterized by the expression of\n                  <jats:italic>CXCL13<\/jats:italic>\n                  ,\n                  <jats:italic>HIF1A<\/jats:italic>\n                  , and\n                  <jats:italic>HLA-DRA,<\/jats:italic>\n                  both correlated with clinical disease severity. Pseudo-time analysis suggests a transition from the inflammatory pre-exhausted CD8T_4 cluster to the cytolytic, terminally exhausted CD8T_5 cluster. The CXCL9-CXCR3 interactions among CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cells, fibroblasts and myeloid cells are implicated in tissue damage. Onset of cGVHD despite frequent oral mucosal FOXP3\u207a regulatory CD4\u207aT cells suggests potential impaired Treg function or CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cell dysfunction. These findings highlight T\n                  <jats:sub>EXEF<\/jats:sub>\n                  cells as key contributors to oral cGVHD pathology and potential therapeutic targets for mitigating sustained tissue injury in cGVHD.\n                <\/jats:p>","DOI":"10.1101\/2025.09.11.675642","type":"posted-content","created":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T01:10:29Z","timestamp":1758071429000},"source":"Crossref","is-referenced-by-count":0,"title":["Exhausted-like effector CD8 T cells mediate immune-stromal interactions at mucosal Chronic Graft-versus-Host Disease onset"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2729-5836","authenticated-orcid":false,"given":"Ana Caroline","family":"Costa-da-Silva","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7804-0673","authenticated-orcid":false,"given":"Rubina","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2080-1740","authenticated-orcid":false,"given":"Marit H.","family":"Aure","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8880-9087","authenticated-orcid":false,"given":"Daniel","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6625-6119","authenticated-orcid":false,"given":"Noemi","family":"Kedei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4044-1642","authenticated-orcid":false,"given":"Damilola F.","family":"Killanin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9346-9219","authenticated-orcid":false,"given":"Ayesha","family":"Javaid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7572-3767","authenticated-orcid":false,"given":"Francis A.","family":"Boksa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6597-4904","authenticated-orcid":false,"given":"Drashty P.","family":"Mody","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6647-0561","authenticated-orcid":false,"given":"Joe T.","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6303-7287","authenticated-orcid":false,"given":"Sukirth M.","family":"Ganesan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua T.","family":"Dodge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3805-0321","authenticated-orcid":false,"given":"Clara H.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Kao-Hsieh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3442-4453","authenticated-orcid":false,"given":"David E.","family":"Kleiner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7736-2056","authenticated-orcid":false,"given":"Christopher G.","family":"Kanakry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9111-9354","authenticated-orcid":false,"given":"Steven Z.","family":"Pavletic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4472-9974","authenticated-orcid":false,"given":"Jacqueline W.","family":"Mays","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025091905300905000_2025.09.11.675642v1.1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2014-08-551994"},{"key":"2025091905300905000_2025.09.11.675642v1.2","doi-asserted-by":"crossref","first-page":"5829","DOI":"10.1182\/bloodadvances.2024012722","article-title":"Decreasing chronic graft-versus-host disease rates in all populations","volume":"8","year":"2024","journal-title":"Blood Adv"},{"key":"2025091905300905000_2025.09.11.675642v1.3","first-page":"504 e501","article-title":"Epidemiology and Treatment of Chronic Graft-versus-Host Disease Post-Allogeneic Hematopoietic Cell Transplantation: A US Claims Analysis","volume":"27","year":"2021","journal-title":"Transplant Cell Ther"},{"key":"2025091905300905000_2025.09.11.675642v1.4","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1056\/NEJMoa2503189","article-title":"Graft-versus-Host Disease Prophylaxis with Cyclophosphamide and Cyclosporin","volume":"393","year":"2025","journal-title":"N Engl J Med"},{"key":"2025091905300905000_2025.09.11.675642v1.5","doi-asserted-by":"crossref","first-page":"903154","DOI":"10.3389\/froh.2022.903154","article-title":"Oral Chronic Graft-Versus-Host Disease","volume":"3","year":"2022","journal-title":"Front Oral Health"},{"key":"2025091905300905000_2025.09.11.675642v1.6","first-page":"6","article-title":"A Review of Oral Chronic Graft-Versus-Host Disease: Considerations for dental hygiene practice","volume":"96","year":"2022","journal-title":"J Dent Hyg"},{"key":"2025091905300905000_2025.09.11.675642v1.7","doi-asserted-by":"crossref","unstructured":"Fall-Dickson, J. M. , Pavletic, S. Z. , Mays, J. W. , and Schubert, M. M. (2019) Oral Complications of Chronic Graft-Versus-Host Disease J Natl Cancer Inst Monogr 2019,","DOI":"10.1093\/jncimonographs\/lgz007"},{"key":"2025091905300905000_2025.09.11.675642v1.8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.bbmt.2016.09.023","article-title":"The Biology of Chronic Graft-versus-Host Disease: A Task Force Report from the National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease","volume":"23","year":"2017","journal-title":"Biol Blood Marrow Transplant"},{"key":"2025091905300905000_2025.09.11.675642v1.9","doi-asserted-by":"crossref","unstructured":"Nguyen, J. T. , Jessri, M. , Costa-da-Silva, A. C. , Sharma, R. , Mays, J. W. , and Treister, N. S . (2024) Oral Chronic Graft-Versus-Host Disease: Pathogenesis, Diagnosis, Current Treatment, and Emerging Therapies Int J Mol Sci 25,","DOI":"10.3390\/ijms251910411"},{"key":"2025091905300905000_2025.09.11.675642v1.10","doi-asserted-by":"crossref","first-page":"3479","DOI":"10.1182\/bloodadvances.2025016170","article-title":"Belumosudil reduces oral chronic graft-versus-host disease tissue inflammation and fibrosis: a ROCKstar companion study","volume":"9","year":"2025","journal-title":"Blood Adv"},{"key":"2025091905300905000_2025.09.11.675642v1.11","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1300657"},{"key":"2025091905300905000_2025.09.11.675642v1.12","doi-asserted-by":"crossref","first-page":"5359","DOI":"10.1182\/bloodadvances.2022009646","article-title":"Mesenchymal stromal cells ameliorate chronic GVHD by boosting thymic regeneration in a CCR9-dependent manner in mice","volume":"7","year":"2023","journal-title":"Blood Adv"},{"key":"2025091905300905000_2025.09.11.675642v1.13","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2006-04-016410"},{"key":"2025091905300905000_2025.09.11.675642v1.14","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.179.10.6547"},{"key":"2025091905300905000_2025.09.11.675642v1.15","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.0802212"},{"key":"2025091905300905000_2025.09.11.675642v1.16","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1200\/JCO.21.01755","article-title":"Naive T-Cell Depletion to Prevent Chronic Graft-Versus-Host Disease","volume":"40","year":"2022","journal-title":"J Clin Oncol"},{"key":"2025091905300905000_2025.09.11.675642v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbmt.2014.12.001"},{"key":"2025091905300905000_2025.09.11.675642v1.18","doi-asserted-by":"crossref","first-page":"770847","DOI":"10.3389\/fimmu.2021.770847","article-title":"Editorial: Regulation of Immunity by Non-Immune Cells","volume":"12","year":"2021","journal-title":"Front Immunol"},{"key":"2025091905300905000_2025.09.11.675642v1.19","doi-asserted-by":"crossref","first-page":"1033490","DOI":"10.3389\/fimmu.2022.1033490","article-title":"Role of endothelial cells in graft-versus-host disease","volume":"13","year":"2022","journal-title":"Front Immunol"},{"key":"2025091905300905000_2025.09.11.675642v1.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2019.08.011"},{"key":"2025091905300905000_2025.09.11.675642v1.21","doi-asserted-by":"crossref","unstructured":"Zima, K. , Purzycka-Bohdan, D. , Szczerkowska-Dobosz, A. , and Gabig-Ciminska, M. (2024) Keratinocyte-Mediated Antigen Presentation in Psoriasis: Preliminary Insights from In Vitro Studies Int J Mol Sci 25,","DOI":"10.3390\/ijms252413387"},{"key":"2025091905300905000_2025.09.11.675642v1.22","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2008-07-168351"},{"key":"2025091905300905000_2025.09.11.675642v1.23","doi-asserted-by":"crossref","first-page":"108805","DOI":"10.1016\/j.isci.2024.108805","article-title":"ignificance of stress keratin expression in normal and diseased epithelia","volume":"27","year":"2024","journal-title":"iScience"},{"key":"2025091905300905000_2025.09.11.675642v1.24","doi-asserted-by":"crossref","unstructured":"Wang, T. H. , Shen, Y. W. , Chen, H. Y. , Chen, C. C. , Lin, N. C. , Shih, Y. H. et al. (2024) Arecoline Induces ROS Accumulation, Transcription of Proinflammatory Factors, and Expression of KRT6 in Oral Epithelial Cells Biomedicines 12,","DOI":"10.3390\/biomedicines12020412"},{"key":"2025091905300905000_2025.09.11.675642v1.25","doi-asserted-by":"publisher","DOI":"10.3390\/cimb46080508"},{"key":"2025091905300905000_2025.09.11.675642v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41385-022-00527-6"},{"key":"2025091905300905000_2025.09.11.675642v1.27","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-49916-4"},{"key":"2025091905300905000_2025.09.11.675642v1.28","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2017-01-758854"},{"key":"2025091905300905000_2025.09.11.675642v1.29","doi-asserted-by":"publisher","DOI":"10.1172\/JCI75935"},{"key":"2025091905300905000_2025.09.11.675642v1.30","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.12998\/wjcc.v8.i10.1793","article-title":"Macrophage regulation of graft-vs-host disease","volume":"8","year":"2020","journal-title":"World J Clin Cases"},{"key":"2025091905300905000_2025.09.11.675642v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.coi.2020.08.006"},{"key":"2025091905300905000_2025.09.11.675642v1.32","doi-asserted-by":"crossref","first-page":"611910","DOI":"10.3389\/fimmu.2021.611910","article-title":"Untangling Local Pro-Inflammatory, Reparative, and Regulatory Damage-Associated Molecular-Patterns (DAMPs) Pathways to Improve Transplant Outcomes","volume":"12","year":"2021","journal-title":"Front Immunol"},{"key":"2025091905300905000_2025.09.11.675642v1.33","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2017.01842"},{"key":"2025091905300905000_2025.09.11.675642v1.34","doi-asserted-by":"crossref","first-page":"105535","DOI":"10.1016\/j.ebiom.2024.105535","article-title":"Clonal GZMK(+)CD8(+) T cells are identified as a hallmark of the pathogenesis of cGVHD-induced bronchiolitis obliterans syndrome after allogeneic hematopoietic stem cell transplantation","volume":"112","year":"2025","journal-title":"EBioMedicine"},{"key":"2025091905300905000_2025.09.11.675642v1.35","doi-asserted-by":"crossref","unstructured":"Mellors, P. W. , Lange, A. N. , Casino Remondo, B. , Shestov, M. , Planer, J. D. , Peterson, A. R. et al. (2025) Shared roles of immune and stromal cells in the pathogenesis of human bronchiolitis obliterans syndrome JCI Insight 10,","DOI":"10.1172\/jci.insight.176596"},{"key":"2025091905300905000_2025.09.11.675642v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/35876"},{"key":"2025091905300905000_2025.09.11.675642v1.37","doi-asserted-by":"publisher","DOI":"10.1084\/jem.187.4.655"},{"key":"2025091905300905000_2025.09.11.675642v1.38","doi-asserted-by":"crossref","first-page":"1151493","DOI":"10.3389\/fimmu.2023.1151493","article-title":"Perspectives on oral chronic graft-versus-host disease from immunobiology to morbid diagnoses","volume":"14","year":"2023","journal-title":"Front Immunol"},{"key":"2025091905300905000_2025.09.11.675642v1.39","doi-asserted-by":"publisher","DOI":"10.1006\/cyto.2001.0923"},{"key":"2025091905300905000_2025.09.11.675642v1.40","doi-asserted-by":"publisher","DOI":"10.1016\/j.intimp.2023.110530"},{"key":"2025091905300905000_2025.09.11.675642v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35238-w"},{"key":"2025091905300905000_2025.09.11.675642v1.42","doi-asserted-by":"crossref","first-page":"491","DOI":"10.3389\/fimmu.2019.00491","article-title":"A Threshold Model for T-Cell Activation in the Era of Checkpoint Blockade Immunotherapy","volume":"10","year":"2019","journal-title":"Front Immunol"},{"key":"2025091905300905000_2025.09.11.675642v1.43","doi-asserted-by":"publisher","DOI":"10.1038\/nature07201"},{"key":"2025091905300905000_2025.09.11.675642v1.44","doi-asserted-by":"publisher","DOI":"10.1101\/2023.03.17.533121"},{"key":"2025091905300905000_2025.09.11.675642v1.45","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms13850"},{"key":"2025091905300905000_2025.09.11.675642v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-021-01058-1"},{"key":"2025091905300905000_2025.09.11.675642v1.47","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2021.04.048"},{"key":"2025091905300905000_2025.09.11.675642v1.48","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"2025091905300905000_2025.09.11.675642v1.49","doi-asserted-by":"crossref","unstructured":"Zappia, L. , and Oshlack, A. (2018) Clustering trees: a visualization for evaluating clusterings at multiple resolutions Gigascience 7,","DOI":"10.1093\/gigascience\/giy083"},{"key":"2025091905300905000_2025.09.11.675642v1.50","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0844-5"},{"key":"2025091905300905000_2025.09.11.675642v1.51","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2011.0118"},{"key":"2025091905300905000_2025.09.11.675642v1.52","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.06.043"},{"key":"2025091905300905000_2025.09.11.675642v1.53","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1161\/ATVBAHA.123.320511","article-title":"Resident Memory T Cells in the Atherosclerotic Lesion Associate With Reduced Macrophage Content and Increased Lesion Stability","volume":"44","year":"2024","journal-title":"Arterioscler Thromb Vasc Biol"},{"key":"2025091905300905000_2025.09.11.675642v1.54","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-020-0762-x"},{"key":"2025091905300905000_2025.09.11.675642v1.55","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-023-02371-y"},{"key":"2025091905300905000_2025.09.11.675642v1.56","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4772-0"},{"key":"2025091905300905000_2025.09.11.675642v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-024-01469-w"},{"key":"2025091905300905000_2025.09.11.675642v1.58","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31369-2"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.09.11.675642","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:34:59Z","timestamp":1768469699000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.09.11.675642"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,16]]},"references-count":58,"URL":"https:\/\/doi.org\/10.1101\/2025.09.11.675642","relation":{},"subject":[],"published":{"date-parts":[[2025,9,16]]},"subtype":"preprint"}}