{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:33:00Z","timestamp":1790836380822,"version":"4.1.0"},"posted":{"date-parts":[[2026,7,9]]},"group-title":"Pathology","reference-count":101,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:00:00Z","timestamp":1783555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["K08DK127246"],"award-info":[{"award-number":["K08DK127246"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"award":["K08DK139370"],"award-info":[{"award-number":["K08DK139370"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01DK090311"],"award-info":[{"award-number":["R01DK090311"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01DK105198"],"award-info":[{"award-number":["R01DK105198"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R24OD017870"],"award-info":[{"award-number":["R24OD017870"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"publisher"}]},{"award":["Autoimmune Hepatitis Pilot Award 2020"],"award-info":[{"award-number":["Autoimmune Hepatitis Pilot Award 2020"]}],"id":[{"id":"https:\/\/ror.org\/005tjs461","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Autoimmune hepatitis (AIH) is a chronic progressive liver disease that despite suggestive serum autoantibodies or plasma cell enrichment, remains functionally a diagnosis of exclusion. Whether the broader cellular composition of the liver might enable improved specificity of diagnosis has not been systematically tested. We prospectively recruited patients undergoing a clinically-indicated liver biopsy for suspected AIH and performed single-nucleus RNA sequencing (snRNA-seq) on biopsy tissue to map the cellular landscape of AIH and its diagnostic mimics. Unsupervised clustering on cell-type abundances alone largely separated AIH from non-AIH samples. Among individual populations, a subset of CD8\u207a T-cells marked by high TOX and PD1 expression was the most discriminating feature: its enrichment perfectly distinguished AIH by both snRNA-seq and\n                  <jats:italic>in situ<\/jats:italic>\n                  density (AUC = 1.00), outperforming plasma cell abundance (AUC = 0.83). CD8\u207aTOX\u207a T-cell enrichment may therefore be the histologic lesion that marks the diagnosis of AIH.\n                <\/jats:p>","DOI":"10.64898\/2026.07.06.734562","type":"posted-content","created":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T09:30:19Z","timestamp":1783589419000},"source":"Crossref","is-referenced-by-count":1,"title":["Hepatic CD8\n                  <sup>+<\/sup>\n                  TOX\n                  <sup>+<\/sup>\n                  T-cells are a hallmark of autoimmune hepatitis"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6510-069X","authenticated-orcid":false,"given":"Marc S.","family":"Sherman","sequence":"first","affiliation":[{"name":"Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel M.","family":"Schafer","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1393-6559","authenticated-orcid":false,"given":"Molly F.","family":"Thomas","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Medicine, Oregon Health and Science University, Portland, Oregon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonya W.","family":"Katzen","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7522-6173","authenticated-orcid":false,"given":"Genevieve","family":"Boland","sequence":"additional","affiliation":[{"name":"Division of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8945-5997","authenticated-orcid":false,"given":"Angela R.","family":"Shih","sequence":"additional","affiliation":[{"name":"Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9792-4271","authenticated-orcid":false,"given":"Georg M.","family":"Lauer","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7461-0408","authenticated-orcid":false,"given":"Alexandra-Chloe","family":"Villani","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9972-1569","authenticated-orcid":false,"given":"Wolfram","family":"Goessling","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026071302000599000_2026.07.06.734562v1.1","doi-asserted-by":"publisher","DOI":"10.1084\/jem.79.5.539"},{"key":"2026071302000599000_2026.07.06.734562v1.2","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/S0016-5085(60)80029-7","article-title":"Autoclasia: A Perpetuating Mechanism in Hepatitis","volume":"38","year":"1960","journal-title":"Gastroenterology"},{"key":"2026071302000599000_2026.07.06.734562v1.3","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1056\/NEJM195102152440702","article-title":"Extreme Hyperglobulinemia in Subacute Hepatic Necrosis","volume":"244","year":"1951","journal-title":"New England Journal of Medicine"},{"key":"2026071302000599000_2026.07.06.734562v1.4","doi-asserted-by":"crossref","first-page":"650","DOI":"10.7326\/0003-4819-61-4-650","volume":"61","year":"1964","journal-title":"Annals of Internal Medicine"},{"key":"2026071302000599000_2026.07.06.734562v1.5","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/imj.1960.9.4.295","article-title":"Plasma Transaminase in Liver Disease","volume":"9","year":"1960","journal-title":"Australasian Annals of Medicine"},{"key":"2026071302000599000_2026.07.06.734562v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-8278(99)80297-9"},{"key":"2026071302000599000_2026.07.06.734562v1.7","doi-asserted-by":"publisher","DOI":"10.1002\/hep.22322"},{"key":"2026071302000599000_2026.07.06.734562v1.8","doi-asserted-by":"publisher","DOI":"10.1002\/hep.22513"},{"key":"2026071302000599000_2026.07.06.734562v1.9","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1177\/2050640617711632","article-title":"Suitability of the simplified autoimmune hepatitis score for the diagnosis of autoimmune hepatitis in a German cohort","volume":"6","year":"2018","journal-title":"United European Gastroenterol J"},{"key":"2026071302000599000_2026.07.06.734562v1.10","doi-asserted-by":"publisher","DOI":"10.1002\/hep.23042"},{"key":"2026071302000599000_2026.07.06.734562v1.11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0092267"},{"key":"2026071302000599000_2026.07.06.734562v1.12","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.autrev.2016.03.001","article-title":"Do anti-smooth muscle antibodies predict development of autoimmune hepatitis in patients with normal liver function? \u2013 A retrospective cohort review","volume":"15","year":"2016","journal-title":"Autoimmunity Reviews"},{"key":"2026071302000599000_2026.07.06.734562v1.13","doi-asserted-by":"publisher","DOI":"10.1002\/hep.31065"},{"key":"2026071302000599000_2026.07.06.734562v1.14","doi-asserted-by":"crossref","first-page":"2088","DOI":"10.1016\/j.cgh.2015.08.012","article-title":"Autoimmune Hepatitis and Overlap Syndromes: Diagnosis and Management","volume":"13","year":"2015","journal-title":"Clinical Gastroenterology and Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.15","doi-asserted-by":"publisher","DOI":"10.1053\/gast.2001.24227"},{"key":"2026071302000599000_2026.07.06.734562v1.16","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.humpath.2018.07.014","article-title":"Histologic features of autoimmune hepatitis: a critical appraisal","volume":"82","year":"2018","journal-title":"Human Pathology"},{"key":"2026071302000599000_2026.07.06.734562v1.17","doi-asserted-by":"publisher","DOI":"10.1002\/hep.1840150403"},{"key":"2026071302000599000_2026.07.06.734562v1.18","doi-asserted-by":"crossref","first-page":"S23","DOI":"10.1016\/0002-9343(94)90186-4","article-title":"Autoimmune hepatitis: Classification, heterogeneity, and treatment","volume":"96","year":"1994","journal-title":"The American Journal of Medicine"},{"key":"2026071302000599000_2026.07.06.734562v1.19","doi-asserted-by":"publisher","DOI":"10.1111\/cei.12558"},{"key":"2026071302000599000_2026.07.06.734562v1.20","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1002\/cld.301","article-title":"Autoimmune hepatitis: Histopathology","volume":"3","year":"2014","journal-title":"Clin Liver Dis (Hoboken)"},{"key":"2026071302000599000_2026.07.06.734562v1.21","first-page":"686","article-title":"Prevalence and clinical significance of portal inflammation, portal plasma cells, interface hepatitis and biliary injury in liver biopsies from patients with non-alcoholic steatohepatitis","volume":"54","year":"2022","journal-title":"Pathology"},{"key":"2026071302000599000_2026.07.06.734562v1.22","doi-asserted-by":"crossref","first-page":"3597","DOI":"10.3748\/wjg.v20.i13.3597","article-title":"Clinicopathological study of primary biliary cirrhosis with interface hepatitis compared to autoimmune hepatitis","volume":"20","year":"2014","journal-title":"World J Gastroenterol"},{"key":"2026071302000599000_2026.07.06.734562v1.23","doi-asserted-by":"publisher","DOI":"10.1002\/hep.24757"},{"key":"2026071302000599000_2026.07.06.734562v1.24","doi-asserted-by":"crossref","unstructured":"Sohal, A. , Nikzad, N. & Kowdley, K. V . Overlap syndromes in autoimmune liver disease: a review. Translational Gastroenterology and Hepatology 10, 33 (2025).","DOI":"10.21037\/tgh-24-140"},{"key":"2026071302000599000_2026.07.06.734562v1.25","doi-asserted-by":"crossref","first-page":"2088","DOI":"10.1016\/j.cgh.2015.08.012","article-title":"Autoimmune Hepatitis and Overlap Syndromes: Diagnosis and Management","volume":"13","year":"2015","journal-title":"Clinical Gastroenterology and Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2010.09.002"},{"key":"2026071302000599000_2026.07.06.734562v1.27","doi-asserted-by":"publisher","DOI":"10.1136\/adc.67.12.1447"},{"key":"2026071302000599000_2026.07.06.734562v1.28","first-page":"968","article-title":"Immune Alterations in Patients With Type 1 Autoimmune Hepatitis Persist Upon Standard Immunosuppressive Treatment","volume":"2","year":"2018","journal-title":"Hepatol Commun"},{"key":"2026071302000599000_2026.07.06.734562v1.29","first-page":"682","article-title":"Assessment of intrahepatic regulatory T cells in children with autoimmune hepatitis","volume":"15","year":"2016","journal-title":"Annals of Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.30","doi-asserted-by":"crossref","unstructured":"Qian, Q. et al. Intrahepatic activated leukocyte cell adhesion molecule induces CD6highCD4+ T cell infiltration in autoimmune hepatitis. Front. Immunol. 13, (2022).","DOI":"10.3389\/fimmu.2022.967944"},{"key":"2026071302000599000_2026.07.06.734562v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2012.02.029"},{"key":"2026071302000599000_2026.07.06.734562v1.32","doi-asserted-by":"publisher","DOI":"10.1002\/hep.29782"},{"key":"2026071302000599000_2026.07.06.734562v1.33","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1007\/s00795-014-0082-z","article-title":"The utility of IgG, IgM, and CD138 immunohistochemistry in the evaluation of autoimmune liver diseases","volume":"47","year":"2014","journal-title":"Med Mol Morphol"},{"key":"2026071302000599000_2026.07.06.734562v1.34","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf1970"},{"key":"2026071302000599000_2026.07.06.734562v1.35","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adc9778"},{"key":"2026071302000599000_2026.07.06.734562v1.36","doi-asserted-by":"crossref","unstructured":"Schafflick, D. et al. Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis. Nat Commun 11, 247 (2020).","DOI":"10.1038\/s41467-019-14118-w"},{"key":"2026071302000599000_2026.07.06.734562v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06708-y"},{"key":"2026071302000599000_2026.07.06.734562v1.38","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.jhep.2021.08.024","article-title":"Infliximab-induced liver injury: Clinical phenotypes, autoimmunity and the role of corticosteroid treatment","volume":"76","year":"2022","journal-title":"Journal of Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.39","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1111\/apt.13159","article-title":"New onset idiosyncratic liver enzyme elevations with biological therapy in inflammatory bowel disease","volume":"41","year":"2015","journal-title":"Aliment Pharmacol Ther"},{"key":"2026071302000599000_2026.07.06.734562v1.40","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1016\/j.cgh.2012.12.025","article-title":"Liver Injury From Tumor Necrosis Factor-\u03b1 Antagonists: Analysis of Thirty-four Cases","volume":"11","year":"2013","journal-title":"Clinical Gastroenterology and Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.41","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1002\/hep.1840180436","article-title":"Toward diagnostic criteria for autoimmune hepatitis","volume":"18","year":"1993","journal-title":"Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.42","doi-asserted-by":"publisher","DOI":"10.1002\/hep.1840180435"},{"key":"2026071302000599000_2026.07.06.734562v1.43","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1080\/00365521.1974.12096884","article-title":"Acute Viral Hepatitis: A Survey of 500 Patients: Clinical, Biochemical, Immunological, and Morphological Features at Time of Diagnosis","volume":"9","year":"1974","journal-title":"Scandinavian Journal of Gastroenterology"},{"key":"2026071302000599000_2026.07.06.734562v1.44","first-page":"914","article-title":"Review by an international group","volume":"2","author":"Acute and chronic hepatitis revisited","year":"1977","journal-title":"Lancet"},{"key":"2026071302000599000_2026.07.06.734562v1.45","doi-asserted-by":"crossref","first-page":"4706","DOI":"10.1038\/s41467-019-12464-3","article-title":"Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease","volume":"10","year":"2019","journal-title":"Nature Communications"},{"key":"2026071302000599000_2026.07.06.734562v1.46","doi-asserted-by":"publisher","DOI":"10.1126\/science.1079490"},{"key":"2026071302000599000_2026.07.06.734562v1.47","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1038\/s41467-021-21928-4","article-title":"Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy","volume":"12","year":"2021","journal-title":"Nature Communications"},{"key":"2026071302000599000_2026.07.06.734562v1.48","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-023-01575-1"},{"key":"2026071302000599000_2026.07.06.734562v1.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1324-y"},{"key":"2026071302000599000_2026.07.06.734562v1.50","doi-asserted-by":"crossref","unstructured":"Tietscher, S. et al. A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer. Nature Communications 14, 98 (2023).","DOI":"10.1038\/s41467-022-35238-w"},{"key":"2026071302000599000_2026.07.06.734562v1.51","doi-asserted-by":"crossref","unstructured":"Heger, L. , Balk, S. , L\u00fchr, J. J. & Dudziak, D . Subsets of CD1c+ DCs: dendritic cell versus monocyte lineage. Frontiers in Immunology 11, 559166 (2020).","DOI":"10.3389\/fimmu.2020.559166"},{"key":"2026071302000599000_2026.07.06.734562v1.52","doi-asserted-by":"publisher","DOI":"10.1126\/science.aah4573"},{"key":"2026071302000599000_2026.07.06.734562v1.53","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s41577-022-00675-7","article-title":"Expanding dendritic cell nomenclature in the single-cell era","volume":"22","year":"2022","journal-title":"Nat Rev Immunol"},{"key":"2026071302000599000_2026.07.06.734562v1.54","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2134-y"},{"key":"2026071302000599000_2026.07.06.734562v1.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.10.003"},{"key":"2026071302000599000_2026.07.06.734562v1.56","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2019.03.009"},{"key":"2026071302000599000_2026.07.06.734562v1.57","doi-asserted-by":"crossref","unstructured":"Hou, J. et al. TREM2 sustains macrophage-hepatocyte metabolic coordination in nonalcoholic fatty liver disease and sepsis. J Clin Invest 131, (2021).","DOI":"10.1172\/JCI135197"},{"key":"2026071302000599000_2026.07.06.734562v1.58","doi-asserted-by":"publisher","DOI":"10.1101\/766113"},{"key":"2026071302000599000_2026.07.06.734562v1.59","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.12.018"},{"key":"2026071302000599000_2026.07.06.734562v1.60","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2408.15954"},{"key":"2026071302000599000_2026.07.06.734562v1.61","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2019.05.015"},{"key":"2026071302000599000_2026.07.06.734562v1.62","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aba7918"},{"key":"2026071302000599000_2026.07.06.734562v1.63","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2020-322404"},{"key":"2026071302000599000_2026.07.06.734562v1.64","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1038\/s41586-025-09989-7","article-title":"Atlas-guided discovery of transcription factors for T cell programming","volume":"651","year":"2026","journal-title":"Nature"},{"key":"2026071302000599000_2026.07.06.734562v1.65","doi-asserted-by":"publisher","DOI":"10.1002\/hep.31739"},{"key":"2026071302000599000_2026.07.06.734562v1.66","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7072"},{"key":"2026071302000599000_2026.07.06.734562v1.67","doi-asserted-by":"crossref","first-page":"1964","DOI":"10.1038\/s41592-025-02793-1","article-title":"Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions","volume":"22","year":"2025","journal-title":"Nat Methods"},{"key":"2026071302000599000_2026.07.06.734562v1.68","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-018-0057-z"},{"key":"2026071302000599000_2026.07.06.734562v1.69","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.11.043"},{"key":"2026071302000599000_2026.07.06.734562v1.70","doi-asserted-by":"crossref","unstructured":"Ma, J. et al. PD1Hi CD8+ T cells correlate with exhausted signature and poor clinical outcome in hepatocellular carcinoma. J Immunother Cancer 7, 331 (2019).","DOI":"10.1186\/s40425-019-0814-7"},{"key":"2026071302000599000_2026.07.06.734562v1.71","doi-asserted-by":"publisher","DOI":"10.1038\/nri3862"},{"key":"2026071302000599000_2026.07.06.734562v1.72","doi-asserted-by":"crossref","unstructured":"Long, J. et al. PD-1+CD8+ T Cell-Mediated Hepatocyte Pyroptosis Promotes Progression of Murine Autoimmune Liver Disease. Adv Sci (Weinh) 12, 2407284 (2024).","DOI":"10.1002\/advs.202407284"},{"key":"2026071302000599000_2026.07.06.734562v1.73","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1038\/s41467-024-46654-5","article-title":"Targeting pathogenic CD8+ tissue-resident T cells with chimeric antigen receptor therapy in murine autoimmune cholangitis","volume":"15","year":"2024","journal-title":"Nat Commun"},{"key":"2026071302000599000_2026.07.06.734562v1.74","doi-asserted-by":"publisher","DOI":"10.1172\/JCI126595"},{"key":"2026071302000599000_2026.07.06.734562v1.75","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-022-01210-5"},{"key":"2026071302000599000_2026.07.06.734562v1.76","doi-asserted-by":"crossref","unstructured":"Xia, Q. et al. The phenotypic and functional characteristics of intrahepatic CD69+CD103+ tissue-resident MAIT cells in primary biliary cholangitis. Journal of Autoimmunity 154, 103442 (2025).","DOI":"10.1016\/j.jaut.2025.103442"},{"key":"2026071302000599000_2026.07.06.734562v1.77","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2026.02.026"},{"key":"2026071302000599000_2026.07.06.734562v1.78","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1542\/peds.29.2.191","article-title":"Plasma Cell Hepatitis: Case Report with Immunologic Studies","volume":"29","year":"1962","journal-title":"Pediatrics"},{"key":"2026071302000599000_2026.07.06.734562v1.79","doi-asserted-by":"crossref","unstructured":"Page, A. R . Plasma-Cell Hepatitis, with Special Attention to Steroid Therapy. Arch Pediatr Adolesc Med 99, 288 (1960).","DOI":"10.1001\/archpedi.1960.02070030290006"},{"key":"2026071302000599000_2026.07.06.734562v1.80","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1055\/s-2008-1040437","article-title":"Ultrastructural Lesion in Autoimmune Hepatitis and Steps of the Immune Response in Liver Tissue","volume":"11","year":"1991","journal-title":"Semin Liver Dis"},{"key":"2026071302000599000_2026.07.06.734562v1.81","doi-asserted-by":"publisher","DOI":"10.1002\/hep.23792"},{"key":"2026071302000599000_2026.07.06.734562v1.82","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2021-324478"},{"key":"2026071302000599000_2026.07.06.734562v1.83","doi-asserted-by":"publisher","DOI":"10.1136\/gut.51.2.259"},{"key":"2026071302000599000_2026.07.06.734562v1.84","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-8278(99)80342-0"},{"key":"2026071302000599000_2026.07.06.734562v1.85","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1111\/hepr.13532","article-title":"Histopathological analysis of autoimmune hepatitis with \u201cacute\u201d presentation: Differentiation from drug-induced liver injury","volume":"50","year":"2020","journal-title":"Hepatology Research"},{"key":"2026071302000599000_2026.07.06.734562v1.86","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1016\/j.jhep.2010.12.041","article-title":"Recurrent Drug-Induced Liver Injury (DILI) with different drugs in the Spanish Registry: The dilemma of the relationship to autoimmune hepatitis","volume":"55","year":"2011","journal-title":"Journal of Hepatology"},{"key":"2026071302000599000_2026.07.06.734562v1.87","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.08.00310.1101\/746743"},{"key":"2026071302000599000_2026.07.06.734562v1.88","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01943-7"},{"key":"2026071302000599000_2026.07.06.734562v1.89","doi-asserted-by":"crossref","unstructured":"Wolf, F. A. , Angerer, P. & Theis, F. J . SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 19, 15 (2018).","DOI":"10.1186\/s13059-017-1382-0"},{"key":"2026071302000599000_2026.07.06.734562v1.90","first-page":"281","article-title":"Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data","volume":"8","year":"2019","journal-title":"cels"},{"key":"2026071302000599000_2026.07.06.734562v1.91","doi-asserted-by":"publisher","DOI":"10.1093\/BIOINFORMATICS\/BTZ625"},{"key":"2026071302000599000_2026.07.06.734562v1.92","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1038\/s41586-024-08411-y","article-title":"A cell atlas foundation model for scalable search of similar human cells","volume":"638","year":"2025","journal-title":"Nature"},{"key":"2026071302000599000_2026.07.06.734562v1.93","doi-asserted-by":"crossref","unstructured":"Love, M. I. , Huber, W. & Anders, S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014).","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2026071302000599000_2026.07.06.734562v1.94","doi-asserted-by":"crossref","first-page":"vbac016","DOI":"10.1093\/bioadv\/vbac016","article-title":"decoupleR: ensemble of computational methods to infer biological activities from omics data","volume":"2","year":"2022","journal-title":"Bioinformatics Advances"},{"key":"2026071302000599000_2026.07.06.734562v1.95","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0336-210.1038\/s41596-020-0336-2"},{"key":"2026071302000599000_2026.07.06.734562v1.96","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad841"},{"key":"2026071302000599000_2026.07.06.734562v1.97","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0"},{"key":"2026071302000599000_2026.07.06.734562v1.98","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad0501"},{"key":"2026071302000599000_2026.07.06.734562v1.99","doi-asserted-by":"crossref","unstructured":"Sherman, M. S. , et al. Harmonizing TUNEL with multiplexed iterative immunofluorescence enriches spatial contextualization of cell death. Cell Reports Methods 5, (2025).","DOI":"10.1016\/j.crmeth.2025.101047"},{"key":"2026071302000599000_2026.07.06.734562v1.100","doi-asserted-by":"crossref","unstructured":"Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Sci Rep 7, 16878 (2017).","DOI":"10.1038\/s41598-017-17204-5"},{"key":"2026071302000599000_2026.07.06.734562v1.101","doi-asserted-by":"crossref","first-page":"4371","DOI":"10.21105\/joss.04371","article-title":"A. anndata: Access and store annotated data matrices","volume":"9","year":"2024","journal-title":"Journal of Open Source Software"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.07.06.734562","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T09:00:19Z","timestamp":1783933219000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.07.06.734562"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,9]]},"references-count":101,"URL":"https:\/\/doi.org\/10.64898\/2026.07.06.734562","relation":{},"subject":[],"published":{"date-parts":[[2026,7,9]]},"subtype":"preprint"}}