{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T19:10:15Z","timestamp":1790536215348,"version":"4.1.0"},"posted":{"date-parts":[[2023,4,7]]},"group-title":"Immunology","reference-count":61,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (\n                  <jats:italic>Rag2<\/jats:italic>\n                  <jats:sup>-\/-<\/jats:sup>\n                  and \u03bcMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum from\n                  <jats:italic>Lyn<\/jats:italic>\n                  <jats:sup>-\/-<\/jats:sup>\n                  <jats:italic>IgD<\/jats:italic>\n                  <jats:sup>+\/-<\/jats:sup>\n                  mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigens. Second, serum from non-obese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, enriched peptides derived from both insulin and predicted pancreatic proteins. Lastly,\n                  <jats:italic>Aire<\/jats:italic>\n                  <jats:sup>-\/-<\/jats:sup>\n                  mouse sera were used to identify numerous auto-antigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 (APS1) carrying recessive mutations in AIRE. Among these were peptides derived from Perilipin-1, a validated autoimmune biomarker of generalized acquired lipodystrophy in humans. Autoreactivity to Perilipin-1 correlated with lymphocyte infiltration in adipose tissue and underscores the approach in revealing previously unknown specificities. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity.\n                <\/jats:p>","DOI":"10.1101\/2023.04.07.535899","type":"posted-content","created":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T01:30:18Z","timestamp":1680917418000},"source":"Crossref","is-referenced-by-count":5,"title":["Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3889-8082","authenticated-orcid":false,"given":"Elze","family":"Rackaityte","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3818-1102","authenticated-orcid":false,"given":"Irina","family":"Proekt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0920-7169","authenticated-orcid":false,"given":"Haleigh S.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akshaya","family":"Ramesh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0710-0544","authenticated-orcid":false,"given":"Jeremy F.","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew F.","family":"Kung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7764-6529","authenticated-orcid":false,"given":"Caleigh","family":"Mandel-Brehm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9477-1388","authenticated-orcid":false,"given":"Colin","family":"Zamecnik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Bair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara E.","family":"Vazquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1897-5063","authenticated-orcid":false,"given":"Sara","family":"Sunshine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9204-2640","authenticated-orcid":false,"given":"Clare L.","family":"Abram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0467-7073","authenticated-orcid":false,"given":"Clifford A.","family":"Lowell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3052-0253","authenticated-orcid":false,"given":"Gabrielle","family":"Rizzuto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0873-192X","authenticated-orcid":false,"given":"Julie","family":"Zikherman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark S.","family":"Anderson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4611-9205","authenticated-orcid":false,"given":"Joseph L.","family":"DeRisi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2023041106200606000_2023.04.07.535899v1.1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1075958"},{"key":"2023041106200606000_2023.04.07.535899v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/83713"},{"key":"2023041106200606000_2023.04.07.535899v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/ni904"},{"key":"2023041106200606000_2023.04.07.535899v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1856"},{"key":"2023041106200606000_2023.04.07.535899v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaut.2013.01.013"},{"key":"2023041106200606000_2023.04.07.535899v1.6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1816721"},{"key":"2023041106200606000_2023.04.07.535899v1.7","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/ana.26380","article-title":"ZSCAN1 Autoantibodies Are Associated with Pediatric Paraneoplastic ROHHAD","volume":"92","year":"2022","journal-title":"Annals of Neurology"},{"key":"2023041106200606000_2023.04.07.535899v1.8","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.52760"},{"key":"2023041106200606000_2023.04.07.535899v1.9","first-page":"59","article-title":"Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy","volume":"72","year":"2022","journal-title":"Diabetes"},{"key":"2023041106200606000_2023.04.07.535899v1.10","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1038\/s41596-018-0025-6","article-title":"PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes","volume":"13","year":"2018","journal-title":"Nature Protocols"},{"key":"2023041106200606000_2023.04.07.535899v1.11","unstructured":"S. E. Vazquez , et al., Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq. eLife 11, e78550 (2022)."},{"key":"2023041106200606000_2023.04.07.535899v1.12","doi-asserted-by":"crossref","unstructured":"M. Raghavan , et al., Proteomewide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum. 2022.06.24.497532 (2022).","DOI":"10.1101\/2022.06.24.497532"},{"key":"2023041106200606000_2023.04.07.535899v1.13","first-page":"1","article-title":"High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display","volume":"2","year":"2020","journal-title":"Brain Communications"},{"key":"2023041106200606000_2023.04.07.535899v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(92)90029-C"},{"key":"2023041106200606000_2023.04.07.535899v1.15","doi-asserted-by":"publisher","DOI":"10.1002\/eji.1830270841"},{"key":"2023041106200606000_2023.04.07.535899v1.16","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20131603"},{"key":"2023041106200606000_2023.04.07.535899v1.17","doi-asserted-by":"crossref","unstructured":"M. Noviski , et al., IgM and IgD B cell receptors differentially respond to endogenous antigens and control B cell fate. eLife 7, e35074 (2018).","DOI":"10.7554\/eLife.35074"},{"key":"2023041106200606000_2023.04.07.535899v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(95)90171-X"},{"key":"2023041106200606000_2023.04.07.535899v1.19","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1301979"},{"key":"2023041106200606000_2023.04.07.535899v1.20","doi-asserted-by":"crossref","unstructured":"J. A. Al-Mughales , Anti-Nuclear Antibodies Patterns in Patients With Systemic Lupus Erythematosus and Their Correlation With Other Diagnostic Immunological Parameters. Front Immunol 13, 850759 (2022).","DOI":"10.3389\/fimmu.2022.850759"},{"key":"2023041106200606000_2023.04.07.535899v1.21","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20160560"},{"key":"2023041106200606000_2023.04.07.535899v1.22","doi-asserted-by":"crossref","unstructured":"T. Tsubata , CD72 is a Negative Regulator of B Cell Responses to Nuclear Lupus Self-antigens and Development of Systemic Lupus Erythematosus. Immune Netw 19, e1 (2019).","DOI":"10.4110\/in.2019.19.e1"},{"key":"2023041106200606000_2023.04.07.535899v1.23","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1300683"},{"key":"2023041106200606000_2023.04.07.535899v1.24","doi-asserted-by":"publisher","DOI":"10.1126\/science.1124978"},{"key":"2023041106200606000_2023.04.07.535899v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/416603a"},{"key":"2023041106200606000_2023.04.07.535899v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04642-z"},{"key":"2023041106200606000_2023.04.07.535899v1.27","doi-asserted-by":"publisher","DOI":"10.1177\/0961203308089990"},{"key":"2023041106200606000_2023.04.07.535899v1.28","unstructured":"L. A. Casciola-Rosen , G. Anhah , A. Rosen , Autoantigens Targeted in Systemic Lupus Erythematmus Are Clustered in Two Populations of Surface Structures on Apoptotic Keratinocytes."},{"key":"2023041106200606000_2023.04.07.535899v1.29","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.4.1721"},{"key":"2023041106200606000_2023.04.07.535899v1.30","doi-asserted-by":"publisher","DOI":"10.1084\/jem.188.12.2267"},{"key":"2023041106200606000_2023.04.07.535899v1.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.autrev.2005.02.002"},{"key":"2023041106200606000_2023.04.07.535899v1.32","doi-asserted-by":"crossref","unstructured":"A.-M. Aubin , et al., The NOD Mouse Beyond Autoimmune Diabetes. Frontiers in Immunology 13 (2022).","DOI":"10.3389\/fimmu.2022.874769"},{"key":"2023041106200606000_2023.04.07.535899v1.33","unstructured":"Early expression of antiinsulin autoantibodies of humans and the NOD mouse: Evidence for early determination of subsequent diabetes | PNAS (January 24, 2023)."},{"key":"2023041106200606000_2023.04.07.535899v1.34","doi-asserted-by":"publisher","DOI":"10.1006\/jaut.2001.0544"},{"key":"2023041106200606000_2023.04.07.535899v1.35","doi-asserted-by":"crossref","unstructured":"N. I. Maria , P. Vogelsang , M. A. Versnel , The clinical relevance of animal models in Sj\u00f6gren\u2019s syndrome: the interferon signature from mouse to man. Arthritis Research & Therapy 17, 172 (2015).","DOI":"10.1186\/s13075-015-0678-2"},{"key":"2023041106200606000_2023.04.07.535899v1.36","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.179.3.1559"},{"key":"2023041106200606000_2023.04.07.535899v1.37","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3000284"},{"key":"2023041106200606000_2023.04.07.535899v1.38","first-page":"2031","article-title":"An aberrant prostate antigen\u2013specific immune response causes prostatitis in mice and is associated with chronic prostatitis in humans","volume":"119","year":"2009","journal-title":"J Clin Invest"},{"key":"2023041106200606000_2023.04.07.535899v1.39","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1056\/NEJMra1713301","article-title":"Autoimmune Polyendocrine Syndromes","volume":"378","year":"2018","journal-title":"N Engl J Med"},{"key":"2023041106200606000_2023.04.07.535899v1.40","doi-asserted-by":"publisher","DOI":"10.1101\/gr.171645.113"},{"key":"2023041106200606000_2023.04.07.535899v1.41","first-page":"71","article-title":"Characterization and Clinical Association of Autoantibodies Against Perilipin 1 in Patients With Acquired Generalized Lipodystrophy","volume":"72","year":"2022","journal-title":"Diabetes"},{"key":"2023041106200606000_2023.04.07.535899v1.42","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.trsl.2014.08.006","article-title":"Luciferase immunoprecipitation systems for measuring antibodies in autoimmune and infectious diseases","volume":"165","year":"2015","journal-title":"Translational Research"},{"key":"2023041106200606000_2023.04.07.535899v1.43","doi-asserted-by":"crossref","unstructured":"J. J. Maguire , R. E. Kuc , A. P. Davenport , \u201cRadioligand Binding Assays and Their Analysis\u201d in Receptor Binding Techniques, Methods in Molecular Biology., A. P. Davenport , Ed. (Humana Press, 2012), pp. 31\u201377.","DOI":"10.1007\/978-1-61779-909-9_3"},{"key":"2023041106200606000_2023.04.07.535899v1.44","doi-asserted-by":"publisher","DOI":"10.1210\/jc.2011-1159"},{"key":"2023041106200606000_2023.04.07.535899v1.45","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.3390\/biology11071055","article-title":"PhIP-Seq Reveals Autoantibodies for Ubiquitously Expressed Antigens in Viral Myocarditis","volume":"11","year":"2022","journal-title":"Biology"},{"key":"2023041106200606000_2023.04.07.535899v1.46","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/s41586-019-0879-y","article-title":"Commonality despite exceptional diversity in the baseline human antibody repertoire","volume":"566","year":"2019","journal-title":"Nature"},{"key":"2023041106200606000_2023.04.07.535899v1.47","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M112.020800"},{"key":"2023041106200606000_2023.04.07.535899v1.48","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp335"},{"key":"2023041106200606000_2023.04.07.535899v1.49","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1210273109"},{"key":"2023041106200606000_2023.04.07.535899v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/nature03523"},{"key":"2023041106200606000_2023.04.07.535899v1.51","doi-asserted-by":"crossref","unstructured":"H. Itabe , T. Yamaguchi , S. Nimura , N. Sasabe , Perilipins: a diversity of intracellular lipid droplet proteins. Lipids in Health and Disease 16, 83 (2017).","DOI":"10.1186\/s12944-017-0473-y"},{"key":"2023041106200606000_2023.04.07.535899v1.52","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20061864"},{"key":"2023041106200606000_2023.04.07.535899v1.53","doi-asserted-by":"crossref","first-page":"4072","DOI":"10.4049\/jimmunol.181.6.4072","article-title":"Effector Mechanisms of the Autoimmune Syndrome in the Murine Model of Autoimmune Polyglandular Syndrome Type 11","volume":"181","year":"2008","journal-title":"The Journal of Immunology"},{"key":"2023041106200606000_2023.04.07.535899v1.54","doi-asserted-by":"publisher","DOI":"10.1007\/s11060-004-1723-1"},{"key":"2023041106200606000_2023.04.07.535899v1.55","doi-asserted-by":"publisher","DOI":"10.1084\/jem.194.8.1151"},{"key":"2023041106200606000_2023.04.07.535899v1.56","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20050693"},{"key":"2023041106200606000_2023.04.07.535899v1.57","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.gpb.2015.09.001","article-title":"Autoantigen Microarray for High-throughput Autoantibody Profiling in Systemic Lupus Erythematosus","volume":"13","year":"2015","journal-title":"Genomics, Proteomics & Bioinformatics"},{"key":"2023041106200606000_2023.04.07.535899v1.58","doi-asserted-by":"crossref","unstructured":"P. Bankhead , et al., QuPath: Open source software for digital pathology image analysis. Sci Rep 7, 16878 (2017).","DOI":"10.1038\/s41598-017-17204-5"},{"key":"2023041106200606000_2023.04.07.535899v1.59","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","year":"2012","journal-title":"Nature methods"},{"key":"2023041106200606000_2023.04.07.535899v1.60","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr595"},{"key":"2023041106200606000_2023.04.07.535899v1.61","unstructured":"FIMO: scanning for occurrences of a given motif | Bioinformatics | Oxford Academic (March 10, 2023)."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.04.07.535899","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:31:33Z","timestamp":1768451493000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.04.07.535899"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,7]]},"references-count":61,"URL":"https:\/\/doi.org\/10.1101\/2023.04.07.535899","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1172\/jci.insight.174976","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2023,4,7]]},"subtype":"preprint"}}