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Autoantibody discov...
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Vazquez, Sara E.Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Univ Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.
(author)
Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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eLife Sciences Publications Ltd,2022
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:uu-492256
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-492256URI
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https://doi.org/10.7554/eLife.78550DOI
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http://kipublications.ki.se/Default.aspx?queryparsed=id:151401947URI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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Phage immunoprecipitation sequencing (PhIP-seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-seq for autoantigen discovery, including our previous work (Vazquez et al., 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), and finally, mild and severe forms of COVID-19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as prodynorphin (PDYN) in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in two patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID-19, including the endosomal protein EEA1. Together, scaled PhIP-seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Mann, Sabrina A.Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Chan Zuckerberg Biohub, San Francisco, CA 94118 USA.
(author)
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Bodansky, AaronUniv Calif San Francisco, Dept Pediat Crit Care Med, San Francisco, CA USA.
(author)
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Kung, Andrew F.Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.
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Quandt, ZoeUniv Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.;Univ Calif San Francisco, Dept Med, San Francisco, CA USA.
(author)
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Ferre, Elise M. N.Natl Inst Allergy & Infect Dis, NIH, Lab Clin Immunol & Microbiol, Fungal Pathogenesis Unit, Bethesda, MD USA.
(author)
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Landegren, Nils,1986-Karolinska Institutet,Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinsk biokemi och mikrobiologi,Karolinska Univ Hosp, Karolinska Inst, Dept Med, Stockholm, Sweden.(Swepub:uu)nillan544
(author)
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Eriksson, DanielUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Karolinska Inst, Ctr Mol Med, Dept Med, Stockholm, Sweden.(Swepub:uu)daner854
(author)
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Bastard, PaulRockefeller Univ, St Giles Lab Human Genet Infect Dis, New York, NY USA.;Necker Hosp Sick Children, Necker Branch, Lab Human Genet Infect Dis, INSERM U1163, Paris, France.;Univ Paris, Imagine Inst, Paris, France.;Necker Hosp Sick Children, Dept Pediat, Paris, France.
(author)
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Zhang, Shen-YingRockefeller Univ, St Giles Lab Human Genet Infect Dis, New York, NY USA.;Necker Hosp Sick Children, Necker Branch, Lab Human Genet Infect Dis, INSERM U1163, Paris, France.;Univ Paris, Imagine Inst, Paris, France.
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Liu, JaminUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Univ Calif San Francisco, Berkeley Univ Calif, San Francisco Grad Program Bioengn, San Francisco, CA USA.
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Mitchell, AntheaUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Chan Zuckerberg Biohub, San Francisco, CA 94118 USA.
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Proekt, IrinaUniv Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.
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Yu, DavidUniv Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.
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Mandel-Brehm, CaleighUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.
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Wang, Chung-YuUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Chan Zuckerberg Biohub, San Francisco, CA 94118 USA.
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Miao, BrendaUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.
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Sowa, GavinUniv Calif San Francisco, Sch Med, San Francisco, CA USA.
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Zorn, KelseyUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.
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Chan, Alice Y.Univ Calif San Francisco, Dept Pediat, Div Pediat Allergy Immunol Bone & Marrow Transplan, Div Pediat Rheumatol, San Francisco, CA USA.
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Tagi, Veronica M.Stanford Univ, Div Stem Cell Transplantat & Regenerat Med, Sch Med, Stanford, CA USA.
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Shimizu, ChisatoUniv Calif San Diego, Rady Childrens Hosp, Kawasaki Dis Res Ctr, La Jolla, CA USA.;Univ Calif San Diego, Dept Pediat, La Jolla, CA USA.
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Tremoulet, AdrianaUniv Calif San Diego, Rady Childrens Hosp, Kawasaki Dis Res Ctr, La Jolla, CA USA.;Univ Calif San Diego, Dept Pediat, La Jolla, CA USA.
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Lynch, KaraUniv Calif San Francisco, Dept Lab Med, San Francisco, CA USA.;Zuckerberg San Francisco Gen, San Francisco, CA USA.
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Wilson, Michael R.Univ Calif San Francisco, Weill Inst Neurosci, San Francisco, CA USA.
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Kaempe, OlleKarolinska Univ Hosp, Karolinska Inst, Dept Med, Stockholm, Sweden.;Univ Bergen, Dept Clin Sci, Bergen, Norway.;Univ Bergen, KG Jebsen Ctr Autoimmune Disorders, Bergen, Norway.;Karolinska Univ Hosp, Ctr Mol Med, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Endocrinol Metab & Diabet, Stockholm, Sweden.
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Dobbs, KerryNIAID, Lab Clin Immunol & Microbiol, NIH, Bethesda, MD USA.
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Delmonte, Ottavia M.NIAID, Lab Clin Immunol & Microbiol, NIH, Bethesda, MD USA.
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Bacchetta, Rosa
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Notarangelo, Luigi D.NIAID, Lab Clin Immunol & Microbiol, NIH, Bethesda, MD USA.
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Burns, Jane C.
(author)
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Casanova, Jean-LaurentRockefeller Univ, St Giles Lab Human Genet Infect Dis, New York, NY USA.;Necker Hosp Sick Children, Necker Branch, Lab Human Genet Infect Dis, INSERM U1163, Paris, France.;Univ Paris, Imagine Inst, Paris, France.;Necker Hosp Sick Children, Dept Pediat, Paris, France.;Howard Hughes Med Inst, New York, NY USA.
(author)
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Lionakis, Michail S.Natl Inst Allergy & Infect Dis, NIH, Lab Clin Immunol & Microbiol, Fungal Pathogenesis Unit, Bethesda, MD USA.
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Torgerson, Troy R.Seattle Childrens Res Inst, Seattle, WA USA.;Univ Washington, Dept Pediat, Seattle, WA USA.
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Anderson, Mark S.Univ Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.
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DeRisi, Joseph L.Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Chan Zuckerberg Biohub, San Francisco, CA 94118 USA.
(author)
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Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Univ Calif San Francisco, Diabet Ctr, San Francisco, CA 94118 USA.Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94118 USA.;Chan Zuckerberg Biohub, San Francisco, CA 94118 USA.
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- By the author/editor
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Vazquez, Sara E.
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Mann, Sabrina A.
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Bodansky, Aaron
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Kung, Andrew F.
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Quandt, Zoe
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Ferre, Elise M. ...
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show more...
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Landegren, Nils, ...
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Eriksson, Daniel
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Bastard, Paul
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Zhang, Shen-Ying
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Liu, Jamin
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Mitchell, Anthea
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Proekt, Irina
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Yu, David
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Mandel-Brehm, Ca ...
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Wang, Chung-Yu
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Miao, Brenda
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Sowa, Gavin
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Zorn, Kelsey
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Chan, Alice Y.
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Tagi, Veronica M ...
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Shimizu, Chisato
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Tremoulet, Adria ...
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Lynch, Kara
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Wilson, Michael ...
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Kaempe, Olle
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Dobbs, Kerry
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Delmonte, Ottavi ...
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Bacchetta, Rosa
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Notarangelo, Lui ...
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Burns, Jane C.
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Casanova, Jean-L ...
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Lionakis, Michai ...
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Torgerson, Troy ...
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Anderson, Mark S ...
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DeRisi, Joseph L ...
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Uppsala University
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