Contents lists available at ScienceDirect Journal of Autoimmunity journal homepage: www.elsevier.com/locate/jautimm Transcriptomic and proteomic analysis of iris tissue and aqueous humor in juvenile idiopathic arthritis-associated uveitis Lena Wildschütz a,* , Doreen Ackermann b , Anika Witten c , Maren Kasper a , Martin Busch a , Shirin Glander c , Harutyun Melkonyan d , Karoline Walscheid a , Christoph Tappeiner e , Solon Thanos d , Andrei Barysenka c , Jörg Koch a , Carsten Heinz a,f , Björn Laffer a,f , Dirk Bauer a , Monika Stoll c , Simone König b , Arnd Heiligenhaus a,f a Department of Ophthalmology and Ophtha-Lab at St. Franziskus-Hospital, Münster, Germany b Interdisciplinary Center for Clinical Research, Core Unit Proteomics, University of Münster, Germany c Core Facility Genomics, University of Münster, Germany d Institute of Experimental Ophthalmology at University of Münster, Germany e Department of Ophthalmology, Inselspital, University of Bern, Bern, Switzerland f Department of Ophthalmology, University of Duisburg-Essen, Essen, Germany ARTICLE INFO Keywords: Juvenile idiopathic arthritis Uveitis B cells Cytokines Plasma cell niche HLA-B27 ABSTRACT Gene and protein expression profiles of iris biopsies, aqueous humor (AqH), and sera in patients with juvenile idiopathic arthritis-associated uveitis (JIAU) in comparison to control patients with primary open-angle glau- coma (POAG) and HLA-B27-positive acute anterior uveitis (AAU) were investigated. Via RNA Sequencing (RNA- Seq) and mass spectrometry-based protein expression analyses 136 genes and 56 proteins could be identified as being significantly differentially expressed (DE) between the JIAU and POAG group. Gene expression of different immunoglobulin (Ig) components as well as of the B cell-associated factors ID3, ID1, and EBF1 was significantly upregulated in the JIAU group as compared to POAG patients. qRT-PCR analysis showed a significantly higher gene expression of the B cell-related genes CD19, CD20, CD27, CD138, and MZB1 in the JIAU group. At the protein level, a significantly higher expression of Ig components in JIAU than in POAG was confirmed. The B cell-associated protein MZB1 showed a higher expression in JIAU patients than in POAG which was confirmed by western blot analysis. Using bead-based immunoassay analysis we were able to detect a significantly higher concentration of the B cell-activating and survival factors BAFF, APRIL, and IL-6 in the AqH of JIAU and AAU patients than in POAG patients. The intraocularly upregulated B cell-specific genes and proteins in iris tissue suggest that B cells participate in the immunopathology of JIAU. The intracameral environment in JIAU may facilitate local effector and survival functions of B cells, leading to disease course typical for anterior uveitis. https://doi.org/10.1016/j.jaut.2019.03.004 Received 23 January 2019; Received in revised form 4 March 2019; Accepted 4 March 2019 Abbreviations: ANA, anti nuclear antibodies; APRIL, a proliferation-inducing ligand; AU, anterior uveitis; AAU, acute anterior uveitis; AqH, aqueous humor; BAFF, B cell-activating factor; BCMA, B cell maturation antigen; BSA, bovine serum albumin; CD, cluster of differentiation; cDNA, complementary desoxyribonucleic acid; CHAPS, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate; DE, differentially expressed; DMARD, disease-modifying anti-rheumatic drug; DTT, Dithiothreitol; f, female; EBF1, early B cell factor 1; FDR, false discovery rate; fw, forward; GAPDH, Glyceraldehyde 3-phosphate dehydrogenase; Gpr83, G Protein- Coupled Receptor 83; HLA, human leukocyte antigen; HKG, housekeeping gene; ID, inhibitor of DNA binding; Ig, immunoglobulin; IL, interleukin; ILAR, International League of Associations for Rheumatology; IOP, intraocular pressure; JIA, juvenile idiopathic arthritis; JIAU, juvenile idiopathic arthritis-associated uveitis; LC-IMS, liquid chromatography coupled ion mobility mass spectrometry; LLPC, long-lived plasma cell; m, male; mRNA, messenger RNA; Mmrn2, Multimerin 2; MTX, methotrexate; MZB1, marginal zone and B1 cell-specific protein; Nedd9, Neural Precursor Cell Expressed; PC, plasma cell; PCA, principle component analysis; POAG, primary open-angle glaucoma; qRT-PCR, quantitative real-time polymerase chain reaction; RA, rheumatoid arthritis; RF, rheumatoid factor; RIN, RNA integrity number; rlog, regularized logarithm; RNA, ribonucleic acid; RNA-Seq, RNA Sequencing; rv, reverse; SD, standard deviation; SE, standard error; SDC-1, Syndecan-1; SDS-PAGE, Sodium dodecyl sulfate polyacrylamide gel electrophoresis; SLE, systemic lupus erythematosus; SS, Sjögren syndrome; SUN, standardization of uveitis nomenclature; TBS-T, Tris-buffered saline with Tween 20; TCEP, tris(2-carboxyethyl)phosphine); Th, T-helper; UPLC, Ultra Performance Liquid Chromatography * Corresponding author. Department of Ophthalmology and Ophtha-Lab at St. Franziskus Hospital, Hohenzollernring 74, 48145, Muenster, Germany. E-mail address: lena.wildschuetz@uveitis-zentrum.de (L. Wildschütz). Journal of Autoimmunity xxx (xxxx) xxx–xxx 0896-8411/ © 2019 Elsevier Ltd. All rights reserved. Please cite this article as: Lena Wildschütz, et al., Journal of Autoimmunity, https://doi.org/10.1016/j.jaut.2019.03.004