DOI: 10.34894/qr1vfz
title: Dataset for "A serum protein network predicts the need for systemic immunomodulatory therapy in autoimmune uveitis"
title: SOMAscan analysis of serum of noninfectious uveitis patients and controls

description: This dataset contains *SOMAscan* targeted proteomics (1305 protein analytes) of serum of 54 patients with non-infectious uveitis (&lt;i&gt;HLA-B27+ anterior uveitis&lt;/i&gt;, &lt;i&gt;idiopathic intermediate uveitis&lt;/i&gt;, &lt;i&gt;HLA-A29+ Birdshot chorioretinopathy&lt;/i&gt;, and 26 sex/age matched healthy controls without ocular inflammatory disease. The raw data files (&lt;i&gt;adat&lt;/i&gt; files with relative fluorescent units for 1305 DNA aptamers for 80 samples), metadata, supplemental table 1-3, and R scripts (markdowns) as presented in: &lt;br&gt;&lt;/br&gt;&lt;i&gt;Kuiper et al. 2021 "A serum protein network predicts the early need for systemic immunomodulatory therapy in non-infectious uveitis"&lt;/i&gt; &lt;dl&gt;see preprint on &lt;a href="https://medrxiv.org/cgi/content/short/2021.09.22.21263286v1"&gt;&lt;i&gt;MedRxiv&lt;/i&gt;&lt;/a&gt;
&lt;br&gt;&lt;/br&gt;&lt;/dl&gt;
This dataset contains: &lt;br&gt;&lt;/br&gt;
&lt;dl&gt;

&lt;dt&gt;Supplemental Table 1-3&lt;/dt&gt;
&lt;ul&gt;&lt;li&gt;&lt;dd&gt;&lt;a href="https://dataverse.nl/api/access/datafile/269069"&gt;Supplemental table 1-3.xml &lt;/a&gt; &lt;sup&gt; xml file &lt;/sup&gt;&lt;/dd&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;dt&gt;Raw SOMAscan data&lt;/dt&gt;
&lt;ul&gt;&lt;li&gt;&lt;dd&gt;&lt;a href="https://dataverse.nl/api/access/datafile/140933"&gt;MED-17-274.hybNorm.plateScale.medNorm.calibrate.20180425.adat&lt;/a&gt; &lt;sup&gt; adat file &lt;/sup&gt;&lt;/dd&gt;&lt;/li&gt;
&lt;li&gt;&lt;dd&gt;&lt;a href="https://dataverse.nl/api/access/datafile/140940"&gt;SOMAscan Quality Statement&lt;/a&gt;&lt;sup&gt; PDF file &lt;/sup&gt;&lt;/dd&gt;&lt;/li&gt;&lt;/ul&gt;

&lt;dt&gt;R scripts with &lt;i&gt;step-by-step&lt;/i&gt; analyses &lt;/dt&gt; 
&lt;ul&gt;&lt;li&gt;&lt;dd&gt; "Figure_1.rmd" (see also &lt;a href="https://dataverse.nl/api/access/datafile/141035"&gt;"Figure_1.html"&lt;/a&gt;)&lt;/dd&gt;&lt;/li&gt;
&lt;li&gt;&lt;dd&gt;"Figure_2.rmd" (see also &lt;a href="https://dataverse.nl/api/access/datafile/141031"&gt;"Figure_2.html"&lt;/a&gt;)&lt;/dd&gt;&lt;/li&gt;
&lt;li&gt;&lt;dd&gt;"Figure_3.rmd" (see also &lt;a href="https://dataverse.nl/api/access/datafile/141032"&gt;"Figure_3.html"&lt;/a&gt;)&lt;/dd&gt;&lt;/li&gt;&lt;/ul&gt;
&lt;dt&gt;Metadata used in the R scripts (above)&lt;/dt&gt; 
&lt;ul&gt;&lt;li&gt;&lt;dd&gt;This includes &lt;a href="https://dataverse.nl/file.xhtml?fileId=140934&version=DRAFT"&gt;data&lt;/i&gt; &lt;/a&gt; generated by &lt;a href="https://www.nature.com/articles/ni.3693"&gt;&lt;i&gt; Rieckmann et al., Nat Immunol. 2018&lt;/i&gt; &lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;dd&gt;This includes &lt;a href="https://dataverse.nl/file.xhtml?fileId=140935&version=DRAFT"&gt;data&lt;/i&gt; &lt;/a&gt; generated by &lt;a href="https://www.science.org/doi/full/10.1126/science.aaq1327"&gt;&lt;i&gt; Emilsson et al., Science 2018&lt;/i&gt; &lt;/a&gt;&lt;/li&gt;
&lt;li&gt;&lt;dd&gt;This includes &lt;a href="https://dataverse.nl/file.xhtml?fileId=140928&version=DRAFT"&gt;data&lt;/i&gt; &lt;/a&gt; generated by &lt;a href="https://academic.oup.com/nar/article/46/D1/D661/4612963"&gt;&lt;i&gt; Selenter et al., Nucleic Acids Res. 2018 &lt;/i&gt; &lt;/a&gt;&lt;/li&gt;
&lt;/dl&gt;
description: R studio, R version 4.0.3 (2020-10-10)
description: Objective biomarkers that can predict a severe disease course of autoimmune uveitis are lacking, and warranted for early identification of high-risk patients to improve visual outcome. The need for non-steroid immunomodulatory therapy (IMT) to control autoimmune uveitis is indicative of a more severe disease course. We used aptamer-based proteomics and a bioinformatic pipeline to uncover the serum protein network of 52 treatment-free patients and 26 healthy controls, and validation cohorts of 114 and 67 patients. Network-based analyses identified a highly co-expressed serum signature (n=85 proteins) whose concentration was consistently low in controls, but varied between cases. Patients that were positive for the signature at baseline showed a significantly increased risk for IMT during follow-up, independent of anatomical location of disease. In an independent cohort (n=114), we established robust risk categories and confirmed that patients with high levels of the signature at diagnosis had a significantly increased risk to start IMT during follow-up. Finally, we further validated the predictive association of the signature in a third cohort of 67 treatment-naive North-American patients. A serum protein signature was highly predictive for IMT in human autoimmune uveitis and may serve as an objective blood biomarker to aid in clinical-decision making.