DOI: 10.5061/dryad.3bk3j9kr1
title: Cystic fibrosis autoantibody signatures associate with Staphylococcus aureus lung infection or cystic fibrosis-related diabetes

description: While cystic fibrosis (CF) lung disease is characterized by persistent
 inflammation and infections, and chronic inflammatory diseases are often
 accompanied by autoimmunity, autooimmune reactivity in CF has not been
 studied in depth. In this work, we undertook an unbiased approach to
 explore the systemic autoantibody repertoire in CF. Our results show
 higher levels of several new autoantibodies in the blood of people with CF
 (PwCF) compared to control subjects. Some of these are IgA autoantibodies
 targeting neutrophil components or autoantigens linked to
 neutrophil-mediated tissue damage in CF. We also found that PwCF with
 higher systemic IgM autoantibody levels have lower prevalence of S. aureus
 infection. On the other hand, IgM autoantibody levels in S.
 aureus-infected PwCF correlate with lung disease severity. Diabetic PwCF
 have significantly higher levels of IgA autoantibodies in their
 circulation compared to nondiabetic PwCF, and several of their IgM
 autoantibodies are associated with worse lung disease. In contrast, in
 nondiabetic PwCF blood levels of IgA autoantibodies correlate with lung
 disease. We have also identified other autoantibodies in CF that are
 associated with P. aeruginosa airway infection. In summary, we have
 identified several new autoantibodies and associations of autoantibody
 signatures with specific clinical features in CF.
description: Autoantibody profiling was performed using an existing
 autoantigen microarray platform developed at the University of Texas
 Southwestern Medical Center Microarray Core. This platform has the
 capacity to display a large number of antigens found in human serum or
 plasma samples on a bio-chip and thereby serves as a high-multiplex
 screening method for the determination of autoantibody specificities. In
 this study, we designed an autoantigen microarray that contains 117
 autoantigens. The protein array chips coated with these autoantigens were
 used for profiling four isotypes of autoantibodies – IgG, IgM, IgA and IgE
 – in human serum samples obtained from healthy control subjects and people
 diagnosed with cystic fibrosis, rheumatoid arthritis and systemic lupus
 erythematosus. The fluorescent signal of fluorescently labelled secondary
 antibodies was acquired with Genepix 7.0 software. The background signals
 were subtracted and signal normalized to internal controls for IgG, IgM,
 IgE and IgA. The final valie for each autoantibody was expressed as
 antibody score which is calculated based on the normalized signal
 intensity (NSI) and the signal-to-noise ratio (SNR) using the formula:
 Ab-score = log<sub>2</sub>(NSI*SNR + 1).
 The normalized and unit variance-scaled Ab-score values were used
 to generate heat maps, organized by unsupervised hierarchical
 co-clustering using Cluster and Treeview software. In the heat maps,
 values were centered by rows, each row represents an autoantibody and each
 column represents a sample (human serum sample). In parallel with the
 above-described antigen array analysis, a whole-chip citrullination was
 also performed to create a corresponding array with the same 117
 autoantigens but all modified by citrullination. A protein citrullination
 kit was used to produce corresponding citrullinated arrays. Antigens that
 had been immobilized to the array chip were incubated with a mixture of
 human recombinant PAD enzymes (PAD 1,2,3,4,6) to produce citrullinated
 antigens. The quality of citrullination was confirmed by antibody-based
 detection of citrullination. Autoantibody reactivities against
 citrullinates autoantigens were measured in the sera the same way as with
 the non-citrullinated autoantigens described.
description: # Cystic fibrosis autoantibody signatures associate with Staphylococcus
 aureus lung infection or cystic fibrosis-related diabetes ## Description
 of the data and file structure Customized autoantigen panel.xls – list of
 the 117 autoantigens included on the autoantigen protein array IgA and
 E_autoAb-Score.xls – derived values of IgA and IgE autoantibody signals of
 citrullinated and non-citrullinated autoantigens IgG and
 M_autoAb-Score.xls - derived values of IgG and IgM autoantibody signals of
 citrullinated and non-citrullinated autoantigens IgA autoantibodies.xls –
 signal and SNR values of IgA autoantibody signals of citrullinated and
 non-citrullinated autoantigens IgE autoantibodies.xls – signal and SNR
 values of IgE autoantibody signals of citrullinated and non-citrullinated
 autoantigens IgG autoantibodies.xls – signal and SNR values of IgG
 autoantibody signals of citrullinated and non-citrullinated autoantigens
 IgM autoantibodies.xls – signal and SNR values of IgM autoantibody signals
 of citrullinated and non-citrullinated autoantigens ## Sharing/Access
 information This data set is linked to the manuscript titled “Cystic
 fibrosis autoantibody signatures associate with Staphylococcus aureus lung
 infection or cystic fibrosis-related diabetes” currently under review at
 Frontiers in Immunology.