Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq

Abstract

The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to more common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people with APS1 and discovered multiple common antibody targets. These novel APS1 autoantigens exhibit tissue-restricted expression, including expression in enteroendocrine cells, pineal gland, and dental enamel. Using detailed clinical phenotyping, we find novel associations between autoantibodies and organ-restricted autoimmunity, including a link between anti-KHDC3L autoantibodies and premature ovarian insufficiency, and between anti-RFX6 autoantibodies and diarrheal-type intestinal dysfunction. Our study highlights the utility of PhIP-Seq for extensively interrogating antigenic repertoires in human autoimmunity and the importance of antigen discovery for improved understanding of disease mechanisms.

REAP: A platform to identify autoantibodies that target the human exoproteome

“…2b) 18,43,47 . We also identified autoantibodies against gastric intrinsic factor (GIF), lipocalin-1 (LCN1), IL-5, IL-6, protein disulfide-isomerase-like protein of the testis (PDILT), and BPI fold containing family member 1 and 2 (BPIFA1/2), which have been previously described in APECED [18][19][20][21]48 . With respect to GIF reactivities, the results seen with REAP demonstrated strong concordance with anti-GIF ELISA results from the same patients ( Fig.…”

“…Error bars represent standard error of the mean. g , Comparison of autoantibody detection frequencies in APECED patient cohorts by REAP, LIPS 18 , ProtoArray 18 , and PhIP-Seq 21 . Frequencies are listed as a percentage inside each circle.…”

“…Because antibodies are themselves large (150 kDa) secreted proteins, they are most likely to recognize and act upon targets that reside within the same extracellular compartment 14 . While state-ofthe-art technologies such as protein/peptide microarrays, proteome-scanning libraries using phage (PhIP-seq) and bacterial display have enabled the discovery of novel autoantibodies in a variety of diseases [15][16][17][18][19][20][21][22][23] , these systems have limited sensitivity to detect autoantibodies against extracellular targets. This is due in part to the inherent difficulty of working with extracellular proteins, which often have unique folding requirements that include signal peptide removal, disulfide bond formation, and posttranslational modifications such as glycosylation.…”

An AIREless Breath: Pneumonitis Caused by Impaired Central Immune Tolerance

“…AIRE is expressed in thymic medullary epithelial cells (mTECs) where it facilitates the negative selection of self-reactive T-lymphocytes. As a transcription regulator, AIRE promotes the expression of peripheral tissue-restricted antigens on mTECs and the clonal deletion of self-reactive T-lymphocytes; in the AIRE-deficient state, these cells escape in the periphery and are both necessary and sufficient to cause tissue-specific autoimmunity as shown by lymphocyte depletion and adoptive transfer experiments in mice ( 2 , 34 – 38 ).…”

“…Several tissue-specific autoantibodies correlate with the development of organ-specific disease in APECED ( 38 , 45 – 47 ). Among these, autoantibodies against bactericidal/permeability-increasing fold-containing family B member 1 (BPIFB1) and the potassium channel regulator KCNRG have been associated with development of APECED pneumonitis ( 3 , 21 , 27 , 48 ).…”