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PhIP-Seq uncovers marked heterogeneity in acute rheumatic fever autoantibodies
Reuben McGregor, Lauren H. Carlton, Timothy J. O’Donnell, Elliot Merritt, Campbell R. Sheen, Florina Chan Mow, William John Martin, Michael G. Baker, Nigel Wilson, Uri Laserson, Nicole J. Moreland
Reuben McGregor, Lauren H. Carlton, Timothy J. O’Donnell, Elliot Merritt, Campbell R. Sheen, Florina Chan Mow, William John Martin, Michael G. Baker, Nigel Wilson, Uri Laserson, Nicole J. Moreland
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Research Article Cardiology

PhIP-Seq uncovers marked heterogeneity in acute rheumatic fever autoantibodies

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Abstract

Acute rheumatic fever (ARF) and associated rheumatic heart disease are serious sequelae after infection with group A Streptococcus (Strep A). Autoantibodies are thought to contribute to pathogenesis, with deeper exploration of the autoantibody repertoire needed to improve mechanistic understanding and identify new biomarkers. Phage immunoprecipitation sequencing (PhIP-Seq) with the HuScan library (>250,000 overlapping 90-mer peptides spanning the human proteome) was utilized to analyze autoreactivity in sera from children with ARF, uncomplicated Strep A pharyngitis, and matched healthy controls. A global proteome-wide increase in autoantigen reactivity was observed in ARF, as was marked heterogeneity between patients. Public epitopes, common between individuals with ARF were rare, and comprised less than 1% of all enriched peptides. Differential analysis identified both unknown and previously identified ARF autoantigens, including PPP1R12B, a myosin phosphatase complex regulatory subunit expressed in cardiac muscle, and members of the collagen protein family, respectively. Pathway analysis found antigens from the disease-relevant processes encompassing sarcomere and heart morphogenesis were targeted. In sum, PhIP-Seq has substantially expanded the spectrum of autoantigens in ARF, and reveals the rarity of public epitopes in the disease. It provides further support for the role of epitope spreading in pathogenesis and has identified PPP1R12B as an enriched autoantigen.

Authors

Reuben McGregor, Lauren H. Carlton, Timothy J. O’Donnell, Elliot Merritt, Campbell R. Sheen, Florina Chan Mow, William John Martin, Michael G. Baker, Nigel Wilson, Uri Laserson, Nicole J. Moreland

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Figure 3

Autoantibody pathway, tissue expression, and localization analysis.

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Autoantibody pathway, tissue expression, and localization analysis.
(A) ...
(A) Volcano plot of differential autoantibody reactivity (PhIP-Seq peptides) between ARF cases and healthy controls. Significant peptides (using DESeq2, adjusted P < 0.05) colored by average binding magnitude, nonsignificant by sample density. Number of peptides significantly elevated in ARF cases compares with healthy controls is indicated; 118 peptides mapping to 81 proteins. Dashed lines indicate thresholds for significance and no change; enriched targets PPP1R12B and COL1A1 labeled. Total magnitude indicated by red scale; ARF significantly elevated magnitude compared with healthy controls by 1-sided Wilcoxon’s test. P = 0.018, r = 0.35. (B) GO pathway enrichment for ARF-associated autoantigens (P < 0.01, 81 proteins represented by 118 peptides in A). Dot size reflects protein count per pathway; fill color indicates enrichment strength. Outlines denote GO categories: Cellular Component (blue), Biological Process (green). Highlighted pathways include Sarcomere and Heart Morphogenesis. Full pathway analysis results with enrichment metrics for all GO terms are provided in Supplemental Dataset 1. (C) Heart muscle expression of ARF-enriched targets (Human Protein Atlas). Upper panel: RNA expression ordered from low to high; tile borders indicate multiple (green) or single (gray) peptide hits. Lower panel: Protein expression by immunohistochemistry; tile borders indicate staining reliability (enhanced, red; supported, orange; approved, pink; uncertain, gray). Red arrows highlight PPP1R12B and COL1A1. (D) Subcellular localization and secretion prediction (Human Protein Atlas). Upper panel: Localization across cellular compartments (purple = presence); borders show reliability. Lower panel: Secreted proteins prediction (violet = predicted secreted). Main locations shaded if proteins predicted secreted as main location. PPP1R12B and COL1A1 indicated by red arrows.

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