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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 5

Orthogonal validation using ELISA.

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Orthogonal validation using ELISA.
(A) Schematic representation of the P...
(A) Schematic representation of the PPP1R12B PhIP-Seq peptide tiling and design of synthetic peptides used for validation. The 3 overlapping PhIP-Seq peptides significantly enriched in ARF (17A, 18B, 19A) localize to a contiguous region of the protein. Two nonoverlapping 45-mer peptides (Pep-1 and Pep-2) were synthesized spanning this region, with Pep-2 fully contained within the recombinant protein used for whole-protein ELISA. Created with Biorender. (B) Whole-protein ELISA responses to PPP1R12B, COL1A1, and CD226 in the discovery cohort (ARF vs. healthy). Violin plots with points; white circle symbols show the median, with IQR as error bars. Horizontal dashed lined indicate the reference threshold of 2 times the median of healthy controls. (C) Median absorbance in PPP1R12B peptide ELISAs in the discovery cohort; dashed lines indicate the reference threshold of 2 times the median of healthy controls. Wilcoxon’s P values (ARF vs. healthy) are shown per peptide. (D) Spearman’s correlation of PhIP-Seq normalized enrichment values for peptide 18B with ELISA absorbance values for PPP1R12B whole protein and Pep-2 with fitted linear regression lines (black) and Spearman’s correlation coefficient with significance shown in black text. (E) Discovery ROC for Pep-2 on the absorbance scale (ARF vs. healthy). The prespecified operating cutoff is marked in red with dotted guides. AUC and 95% CI are shown on the plot. (F) Independent validation cohort (ARF, healthy, and Strep A–positive pharyngitis controls): distribution of Pep-2 absorbance with the prespecified discovery cutoff (red dashed line). Wilcoxon’s P values are shown throughout in black text.

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