Identification of significant potential signaling pathways and differentially expressed proteins in patients with wheat intolerance based on quantitative proteomics

Abstract

Wheat intolerance has various systemic manifestations that can affect people's quality of life, and few studies have focused on the mechanism of wheat intolerance and the signaling pathways involved in wheat intolerance have not been fully identified. We compared the protein profiles of patients with wheat intolerance with those of healthy controls using LASSO (least absolute shrinkage and selection operator) and PLS (partial least squares regression) to obtain DEPs (differentially expressed proteins) for GO (Gene Ontology) analysis, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, and PPI (protein-protein interaction) network analysis. Internal validation and external validation were conducted for target proteomics testing. The correlation between differently expressed protein and the wheat-specific IgG antibody concentration was analyzed. Then ROC curve (receiver operating characteristic curve) was generated to validate the differentially expressed proteins. We identified 33 DEPs as significant candidate proteins of wheat intolerance. These proteins were mainly enriched in complement and coagulation cascade pathways, immune activation, and immune response-related pathways. After internal and external target proteomics validation, CFHR3 (complement factor H-related protein 3) was identified as a key protein that may have an important role in wheat intolerance. We found CFHR3 protein expression abundance and the wheat-specific IgG antibody concentration were significantly negatively correlated (P = 0.035; Spearman correlation coefficient r = -0.565). The AUC (median area under the ROC curve) of CFHR3 is 0.857 in external verification data. This study provides insights into wheat intolerance that can be used to further explore the pathogenesis of this condition. SIGNIFICANCE: Proteomics has performed important potential in food allergy research and is conducive to improving our comprehension on molecular mechanisms of food allergy. The present study identified significant signaling pathways and differentially expressed proteins in patients with wheat intolerance by means of bioinformatics from the viewpoint of mass spectrometry-based proteomics, which provided insights into further research on the pathogenesis and timely diagnosis of wheat intolerance.

Keywords: CFHR3; Complement and coagulation cascades; Differentially expressed protein; Serum proteomics; Signaling pathways; Wheat intolerance.