Peptides Derived From Mismatched Paternal Human Leukocyte Antigen Predicted to Be Presented by HLA-DRB1, -DRB3/4/5, -DQ, and -DP Induce Child-Specific Antibodies in Pregnant Women

Abstract

Predicted Indirectly ReCognizable Human Leukocyte Antigen (HLA) Epitopes (PIRCHE) are known to be a significant risk factor for the development of donor HLA-specific antibodies after organ transplantation. Most previous studies on PIRCHE limited their analyses on the presentation of the HLA-DRB1 locus, although HLA-DRB3/4/5, -DQ, and -DP are also known for presenting allopeptides to CD4+ T cells. In this study, we analyzed the impact of predicted allopeptides presented by these additional loci on the incidence of HLA-specific antibodies after an immunization event. We considered pregnancy as a model system of an HLA immunization and observed child-specific HLA antibody (CSA) development of 231 mothers during pregnancy by samples being taken at delivery. Our data confirm that PIRCHE presented by HLA-DRB1 along with HLA-DRB3/4/5, -DQ, and -DP are significant predictors for the development of CSA. Although there was limited peptidome overlap observed within the mothers' presenting HLA proteins, combining multiple presenting loci in a single predictor improved the model only marginally. Prediction performance of PIRCHE further improved when normalizing scores by the respective presenters' binding promiscuity. Immunogenicity analysis of specific allopeptides could not identify significant drivers of an immune response in this small cohort, suggesting confirmatory studies.

Keywords: HLA; T-cell epitope; T-cell help; antibody formation; pregnancy.

Figure 1

Flowchart of identifying child-HLA-derived peptides presented by HLA Class II proteins. HLA, human leukocyte antigen.

Figure 2

Distributions of HLA mismatches and presented allopeptides. (A) Total number of HLA mismatches within all pregnancies. (B) Number of unique allopeptides predicted to be presented by maternal HLA considering IC50 threshold. (C) Distribution of allopeptide numbers per source locus dependent on IC50 threshold. HLA, human leukocyte antigen.

Figure 3

Peptide position of allopeptides dependent on presenting locus (line colors) and presented locus (panel) and polymorphy indication. Amino acid variation is shown with inverted gray bars, and exon limits are indicated by dotted vertical lines. Position (x-axis) is numbered continuously based on the IMGT alignment file, including leader peptides and deletions. (A) HLA-A-derived peptides. (B) HLA-B-derived peptides. (C) HLA-C-derived peptides. (D) HLA-DRB1-derived peptides. (E) HLA-DRB3/4/5-derived peptides. (F) HLA-DQA1-derived peptides. (G) HLA-DQB1-derived peptides. (H) HLA-DPA1-derived peptides. (I) HLA-DPB1-derived peptides. HLA, human leukocyte antigen.

Figure 4

Allopeptide number distributions depending on maternal presenting (y-axis) and paternal presented locus (x-axis). Inner circle size, 25th percentile; colored center circle size, median; outer circle size, 75th percentile; color, coefficient of variation.

Figure 5

Boxplots [pooling HLA mismatches by (A) HLA Class I, (B) HLA Class II and (C) across all HLA] showing scaled PS, stratified by CSA⁺ incidence (color) and maternal presenting locus (x-axis). Boxplots depict the median (horizontal line), mean (plus), and first to third quartile (box); the highest and lowest values within 1.5× IQR (whiskers) and outliers (circles), respectively. Ns, p > 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. HLA, human leukocyte antigen; PS, PIRCHE score; CSA, child-specific HLA antibody; IQR, interquartile range.

Figure 6

Immunogenic allopeptides and their composition. (A) Scatterplot of all presented allopeptides, indicating their relative immunogenicity (y-axis), frequency (x-axis), and maternal presenting locus (color and symbol). Quadrant (I) indicates highly immunogenic, yet rare allopeptides; quadrant (II) indicates frequent immunogenic allopeptides; quadrant (III) indicates rare allopeptides that were not or only rarely co-occurring with CSA; quadrant (IV) indicates frequent allopeptides that were rarely co-occurring with CSA; asterisks indicate peptides, which are characterized in Supplementary Table 2 . (B) Logo plot showing amino acid composition of all core allopeptides, considering identical peptides presented on different loci multiple times. (C) Logo plot for allopeptides frequently co-occurring with CSA. (D) Logo plot for allopeptides rarely co-occurring with CSA. (E) Difference in position probability matrices of peptides in (C, D), *p ≤ 0.05. Amino acid abbreviations in panels (B–E) follow IUPAC one-letter codes. CSA, child-specific human leukocyte antigen antibody.