HLA class II immunopeptidomics reveals that co‐inherited HLA‐allotypes within an extended haplotype can improve proteome coverage for immunosurveillance

Abstract

Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA‐DR, ‐DQ, and ‐DP. These molecules share approximately 70% sequence similarity and all present peptide ligands to circulating T cells. While the peptide repertoires of numerous HLA‐DR, ‐DQ, and ‐DP allotypes have been examined, there have been few reports on the combined repertoire of these co‐inherited molecules expressed in a single cell as an extended HLA haplotype. Here we describe the endogenous peptide repertoire of a human B lymphoblastoid cell line (C1R) expressing the class II haplotype HLA‐DR12/DQ7/DP4. We have identified 71350 unique naturally processed peptides presented collectively by HLA‐DR12, HLA‐DQ7, or HLA‐DP4. The resulting “haplodome” is complemented by the cellular proteome defined by standard LC‐MS/MS approaches. This large dataset has shed light on properties of these class II ligands especially the preference for membrane and extracellular source proteins. Our data also provides insights into the co‐evolution of these conserved haplotypes of closely linked and co‐inherited HLA molecules; which together increase sequence coverage of cellular proteins for immune surveillance with minimal overlap between each co‐inherited HLA‐class II allomorph.

HLA-Glyco: A large-scale interrogation of the glycosylated immunopeptidome

“…Consistently, glycosylated and non-glycosylated peptides from Ramarathinam et al 2021 showed similar binding properties, indicating that the detected glycosylation fit within the known HLA-binding cores (two-tailed Fisher's exact test, P-value: 0.48). Interestingly, .…”

“…We carefully selected a case study on a human B lymphoblastoid cell line (C1R) from Ramarathinam et al . 2021 36 . The purification protocol of the HLA-bound peptides in this study was performed sequentially with pan anti-class I, followed by class II anti-DP ( Fig.…”

“…We selected 8 immunopeptidomic studies [31][32][33][34][35][36][37][38] , prioritizing studies with a large amount of highresolution mass spectrometry data and included a variety of instruments as a means to reduce instrumental bias (see Methods). Based on our careful curation and annotation of these data, our collection of 732 different HLA class II mass spectrometry samples incorporated 90.8% of HLA-typed data (Fig.…”

“…Such a deconvolution strategy requires manual intervention to choose the number of HLA motifs (i.e., number of clusters) and assign each discovered motif to one of the expressed HLA alleles of a given sample. We carefully selected a case study on a human B lymphoblastoid cell line (C1R) from Ramarathinam et al 2021 36 .…”

Abundance, Betweenness Centrality, Hydrophobicity, and Isoelectric Points Are Relevant Factors in the Processing of Parental Proteins of the HLA Class II Ligandome

“…To expand the results obtained in the current study to other HLA-DR and -DP allotypes as well as the HLA-DQ locus, the analysis of the 5856 parental proteins containing HLA class II ligands previously reported − was carried out. Up to 86% of our parental protein data set was present in the pool of these studies.…”