Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome

Abstract

The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.

Diverse HLA-I Peptide Repertoires of the APC Lines MUTZ3-Derived Immature and Mature Dendritic Cells and THP1-Derived Macrophages

“…The dominance of nanopeptides was also observed in the shared peptides between MUTZ3 iDC and MUTZ3 mDC, and in the HLA-A*02:01-bound peptides shared among the MUTZ3 DCs and THP1MF. This dominance of nanopeptides has also been observed in other cell lines and patient tumor samples (37)(38)(39)(40), and indicates that nine amino acids is the optimum length for MHC I-binding peptides. Decapeptides were the second most dominant and constituted 22 and 25% for MUTZ3 iDC and MUTZ3 mDC and 12% for THP1.…”

“…First, the source proteins were derived from almost all subcellular locations, with the nucleus, cytoplasm, plasma membrane, and endoplasmic reticulum the most dominant (Fig. 5), which is similar for the HLA-I peptidome of melanoma tumor samples reported earlier (37,38), but different for other human samples such as the B lymphoblastoid cell line, where no source proteins from plasma membrane were found (39), and multiple sclerosis autopsy samples, where cytoplasm and plasma membrane were the most dominant, 34 and 24%, respectively (40). Second, the source proteins were involved in various molecular functions but especially in cell communication/signal transduction, protein metabolism, and transcription factor activity/regulator activity, and the proportion of source proteins per molecular function was similar.…”

“…Second, the source proteins were involved in various molecular functions but especially in cell communication/signal transduction, protein metabolism, and transcription factor activity/regulator activity, and the proportion of source proteins per molecular function was similar. In contrast, in the B lymphoblastic cell line 721.221, the source proteins were dominantly involved in declining prominence in metabolism, cell growth and/or maintenance, cell communication, and stress response (39), and in multiple sclerosis autopsy samples, they were dominantly involved in cellular assembly and organization, nervous system development and function, cellular growth, and proliferation (40). The similarities in source protein peptide sampling in MUTZ3 DCs and THP1MF, although unconfirmed, would imply similarities in protein turnover, because protein turnover correlates with source protein peptide sampling (43,44).…”

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

“…We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. The immunopeptidome is referred to as the collection of peptides associated with and presented by major histocompatibility complex (MHC) molecules (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). MHC-associated peptides are recognized by T lymphocytes that are in turn activated to eliminate abnormal cells such as pathogen-infected and cancer cells.…”

Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma

“…Determining MHC alleles is straightforward in inbred mouse strains but is more complex in humans due to the polymorphic nature of the human leukocyte antigen (HLA) resulting in over 6,500 unique HLA alleles [47]. Any given patient has at least 6 alleles that each may require different algorithms for predicting peptide binding.…”