HLA-F Allele-Specific Peptide Restriction Represents an Exceptional Proteomic Footprint

Abstract

Peptide-dependent engagement between human leucocyte antigens class I (HLA-I) molecules and their cognate receptors has been extensively analyzed. HLA-F belongs to the non-classical HLA-Ib molecules with marginal polymorphic nature and tissue restricted distribution. The three common allelic variants HLA-F*01:01/01:03/01:04 are distinguished by polymorphism outside the peptide binding pockets (residue 50, α1 or residue 251, α3) and are therefore not considered relevant for attention. However, peptide selection and presentation undergoes a most elaborated extraction from the whole available proteome. It is known that HLA-F confers a beneficial effect on disease outcome during HIV-1 infections. The interaction with the NK cell receptor initiates an antiviral downstream immune response and lead to delayed disease progression. During the time of HIV infection, HLA-F expression is upregulated, while its interaction with KIR3DS1 is diminished. The non-polymorphic nature of HLA-F facilitates the conclusion that understanding HLA-F peptide selection and presentation is essential to a comprehensive understanding of this dynamic immune response. Utilizing soluble HLA technology we recovered stable pHLA-F*01:01, 01:03 and 01:04 complexes from K562 cells and analyzed the peptides presented. Utilizing a sophisticated LC-MS-method, we analyzed the complete K562 proteome and matched the peptides presented by the respective HLA-F subtypes with detected proteins. All peptides featured a length of 8 to 24 amino acids and are not N-terminally anchored; the C-terminus is preferably anchored by Lys. To comprehend the alteration of the pHLA-F surface we structurally compared HLA-F variants bound to selected peptides. The peptides were selected from the same cellular content; however, no overlap between the proteomic source of F*01:01, 01:03 or 01:04 selected peptides could be observed. Recognizing the balance between HLA-F expression, HLA-F polymorphism and peptide selection will support to understand the role of HLA-F in viral pathogenesis.

The Loss of HLA-F/KIR3DS1 Ligation Is Mediated by Hemoglobin Peptides

“…In all investigations concerning the interaction between HLA-F and its cognate immune receptors, only HLA-F*01:01 and HLA-F*01:01 OC were examined [5,6]. Our peptide sequence analysis from HLA-F allelic variants featured hemoglobin subunit beta (HBB) peptide (VNVDEVGGEALGR) as dominant and shared [8]. Since HBB is upregulated during HIV infection and presented by all three allelic variants of HLA-F, we suggest that peptide presentation is involved in the obstacle of reducing interaction between HLA-F and KIR3DS1 in HIV infection.…”

“…However, polymorphism of other HLA-Ib molecules HLA-E and HLA-G that should also not interfere with peptide selection, binding, and presentation impacts their immune function significantly [22,34]. Recently, it has been shown that the polymorphism of HLA-F allelic variants does not influence peptide features of presented peptides [8]. The pHLA structure of HLA-F differs from the classical pHLA structure [6,7].…”

“…For proteome analysis, 1 × 10 6 CD4 + T cells from therapy-naïve patients with HIV (approved by the ethics committee of Hannover Medical School; code 2411-2014) and CD4 + /HIV − T cells were lysed in 100 µL RIPA buffer as previously described [8]. Protein concentration was ascertained using the bicinchoninic acid assay (BCA) protein quantitation kit (Interchim, San Diego, CA, USA).…”

“…Recently, it has been demonstrated that HLA-F is able to assemble with β2m and to bind and present peptides like classical HLA-I molecules [6,7]. Of note, peptides selected and presented by HLA-F exhibit unusual length [6,8]; further analysis revealed that the peptides are exclusively C terminal anchored; the unique structure of the HLA-F peptide-binding region (PBR) impedes the classical pocket A and pocket B engagement and enables the binding of these long peptides [6,8]. However, peptide-HLA-F complexes (pHLA-F) are ligands for immunoglobulin-like transcript receptor-2 (ILT-2) [6,9].…”