HLA-G peptide preferences change in transformed cells: impact on the binding motif

Abstract

HLA-G is known for its strictly restricted tissue distribution. HLA-G expression could be detected in immune privileged organs and many tumor entities such as leukemia, multiple myeloma, and non-Hodgkin and Hodgkin’s lymphoma. This functional variability from mediation of immune tolerance to facilitation of tumor immune evasion strategies might translate to a differential NK cell inhibition between immune-privileged organs and tumor cells. The biophysical invariability of the HLA-G heavy chain and its contrary diversity in immunity implicates a strong influence of the bound peptides on the pHLA-G structure. The aim was to determine if HLA-G displays a tissue-specific peptide repertoire. Therefore, using soluble sHLA-G technology, we analyzed the K562 and HDLM-2 peptide repertoires. Although both cell lines possess a comparable proteome and recruit HLA-G-restricted peptides through the same peptide-loading pathway, the peptide features appear to be cell specific. HDLM-2 derived HLA-G peptides are anchored by an Arg at p1 and K562-derived peptides are anchored by a Lys. At p2, no anchor motif could be determined while peptides were anchored at pΩ with a Leu and showed an auxiliary anchor motif Pro at p3. To appreciate if the peptide anchor alterations are due to a cell-specific differential peptidome, we performed analysis of peptide availability within the different cell types. Yet, the comparison of the cell-specific proteome and HLA-G-restricted ligandome clearly demonstrates a tissue-specific peptide selection by HLA-G molecules. This exclusive and unexpected observation suggests an exquisite immune function of HLA-G.

HLA-F*01:01 presents peptides with N-terminal flexibility and a preferred length of 16 residues

“…According to the method described by Bade-Doeding et al (Bade-Doeding et al 2011 ), HEK293T cells were transfected with the target plasmid along with the packaging and envelope vectors psPAX2 and pmD2G. LCL721.221 cells were stably transduced; the expression of trimeric sHLA-F*01:01 molecules was confirmed by ELISA as previously described (Celik et al 2018b ).…”

“…HLA-Ib molecules are involved in a diverse range of functions in adaptive and innate immunity. In recent years, knowledge about the function (Wagner et al 2017 ; Kraemer et al 2015 ; Celik et al 2018a ) and biophysical features (Celik et al 2018b ; Celik et al 2016 ; Petrie et al 2008 ) of HLA-Ib molecules are engaged in the fundamental understanding of tumor immunosurveillance, pathogen recognition, regulation of autoimmunity and virus-induced immunopathology (Kochan et al 2013 ; Rebmann et al 2014 ; Hofstetter et al 2011 ), their upregulation during pathogenic episodes support the mediation of immune tolerance (Celik et al 2018b ). During viral infection, HLA-E is upregulated on the cell surface and avoids the recognition of infected HLA-Ia empty cells by NK cell (Kraemer et al 2014 ).…”

“…Before being presented by an HLA-Ib molecule, the selection criteria are understandably more severe due to the limited polymorphisms in HLA-Ib molecules (Braud et al 1997 ). While peptide/HLA-E expression levels are highly dependent on cellular stress (van Hall et al 2010 ; Sasaki et al 2016 ), HLA-G selects tissue-specific peptides (Celik et al 2018b ) that are independent of peptide anchor motifs (Celik et al 2018a ). The restricted interaction between peptide/HLA-F (pHLA-F) complexes and the NK cell receptor KIR3DS1 during HIV infection suggests that understanding HLA-F peptide selection and presentation is functionally important.…”

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

“…These observations agree with prior structural analyses that have reported more shallow HLA-C binding clefts 24 , as higher abundance and elevated hydrophobicity of cognate peptides could compensate for decreased binding stability. We noted that HLA-G peptides had an even stronger bias towards lower cleavability scores, possibly due to the lack of HLA-G training data for the cleavability predictor and may suggest differential protease activity in shaping the HLA-G ligandome 25 . Other differences with smaller effect sizes were also observed which altogether prompted us to model extrinsic properties per HLA loci in pan-allele predictors.…”

Dynamic Interaction between Immune Escape Mechanism and HLA-Ib Regulation

“…In terms of peptide presentation, HLA-G differs from other HLA-Ib molecules like HLA-E that presents a very restricted peptide repertoire derived from the signal sequence of other HLA molecules irrespectively of the HLA-E-expressing tissue [7]. In contrast, HLA-G is considered to be a classical peptide presenter like HLA-Ia molecules; however, its peptide repertoire is restricted to the tissue distribution and cell type [7,69,70]. Peptide identification of HLA subtypes is usually performed by affinity purification of the desired HLA molecule from a selected tissue/cell type followed by peptide isolation and mass spectrometric sequencing.…”