Influenza B-derived peptide presentation by HLA-B*07:02, -B*08:01 and -B*35:01
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ABSTRACT: Analysis of peptide presentation by Human Leukocyte Antigen (HLA) class I of influenza B infected C1R cells expressing HLA-B*07:02, -B*08:01 or -B*35:01.
Project description:Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex (MHC) (human leukocyte antigen (HLA) in humans). These HLA-peptide complexes are presented on the cell surface for immune T cell recognition. Immunopeptidomics utilizes tandem mass spectrometry (MS/MS) to identify and quantify peptides bound to HLA molecules. The dataset deposited here contains the DDA runs used to generate the spectral libraries of the HLA-bound peptides purified and isolated from C1R-B*57:01 and C1R-A*02:01 cell lines.
Project description:Analysis of the immunopeptidome of Human Leukocyte Antigen (HLA)-A*11:01 during influenza infection. Analyses were performed using the Class I reduced C1R cell line transfected with the HLA class I allele HLA-A*11:01.
Project description:Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex (MHC) (human leukocyte antigen (HLA) in humans). These HLA-peptide complexes are presented on the cell surface for immune T cell recognition. Immunopeptidomics utilizes tandem mass spectrometry (MS/MS) to identify and quantify peptides bound to HLA molecules. Data-independent acquisition (DIA) has emerged as a powerful strategy for deep proteome-wide profiling, but DIA application to immunopeptidomics analyses has so far seen limited use. The dataset deposited here contains the DIA data of the HLA-bound peptides purified and isolated from C1R-B*57:01 and C1R-A*02:01 cell lines.
Project description:HLA-C expresion varies widely across the different HLA-C alleles. MicroRNA binding can partly explain the differences in HLA-C allele expression however other contributing factors still remain undetermined. Here we use two common HLA-C alleles, HLA-C*05:01 and HLA-C*07:02, to explore differences in expression levels. Using functional, structural and peptide repertoire comparisons we demonstrate that HLA-C expression levels are not only modulated at the RNA level but also at the protein level. This dataset contains RAW data and database search results for HLA-C*05:01 and HLA-C*07:02 from the 721.221 cell line.
Project description:Characterisation of peptide ligands of Major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I allele HLA-B*57:01.
Project description:Characterisation of peptide ligands of Major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I allele HLA-B*58:01.
Project description:A novel modified HLA-B*57:01-restricted epitope was identified in one of the reversed-phase fractions following immunoaffinity purification of HLA-peptide complexes from C1R cells expressing HIV envelope protein. Also includes six immunopeptidome datasets from several B57 and env transfected cell lysates.
Project description:Characterisation of peptides presented by the Human Leukocyte Antigen (HLA) class I molecule HLA-B*15:02 in the presence and absence of carbamazepine (CBZ), and related molecules carbamazepine-10,11-epoxide (ECBZ) and oxcarbazepine (OXC).
Project description:Characterisation of peptide ligands of Major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I allele HLA-A*01:01, or HLA-A*02:01, HLA-A*24:02. In addition, public mass spectrometry (MS) datasets of HLA-I and HLA-II immunopeptidome derived from patients’ samples, PBMC or cell lines, and shotgun proteomics from trypsin/elastase digestion were analysed.
Project description:Human leukocyte antigen (HLA) - B*51:01 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are two strong predisposing genetic factors to Behçet's disease (BD). Previous studies have focused on two subgroups of HLA-B*51 peptidome containing Proline (Pro) or Alanine (Ala) at position 2 (P2). Little is known about the unconventional non-Pro/Ala2 HLA-B*51-bound peptides. We aimed to study the features of this novel sub-peptidome, and investigate its regulation by ERAP1. CRISPR-Cas9 was used to generate an HLA-ABC-knockout HeLa cell line (HeLa.ABC-KO), which was subsequently transduced to express HLA-B*51:01 (HeLa.ABC-KO.B51). ERAP1 was silenced using lentiviral shRNA. Peptides bound to HLA-B*51:01 were eluted and analyzed by Mass Spectrometry. The characteristics of non-Pro/Ala2, Pro2 and Ala2 peptides, and their alteration by ERAP1 silencing were investigated. Effects of ERAP1 silencing on cell surface expression of HLA-B*51:01 were studied using flow cytometry. More than 20% of peptides eluted from HLA-B*51:01 lacked Proline or Alanine at P2. This unconventional group of HLA-B*51:01-bound peptides was enriched for 8-mers (with fewer 9-mers) compared to Pro2 and Ala2 sub-peptidomes, and had similar N-terminal and C-terminal residue usages to Ala2 peptides with the exception of the less abundant Leucine at position Ω. Knockdown of ERAP1 increased the percentage of non-Pro/Ala2 to approximately 40%, increased the percentage of longer (10-mer and 11-mer) peptides eluted from HLA-B*51:01 complexes, and abrogated the predominance of Leucine at P1. Interestingly knockdown of ERAP1 altered the length and N-terminal residue usage of non-Ala2&Pro2 and Ala2 but not the Pro2 peptides. Finally, ERAP1 silencing regulated the expression levels of cell surface HLA-B*51 in a cell type - dependent manner. The HLA-B*51:01 peptidome includes a surprisingly high proportion of unconventional non-Pro/Ala2 peptides which are increased by ERAP1 silencing, mimicking the loss-of-function BD risk variant.