PXD013064

PXD013064 is an original dataset announced via ProteomeXchange.

Title	IDENTIFICATION OF AN UNCONVENTIONAL SUBPEPTIDOME BOUND TO THE BEHÇET’S DISEASE - ASSOCIATED HLA–B*51:01 THAT IS REGULATED BY ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 (ERAP1)
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.
HostingRepository	PRIDE
AnnounceDate	2020-03-18
AnnouncementXML	Submission_2020-03-18_05:13:27.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD013064
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Nicola Ternette
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-12 08:57:27	ID requested
⏵ 1	2020-03-18 05:13:28	announced

Chen L, Shi H, Koftori D, Sekine T, Nicastri A, Ternette N, Bowness P, et's Disease-associated HLA-B*51:01 that is Regulated by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1). Mol Cell Proteomics, 19(5):871-883(2020) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biomedical

submitter keyword: ERAP1

HLA–B*51:01

BEHÇET’S DISEASE

Nicola Ternette
contact affiliation	University of Oxford
contact email	nicola.ternette@ndm.ox.ac.uk
lab head
Nicola Ternette
contact affiliation	University of Oxford
contact email	nicola.ternette@ndm.ox.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD013064
     1. Label: PRIDE project
     2. Name: IDENTIFICATION OF AN UNCONVENTIONAL SUBPEPTIDOME BOUND TO THE BEHÇET’S DISEASE - ASSOCIATED HLA–B*51:01 THAT IS REGULATED BY ENDOPLASMIC RETICULUM AMINOPEPTIDASE 1 (ERAP1)