Dataset Information

Cervical Cancer Tissue Immunopeptidomics

ABSTRACT: 10 cervical cancer tissue tumour resections were analysed using an immunopeptidomics workflow.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Female Reproductive System

DISEASE(S): Cervix Carcinoma

SUBMITTER: Nicola Ternette

LAB HEAD: Nicola Ternette

PROVIDER: PXD046182 | Pride | 2024-01-26

REPOSITORIES: pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	HFX0063_IPP180_Xu_CT_1-2_even.mgf	Mgf
	HFX0063_IPP180_Xu_CT_1-2_even.raw	Raw
	HFX0063_IPP180_Xu_CT_1-2_odd.mgf	Mgf
	HFX0063_IPP180_Xu_CT_1-2_odd.raw	Raw
	HFX0063_IPP180_Xu_CT_10-2_even.mgf	Mgf

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Publications

MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer.

Liao Hanqing H Barra Carolina C Zhou Zhicheng Z Peng Xu X Woodhouse Isaac I Tailor Arun A Parker Robert R Carré Alexia A Borrow Persephone P Hogan Michael J MJ Paes Wayne W Eisenlohr Laurence C LC Mallone Roberto R Nielsen Morten M Ternette Nicola N

Nature communications 20240122 1

Understanding the nature and extent of non-canonical human leukocyte antigen (HLA) presentation in tumour cells is a priority for target antigen discovery for the development of next generation immunotherapies in cancer. We here employ a de novo mass spectrometric sequencing approach with a refined, MHC-centric analysis strategy to detect non-canonical MHC-associated peptides specific to cancer without any prior knowledge of the target sequence from genomic or RNA sequencing data. Our strategy i ...[more]

PMID: 38253617

Similar Datasets

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.