PXD019774

PXD019774 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic analysis unveils the expression of cancer associated and specific antigen-derived HLA Class ǀ immunopeptides in melanoma and EGFR mutant lung adenocarcinoma
Description	Immunotherapy has shown great therapeutic potential for cancers with high tumor mutational burden (TMB), but much less promise for cancers with low TMB. One primary approach for adoptive lymphocyte transfer-based immunotherapy is to target the somatic mutated peptide neoantigens and cancer testis (CT) antigens recognized by cytotoxic T cells. Here, we employed mass spectrometry (MS)-based proteogenomic large-scale profiling to identify potential immunogenic human leukocyte antigen (HLA) Class ǀ- associated peptides in both melanoma, a “hot tumor”, and EGFR mutant lung adenocarcinoma, a “cold tumor”. We uncovered 19 common driver oncogene-derived peptides and more than 1000 post-translationally modified peptides (PTM) representing 58 different PTMs. We constructed a CT antigen database with 286 antigens by compiling reputed CT antigen resources and “in-house” genomic data and used this to identify 45 CT antigen-derived peptides from the identified HLA peptidome. Using integrated next generation sequencing data, we discovered 12 neopeptides in EGFR mutant lung cancer cell lines. Finally, we report a novel approach for non-canonical peptide discovery, whereby we leveraged a deep learning-based de novo search and a high confidence annotated long noncoding RNA (LncRNA) database to identify 44 lncRNA-derived peptides. Findings of this study, for the first time, provide evidence for a large pool of actionable cancer antigen-derived peptides for use in mutant EGFR lung cancer immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:30:35.632.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yue Andy Qi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-15 02:50:17	ID requested
1	2021-12-07 09:52:07	announced
⏵ 2	2024-10-22 05:30:36	announced	2024-10-22: Updated project metadata.

10.1016/j.mcpro.2021.100136;

Qi YA, Maity TK, Cultraro CM, Misra V, Zhang X, Ade C, Gao S, Milewski D, Nguyen KD, Ebrahimabadi MH, Hanada KI, Khan J, Sahinalp C, Yang JC, Guha U, Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma. Mol Cell Proteomics, 20():100136(2021) [pubmed]

submitter keyword: HLA immunopeptidome,immunotherapy, neoantigen, melanoma, lung cancer

Udayan Guha
contact affiliation	Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892
contact email	udayan.guha@nih.gov
lab head
Yue Andy Qi
contact affiliation	National Cancer Institute/NIH
contact email	andy.qi@nih.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/12/PXD019774

PRIDE project URI

• PRIDE
  1. PXD019774
     1. Label: PRIDE project
     2. Name: Proteogenomic analysis unveils the expression of cancer associated and specific antigen-derived HLA Class ǀ immunopeptides in melanoma and EGFR mutant lung adenocarcinoma