PXD055609

PXD055609 is an original dataset announced via ProteomeXchange.

Title	Immunogenic noncoding cryptic peptides dominate the antigenic landscape of ovarian cancer
Description	Increased infiltration of CD3+ and CD8+ T cells into ovarian cancer (OC) tumors is linked to better prognosis, but the specific antigens involved are unclear. Recent data suggests that HLA-I can present peptides from noncoding genomic regions, known as noncanonical or cryptic peptides, but their immunogenicity is underexplored. To address this, we used immunopeptidomic analysis and RNA sequencing on five metastatic OC tumors, identifying around 311 cryptic peptides total, with 40 to 83 per patient. Over 90% of these were novel, with only 9 matching existing datasets. Despite comprising less than 1% of total peptides, noncoding cryptic peptides were more abundant than other antigen types in OC samples. Notably, about 70% of the prioritized cryptic peptides elicited T cell activation, indicated by increased 4-1BB and IFNγ expression in autologous CD8+ T cells. This study reveals noncoding cryptic peptides as a significant class of immunogenic antigens in OC.
HostingRepository	PRIDE
AnnounceDate	2025-01-14
AnnouncementXML	Submission_2025-01-14_11:30:54.126.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); monohydroxylated residue; deamidated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-05 19:42:32	ID requested
⏵ 1	2025-01-14 11:30:54	announced

Dataset with its publication pending

submitter keyword: Immunopeptidomics, Proteogenomics, Noncanonical peptides, Neoantigens

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
contact email	Pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055609
     1. Label: PRIDE project
     2. Name: Immunogenic noncoding cryptic peptides dominate the antigenic landscape of ovarian cancer