PXD041585

PXD041585 is an original dataset announced via ProteomeXchange.

Title	Small open reading frame-encoded protein production is modulated by nonsense-mediated decay in breast cancer
Description	Peptides from low abundance non-canonical proteins encoded by the human genome are presented by the major histocompatibility complex and serve as potential neoantigens or therapeutic targets. However, their prevalence in the genome is unclear. We identified several non-canonical proteins produced by breast cancer cell lines using proteogenomics approach. Although these proteins were detectable, the transcripts and corresponding proteins showed low abundance and inconsistent expression pattern. Targeting the nonsense-mediated decay pathway by UPF1-knockdown increased the levels of both non-coding transcripts and non-canonical proteins, suggesting they are subjected to degradation by conserved quality control mechanisms in cells. We also observed increased expression of unannotated transcripts and human leukocyte antigen transcripts associated with antigen presentation. These observations suggest that UPF1 has a role in regulating or suppressing transcriptional noise and that modulating the expression level of UPF1 could expand the reservoir of neoantigens and increase neoantigen presentation, potentially augmenting immunotherapeutic responses in cancers.
HostingRepository	PRIDE
AnnounceDate	2024-01-28
AnnouncementXML	Submission_2024-01-28_07:19:34.020.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	PARTHIBAN PERIASAMY
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-17 07:51:12	ID requested
⏵ 1	2024-01-28 07:19:34	announced

10.1101/2023.08.26.554966;

submitter keyword: Human, breast cancer cell lines, non-canonical proteins, LC-MS/MS

HARSHA GOWDA
contact affiliation	Cancer Precision Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
contact email	parthiban_periasamy@imcb.a-star.edu.sg
lab head
PARTHIBAN PERIASAMY
contact affiliation	Institute of Molecular and Cell Biology, A*-Star
contact email	parthiban_periasamy@imcb.a-star.edu.sg
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/2024/01/PXD041585

PRIDE project URI

• PRIDE
  1. PXD041585
     1. Label: PRIDE project
     2. Name: Small open reading frame-encoded protein production is modulated by nonsense-mediated decay in breast cancer