PXD041688

PXD041688 is an original dataset announced via ProteomeXchange.

Title	The ribosomal P-stalk regulates MHC I antigen presentation
Description	MHC I antigen processing and presentation (APP) is a highly regulated process that enables CD8+ T cell immunosurveillance. APP begins with the ribosomal synthesis of a source antigen, yet the role of ribosomes, particularly specialized ribosomes, in antigen presentation is poorly understood. Here, we show that the presence of the “P-stalk” on the ribosome enhances antigen presentation. The addition of the P-stalk to the ribosome is stimulated by cytokines that upregulate APP components, and knockdown of one of the P-stalk proteins (P1) reduces T cell recognition of tumor cells. Mechanistically, we show that P1-containing ribosomes exhibit enhanced translation of MHC class I molecules and accessory APP components. Finally, analysis of patient data reveals that the mRNA expression of the P-stalk proteins positively correlates with CD8+ T cell infiltration, a trend not seen for other ribosomal proteins. In all, we demonstrate that the presence of the P-stalk defines a specialized ribosome population that enhances antigen presentation, something that may be exploited by cancer cells to escape immunosurveillance.
HostingRepository	PRIDE
AnnounceDate	2025-12-02
AnnouncementXML	Submission_2025-12-02_08:22:31.172.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Onno Bleijerveld
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-20 08:57:45	ID requested
⏵ 1	2025-12-02 08:22:32	announced

10.1016/j.cell.2024.09.039;

Dopler A, Alkan F, Malka Y, van der Kammen R, Hoefakker K, Taranto D, Kocabay N, Mimpen I, Ramirez C, Malzer E, Isaeva OI, Kerkhoff M, Gangaev A, Silva J, Ramalho S, Hoekman L, Altelaar M, Beijersbergen R, Akkari L, Yewdell JW, Kvistborg P, Faller WJ, P-stalk ribosomes act as master regulators of cytokine-mediated processes. Cell, 187(24):6981-6993.e23(2024) [pubmed]

submitter keyword: ribosomal, P1, T cell, CD8,LC-MSMS, P-stalk

Onno Bleijerveld
contact affiliation	Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands.
contact email	O.bleijerveld@nki.nl
lab head
Onno Bleijerveld
contact affiliation	The Netherlands Cancer Institute
contact email	o.bleijerveld@nki.nl
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/2025/12/PXD041688

PRIDE project URI

• PRIDE
  1. PXD041688
     1. Label: PRIDE project
     2. Name: The ribosomal P-stalk regulates MHC I antigen presentation