PXD050950

PXD050950 is an original dataset announced via ProteomeXchange.

Title	Qualitative and quantitative proteomic analysis of cancer-PD1 interactome in osteosarcoma cells
Description	The PD-1 immune checkpoint is the target for cancer immunotherapy, which has recently revolutionized cancer treatment approaches. Interestingly, PD-1 is not only expressed by immune cells but also by cancer cells, however contradictory reports are available regarding its significance. The role and PD-1 protein-protein interactions have been well characterized in the immune cells, yet little is known regarding the cancer-expressed PD-1 interactome. Considering the distinct role PD-1 plays in these types of cells and high mutational burden in cancer, the PD-1 interactome may differ significantly from our current understanding. We used U2OS cells as a cellular model of osteosarcoma to investigate the PD-1 protein-protein interactions in cancer. Apart from the wild-type PD-1, the study included two phosho-tyrosine PD-1 mutants (Y223 and Y248), where tyrosine was substituted with phenylalanine. PD-1 phosphorylation at residues Y223 and particularly Y248, was reported critical for the PD-1 downstream signaling in immune cells. Therefore, including these protein variants in the study enabled identification of phospho-PD-1 dependent protein interactions. The PD-1 interacting proteins were isolated through PD-1 pull-down performed in U2OS cells overexpressing PD-1 protein fused with V5 and Twin-Strep tags. The interacting proteins were purified on StrepTactin magnetic beads and eluted into SDS reducing buffer. Quantitative bottom-up mass spectrometry analysis and bioinformatic processing identified 52 interacting protein candidates (FDR<1%) for the WT PD-1 and 79 proteins for each of the phospho-tyrosine mutants. 36 proteins were shared across all PD-1 protein variants, 8 proteins were unique for the WT PD-1, implicating that the latter require the functional phosphorylation of PD-1 tyrosine residues.
HostingRepository	PRIDE
AnnounceDate	2025-03-06
AnnouncementXML	Submission_2025-03-06_05:42:58.302.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jakub Faktor
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-25 05:22:23	ID requested
⏵ 1	2025-03-06 05:42:59	announced

10.1186/s12964-024-01935-w;

Dziubek K, Faktor J, Lokhande KB, Shrivastava A, Papak I, Chrusciel E, Pilch M, Hupp T, Marek-Trzonkowska N, Singh A, Parys M, Kote S, PD-1 interactome in osteosarcoma: identification of a novel PD-1/AXL interaction conserved between humans and dogs. Cell Commun Signal, 22(1):605(2024) [pubmed]

submitter keyword: cancer-intrinsic PD-1,PD-1, interactome, osteosarcoma

Sachin Kote
contact affiliation	International Centre for Cancer Vaccine Science, University of Gdansk
contact email	sachin.kote@ug.edu.pl
lab head
Jakub Faktor
contact affiliation	University of Gdansk Kladki 24 Gdansk
contact email	jakub.faktor@ug.edu.pl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050950
     1. Label: PRIDE project
     2. Name: Qualitative and quantitative proteomic analysis of cancer-PD1 interactome in osteosarcoma cells