PXD053550

PXD053550 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic Characterization of Skull-base Chordoma
Description	Skull-base chordoma (SBC) is a rare, aggressive bone cancer with a high recurrent rate. Genomic studies of SBC have improved our understanding of the disease’s biology. However, the molecular biological characteristics and the effective therapy of SBC remain unknown. Here, we carried out an integrative genomics, transcriptomics, proteomics, and phosphoproteomics analysis of 187 skull-base chordoma tumors. We identified chromosome instability (CIN) as a prognostic predictor and a potential therapeutic target in SBCs. Multi-omic data revealed downstream effects of CIN, in which, RPRD1B served as a putative therapeutic target for radiotherapy resistant SBC patients. Chromosome 1q gain was significantly enriched in CIN+ SBCs, and associated with upregulated mitochondrial functions, which led to inferior clinical outcomes. Immune subtyping identified an immune cold SBC subtype with CIN+ feature, and elucidated an association between losses of chromosome 9p/10q and immune evasion. In addition, proteomics-based classification of SBCs revealed that P-II and P-III subtype tumors had both CIN+ and immune cold features; however, P-II tumors with apoptosis suppression features were more invasive. These identified molecular features of CIN were further confirmed in 17 pairwise SBC patients. Our observations and the multi-omic data resources might guide research into the biology and treatment of SBC.
HostingRepository	iProX
AnnounceDate	2024-07-01
AnnouncementXML	Submission_2024-07-01_21:35:13.383.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ziyan Xu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	acetylated residue; phosphorylated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-01 21:33:09	ID requested
⏵ 1	2024-07-01 21:35:13	announced

Dataset with its publication pending

submitter keyword: SBC

Chen Ding
contact affiliation	Fudan University
contact email	chend@fudan.edu.cn
lab head
Ziyan Xu
contact affiliation	Fudan University
contact email	zyan-Xu@outlook.com
dataset submitter

iProX dataset URI