PXD072410-1

PXD072410 is an original dataset announced via ProteomeXchange.

Title	Integrated LiP-MS and 4D proteomics define a coordinated protein conformation–expression atlas in hepatocellular carcinoma
Description	Hepatocellular carcinoma (HCC) exhibits pronounced spatial heterogeneity, yet its underlying molecular mechanisms remain incompletely understood. Conventional proteomic approaches primarily focus on abundance changes, offering limited insights into protein conformational regulation. In this study, we constructed a multi-region protein conformation-expression atlas of HCC by integrating limited proteolysis mass spectrometry with 4D label-free quantitative proteomics across tumor, peritumor-near, and peritumor-far tissues. Our analysis revealed widespread remodeling of protein conformation and expression across tissue regions. We identified conformation-specific altered proteins (CSAPs) that exhibited structural changes independent of abundance, highlighting an underappreciated regulatory layer in HCC. Additionally, conformation–expression coupled proteins (CECPs) were defined as proteins showing coordinated alterations in both conformation and expression. CECPs displayed two distinct spatial patterns—spatially conserved and region-specific—reflecting both common and localized functional adaptations. Directional concordance analysis revealed that structural and abundance changes were highly aligned, suggesting that conformational remodeling may contribute to or reflect expression regulation. Functional enrichment indicated that CECPs were predominantly involved in metabolic and redox-related pathways, RNA processing, and signal transduction. Among the top 30 hub CECPs identified by protein-protein interaction network analysis, ACLY, ALDH18A1, GMPS, and DHX9 exhibited consistent increases in conformation, protein abundance, and mRNA expression, with altered regions localized to catalytic or regulatory domains. Their elevated levels correlated with poorer prognosis, highlighting their potential functional relevance in HCC progression. Overall, our findings highlight conformational remodeling as a significant regulatory layer. This atlas provides a framework for understanding protein-level regulation in HCC and may guide the identification of conformation-sensitive biomarkers and therapeutic targets.
HostingRepository	iProX
AnnounceDate	2025-12-24
AnnouncementXML	Submission_2026-07-10_01:19:03.966.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhendong Chen
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-24 18:08:15	ID requested
⏵ 1	2026-07-10 01:19:04	announced

Dataset with its publication pending

submitter keyword: Hepatocellular carcinoma, Limited proteolysis mass spectrometry, 4D label-free proteomics, Conformational remodeling, Proteomics

Dandan Xiong
contact affiliation	the First Affiliated Hospital of Guangxi Medical University
contact email	xiongdandan@gxmu.edu.cn
lab head
Zhendong Chen
contact affiliation	the First Affiliated Hospital of Guangxi Medical University
contact email	chenzhendong_7315@163.com
dataset submitter

iProX dataset URI