PXD083820-1

PXD083820 is an original dataset announced via ProteomeXchange.

Title	Integrative proteomics and acetylomics reveal TOPK as a regulator of mitochondrial metabolism and proteostasis in hepatocellular carcinoma.
Description	Hepatocellular carcinoma (HCC) remains one of the deadliest malignancies worldwide, with limited treatment options and poorly understood oncogenic drivers at the post-translational level. PDZ-binding kinase (TOPK, also known as PBK) is overexpressed across multiple solid tumours, yet its molecular footprint in HCC—particularly at the proteomic and acetylome levels—has never been systematically defined. Methods: TOPK expression and prognostic significance were assessed in the TCGA-LIHC cohort (n = 371) and validated by GEPIA2 and immunohistochemistry in clinical specimens. siRNA-mediated TOPK knockdown was performed in HepG2 and Huh-7 cells, followed by CCK-8, wound-healing, and Western blot assays. Downstream molecular consequences were interrogated by Orbitrap Astral DIA-based quantitative proteomics and DIA-based acetylome profiling. Results: TOPK was markedly overexpressed in HCC tumour versus normal tissue (p < 0.0001) and associated with advanced tumour stage and significantly shorter overall survival (HR = 1.6, log-rank p = 0.0061). TOPK expression positively correlated with CTNNB1, AXIN1, APC, AFP, and TP53. Immunohistochemistry confirmed progressive TOPK protein accumulation from TNM Stage I to Stage III. In vitro, TOPK knockdown suppressed cell proliferation and migration, downregulated AFP-L3 and Bcl-2, and reversed epithelial-to-mesenchymal transition markers. Pan-acetyl-lysine blotting revealed a broad reduction in global protein acetylation. Quantitative proteomics identified 250 differentially expressed proteins (157 upregulated, 93 downregulated), with downregulated proteins enriched in oxidative phosphorylation, mitochondrial inner membrane, and chromatin methyltransferase functions, and upregulated proteins concentrated in lipid and sterol biosynthesis. Acetylome profiling identified 860 differentially acetylated sites (516 hyperacetylated, 344 hypoacetylated), converging on hypoacetylation of TCA cycle, glycolysis, and oxidative phosphorylation enzymes alongside hyperacetylation of ribosomal and Hsp70 chaperone networks—most prominently HSPA4L-K564 (log2FC = +3.78). Conclusions: TOPK functions as a multidimensional oncogenic regulator in HCC, sustaining tumour cell survival, invasion, and mitochondrial bioenergetics while governing the global lysine acetylation landscape. The convergent suppression of mitochondrial metabolism at both proteomic and acetylation levels upon TOPK depletion defines a novel form of metabolic and proteostatic synthetic vulnerability, nominating TOPK as a therapeutic target whose inhibition may be strategically combined with mitochondria-targeting agents in HCC.
HostingRepository	iProX
AnnounceDate	2026-09-08
AnnouncementXML	Submission_2026-09-08_00:48:05.889.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Meijian Yang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2026-09-08 00:45:49	ID requested
⏵ 1	2026-09-08 00:48:06	announced

Dataset with its publication pending

submitter keyword: hepatocellular carcinoma, TOPK/PBK, proteomics, acetylomics, mitochondrial metabolism, epithelial-to-mesenchymal transition, lysine acetylation, post-translational modification

Meijian Yang
contact affiliation	Hebei Medical University
contact email	ymeijianhb@163.com
lab head
Meijian Yang
contact affiliation	Hebei Medical University
contact email	ymeijianhb@163.com
dataset submitter

iProX dataset URI