PXD061119

PXD061119 is an original dataset announced via ProteomeXchange.

Title	Multi-omic analysis reveals a CAF-stemness-governed classification in HCC liver transplant recipients
Description	In patients with hepatocellular carcinoma (HCC) meeting the Milan criteria, liver transplantation (LT) is an effective therapy. This study aims to define the survival-related molecular biological features helping precisely identifying the patients with HCC beyond the Milan criteria who have acceptable outcomes. In the derivation cohort (n = 122), integrated analyses of tumor tissues are conducted using RNA sequencing (RNA-seq), proteomic landscape and transposase-accessible chromatin sequencing (ATAC-seq). Based on transcriptomics, three subgroups that significantly differ in overall survival were identified in the derivation cohort, and these findings are validated in an independent cohort. In-depth bioinformatics analysis using RNA-seq and proteomics reveals that the promotion of cancer stemness by cancer-associated fibroblasts (CAFs) can be responsible for the negative biological characteristics observed in high-risk HCC patients. The ATAC-seq identifies key factors regulating transcription, which may bridge CAF infiltration and stemness. Finally, we demonstrate that the CAF-derived CXCL12 sustains the stemness of HCC cells by promoting XRCC5 through CXCR4.
HostingRepository	iProX
AnnounceDate	2025-02-24
AnnouncementXML	Submission_2025-07-16_00:37:07.697.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sunbin Ling
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-24 00:02:42	ID requested
1	2025-02-24 00:03:02	announced
⏵ 2	2025-07-16 00:37:08	announced	2025-07-16: Add info.

Ling S, Yu J, Zhan Q, Gao M, Liu P, Wu Y, Zhang L, Shan Q, Liu H, Wang J, Cai S, Zhou W, Que Q, Wang S, Hong J, Xiang J, Xu S, Liu J, Peng X, Wang N, Wang W, Xie H, Cai J, Wang L, Zheng S, Xu X, Multi-omic analysis reveals a CAF-stemness-governed classification in HCC liver transplant recipients beyond the Milan criteria. Nat Commun, 16(1):4392(2025) [pubmed]

submitter keyword: hepatocellular carcinoma, liver transplantation, molecular subtypes, cancer-associated fibroblast

stemness

Sunbin Ling
contact affiliation	Hangzhou Medical College
contact email	lsb0330@zju.edu.cn
lab head
Sunbin Ling
contact affiliation	Hangzhou Medical college
contact email	lsb0330@zju.edu.cn
dataset submitter

iProX dataset URI