PXD063677

PXD063677 is an original dataset announced via ProteomeXchange.

Title	Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma
Description	Medullary thyroid carcinoma (MTC) is a rare and aggressive neuroendocrine tumor. Our study involves 482 retrospective MTC formalin-fixed, paraffin-embedded (FFPE) samples from 452 patients, collected from 10 Chinese clinical centers. Quantification of 10,092 proteins were achieved via diaPASEF, and 87.8% patients were found to harbor at least one mutation. International MTC grading system, concurrent papillary thyroid carcinoma (PTC), and lymph node metastasis were identified as significant risk factors. Notably, RET mutations M918T and S891A were associated with high recurrence risk in sporadic and hereditary MTC, respectively. Pathway analyses highlighted enhanced collagen biosynthesis linked to poor prognosis. Ubiquitinomics showed downregulated E3 ligases CUL4B and TRIM32 linked to structural recurrence. Unsupervised clustering identified three molecular subtypes with distinct clinical outcomes and characteristics. To address the need for precise risk stratification, we developed a machine learning model using clinical, genomic, and proteomic data to predict individualized recurrence risk. Our integrated model, comprising 20 features (2 clinical factors and 18 proteins), achieved 84.8% accuracy and an AUC of 0.87 in the independent test dataset. As a comprehensive multi-center, multi-omics study of MTC, our work provides critical insights into MTC heterogeneity and aggressiveness while offering a robust framework for personalized patient management and follow-up strategies.
HostingRepository	PRIDE
AnnounceDate	2025-11-18
AnnouncementXML	Submission_2025-11-18_10:53:14.820.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yan Zhou
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-06 13:45:51	ID requested
⏵ 1	2025-11-18 10:53:15	announced

Dataset with its publication pending

submitter keyword: None

Tiannan Guo
contact affiliation	Westlake University
contact email	guotiannan@westlake.edu.cn
lab head
Yan Zhou
contact affiliation	Westlake University
contact email	zhouyan@westlake.edu.cn
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/11/PXD063677

PRIDE project URI

• PRIDE
  1. PXD063677
     1. Label: PRIDE project
     2. Name: Multi-center multi-omics integration predicts individualized prognosis in medullary thyroid carcinoma