PXD057863

PXD057863 is an original dataset announced via ProteomeXchange.

Title	Thromboxane-A Synthase 1 as a Potential Dual Biomarker for Metastatic Prostate Cancer and Atherosclerosis: Insights from a Nanomedicine Protein Corona, Machine Learning, and Actual Causality Approaches
Description	Prostate cancer (PC) is the most common cancer among men in the United States, while atherosclerosis (ASCVD) is the most prevalent cardiovascular disease (CVD) associated with it. CVD, particularly ASCVD, has been shown to contribute to metastatic prostate cancer (mPC) progression. Identifying blood-based biomarkers for these diseases is essential, yet current diagnostics face challenges in detecting low-abundance proteins in plasma. METHODS: This study introduces a nanomedicine platform that uses nanoparticle protein coronas, combined with mass spectrometry (MS)-based bottom up proteomics (BUP), machine learning, and actual causality analysis, to enable biomarker detection for ASCVD and mPC. Protein corona profiles were generated from 35 plasma samples divided into four groups: mPC with ASCVD, non-metastatic PC (nmPC) with ASCVD, mPC without ASCVD, and nmPC without ASCVD. BUP identified and quantified the proteins in the corona samples and discovered the differentially expressed proteins between different groups. LASSO (Least Absolute Shrinkage and Selection Operator) regularization within a logistic regression model was applied to determine proteins closely linked to ASCVD and mPC. Causality analysis then evaluated the proteins identified, focusing on those that could be considered causal factors in both ASCVD and mPC.
HostingRepository	PRIDE
AnnounceDate	2025-11-21
AnnouncementXML	Submission_2025-11-21_12:16:37.663.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-13 14:00:59	ID requested
⏵ 1	2025-11-21 12:16:38	announced

10.1016/j.cej.2025.161134;

Guha A, Sadeghi SA, Kunhiraman HH, Fang F, Wang Q, Rafieioskouei A, Grumelot S, Gharibi H, Saei AA, Sayadi M, Weintraub NL, Horibata S, Yang PC, Bonakdarpour B, Ghassemi M, Sun L, Mahmoudi M, AI-Driven Prediction of Cardio-Oncology Biomarkers Through Protein Corona Analysis. Chem Eng J, 509():(2025) [pubmed]

submitter keyword: protein corona, Bottom up proteomics, Machin learning,Human Plasma

Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD057863
     1. Label: PRIDE project
     2. Name: Thromboxane-A Synthase 1 as a Potential Dual Biomarker for Metastatic Prostate Cancer and Atherosclerosis: Insights from a Nanomedicine Protein Corona, Machine Learning, and Actual Causality Approaches