PXD063231

PXD063231 is an original dataset announced via ProteomeXchange.

Title	Spatial Proteomics Profiling of Vascular Smooth Muscle Cells and Atherosclerotic Plaques in a Diabetic Atherosclerosis Mouse Model
Description	This project presents a spatial proteomic investigation of vascular smooth muscle cells (VSMCs) and atherosclerotic plaque regions in a diabetic mouse model of atherosclerosis (DMAS). Using ApoE-/- mice fed with a high-fat diet and treated with low-dose streptozotocin (STZ) to induce a diabetic phenotype, we performed laser capture microdissection (LCM) to separately isolate plaque regions and adjacent VSMC-rich areas of the aortic arch. Subsequently, spatially resolved proteomic profiling was carried out using LC-MS/MS, followed by quantitative analysis based on iBAQ values. Differentially expressed proteins between plaque and VSMC regions were identified and enriched pathway analysis revealed significant alterations in oxidative stress response, insulin signaling, mitochondrial function, RNA transport, and extracellular matrix remodeling under diabetic conditions. Of particular interest, the spatial proteomics data highlighted a marked downregulation of the nuclear pore complex protein Nup93 in VSMCs from diabetic mice, implicating impaired nuclear transport and dysregulation of RNA alternative splicing. This finding was supported by transcriptomic integration and functional analyses that revealed aberrant splicing of SerpinE2, a gene associated with cell proliferation and ECM accumulation. This dataset provides region-specific, high-resolution proteomic profiles of vascular tissues in a diabetic atherosclerosis model. It serves as a valuable resource for investigating the spatial heterogeneity of vascular pathology and the molecular mechanisms underlying diabetes-accelerated atherosclerosis. The raw and processed data can be used to explore protein expression dynamics, identify spatiotemporal biomarkers, and validate candidate targets such as Nup93 and SerpinE2 involved in VSMC phenotypic switching.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-28_16:39:15.084.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuan Xiaojing
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-23 01:36:20	ID requested
⏵ 1	2025-09-28 16:39:15	announced

10.1016/j.mcpro.2025.101029;

Yuan X, Zhang Q, Li J, Zhang Z, Ye S, Zhou W, Nup93-Mediated RNA Alternative Splicing Associated With Diabetic Atherosclerosis. Mol Cell Proteomics, 24(9):101029(2025) [pubmed]

submitter keyword: Diabetes mellitus

Atherosclerosis

Spatial proteomic technology

Xiaojing Yuan
contact affiliation	The First Affiliated Hospital of USTC, Affiliated to Anhui Medical University, Hefei, Anhui
contact email	yuanxj1123@mail.ustc.edu.cn
lab head
Yuan Xiaojing
contact affiliation	The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China
contact email	yuanxj1123@mail.ustc.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/2025/09/PXD063231

PRIDE project URI

• PRIDE
  1. PXD063231
     1. Label: PRIDE project
     2. Name: Spatial Proteomics Profiling of Vascular Smooth Muscle Cells and Atherosclerotic Plaques in a Diabetic Atherosclerosis Mouse Model