PXD068148-1

PXD068148 is an original dataset announced via ProteomeXchange.

Title	Vulnerable Carotid Artery Plaques Exhibit Proteolysis, Metabolic Reprogramming and Inflammation
Description	Carotid plaque vulnerability is a current feature that aids in the decision making for ischemic stroke risk prevention. Proteomic analysis of plaque tissue can reveal molecular indicators of instability that complement imaging findings. We sought to identify a proteomic signature distinguishing vulnerable from stable carotid plaques in patients undergoing endarterectomy, with the aim of uncovering candidate biomarkers for potential diagnostic and therapeutic targets. 28 carotid plaque specimens were collected from 27 patients (including one patient with bilateral endarterectomy). Samples were classified as vulnerable (n=14) or non-vulnerable (n=14) based on pre-operative magnetic resonance angiography (MRA) with vessel wall imaging (VWI). Tandem mass tag-based multiplexing strategy followed by mass spectrometry analysis was used to profile the proteomes of all samples. Normalized and log2-transformed protein intensities were compared using two-sample t-tests with unequal variances, and P-values were adjusted for multiple testing with the Benjamini–Hochberg method to obtain false discovery rate q-values. Proteins with q≤0.25 were designated high-confidence candidates, and those with p<0.05 but q>0.25 were considered exploratory. From 3267 proteins identified, 398 reached nominal significance (p<0.05). From those, 29 reached at least log₂ fold change of 1, and fifteen were significant for q≤0.25. All were up-regulated in vulnerable lesions and these included: matrix-degrading enzymes (MMP7, MMP9, MMP1, ADAMDEC1); neutrophil-derived effectors (AZU1, CAMP, LTF, MPO); inflammatory regulators (IL1RN, IL4I1); glycolytic enzymes (HK3, HK2); and lipid-handling proteins (PLA2G7, APOB, PON1). An additional 17 exploratory proteins showed nominal significance (p<0.05, q>0.25) with at least log₂ fold change of 1, and 366 proteins with nominal significance but with a log₂ fold change less than 1 are reported. Our proteomic profiling delineates a robust vulnerability signature marked by enhanced proteolysis, neutrophil activation, inflammatory signaling, metabolic reprogramming, and lipid dysregulation. The high-confidence proteins offer promising tissue biomarkers for identifying unstable carotid plaques, while exploratory candidates warrant further validation.
HostingRepository	PRIDE
AnnounceDate	2026-02-23
AnnouncementXML	Submission_2026-02-22_18:42:08.147.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-07 22:10:57	ID requested
⏵ 1	2026-02-22 18:42:09	announced

Sandoval CP, Meschia JF, Prudencio M, Gendron T, Jacobs C, Beegle RD, Sandhu SJS, Mangalaparthi KK, Sung J, Zhao X, Nassar A, Farres H, Petrucelli L, Pandey A, Erben Y, Proteomic signatures of carotid plaque vulnerability: Proteolysis, inflammation, metabolic reprogramming, and lipid dysregulation. JVS Vasc Sci, 7():100404(2026) [pubmed]

10.1016/j.jvssci.2025.100404;

submitter keyword: Carotid artery disease, proteomics, stroke, vulnerable features, risk stratification

Akhilesh Pandey
contact affiliation	Professor Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/2026/02/PXD068148

PRIDE project URI

• PRIDE
  1. PXD068148
     1. Label: PRIDE project
     2. Name: Vulnerable Carotid Artery Plaques Exhibit Proteolysis, Metabolic Reprogramming and Inflammation