PXD055505-1

PXD055505 is an original dataset announced via ProteomeXchange.

Title	The exploration of brain-body interactions of brain injury reveals organ-specific and diverse signatures
Description	The importance of brain-body interactions in the progresses of diseases are increasingly noticed, and understanding the associated processes could vastly improve the health of whole organism. A comprehensive, whole-organism analysis of organ dynamics to identify the molecular processes within and between organs after brain injury caused by ischemic stroke has been lacking. Mice models of 24 hours ischemic brain injury are constructed. Proteomics and metabolomics are used to detect the changes of organ’s proteome and metaboleome, respectively, and multiple bioinformatics analysis are performed to investigate the changing signatures across organs after stroke. Then, the organ proteomics data combined with aging mouse organ transcriptome data and mouse organ scRNA-seq data to reveal the biological age of organs and cellular resource of differentially expressed proteins (DEPs) of organs after stroke, respectively. Finally, we cross-referenced stroke-related DEPs in plasma with their corresponding protein expression in each organ to investigate the original source of plasma proteins by using spearman’s correlation analysis. Bioinformatics analysis showing the synchronization and asynchronization of the stroke-related proteins involved in multiple regulatory pathways are universally across organs. Although significant inter-organ correlations exist without influenced by stroke, the protein expression changes may better reflect the inter-organ correlation after brain injury by sharing some common changing signatures. Then, hundreds of DEPs in organs with the greatest numbers of DEPs are revealed in heart, and they are unique and common expressed between organs. Notably, an integrate analysis of these DEPs with mouse aging RNA-seq data reveal ageing-like changes in organs, suggesting increased biological ages of organs. Furthermore, a conjoint analysis of our proteomic data with scRNA-seq data confirms the cellular source of DEPs originated from intrinsic cells and immune cells, and the latter are widely located and activated in organs. Finally, we find that some DEPs in plasma are highly correlated with corresponding protein levels in distinct organs, potentially resulting in the stroke of the systemic circulation. Together, this study demonstrates a similar yet asynchronous inter- and intra-organ progression of stroke, providing a fundamental resource for understanding the molecular mechanisms underlying brain-body interaction and potential interventions for brain injury.
HostingRepository	PRIDE
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-24_23:05:18.840.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yuanhong Deng
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-03 03:25:43	ID requested
⏵ 1	2025-08-24 23:05:19	announced

10.1016/j.isci.2025.113103;

Deng YH, Wang H, Zhang JH, Wang YF, Wang MY, Pan XR, Zhang YD, Gan YH, He Y, Xie F, Feng XS, Xie JX, Liu BT, Wang JT, Zhang XX, Wang PF, Li J, Yu SG, Yang QW, Bai MZ, Tang Y, Xiong XY, Integrated omics identifies molecular networks of brain-body interactions of brain injury. iScience, 28(8):113103(2025) [pubmed]

submitter keyword: proteomics, ischemic stroke, brain-body interactions,Brain injury

Yuanhong Deng
contact affiliation	School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
contact email	2007dyh@163.com
lab head
Yuanhong Deng
contact affiliation	School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
contact email	2007dyh@163.com
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/2025/08/PXD055505

PRIDE project URI

• PRIDE
  1. PXD055505
     1. Label: PRIDE project
     2. Name: The exploration of brain-body interactions of brain injury reveals organ-specific and diverse signatures