PXD022850

PXD022850 is an original dataset announced via ProteomeXchange.

Title	Integrative multi-omics analysis to characterize human brain ischemia
Description	1. Rationale: Stroke is still a major cause of death and disability worldwide. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome. The use of high-throughput unbiased omics approaches, such as proteomics and transcriptomics, might aid to deepen the knowledge of stroke at the molecular level. Moreover, the integration of omics data is needed to depict the existing interaction between different molecular units and interpret the results in a global biological context. 2. Objective: Our aim was to identify and verify protein and gene expression changes that occur in the human brain after ischemia through an integrative approach to join and combine the information of both omics analyses. The translational potential of our results was explored in a pilot study with blood samples from ischemic stroke patients. 3. Methods and results: Proteomics and transcriptomics discovery studies were performed in human brain samples from deceased stroke patients, unveiling 128 proteins and 2716 genes significantly dysregulated after cerebral ischemia. Afterwards, integrative bioinformatics analyses joining both datasets exposed several canonical pathways altered in the ischemic area, such as neurotransmitters release or matrisome regulation, highlighting the most influential molecules in these pathways. To conduct the verification phase, 28 genes and 9 proteins were selected to be validated in independent human brain samples by means of orthogonal techniques. Our results were confirmed for NCDN, RAB3C, ST4A1, DNM1L, A1AG1, A1AT, JAM3, VTDB, ANXA1, ANXA2 and IL8. Finally, the blood circulating levels of the validated protein candidates were explored in ischemic stroke patients over the acute phase of the disease. Protein fluctuations along the first week after onset were detected for A1AG1 and A1AT. 4. Conclusion: The results presented here expand the knowledge of stroke pathology, revealing new key molecules that can be further explored as biomarkers and/or therapeutic targets of ischemic stroke.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:34:13.702.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laura Ramiro
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-01 06:52:33	ID requested
1	2022-12-21 03:22:35	announced
⏵ 2	2023-11-14 08:34:14	announced	2023-11-14: Updated project metadata.

Ramiro L, Garc, í, a-Berrocoso T, Brians, ó F, Goicoechea L, Simats A, Llombart V, Gonzalo R, Hainard A, Mart, í, nez-Saez E, Canals F, Sanchez JC, S, á, nchez-Pla A, Montaner J, Integrative Multi-omics Analysis to Characterize Human Brain Ischemia. Mol Neurobiol, 58(8):4107-4121(2021) [pubmed]

submitter keyword: proteomics, integrative analysis,Ischemic stroke, transcriptomics

Joan Montaner
contact affiliation	Neurovascular Research Laboratory, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. Institute de Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC/University of Seville & Department of Neurology, Hospital Universitario Virgen Macarena, Seville.
contact email	joan.montaner@vhir.org
lab head
Laura Ramiro
contact affiliation	Vall d'Hebron Institute of Research
contact email	laura.ramirop@gmail.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/2022/12/PXD022850

PRIDE project URI

• PRIDE
  1. PXD022850
     1. Label: PRIDE project
     2. Name: Integrative multi-omics analysis to characterize human brain ischemia