PXD048864-1

PXD048864 is an original dataset announced via ProteomeXchange.

Title	Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers
Description	HIGHTLIGHTS - Improved protocol for ISF collection using microdialysis and CSF sampling in mice. - Combined LC‒MS/MS proteomics ISF and CSF analyses for the validation and description of potential new AD biomarkers. - ISF proteomics analysis to track disease progression at the neuronal and glial levels. - Identification of new biomarker candidates for Alzheimer’s disease. ABSTRACT Background: Mass spectrometry (MS)-based cerebrospinal fluid (CSF) proteomics is an important method for discovering biomarkers of neurodegenerative diseases. CSF serves as a reservoir for interstitial fluid (ISF), and extensive communication between the two fluid compartments helps to remove waste products from the brain. New method: We performed proteomic analyses of both CSF and ISF fluid compartments using intracerebral microdialysis to validate and detect novel biomarkers of Alzheimer's disease (AD) in APPtg and C57Bl/6J control mice. Results: We identified up to 625 proteins in ISF and 4,483 proteins in CSF samples. By comparing the biofluid profiles of APPtg and C57Bl/6J mice, we detected 37 and 108 significantly up- and downregulated candidates, respectively. In ISF, 7 highly regulated proteins, such as Gfap, Aldh1l1, Gstm1, and Txn, have already been implicated in AD progression, whereas in CSF, 9 out of 14 highly regulated proteins, such as Apba2, Syt12, Pgs1 and Vsnl1, have also been validated to be involved in AD pathogenesis. In addition, we also detected new interesting regulated proteins related to the control of synapses and neurotransmission (Kcna2, Cacng3, and Clcn6) whose roles as AD biomarkers should be further investigated. Comparison with existing methods: This newly established combined protocol provides better insight into the mutual communication between ISF and CSF as an analysis of tissue or CSF compartments alone. Conclusions: The use of multiple fluid compartments, ISF and CSF, for the detection of their biological communication enables better detection of new promising AD biomarkers. KEYWORDS Alzheimer’s disease, CSF, ISF, proteomics, biomarkers, microdialysis, mass spectrometry, protein identification, neurodegeneration, brain fluids, expression profiles DATA AVAILABILITY DOI: 10.17605/OSF.IO/VWQ58 PUBLICATIONS using this dataset: 1) Gorska et al. 2024, Journal of Neuroscience Methods https://doi.org/10.1016/j.jneumeth.2024.110239 2) to come
HostingRepository	PRIDE
AnnounceDate	2024-08-28
AnnouncementXML	Submission_2024-08-28_01:53:29.716.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jens Pahnke
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF fleX

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-24 23:35:12	ID requested
⏵ 1	2024-08-28 01:53:30	announced

10.1016/J.JNEUMETH.2024.110239;

submitter keyword: proteomics, ISF,Alzheimer’s disease, mass spectrometry, CSF, biomarkers, microdialysis, neurodegeneration, brain fluids, expression profiles, protein identification

Jens Pahnke
contact affiliation	University of Oslo, Oslo University Hospital, University of Lübeck, University of Latvia, Tel Aviv University www.pahnkelab.eu
contact email	jens.pahnke@gmail.com
lab head
Jens Pahnke
contact affiliation	University of Oslo, University of Lübeck, University of Latvia, Tel Aviv University
contact email	jens.pahnke@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/2024/08/PXD048864

PRIDE project URI

• PRIDE
  1. PXD048864
     1. Label: PRIDE project
     2. Name: Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers