PXD008354

PXD008354 is an original dataset announced via ProteomeXchange.

Title	The Proteomic Landscape in the Vitreous of Patients With Age-Related and Diabetic Retinal Disease
Description	In contrast to neovascular age-related macular degeneration (nAMD), no treatment option exists for dry AMD. The identification of specific biomarkers is required to facilitate diagnosis and therapy of dry AMD. We thus measured the proteome of 34 vitreous humor samples (dry AMD: n = 6, nAMD: n = 10, PDR: n = 9, ERM: n = 9). Samples were immunodepleted for high abundant blood proteins and analyzed by LC-MS/MS with a shotgun approach. Data from dry AMD, nAMD and PDR were compared to the ERM patient group, which was used as reference group. A bioinformatic pipeline was used for label-free relative quantification of proteins and to perform cluster analysis, gene ontology classification and gene set enrichment analysis. A selection of differentially regulated proteins was validated by ELISA. A total of 677 proteins were identified and relatively quantified in the four patient groups. Different clusters of regulated proteins for each patient group were identified and showed characteristic enrichment of specific pathways, like ‘oxidative stress’ for dry AMD, ‘focal adhesion’ for nAMD and ‘complement and coagulation cascade’ for PDR patients. We’ve identified CHLE to be specifically upregulated in dry AMD and RNAS1 together with CPVL to be upregulated in both forms of AMD. The description of pathways specific for the different patient groups and the identification of differentially regulated proteins provide a first step towards the definition of biomarkers for dry AMD. To validate these data and to unravel the mechanistic connection of identified proteins to dry AMD, larger patient cohorts need to be investigated.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:36.686.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Schori
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-04 00:48:12	ID requested
1	2018-07-23 08:21:28	announced
2	2018-07-23 23:58:33	announced	Updated project metadata.
3	2018-07-24 00:14:03	announced	Updated project metadata.
⏵ 4	2023-11-14 08:49:37	announced	2023-11-14: Updated project metadata.

Schori C, Trachsel C, Grossmann J, Zygoula I, Barthelmes D, Grimm C, The Proteomic Landscape in the Vitreous of Patients With Age-Related and Diabetic Retinal Disease. Invest Ophthalmol Vis Sci, 59(4):AMD31-AMD40(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: PDR, proliferative diabetic retinopathy, dry AMD, age-related macular degeneration, neovascular AMD, epiretinal membrane, vitreous proteome,human, biomarker, vitreous humor, nAMD, ERM

Christian Grimm
contact affiliation	Lab for Retinal Cell Biology, Department of Ophthalmology, University of Zürich, Wagistrasse 14, Schlieren, CH 8952, Switzerland
contact email	cgrimm@opht.uzh.ch
lab head
Christian Schori
contact affiliation	University of Zurich
contact email	christian.schori@usz.ch
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/2018/07/PXD008354

PRIDE project URI

• PRIDE
  1. PXD008354
     1. Label: PRIDE project
     2. Name: The Proteomic Landscape in the Vitreous of Patients With Age-Related and Diabetic Retinal Disease