PXD023199

PXD023199 is an original dataset announced via ProteomeXchange.

Title	The proteome of granulovacuolar degeneration and neurofibrillary tangles in Alzheimer’s disease
Description	By combining immunohistochemistry (IHC) and laser microdissection (LMD) we isolated neurons with GVD and those bearing tangles separately from human post-mortem AD hippocampus (n=12) using their typical markers casein kinase (CK)1δ and phosphorylated tau (AT8). Control neurons were isolated from cognitively healthy cases (n=12). 3000 neurons per sample were used for proteome analysis by label free LC-MS/MS. In total 2596 proteins were quantified across samples and a significant change in abundance of 115 proteins in GVD and 197 in tangle bearing neurons was observed compared to control neurons. With IHC the presence of PPIA, TOMM34, HSP70, CHMP1A, TPPP and VXN was confirmed in GVD containing neurons. We found multiple proteins localizing specifically to the GVD bodies, with VXN and TOMM34 being the most prominent new protein markers for GVD bodies. In general, protein groups related protein folding, proteasomal function, the endolysosomal pathway, microtubule and cytoskeletal related function, RNA processing and glycolysis were found to be changed in GVD neurons. In addition to these protein groups, tangle bearing neurons show a decrease in ribosomal proteins, as well as in various proteins related to protein folding.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_15:19:39.454.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frank Koopmans
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-17 06:17:30	ID requested
⏵ 1	2021-09-09 15:19:40	announced

Hondius DC, Koopmans F, Leistner C, Pita-Illobre D, Peferoen-Baert RM, Marbus F, Paliukhovich I, Li KW, Rozemuller AJM, Hoozemans JJM, Smit AB, The proteome of granulovacuolar degeneration and neurofibrillary tangles in Alzheimer's disease. Acta Neuropathol, 141(3):341-358(2021) [pubmed]

submitter keyword: Alzheimer´s disease, Granulovacuolar degeneration, Tau, Neurofibrillary tangles, Proteomics, Neuropathology

Li, Ka Wan
contact affiliation	Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, The Netherlands
contact email	k.w.li@vu.nl
lab head
Frank Koopmans
contact affiliation	VU University
contact email	frank.koopmans@vu.nl
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/2021/09/PXD023199

PRIDE project URI

• PRIDE
  1. PXD023199
     1. Label: PRIDE project
     2. Name: The proteome of granulovacuolar degeneration and neurofibrillary tangles in Alzheimer’s disease