PXD004241

PXD004241 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells
Description	Despite affecting up to 70% of HIV+ patients and being the leading cause of dementia in patients under 40 years, the molecular mechanisms involved in the onset of HAND are not well understood. To address this, we performed SILAC-based quantitative proteomic analysis on HIV-Tat treated SH-SY5Y neuroblastoma cells. Isolated protein was fractionated by SDS-PAGE and analysed by nLC-MS/MS on an Orbitrap Velos. Using MaxQuant, we identified and quantitation 3077 unique protein groups. Statistical analysis identified 407 differentially regulated proteins, of which 29 were identified as highly significantly and stably dysregulated using an additional standard deviation-based cutoff. GO-term analysis shows dysregulation in both protein translation machinery as well as cytoskeletal regulation which have both been implicated in other dementias. In addition, several key cytoskeletal regulatory proteins such as ARHGEF17, the Rho GTPase, SHROOM3 and CMRP1 are down-regulated. Together, we show that HIV-Tat can dysregulate neuronal cytoskeletal regulatory proteins which could lead to the major HAND clinical manifestation - synapse loss.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:29:48.064.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tariq Ganief
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-31 00:13:14	ID requested
1	2017-01-29 23:48:24	announced
⏵ 2	2024-10-22 04:29:56	announced	2024-10-22: Updated project metadata.

Ganief T, Gqamana P, Garnett S, Hoare J, Stein DJ, Joska J, Soares N, Blackburn JM, Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells. Proteomics, 17(6):(2017) [pubmed]

10.1002/pmic.201600236;

curator keyword: Biomedical

submitter keyword: proteomics,neuroblastoma, network analysis

Jonathan Blackburn
contact affiliation	Institute of Infectious Disease & Molecular Medicine and Department of Integrative Biomedical Sciences, UCT.
contact email	jonathan.blackburn@uct.ac.za
lab head
Tariq Ganief
contact affiliation	Proteome centre Tubingen
contact email	tariq.ganief@ifiz.uni-tuebingen.de
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/2017/01/PXD004241

PRIDE project URI

• PRIDE
  1. PXD004241
     1. Label: PRIDE project
     2. Name: Quantitative proteomic analysis of HIV-1 Tat-induced dysregulation in SH-SY5Y neuroblastoma cells