PXD041795

PXD041795 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS of HEK-293 inducibly expressing TDP-43 protein (WT and 3 non-functional mutants)
Description	Aggregation of the RNA-binding protein TDP-43 is the key neuropathological feature of neurodegenerative diseases, including ALS and FTLD. TDP-43 is a ubiquitously expressed, nucleic acid-binding protein essential for human development. In physiological conditions, TDP-43 is predominantly nuclear, forms physiological oligomers and performs a wide variety of functions in the metabolism of RNA. However, whether oligomerization is required for TDP-43 functionality and whether oligomerization and RNA binding are intertwined, and if so how, remains poorly understood. To study this question, we generated three GFP-tagged human TDP-43 variants with either six point mutations that disrupt TDP-43 oligomerization (6M), five point mutations within the RNA-recognition motifs that disrupt RNA binding (RBDm) or both (6M&RBDm), and developed the corresponding four (TDP-43 WT and 3 mutants) isogenic HEK-293 cell lines expressing a single copy of GFP-TDP-43 under the control of a doxycycline-inducible promoter. Here, we induced the expression of all four TDP-43 constructs and studied the effects of the mild overexpression of the different TDP-43 variants on the human cell proteome.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:04:57.570.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuela Pérez Berlanga
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-25 04:06:20	ID requested
1	2023-08-31 07:03:26	announced
⏵ 2	2023-11-14 09:04:58	announced	2023-11-14: Updated project metadata.

P, é, rez-Berlanga M, Wiersma VI, Zbinden A, De Vos L, Wagner U, Foglieni C, Mallona I, Betz KM, Cl, é, ry A, Weber J, Guo Z, Rigort R, de Rossi P, Manglunia R, Tantardini E, Sahadevan S, Stach O, Hruska-Plochan M, Allain FH, Paganetti P, Polymenidou M, Loss of TDP-43 oligomerization or RNA binding elicits distinct aggregation patterns. EMBO J, 42(17):e111719(2023) [pubmed]

submitter keyword: Human, kidney, TDP-43, LC-MS/MS

Magdalini Polymenidou
contact affiliation	Polymenidou group Department of Quantitative Biomedicine University of Zurich Switzerland
contact email	magdalini.polymenidou@uzh.ch
lab head
Manuela Pérez Berlanga
contact affiliation	University of Zurich
contact email	manuela.perezberlanga@uzh.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/2023/08/PXD041795

PRIDE project URI

• PRIDE
  1. PXD041795
     1. Label: PRIDE project
     2. Name: LC-MS/MS of HEK-293 inducibly expressing TDP-43 protein (WT and 3 non-functional mutants)