PXD042302-3

PXD042302 is an original dataset announced via ProteomeXchange.

Title	Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.
Description	The unique architecture of glomerular podocytes is integral to kidney filtration. Interdigitating foot processes extend from the podocyte cell body, wrap around fenestrated capillaries, and form specialized junctional complexes termed slit diaphragms to create a molecular sieve. However, the full complement of proteins which maintain foot process integrity, and how this localized proteome changes with disease, remains to be elucidated. Proximity-dependent biotin identification (BioID) enables the identification of spatially localized proteomes. To this end, we developed a novel in vivo BioID knock-in mouse model. We utilized the slit diaphragm protein podocin (Nphs2) to create a podocin-BioID fusion. Podocin-BioID localizes to the slit diaphragm and biotin injection leads to podocyte-specific protein biotinylation. We isolated the biotinylated proteins and performed mass spectrometry to identify proximal interactors. Gene ontology analysis of 54 proteins specifically enriched in our podocin-BioID sample revealed ‘cell junctions’, ‘actin binding’, and ‘cytoskeleton organization’ as top terms. Known foot process components were identified and we further uncovered two novel proteins: the tricellular junctional protein Ildr2 and the CDC42 and N-WASP interactor Fnbp1l. We confirmed Ildr2 and Fnbp1l are expressed by podocytes and partially colocalize with podocin. Finally, we investigated how this proteome changes with age and uncovered a significant increase in Ildr2. This was confirmed by immunofluorescence on human kidney samples and suggests altered junctional composition may preserve podocyte integrity. Together, these assays have led to new insights into podocyte biology and supports the efficacy of utilizing BioID in vivo to interrogate spatially localized proteomes in health, aging, and disease.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:50:26.230.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gary Gerlach
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-17 14:09:53	ID requested
1	2023-06-23 09:10:12	announced
2	2023-11-14 09:01:39	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:50:27	announced	2024-10-22: Updated project metadata.

10.3389/fcell.2023.1195037;

Gerlach GF, Imseis ZH, Cooper SL, Santos AN, O'Brien LL, Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process. Front Cell Dev Biol, 11():1195037(2023) [pubmed]

submitter keyword: Aging, Ildr2, Fnbp1l,Podocytes, BioID Proximity Labeling, Foot Process

Lori O'Brien
contact affiliation	Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
contact email	lori_obrien@med.unc.edu
lab head
Gary Gerlach
contact affiliation	The University of North Carolina at Chapel Hill
contact email	garygerlach@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/2023/06/PXD042302

PRIDE project URI

• PRIDE
  1. PXD042302
     1. Label: PRIDE project
     2. Name: Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process.