PXD047028

PXD047028 is an original dataset announced via ProteomeXchange.

Title	Proteomic and computational analyses followed by functional validation of protective effects of trigonelline against calcium oxalate-induced renal cell deteriorations
Description	Trigonelline is a phytoalkaloid commonly found in green and roasted coffee beans. It is also found in decaffeinated coffee. Previous report has shown that trigonelline-rich plant extract exhibits anti-lithiatic effects in a nephrolithiatic rat model. Nevertheless, cellular mechanisms underlying the anti-lithiatic properties of trigonelline remain hazy. Herein, we used nanoLC-ESI-Qq-TOF MS/MS and MaxQuant algorithm to perform label-free quantitative proteomics to identify trigonelline-induced changes in protein expression in MDCK renal cells. From a total of 1,006 and 1,011 proteins identified from control and trigonelline-treated cells, respectively, levels of 62 (23 up-regulated and 39 down-regulated) proteins were significantly changed by trigonelline. Functional enrichment and reactome pathway analyses showed that these 62 altered proteins were related to stress response, cell cycle and cell polarity. Functional validation by corresponding experimental assays revealed that trigonelline prevented calcium oxalate monohydrate crystal-induced renal cell deteriorations by inhibiting crystal-induced overproduction of intracellular reactive oxygen species, cell cycle shift from G0/G1 to G2/M phase, tight junction disruption, and epithelial-mesenchymal transition in renal epithelial cells. These findings provide cellular mechanisms and convincing evidence for the renoprotective effects of trigonelline, particularly in kidney stone prevention.
HostingRepository	PRIDE
AnnounceDate	2024-11-19
AnnouncementXML	Submission_2024-11-18_17:14:20.725.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Visith Thongboonkerd
SpeciesList	scientific name: Canis familiaris (Dog) (Canis lupus familiaris); NCBI TaxID: 9615;
ModificationList	No PTMs are included in the dataset
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-16 12:00:40	ID requested
⏵ 1	2024-11-18 17:14:21	announced

Peerapen P, Boonmark W, Putpeerawit P, Sassanarakkit S, Thongboonkerd V, Proteomic and computational analyses followed by functional validation of protective effects of trigonelline against calcium oxalate-induced renal cell deteriorations. Comput Struct Biotechnol J, 21():5851-5867(2023) [pubmed]

10.1016/j.csbj.2023.11.036;

submitter keyword: Anti-lithiatic

Bioactive compound

Bioinformatics

Coffee

Kidney stone

Proteomics

Reactome

Prof. Visith Thongboonkerd
contact affiliation	Medical Proteomics Unit, Research departmetn, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
contact email	vthongbo@yahoo.com
lab head
Visith Thongboonkerd
contact affiliation	Mahidol University
contact email	sirirajms@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/2024/11/PXD047028

PRIDE project URI

• PRIDE
  1. PXD047028
     1. Label: PRIDE project
     2. Name: Proteomic and computational analyses followed by functional validation of protective effects of trigonelline against calcium oxalate-induced renal cell deteriorations