PXD012196-1

PXD012196 is an original dataset announced via ProteomeXchange.

Title	An integrative multi-omics approach uncovers the regulatory role of Cdk7 and Cdk4 in autophagy induced by silica nanoparticles
Description	The abnormal induction of macroautophagy/autophagy, a highly conserved lysosome-based degradation pathway, has been postulated as a major toxicity of nanomaterials, whereas little is known on the exact molecular mechanisms. Here, we treated mammalian cells with 16 nm silica nanoparticles (SiNPs), conducted a transcriptomic, proteomic and phosphoproteomic profiling during autophagy, and detected up to 7208 (25.09%) genes potentially regulated in at least one level. To identify key regulators, we developed a new algorithm of computational prediction of master protein kinases (cMAK) to integrate the multi-omics data. Using cMAK, we predicted 21 candidates and validated a Cdk7-Cdk4 cascade to be functionally important, while the silence or inhibition of Cdk4 or Cdk7 significantly attenuated the autophagic induction and greatly diminished autophagosome formation. Our studies not only established a powerful method for predicting potentially regulatory kinases from the multi-omics data, but also revealed a novel mechanism of SiNPs-triggered autophagy through activating the Cdk7-Cdk4 cascade.
HostingRepository	iProX
AnnounceDate	2018-12-28
AnnouncementXML	Submission_2019-12-01_20:49:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chenwei Wang
SpeciesList	scientific name: Rattus norvegicus; NCBI TaxID: 10116;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-28 18:19:53	ID requested
⏵ 1	2019-12-01 20:49:48	announced
2	2020-09-03 21:10:43	announced	2020-09-04: Update publication information

Dataset with its publication pending

submitter keyword: autophagy, silica nanoparticles, protein kinase, phosphoproteomics, Cdk4, Cdk7

Xue Yu
contact affiliation	Huazhong University of Science and Technology
contact email	xueyu@hust.edu.cn
lab head
Chenwei Wang
contact affiliation	Huazhong University of Science and Technology
contact email	reviewerfly2018@gmail.com
dataset submitter

iProX dataset URI