PXD068352-1

PXD068352 is an original dataset announced via ProteomeXchange.

Title	Quantitative Phosphoproteomics Reveals TGFβ Signaling Regulates Autophagy through Protein Phosphorylation during Palatogenesis
Description	Cleft palate (CP) are common craniofacial birth defects, with the TGFβ pathway playing critical roles. Protein phosphorylation is key in conserved signaling pathways. Recent evidence links autophagy to regulating mouse embryonic palatal mesenchyme (MEPM) cells, but its interaction with TGFβ-activated phosphorylation cascades remains largely unknown. Here, we investigated the interplay between these pathways during pala-togenesis. H&E and IHC analyses revealed increased expression of Beclin 1 and LC3 during the critical period of palatal shelves elevation and fusion (E13.5-E15.5). Bulk RNA sequencing (Bulk RNA-seq) further revealed enrichment of autophagy-related pathways and their interaction with TGFβ signaling. To characterize phosphorylation regulation, TMT-based quantitative phosphoproteomics with TiO₂ enrichment and high-resolution LC-MS/MS was done on TGFβ2-treated MEPM cells. We identified 23,471 peptides and 3,952 proteins, including 6,339 phosphopeptides corresponding to 2,195 phosphoproteins. Differential analysis found 477 upregulated and 53 downregulated phosphopeptides. Functional enrichment showed significant involvement of mTOR, MAPK, and autoph-agy/mitophagy pathways. Kinase-substrate enrichment analysis highlighted CSNK2A, MAPKs, and CDKs as key regulators, while network reconstruction showed cross-talk between TGFβ, autophagy, and phosphorylation signaling cascades. Our results demonstrate that TGFβ2 not only reshapes the MEPM phosphoproteome but also induces autophagy through multiple kinase-mediated pathways, providing novel insights into the molecular mechanisms underlying palatogenesis.
HostingRepository	iProX
AnnounceDate	2025-09-14
AnnouncementXML	Submission_2025-11-25_23:02:57.159.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xia Peng
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	phosphorylated residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-14 00:07:31	ID requested
⏵ 1	2025-11-25 23:02:57	announced

Dataset with its publication pending

submitter keyword: Mouse embryonic palatal mesenchyme (MEPM) cell

TGFβ2

Phosphoproteomics

Autophagy Palatogenesis

Juan Du
contact affiliation	Capital Medical University School of Stomatology
contact email	juandug@ccmu.edu.cn
lab head
Xia Peng
contact affiliation	Capital Medical University School of Stomatology
contact email	18834183343@163.com
dataset submitter

iProX dataset URI