PXD078584-1

PXD078584 is an original dataset announced via ProteomeXchange.

Title	Multi-omics integration reveals convergent extracellular matrix remodeling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells
Description	Adipose tissue dysfunction is a hallmark of obesity and type 2 diabetes mellitus, yet the full molecular complexity of adipocyte differentiation remains incompletely characterized. Single-omics approaches capture only partial dimensions of this multi-layered biological transition. Here, we applied a comprehensive five-layer multi-omics framework to dissect adipocyte differentiation from mouse embryonic stem cells (mESCs) at day 30 under adipogenic and non-differentiating conditions, integrating transcriptomic, proteomic, secretomic, metabolomic, and lipidomic profiling across matched biological replicates. Principal component analysis demonstrated robust condition-specific separation across all molecular layers, with transcriptomics exhibiting the strongest discriminatory power. MultiOmics Factor Analysis (MOFA+) identified a dominant shared latent factor strongly associated with adipogenic condition (Wilcoxon p = 2.9 × 10⁻⁵), capturing coordinated variance across transcriptomic, proteomic, lipidomic, and metabolomic layers, while secretomic variance was partially independent. Gene Ontology enrichment analyses converged upon extracellular matrix organization and lipid metabolic reprogramming as the principal biological themes driving differentiation across modalities. Interaction network analysis identified lipid metabolic enzymes — including phospholipases, ceramide synthases, and acyltransferases — and extracellular matrix regulators as high-degree network hubs, rather than canonical PPARγdriven transcription factors alone. Targeted qPCR validation of six prioritized candidates confirmed significant upregulation of Lpl and Plg and downregulation of Acer3 in differentiated cells, alongside directionally concordant changes in Itga5, Igfbp6, and Pik3cg. These findings establish that mESC adipogenesis is governed by a systems-level program integrating transcriptional activation, structural ECM remodeling, and lipid enzymatic reprogramming, and nominate novel regulatory hubs with relevance to metabolic disease pathophysiology.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_16:10:17.833.xml
DigitalObjectIdentifier	https://doi.org/10.6019/PXD078584
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Liaqat Ali
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2026-05-20 00:10:24	ID requested
⏵ 1	2026-06-07 16:10:18	announced

10.1080/21623945.2026.2680625;

Al-Sayegh M, Khalili M, Alzaabi M, Sultana M, Ali L, Ali M, El-Hadidi M, Multi-omics integration reveals convergent extracellular matrix remodelling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells. Adipocyte, 15(1):2680625(2026) [pubmed]

10.6019/PXD078584;

ProteomeXchange project tag: Diabetes (B/D-HPP), Stems Cells (B/D-HPP)

submitter keyword: adipogenesis

mouse embryonic stem cells

multi-omics integration

extracellular matrix remodeling

lipidomics

MOFA+

Multi-Omics Factor Analysis

Mohamed Al-Sayegh
contact affiliation	New York University Abu Dhabi, Division of Biology, Saadiyaat Island, Abu Dhabi, United Arab Emirates New York University Abu Dhabi, Center of Genomics and System Biology, Saadiyaat Island, Abu Dhabi, United Arab Emirates
contact email	ma3803@nyu.edu
lab head
Liaqat Ali
contact affiliation	New York University Abu Dhabi
contact email	la77@nyu.edu
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/2026/06/PXD078584

PRIDE project URI

• PRIDE
  1. PXD078584
     1. Label: PRIDE project
     2. Name: Multi-omics integration reveals convergent extracellular matrix remodeling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells