Dataset Information

Multi-omics integration reveals convergent extracellular matrix remodeling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Stem Cell, Cell Culture

DISEASE(S): Type 2 Diabetes Mellitus

SUBMITTER: Liaqat Ali

LAB HEAD: Mohamed Al-Sayegh

PROVIDER: PXD078584 | Pride | 2026-06-08

REPOSITORIES: Pride

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			Action	DRS
	03032025_Alsayegh_Quantified_Proteins_Result.mzTab	Mztab
	03032025_Alsayegh_RFrac10_1.raw	Raw
	03032025_Alsayegh_RFrac1_1.raw	Raw
	03032025_Alsayegh_RFrac2_1.raw	Raw
	03032025_Alsayegh_RFrac3_1.raw	Raw

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Multi-omics integration reveals convergent extracellular matrix remodelling and lipid metabolic reprogramming as central axes of adipocyte differentiation from mouse embryonic stem cells.

Al-Sayegh M M Khalili M M Alzaabi M M Sultana M M Ali L L Ali M M El-Hadidi M M

Adipocyte 20260602 1

Adipogenesis from mouse embryonic stem cells (mESCs) offers a tractable model for dissecting early adipocyte commitment, yet the mechanisms coordinating this transition across multiple biological layers remain incompletely understood. Here we present the first simultaneous five-layer multi-omics characterization of mESC-derived adipocyte differentiation, integrating transcriptomics, proteomics, secretomics, lipidomics, and metabolomics from matched adipogenic (Pos) and non-differentiating (Neg) ...[more]

PMID: 42228580

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