biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsDomenico MemoliIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15370Lipedema is a chronic, progressive adipose disorder affecting predominantly women, characterized by painful, symmetrical accumulation of subcutaneous fat in the limbs, and typically resistant to diet or exercise. The underlying pathophysiology of advanced stages remains poorly defined, and no validated biomarkers or molecular targets currently guide diagnosis or therapy. In this observational study, we employed a comprehensive multi-omics strategy to investigate the molecular and metabolic landscape of late-stage lipedema in female patients. Genome-wide DNA methylation profiling revealed over 5,000 differentially methylated CpG sites, impacting genes involved in receptor tyrosine kinase signaling, phospho-metabolism, and immune regulation. Transcriptome analysis identified pronounced downregulation of mitochondrial functions, including oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and fatty acid β-oxidation, along with sirtuin pathway disruption and extracellular matrix remodelling. Integrative analysis pinpointed AKT1, a serine/threonine kinase involved in metabolism and survival, as a putative central regulator. A hypomethylated promoter region in AKT1 was associated with increased gene expression and protein phosphorylation. Metabolomic profiling of adipose tissue revealed altered levels of AKT1-linked metabolites, including L-arginine, NADP, ATP, guanosine, glycerol, and glutamate, suggesting coordinated dysregulation of amino acid metabolism, redox homeostasis, and energy production. Trans-omic network analysis further confirmed AKT1 as a central metabolic hub integrating epigenetic, transcriptomic, and metabolic alterations. Our findings identify epigenetically activated AKT1 signaling as a potential pathogenic driver of metabolic reprogramming in advanced lipedema and propose AKT1 as a candidate biomarker and therapeutic target to support disease stratification and intervention strategies.biostudies-arrayexpressNucleic Acid Extraction - RNA was extracted using TRIzol™ Reagent (Invitrogen, #15596026) according to the manufacturer's protocol. Briefly, 1 ml of TRIzol was added to ~150 mg of pulverized adipose tissue, followed by homogenization and phase separation. RNA was quantified with Qubit 2.0 fluorimeter using Qubit RNA HS assay kit (Termo Fisher Scientifc, USA), and the assessment of nucleic acids integrity (RNA Integrity Number) was performed with Agilent 4150 TapeStation System (Agilent Technologies, USA).Sample Collection - Total RNA was isolated from adipose tissue samples obtained from 8 patients (4 with lipedema and 4 healthy individuals). Tissues were snap-frozen in liquid nitrogen immediately after collection and stored at −80 °C until further processing. Prior to RNA extraction, samples (~150 mg each) were cryopulverized using the CP02 cryoPREP® Automated Dry Pulverizer (Covaris).Sequencing - the Novaseq 6000s4 v 1.5 platform (Illumina Inc.) using 2 × 100 bpLibrary Construction - Indexed libraries were prepared starting from 200 ng total RNA according to TruSeq Stranded Total RNA Library Prep Gold (Cat. 20020599, Illumina, San Diego, California, USA)OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesDomenico MemolifalseRNASeq - Epigenetic Activation of AKT1 Drives Metabolic Reprogramming in Advanced-Stage Lipedema: A Multi-Omics StudyLipedema is a chronic, progressive adipose disorder affecting predominantly women, characterized by painful, symmetrical accumulation of subcutaneous fat in the limbs, and typically resistant to diet or exercise. The underlying pathophysiology of advanced stages remains poorly defined, and no validated biomarkers or molecular targets currently guide diagnosis or therapy. In this observational study, we employed a comprehensive multi-omics strategy to investigate the molecular and metabolic landscape of late-stage lipedema in female patients. Genome-wide DNA methylation profiling revealed over 5,000 differentially methylated CpG sites, impacting genes involved in receptor tyrosine kinase signaling, phospho-metabolism, and immune regulation. Transcriptome analysis identified pronounced downregulation of mitochondrial functions, including oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and fatty acid β-oxidation, along with sirtuin pathway disruption and extracellular matrix remodelling. Integrative analysis pinpointed AKT1, a serine/threonine kinase involved in metabolism and survival, as a putative central regulator. A hypomethylated promoter region in AKT1 was associated with increased gene expression and protein phosphorylation. Metabolomic profiling of adipose tissue revealed altered levels of AKT1-linked metabolites, including L-arginine, NADP, ATP, guanosine, glycerol, and glutamate, suggesting coordinated dysregulation of amino acid metabolism, redox homeostasis, and energy production. Trans-omic network analysis further confirmed AKT1 as a central metabolic hub integrating epigenetic, transcriptomic, and metabolic alterations. Our findings identify epigenetically activated AKT1 signaling as a potential pathogenic driver of metabolic reprogramming in advanced lipedema and propose AKT1 as a candidate biomarker and therapeutic target to support disease stratification and intervention strategies.2025-08-12T00:00:00Z2025-08-12T21:50:30.685Z2025-07-18T22:05:36.817ZE-MTAB-15370ERP176949EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184