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PROVIDER: PRJNA1251999 | ENA |
REPOSITORIES: ENA
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Project description:- Background & Aims: Considering the escalating prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) and MASLD-related fibrosis, accurate non-invasive biomarkers for diagnosis and staging of fibrosis are urgently needed. This study Aims to develop a blood-based biomarker panel for fibrosis detection in individuals with MASLD. - Approach & Results: Using a translational diet-induced LDLr-/-.Leiden MASLD mouse model, candidate biomarkers were identified focused on the mechanism of collagen deposition, by integrating hepatic gene expression and new extracellular matrix deposition, as detected by dynamic D2O-labeling. To translate these findings to humans, gene expression profiles and biomarkers were analyzed in liver biopsies and serum samples from 67 individuals with histologically characterized MASLD and variable degrees of fibrosis. This led to the selection of three biomarkers for a blood-based fibrosis biomarker panel: IGFBP7, SSc5D and Sema4D. The accuracy of the biomarker panel was tested in a separate cohort of 128 individuals with histologically characterized MASLD across different stages of fibrosis. A Light Gradient Boosting Machine (LGBM) model was applied to predict fibrosis stage in MASLD (F0/F1: AUC = 0.90; F2: AUC = 0.91; F3/F4: AUC = 0.87). - Conclusion & Discussion: Using a translational Approach to identify collagen turnover related proteins indicative of fibrosis, we developed an accurate blood-based biomarker panel to detect and stage hepatic fibrosis in individuals with MASLD.
2024-05-17 | GSE240729 | GEO
Project description:Gene expression profiles in the Leiden Longevity Study
| PRJNA117477 | ENA
Project description:Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide, but its pathophysiological mechanisms remain elusive. It is a progressive disease, encompassing hepatic steatosis, steatohepatitis with(out) fibrosis and ultimately cirrhosis and hepatocellular carcinoma. DNA methylation (DNAm) is dysregulated in MASLD and may underpin key pathogenic mechanisms. Additionally, aging is associated with MASLD and shares common processes of chronic inflammation and oxidative stress. Therefore, this study focuses on DNAm changes in relation to MASLD progression and epigenetic age acceleration (EAA). Results: Liver biopsies from 22 MASLD patients were analyzed using Infinium MethylationEPIC BeadChip arrays. Strikingly, progression of MASLD was characterized by gradual DNAm changes, revealing associated KEGG pathways. Additionally, Horvath’s EAA significantly correlated with MASLD stage and individual histological MASLD parameters while LiverClock’s EAA correlated only with MASLD stage. In contrast, both Horvath’s intrinsic EAA and HepClock’s EAA showed no significant correlations. Integrative analyses, leveraging both gradual MASLD and Horvath’s EAA DNAm signatures, gene expression (n = 118), and a MASLD-specific transcriptional regulatory network, identified (regulon-specific) transcription factors implicated in MASLD and EAA progression, representing a transcription factor-network of redox (ferroptosis), immune, and metabolic/endocrine related epigenetic processes. Conclusion: Gradual DNAm changes were found to align with progression of MASLD and EAA, with EAA a potential non-biased quantitative biomarker for MASLD. Integrative analysis highlighted potential new therapeutic transcription factor targets, with special emphasis on AEBP1 and emerging nuclear receptors including CAR(NR1I3), MR(NR3C2), GR(NR3C1), and ESRRG, underscoring the potential of epigenetic redox-metabolic therapies for MASLD
2025-08-11 | GSE294806 | GEO
Project description:This study aimed to establish and characterize an in vitro model of human intestinal organoids isolated from duodenal samples of patients with non-fibrotic MASLD and those with MASLD-cirrhosis. Whole transcriptome analysis and the energetic and redox status of the organoids were assessed to characterize intestinal functional impairment in the context of MASLD. We used microarrays to detail the whole transcriptome dysregulation underlying intestinal dysfunction in organoids isolated from chirrotic versus non-fibrotic MASLD patients.
2025-09-04 | GSE299719 | GEO
Project description:The molecular mechanisms underlying the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD) remain largely unclear. Emerging evidence suggests that microRNAs (miRNAs) play a critical role in transcriptional regulation by targeting genes involved in MASLD and other metabolic disorders, this study aims to elucidate the role of miR-93 in lipid metabolism and its impact on MASLD progression.
2025-04-14 | GSE277560 | GEO
Project description:Abstract Obesity has been linked to vascular dysfunction, cognitive impairment and neurodegenerative diseases. However, experimental models that recapitulate brain pathology in relation to obesity and vascular dysfunction are still lacking. In this study we performed the histological and histochemical characterization of brains from Ldlr-/-.Leiden mice, an established model for obesity and associated vascular disease. 18 week-old and 50 week-old Ldlr-/-.Leiden male mice were compared with age-matched C57BL/6J mice. We then assessed the effect of high-fat diet (HFD)-induced obesity on brain pathology in Ldlr-/-.Leiden mice and tested whether a treatment with an anti-complement component 5 antibody, a terminal complement pathway inhibitor recently shown to reduce vascular disease, can attenuate neurodegeneration and neuroinflammation. Histological analyses were complemented with Next Generation Sequencing (NGS) analyses of the hippocampus to unravel molecular pathways underlying brain histopathology. We show that Ldlr-/-.Leiden mice have more severe neurodegeneration and show an age-dependent astrogliosis that is not observed in age-matched C57BL/6J controls. This was substantiated by pathway enrichment analysis using the NGS data which showed that oxidative phosphorylation, EIF2 signaling and mitochondrial dysfunction pathways, all associated with neurodegeneration, were significantly altered in the hippocampus of Ldlr-/-.Leiden mice compared with controls. Obesity-inducing HFD-feeding did not aggravate neurodegeneration and astrogliosis. However, brains from HFD-fed Ldlr-/-.Leiden mice showed reduced IBA-1 immunoreactivity and increased CD68 immunoreactivity compared with chow-fed controls, indicating an altered overall microglial immunophenotype by HFD feeding. The systemic administration of an anti-C5 treatment partially restored the HFD effect on microglial immunophenotype. In addition, NGS data of hippocampi from Ldlr-/-.Leiden mice showed that HFD affected multiple molecular pathways: HFD notably inactivated synaptogenesis and activated neuroinflammation pathways. The anti-C5 treatment restored the HFD-induced effect on molecular pathways to a large extent. This study shows that the Ldlr-/-.Leiden mouse model is suitable to study brain histopathology and associated biological processes in a context of obesity and provides evidence of the potential therapeutic value of anti-complement therapy against obesity-induced neuroinflammation.
2023-06-18 | GSE234425 | GEO
Project description:We’ve previously demonstrated that hepatocytes with Tbx3 deletions have increased cellular fitness and clonally expand during metabolic-dysfunction associated steatotic liver disease (MASLD) development. TBX3 is a transcription factor that is critical for embryonic development, but has never been studied within the context of MASLD. Here, we show that somatic mutations in TBX3 are found in human patients with MASLD. Liver specific deletion of Tbx3 in mice protects against diet induced MASLD through upregulating VLDL-TG particle secretion. TBX3 transcriptionally suppresses the conventional secretory pathway and cholesterol biosynthesis. Hdlbp is a direct target of TBX3 that is responsible for altered VLDL secretion. In contrast to WT TBX3, TBX3 harboring somatic mutations found in humans failed to suppress VLDL secretion in vivo. In conclusion, mutations in TBX3 promote clonal expansion during MASLD development through increased lipid disposal, demonstrating clonal fitness can benefit the liver even at the cost of hyperlipidemia.
2025-06-30 | GSE300981 | GEO
Project description:DNA demethylation is regulated by the TET family proteins, whose enzymatic activity requires 2-oxoglutarate (2-OG) and iron that both are elevated in MASLD. We aimed to investigate liver TET1 in MASLD progression. Depleting TET1 substantially alleviated MASLD progression. Whole body Knockout of TET1 (TKO) slightly improved diet induced obesity and glucose homeostasis. Intriguingly, hepatic cholesterols, triglycerides, were significantly decreased upon TET1 depletion. Moreover, targeting TET1 with a small molecule inhibitor significantly suppressed MASLD progression. Liver TET1 plays a deleterious role in MASLD, suggesting the potential of targeting TET1 in hepatocytes to suppress MASLD.
2025-03-04 | GSE286394 | GEO
Project description:Metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are two common liver disorders characterized by abnormal lipid accumulation. Our study found reduced levels of GTPase-activating protein-binding protein1（G3BP1）in patients with MASLD and MASH, suggesting its involvement in these liver disorders. Hepatocyte-specific G3BP1 knockout (G3BP1 HKO) mice had more severe MASLD and MASH than their corresponding controls. Intriguingly, the G3BP1 HKO MASLD model mice exhibit dysregulated autophagy, and biochemical analyses demonstrated that G3BP1 promotes autophagosome-lysosome fusion through direct interactions with the SNARE proteins STX17 and VAMP8. We also show that hepatic knockout of G3BP1 promotes de novo lipogenesis, and ultimately found that G3BP1 is required for the nuclear translocation of the well-known liver-lipid-regulating transcription factor TFE3. Taken together, our results suggest that G3BP1 should be investigated as a potential target for developing medical interventions to treat MASLD and MASH.
2025-08-06 | GSE304454 | GEO
Project description:Abdominal obesity increases the risk for non-alcoholic fatty liver disease (NAFLD), now known as metabolic dysfunction-associated steatotic liver disease (MASLD). To elucidate the directional cell-type level biological mechanisms underlying the association between abdominal obesity and MASLD, we integrated adipose and liver single nucleus RNA-sequencing and bulk cis-expression quantitative trait locus (eQTL) data with the UK Biobank genome-wide association study (GWAS) data using colocalization. Then we used colocalized cis-eQTL variants as instrumental variables in Mendelian randomization (MR) analyses, followed by functional validation experiments on the target genes of the cis-eQTL variants. We identified 17 colocalized abdominal obesity GWAS variants, regulating 17 adipose cell-type marker genes. Incorporating these 17 variants into MR discovers a putative tissue-of-origin, cell-type-aware causal effect of abdominal obesity on MASLD consistently with multiple MR methods without significant evidence for pleiotropy or heterogeneity. Single cell data confirm the adipocyte-enriched mean expression of the 17 genes. Our cellular experiments across human adipogenesis identify risk variant -specific epigenetic and transcriptional mechanisms. Knocking down two of the 17 genes, PPP2R5A and SH3PXD2B, shows a marked decrease in adipocyte lipidation and significantly alters adipocyte function and adipogenesis regulator genes, including DGAT2, LPL, ADIPOQ, PPARG, and SREBF1. Furthermore, the 17 genes capture a characteristic MASLD expression signature in subcutaneous adipose tissue. Overall, we discover a significant cell-type level effect of abdominal obesity on MASLD and trace its biological effect to adipogenesis (Lee et. al, eBioMedicine 2024).
2024-07-11 | GSE269929 | GEO