Ontology highlight
ABSTRACT:
PROVIDER: PRJNA606577 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11080587_1.fastq.gz | Fastqsanger.gz | |||
| SRR11080587_2.fastq.gz | Fastqsanger.gz | |||
| SRR11080588_1.fastq.gz | Fastqsanger.gz | |||
| SRR11080588_2.fastq.gz | Fastqsanger.gz | |||
| SRR11080589_1.fastq.gz | Fastqsanger.gz |
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Project description:Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD to date. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
2024-04-10 | PXD046335 | Pride
Project description:Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients with all stages of NAFLD and controls were analysed by array-based DNA methylation and mRNA expression profiling. Bisulphite converted DNA from the 85 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-08-08 | E-GEOD-48325 | biostudies-arrayexpress
Project description:Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-drivencellular change.
2024-04-09 | GSE261297 | GEO
Project description:Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. In this study liver metabolic activity and functionality in NAFLD was charted by integrating global transcriptomic data within a genome-scale model of human metabolism. Gene expression was measured in the human liver of eight subjects with extreme steatosis diagnosed with NAFLD (liver fat % range 20-80%), and eight healthy, but obese subjects with low liver fat content (liver fat % range 0-10%). This dataset is part of the TransQST collection.
2016-06-01 | E-MTAB-4231 | biostudies-arrayexpress
Project description:Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients with all stages of NAFLD and controls were analysed by array-based DNA methylation and mRNA expression profiling.
2013-08-08 | GSE48325 | GEO
Project description:Expression data from human non-alcoholic fatty liver disease stages
2025-01-24 | E-GEOD-63067 | ExpressionAtlas
Project description:Fatty liver disease (FLD) caused by metabolic dysfunction is the leading cause of liver disease, and the prevalence is rising, especially in women. Although during reproductive age women are protected against FLD, for still unknown and understudied reasons some develop rapidly progressive disease at menopause. Patatin-like phospholipase domain containing 3 (PNPLA3) p.I148M variant accounts for the largest fraction of inherited FLD variability. Hepatic gene expression profile of 125 obese individuals stratified by sex and PNPLA3 genotype revealed higher PNPLA3 mRNA levels in women carrying PNPLA3 p.I148M variant. Furthermore, we showed that there is an estrogen receptor-alpha (ERα) binding site within the PNPLA3 enhancer sequence, suggesting a specific multiplicative interaction between female sex and PNPLA3 p.I148M in determining FLD.
2023-09-20 | GSE239422 | GEO
Project description:Non-alcoholic fatty liver (NAFL) has the potential to progress to non-alcoholic steatohepatitis (NASH) or to promote type 2 diabetes mellitus (T2DM). However, NASH and T2DM do not always develop coordinately. We established rat models of NAFL, NASH, and NAFL + T2DM to recapitulate different phenotypes associated with NAFLD and its progression. Microarrays were used to identify hepatic gene expression changes in each of these models. The goal is to identify a predictor of different NAFLD progressions. Non-alcoholic fatty liver disease (NAFLD) is recognized as a low-grade systemic inflammatory state with both hepatic and extra-hepatic manifestations. We aimed to identify common key regulators and adaptive pathways in different NAFLD phenotypes. NAFL, NASH and NAFL+T2DM rat models were used to represent simple fatty liver, fatty liver with severe hepatic manifestations, and fatty liver with severe metabolic manifestations, respectively. We applied microarray analysis to characterize the key regulators and adaptive pathways in different NAFLD phenotypes. There are 12 samples in our study which belonged to 4 groups, and each group contains 3 different samples.
2015-01-23 | E-GEOD-65220 | biostudies-arrayexpress
Project description:Non-alcoholic fatty liver disease (NAFLD) is characterized by a series of pathological changes that can progress from simple fatty liver disease to non-alcoholic steatohepatitis (NASH). The objective of this study is to describe changes in global gene expression associated with the progression of NAFLD. This study is focused on the expression levels of genes responsible for the absorption, distribution, metabolism and excretion (ADME) of drugs. Differential gene expression between three clinically defined pathological groups; normal, steatosis and NASH was analyzed. The samples were diagnosed as normal, steatotic, NASH with fatty liver (NASH fatty) and NASH without fatty liver (NASH NF). Genome-wide mRNA levels in samples of human liver tissue were assayed with Affymetrix GeneChipM-. Human 1.0ST arrays
2011-07-12 | E-MEXP-3291 | biostudies-arrayexpress
Project description:We aimed to develop an in vitro system that would recapitulate the key features of Non-Alcoholic Fatty Liver Disease (NAFLD). We took advantage of human pluripotent stem cells (hIPSCs) to establish 3D cultures of hIPSCs-derived hepatocytes to study NAFLD pathogenesis in vitro. Cultures were challenged with free fatty acid to mimic NAFLD, and transcriptomic analyses were used to confirm the presence of a NAFLD signature.
2023-10-01 | E-MTAB-10598 | biostudies-arrayexpress