SE-driven metabolic reprogramming in ADPKD (kidney RNA-seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA611748 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11280572.fastq.gz | Fastqsanger.gz | |||
| SRR11280573.fastq.gz | Fastqsanger.gz | |||
| SRR11280574.fastq.gz | Fastqsanger.gz | |||
| SRR11280575.fastq.gz | Fastqsanger.gz |
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Project description:Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we establish a prominent role for SEs in regulating metabolic gene expression and ADPKD progression. Characterization of cis-acting SE landscapes in cystic renal epithelial cells reveals extensive remodeling of SEs during cystogenesis. Gene ontology analysis indicates that SE-associated transcripts in the metabolic pathway category are most significantly enriched in cystic cells. Cystic cells are highly sensitive to the inhibition of cyclin-dependent kinase 7 (CDK7), a critical component of the trans-acting SE complex. THZ1, a specific CDK7 inhibitor, exerts a potent anti-cystogenesis effect in ADPKD cells and mouse models. Integrative analyses of transcriptomics and SE profiling identify AMP deaminase 3 (AMPD3) as a SE-driven metabolic gene. Up-regulation of AMPD3 in cystic cells results in reduced AMP level and decreased AMPK activity, while inhibition of AMPD3 suppresses cyst development in a zebrafish ADPKD model. In a cohort of ADPKD patients, CDK7 expression is frequently elevated, and its expression is significantly correlated with AMPD3 expression and disease severity. Taken together, our findings elucidate a mechanism by which SE controls metabolic gene transcription during cystogenesis, and identifies SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment.
2020-05-16 | GSE146714 | GEO
Project description:Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we establish a prominent role for SEs in regulating metabolic gene expression and ADPKD progression. Characterization of cis-acting SE landscapes in cystic renal epithelial cells reveals extensive remodeling of SEs during cystogenesis. Gene ontology analysis indicates that SE-associated transcripts in the metabolic pathway category are most significantly enriched in cystic cells. Cystic cells are highly sensitive to the inhibition of cyclin-dependent kinase 7 (CDK7), a critical component of the trans-acting SE complex. THZ1, a specific CDK7 inhibitor, exerts a potent anti-cystogenesis effect in ADPKD cells and mouse models. Integrative analyses of transcriptomics and SE profiling identify AMP deaminase 3 (AMPD3) as a SE-driven metabolic gene. Up-regulation of AMPD3 in cystic cells results in reduced AMP level and decreased AMPK activity, while inhibition of AMPD3 suppresses cyst development in a zebrafish ADPKD model. In a cohort of ADPKD patients, CDK7 expression is frequently elevated, and its expression is significantly correlated with AMPD3 expression and disease severity. Taken together, our findings elucidate a mechanism by which SE controls metabolic gene transcription during cystogenesis, and identifies SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment.
2020-05-16 | GSE141280 | GEO
Project description:Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we establish a prominent role for SEs in regulating metabolic gene expression and ADPKD progression. Characterization of cis-acting SE landscapes in cystic renal epithelial cells reveals extensive remodeling of SEs during cystogenesis. Gene ontology analysis indicates that SE-associated transcripts in the metabolic pathway category are most significantly enriched in cystic cells. Cystic cells are highly sensitive to the inhibition of cyclin-dependent kinase 7 (CDK7), a critical component of the trans-acting SE complex. THZ1, a specific CDK7 inhibitor, exerts a potent anti-cystogenesis effect in ADPKD cells and mouse models. Integrative analyses of transcriptomics and SE profiling identify AMP deaminase 3 (AMPD3) as a SE-driven metabolic gene. Up-regulation of AMPD3 in cystic cells results in reduced AMP level and decreased AMPK activity, while inhibition of AMPD3 suppresses cyst development in a zebrafish ADPKD model. In a cohort of ADPKD patients, CDK7 expression is frequently elevated, and its expression is significantly correlated with AMPD3 expression and disease severity. Taken together, our findings elucidate a mechanism by which SE controls metabolic gene transcription during cystogenesis, and identifies SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment.
2020-05-16 | GSE141279 | GEO
Project description:SE-driven metabolic reprogramming in ADPKD
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Project description:SE-driven metabolic reprogramming in ADPKD (RNA-Seq)
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Project description:SE-driven metabolic reprogramming in ADPKD (ChIP-Seq)
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2020-05-16 | GSE141281 | GEO
Project description:We have previously described global hypomethylation and site-specific DNA methylation changes which are associated with disease-state renal tissue in Autosomal Dominant Polycystic Kidney Disease (ADPKD). However, to-date there are no available data on the pattern of DNA methylation across an ADPKD kidney. Here we describe the methylome of eight individual cysts from a single ADPKD patient and peform an intra-individual analysis to identify regions of DNA methylation variability.
2020-01-14 | GSE142664 | GEO
Project description:To elucidate the molecular pathways that modulate renal cyst growth in autosomal dominant polycystic kidney disease (ADPKD) Keywords: Disease state analysis
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Project description:We performed a proteomic analysis of kidneys samples from mice with ADPKD and 3az- treated mice with ADPKD to explore the mechanisms of 3az treatment in ADPKD. Over 5000 proteins were obtained in kidney tissues from ADPKD group and drug administration group. Among them, 112 and 135 proteins were found up- and down-regulation between two groups, respectively. Gene Ontology (GO) analysis of these dysregulated proteins preliminarily revealed that the proteins regulated by 3az were mainly enriched in many biological processes. In particular, microtubule-based processes, microtubule cytoskeleton formation and mitotic cell cycle changed most significantly and were enriched in a great many of dysregulated proteins following 3az treatment in ADPKD mice. GSEA enrichment analysis demonstrated that compound 3az can down-regulate the proliferation ability of kidney in ADPKD mice. Microtubule-based processes and microtubule cytoskeleton formation have been reported to be associated with retard of cell proliferation and renal cyst expansion.
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