Project description:To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8). We pulled down the DNA with specific antibodies of interests against histone tail modifications in the human rebal tubule epithelial cells. The result can be interpretated with ChromHMM for different states.
Project description:To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8).
Project description:Kidney failure, the decrease of kidney function below a threshold necessary to support life, is a major cause of morbidity and mortality in humans. Kidney function is highly heritable; yet, the cellular and molecular mechanisms which contribute to differences in human kidney function remain obscure. We performed a genome wide association study (GWAS), identifying 430 loci affecting kidney function in middle-aged adults. To investigate which cell types are affected by these loci, we integrated the GWAS with human kidney candidate cis-regulatory elements (cCREs), identified using scATAC-seq. 56% of kidney function heritability localized to kidney tubule epithelial cCREs and an additional 7% to kidney podocyte cCREs. Thus, most of the heritable differences in adult kidney function is due to altered gene expression in these two cell types. Using enhancer assays, allele-specific scATAC-seq and machine learning, we found that many kidney function variants alter cCRE chromatin accessibility and function. Using CRISPRi, we determined which genes some of these cCREs regulate, implicating NDRG1, CCNB1 and STC1 in human kidney function. This work provides an experimental approach to identify the variants, regulatory elements and genes involved in human traits and disease.
Project description:We used bulk and single-cell ATAC-seq to measure chromatin accessibilty in human kidneys. This allowed us to define candidate cis-regulatory elements of each human kidney cell type and identify the role of podocyte and tubule regulatory elements in human kidney function.
Project description:Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl ̶ coenzyme A mutase (MUT). How MUT deficiency triggers mitochondrial alterations and cell damage remains unknown, preventing the development of disease-modifying therapies. To assess the effect of MUT deficiency on gene expression we investigated the transcriptome of in kidney cells derived from healthy controls or patients with MMA who harbor inactivating mutations in MUT. Microarray data indicate that MUT deficiency induces a profound and global change in gene expression that may be in part responsible of cellular alterations observed in patient cells.
Project description:Global gene expression in the primary cultured mouse kidney proximal tubule cells treated either DMSO or 1uM GW4064 (a FXR agonist) was compared. Results provide insight into mechanisms underlying effects of FXR activation on gene expression in mouse kidney proximal tubule cells. Male C57/BJ mice aged 6 weeks were sacrificed under anesthesia and kidney proximal tubule cells were cultured until confluent. Cells were treated with either GW4064 (1uM) or equal amount of DMSO and incubated for 24 hours. 4 total RNA samples per group were analyzed and gene expression was compared between the groups.
Project description:Injury to the proximal tubule plays a central role in the initiation and progression of kidney fibrosis, and rates of chronic kidney disease progresses approximately 50% faster in males compared to females. We applied Translating Ribosome Affinity Purification (TRAP) followed by RNA-sequencing to characterize the cell-specific proximal tubule transcriptional landscape during fibrosis in male vs. female mice.
Project description:TGFbeta is the major cytokine driver of fibrosis in the kidney and other tissue. Epithelial-mesenchymal transition has been postulated to contibrute to renal fibrosis in diseases such as diabetic nephropathy. We wished to identify novel genes that were upregulated in human kidney epithelial cells in response to TGFb1.The transcriptional responses for human proximal tubule epithelial cells to 10 ng/ml TGFbeta1 was examined over 24 and 48 hr