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Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [microarray]

ABSTRACT: Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [microarray]

PROVIDER: PRJNA608118 | ENA |

REPOSITORIES: ENA

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Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction.

Project description:Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction.

| PRJNA608120 | ENA

Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [sequencing]

Project description:Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [sequencing]

| PRJNA608119 | ENA

Integrative multi-omics analysis in sepsis-associated liver dysfunction

Project description:we conducted integrative multiple levels of omics data including transcriptome, phosphoproteome, proteome and metabolome in different time-course of sepsis-associated liver dysfunction (SALD). This is the first trial to suggest the statistical pathway of integrative multi-omics data in sepsis. Given the increasing number of studies collecting multi-omics data but limited overview of the methodological framework for integrative analyses (Liu, Ding et al. 2013, Petersen, Zeilinger et al. 2014, Shah, Bonder et al. 2015), integrative approach in sepsis with liver dysfunction in this study will provide novel insights into the development of sepsis and ultimately offer new tools for overcoming the present diagnostic limitation. Therefore, a combined multi-omics dataset will give better accessibility of adoption in disease, and insight to identify the promising candidates for therapeutic strategies.

2023-06-21 | PXD025800 | Pride

Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [microarray]

Project description:We report novel epigenetic mechanisms of epigenetic memory and its role in regulation of transporter genes in diabetic renal proximal tubules. We have generated RNA-seq, ATAC-seq and Infinium EPIC methylation array datasets from human primary proximal tubule epithelial cells from non-diabetic healthy controls and from patients with history of Type II Diabetes. Analyses of RNA-seq, ATAC-seq and Methylaiton EPIC array data.

2020-10-28 | GSE145745 | GEO

Integrative Omics Analysis for Colorectal Cancer and Metastasis

Project description:The pathogenesis of Colorectal cancer (CRC) metastasis remains unclear.We collect clinical data from our center and use Integrative omics to analyze and predict candidate biomarkers of colorectal cancer and distant metastasis.

| 2743637 | ecrin-mdr-crc

Integrative omics analyses reveal epigenetic memory in diabetic cells regulating genes associated with kidney dysfunction. [sequencing]

2020-10-28 | GSE145746 | GEO

chinse healthy integrative omics project cohort

Project description:chinse healthy integrative omics project

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Integrative omics analysis in HCC samples

Project description:Integrative omics analysis in HCC samples

| PRJNA327799 | ENA

Integrative Omics Analyses Reveal Epigenetic Memory in Diabetic Renal Cells Regulating Genes Associated With Kidney Dysfunction.

Project description:Diabetic kidney disease (DKD) is a major complication of diabetes and the leading cause of end-stage renal failure. Epigenetics has been associated with metabolic memory in which prior periods of hyperglycemia enhance the future risk of developing DKD despite subsequent glycemic control. To understand the mechanistic role of such epigenetic memory in human DKD and to identify new therapeutic targets, we profiled gene expression, DNA methylation, and chromatin accessibility in kidney proximal tubule epithelial cells (PTECs) derived from subjects with and without type 2 diabetes (T2D). T2D-PTECs displayed persistent gene expression and epigenetic changes with and without transforming growth factor-β1 treatment, even after culturing in vitro under similar conditions as nondiabetic PTECs, signified by deregulation of fibrotic and transport-associated genes (TAGs). Motif analysis of differential DNA methylation and chromatin accessibility regions associated with genes differentially regulated in T2D revealed enrichment for SMAD3, HNF4A, and CTCF transcription factor binding sites. Furthermore, the downregulation of several TAGs in T2D (including CLDN10, CLDN14, CLDN16, SLC16A2, and SLC16A5) was associated with promoter hypermethylation, decreased chromatin accessibility, and reduced enrichment of HNF4A, histone H3-lysine-27-acetylation, and CTCF. Together, these integrative analyses reveal epigenetic memory underlying the deregulation of key target genes in T2D-PTECs that may contribute to sustained renal dysfunction in DKD.

| S-EPMC7576555 | biostudies-literature

Modeling Diabetic Endothelial Dysfunction with Patient-Specific Induced Pluripotent Stem Cells

Project description:Diabetes is a known risk factor for various cardiovascular complications, mediated by endothelial dysfunction. Despite the high prevalence of this metabolic disorder, there is a lack of in vitro models that recapitulate the complexity of genetic and environmental factors associated with diabetic endothelial dysfunction. Here, we utilized human induced pluripotent stem cell (iPSC)-derived endothelial cells (ECs) to develop in vitro models of diabetic endothelial dysfunction. We found that the diabetic phenotype was recapitulated in diabetic patient-derived iPSC-ECs, even in the absence of a diabetogenic environment. Subsequent exposure with culture conditions that mimic the diabetic clinical chemistry induced a diabetic phenotype in healthy iPSC-ECs but did not affect the already dysfunctional diabetic iPSC-ECs. RNA-seq analysis revealed extensive transcriptome-wide differences between cells derived from healthy individuals and diabetic patients. The in vitro disease models were used as a screening platform which identified angiotensin receptor blockers (ARBs) that improved endothelial function in vitro for each patient. In summary, we present in vitro models of diabetic endothelial dysfunction using iPSC technology, taking into account the complexity of genetic and environmental factors in the metabolic disorder. Our study provides novel insights into the pathophysiology of diabetic endothelial dysfunction and highlights the potential of iPSC-based models for drug discovery and personalized medicine.

2023-07-05 | GSE236430 | GEO

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