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Expression data from human pancreatic islets

ABSTRACT: Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Islets from cadaver donors (54 non-diabetic and 9 diabetic) were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChipM-BM-. Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

ORGANISM(S): Homo sapiens

SUBMITTER: Joao Fadista

PROVIDER: E-GEOD-38642 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets.

Taneera Jalal J Lang Stefan S Sharma Amitabh A Fadista Joao J Fadista Joao J Zhou Yuedan Y Ahlqvist Emma E Jonsson Anna A Lyssenko Valeriya V Vikman Petter P Hansson Ola O Parikh Hemang H Korsgren Olle O Soni Arvind A Krus Ulrika U Zhang Enming E Jing Xing-Jun XJ Esguerra Jonathan L S JL Wollheim Claes B CB Salehi Albert A Rosengren Anders A Renström Erik E Groop Leif L

Cell metabolism 20120701 1

Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified gene coexpression and protein-protein interaction networks that were strongly associated with islet insulin secretion and HbA(1c). We integrated our data to form a rank list of putative T2D genes, of whi ...[more]

PMID: 22768844

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Expression data from human pancreatic islets

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2012-10-23 | E-GEOD-41762 | biostudies-arrayexpress

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Gene expression from human pancreatic islet

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Project description:Pancreatic islets are central in type 2-diabetes development, which coincides with increased activity of innate immunity. Intriguingly, human pancreatic islets express many complement genes. The most highly expressed gene was the complement inhibitor CD59 that is GPI anchored to the cell membrane, which unexpectedly was found in high amounts intracellularly in beta cells. Silencing of CD59 strongly suppressed insulin secretion. Importantly, this suppression was unrelated to established CD59 functions, but rather depletion of intracellular CD59. Imaging experiments identified a distal site of inhibition in the exocytotic pathway, but prior to emptying of the insulin granules. Proximity Ligation Assays pin-pointed the mechanism to impaired turnover of exocytosis-regulating SNARE-proteins and CD59 was detected in complex with VAMP2 and syntaxin. CD59 was downregulated by 24-h glucose incubations in human islets, rat cell lines and in islets from three rodent diabetes models. Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChipM-BM-. Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

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ATAC-seq on human pancreatic islets

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DNA methylation profiling of male human pancreatic islets identifies loci for type 2 diabetes

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2012-04-22 | E-GEOD-21232 | biostudies-arrayexpress

Single-cell multiome (ATAC and RNA) landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

Project description:We used single cell multiome (ATAC and RNA) sequencing to profile 85266 islet cells from 20 individuals, including islets from non-diabetic, pre-diabetic and type 2 diabetic (T2D) donors. We characterize changes in regulatory programs of islet cell types and subtypes in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.

2023-02-07 | GSE200044 | GEO

Single-cell chromatin landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

Project description:In this study, we used single cell nucleus ATAC-seq (snATAC-seq) to profile 218,973 islet cells from 34 individuals, including islets from non-diabetic, pre-diabetic and type 2 diectic (T2D) donors. We characterize changes in regulatory programs of islet cell types in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.

2023-02-07 | GSE169453 | GEO

Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-17 | E-GEOD-50398 | biostudies-arrayexpress

Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [partially pancreatectomized patient cohort]

Project description:Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). This signature includes 19 genes, of which 9 have never been previously reported to be differentially expressed in T2D islets. The PPP cohort also includes samples from individuals with impaired glucose tolerance (IGT) or recent onset diabetes associated with a pancreatic exocrine disorder (T3cD). Notably, none of the 19 signature genes of T2D islets were significantly dysregulated in islets of subjects with IGT or T3cD, suggesting that their changed expression reflects beta cell deterioration rather than a deficit preceding it.

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