Transcriptional profiling of type 1 diabetes genes on chromosome 21 in a rat beta-cell line and human pancreatic islets

Abstract

We recently finemapped a type 1 diabetes (T1D)-linked region on chromosome 21, indicating that one or more T1D-linked genes exist in this region with 33 annotated genes. In the current study, we have taken a novel approach using transcriptional profiling in predicting and prioritizing the most likely candidate genes influencing beta-cell function in this region. Two arraybased approaches were used, a rat insulinoma cell line (INS-1ab) overexpressing pancreatic duodenum homeobox 1 (pdx-1) and treated with interleukin 1b (IL-1b) as well as human pancreatic islets stimulated with a mixture of cytokines. Several candidate genes with likely functional significance in T1D were identified. Genes showing differential expression in the two approaches were highly similar, supporting the role of these specific gene products in cytokine-induced beta-cell damage. These were genes involved in cytokine signaling, oxidative phosphorylation, defense responses and apoptosis. The analyses, furthermore, revealed several transcription factor binding sites shared by the differentially expressed genes and by genes demonstrating highly similar expression profiles with these genes. Comparable findings in the rat beta-cell line and human islets support the validity of the methods used and support this as a valuable approach for gene mapping and identification of genes with potential functional significance in T1D, within a region of linkage.

The pancreatic β cell and type 1 diabetes: innocent bystander or active participant?

“…Studies within a T1DM-associated linkage region on chromosome 21 have also identified several genes with altered expression following cytokine exposure [71], including carbonyl transferase ( CBR1 ), which functions as a nitrosylated glutathione reductase important for β cell survival during oxidative stress [72], and the E3 ligase protein tetratricopeptide repeat domain 3 ( TTC3 ), which facilitates the ubiquitination and degradation of the survival factor Akt/PKB [73]. …”

Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression

“…None had classical type 1 diabetes–associated HLA-DR risk genotypes (DR1/3, DR11/52, DR4/5, DR2/5, DR6/13, DR4/6, DR4/5, and one donor missing HLA-DR genotype). Islet preparation, cytokine stimulation, including tumor necrosis factor-α (TNF-α; 5,000 units/mL), interferon-γ (IFN-γ; 750 units/mL), and interleukin (IL)-1β (75 units/mL) for 48 h, and RNA extraction have been described previously (7,22,23). …”

“…Network- or pathway-based approaches have been used to identify multiple disease genes for various diseases (7–12). This includes enrichment in predefined pathways by, for example, Kyoto Encyclopedia of Genes and Genomes (KEGG) (13) (http://www.genome.jp) and Gene Ontology (GO) terms (14) (http://www.geneontology.org).…”

Human Carbonyl Reductases

“…From several candidate genes, some evidence was observed for an association of variants of the CBR1 gene to T1D [24]. A later study revealed down-regulation of CBR1 mRNA in human islets following exposure to a mixture of cytokines, modeling the pathogenetic process in the target organ of T1D [134]. This down-regulation by cytokines may be an important mechanism, potentially making -cells more vulnerable toward oxidative stress [133].…”