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Genome-wide identification of palmitate-regulated immediate early genes and target genes in pancreatic beta-cells reveals a central role of NF-κB

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Abstract

Free fatty acid-induced pancreatic β-cell dysfunction plays a key role in the pathogenesis of type 2 diabetes. We conducted gene expression microarray analysis to comprehensively investigate the transcription machinery of palmitate-regulated genes in pancreatic β-cells in vitro. In particular, mouse pancreatic βTC3 cells were treated with palmitate in the presence or absence of cycloheximide (CHX), which blocks protein synthesis and thereby allows us to distinguish immediate early genes (IEGs) from their target genes. The microarray experiments identified 34 palmitate-regulated IEGs and 74 palmitate-regulated target genes. In silico promoter analysis revealed that transcription factor binding sites for NF-κB were over-represented, regulating approximately one-third of the palmitate-regulated target genes. In cells treated with CHX, nfkb1 showed an up-regulation by palmitate, suggesting that NF-κB could be an IEG. Functional enrichment analysis of 27 palmitate-regulated genes with NF-κB binding sites showed an over-representation of genes involved in immune response, inflammatory response, defense response, taxis, regulation of cell proliferation, and regulation of cell death pathways. Electrophoretic mobility shift assay showed that palmitate stimulates NF-κB activity both in the presence and absence of CHX. In conclusion, by identifying IEGs and target genes, the present study depicted a comprehensive view of transcription machinery underlying palmitate-induced inflammation and cell proliferation/death in pancreatic β-cells and our data demonstrated the central role of NF-κB.

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Abbreviations

FFA:

Free fatty acid

CHX:

Cycloheximide

IEG:

Immediate early gene

TF:

Transcription factor

TFBS:

Transcription factor binding site

DEG:

Differentially expressed genes

MMP:

Matrix metalloproteinase

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Acknowledgments

This work was supported by Grants from the National Research Foundation (M10753020005-07N5302-00500), the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program and Seoul National University Hospital intramural research fund (0620083589), South Korea. We thank Dominique Glauser for helpful discussion on the confounding effects of cycloheximide.

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Authors and Affiliations

  1. Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea

    Hyung Jin Choi, Se-Hee Lee, You Ri Lee, Jiyon Shin, Kyong Soo Park & Young Min Cho

  2. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea

    Seungwoo Hwang

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  1. Hyung Jin Choi
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Correspondence to Young Min Cho.

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Hyung Jin Choi and Seungwoo Hwang contributed equally to this manuscript.

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Choi, H.J., Hwang, S., Lee, SH. et al. Genome-wide identification of palmitate-regulated immediate early genes and target genes in pancreatic beta-cells reveals a central role of NF-κB. Mol Biol Rep 39, 6781–6789 (2012). https://doi.org/10.1007/s11033-012-1503-5

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