A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility

  1. Mark P. Keller1,
  2. YounJeong Choi2,3,
  3. Ping Wang2,3,
  4. Dawn Belt Davis1,
  5. Mary E. Rabaglia1,
  6. Angie T. Oler1,
  7. Donald S. Stapleton1,
  8. Carmen Argmann4,
  9. Kathy L. Schueler1,
  10. Steve Edwards4,
  11. H. Adam Steinberg1,
  12. Elias Chaibub Neto3,
  13. Robert Kleinhanz4,
  14. Scott Turner5,
  15. Marc K. Hellerstein6,7,
  16. Eric E. Schadt4,
  17. Brian S. Yandell2,3,8,
  18. Christina Kendziorski2, and
  19. Alan D. Attie1,9
  1. 1 Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53076, USA;
  2. 2 Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, Wisconsin 53076, USA;
  3. 3 Department of Statistics, University of Wisconsin, Madison, Wisconsin 53076, USA;
  4. 4 Rosetta Inpharmatics, Seattle, Washington 98109, USA;
  5. 5 KineMed, Emeryville, California 94608, USA;
  6. 6 Department of Nutritional Sciences and Toxicology, University of California at Berkeley, California 94720, USA;
  7. 7 Division of Endocrinology and Metabolism, Department of Medicine, University of California at San Francisco, San Francisco, California 94110, USA;
  8. 8 Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53076, USA

Abstract

Insulin resistance is necessary but not sufficient for the development of type 2 diabetes. Diabetes results when pancreatic beta-cells fail to compensate for insulin resistance by increasing insulin production through an expansion of beta-cell mass or increased insulin secretion. Communication between insulin target tissues and beta-cells may initiate this compensatory response. Correlated changes in gene expression between tissues can provide evidence for such intercellular communication. We profiled gene expression in six tissues of mice from an obesity-induced diabetes-resistant and a diabetes-susceptible strain before and after the onset of diabetes. We studied the correlation structure of mRNA abundance and identified 105 co-expression gene modules. We provide an interactive gene network model showing the correlation structure between the expression modules within and among the six tissues. This resource also provides a searchable database of gene expression profiles for all genes in six tissues in lean and obese diabetes-resistant and diabetes-susceptible mice, at 4 and 10 wk of age. A cell cycle regulatory module in islets predicts diabetes susceptibility. The module predicts islet replication; we found a strong correlation between 2H2O incorporation into islet DNA in vivo and the expression pattern of the cell cycle module. This pattern is highly correlated with that of several individual genes in insulin target tissues, including Igf2, which has been shown to promote beta-cell proliferation, suggesting that these genes may provide a link between insulin resistance and beta-cell proliferation.

Footnotes

  • ↵9 Corresponding author.

    ↵9 E-mail adattie{at}wisc.edu; fax (608) 263-9609.

  • [Supplemental material is available online at www.genome.org. Primary expression data for all arrays used in this study have been submitted to Gene Expression Omnibus under accession no. GSE10785.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.074914.107.

    • Received November 28, 2007.
    • Accepted March 12, 2008.
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  1. Published in Advance March 17, 2008, doi: 10.1101/gr.074914.107 Genome Res. 18: 706-716 Copyright © 2008, Cold Spring Harbor Laboratory Press

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