Transcription Factors as Susceptibility Genes in Type 2 Diabetes

Coordinating Institution: Université du Luxembourg
Contracting Partner(s): University of Kuopio, Finland
From: 01/12/2008
To: 30/11/2010
Budget: 275,000.00€
Contact(s): Carlberg Carsten

Summary

Genome-wide association studies have identified some 20 genomic regions that alter the risk of type 2 diabetes (T2D) in the European population. Four of these regions code for the transcription factors, the peroxisome proliferator-activated receptor (PPAR) g, T cell factor 7-like 2 (TCF7L2), hepatocyte nuclear factor 1 b (HNF1b, also known as TCF2) and hematopoietically expressed homeobox (HHEX). PPAR g and TCF2 have strong physiological links to diabetes, whereas for TCF7L2 and HHEX the mechanism of action in the disease is largely unknown. Our focus on gene regulation is based on the understanding that only the diversity of regulatory networks enables the human organism to respond in subtle ways to an extensive variety of challenges, such as the ones that accumulate during aging-related diseases. Our key hypothesis is that insights into the target genes of the transcription factors PPARg, TCF7L2, TCF2 and HHEX allow a mechanistic understanding of the development of T2D. We assume that a human individual’s susceptibility to these diseases depends on regulatory SNPs in binding sites for these four transcription factors. These regulatory SNPs can be used in personalized predictive medicine as easy accessible biomarkers. The project is subdivided into the following specific aims: 1. Identification and validation of primary responding genes of the transcription factors PPARg, TCF7L2, TCF2 and HHEX in cell lines mainly affected in metabolic syndromes, i.e. in hepatocytes, macrophages, adipocytes, myocytes and pancreatic beta-cells (by microarrays and real-time qPCR). 2. Performing an in silico screening of the whole human (and mouse) genome for binding sites of PPARg, TCF7L2, TCF2 and HHEX and validation of selected candidate response elements in living cells (by ChIP assays/massively parallel sequencing). Results: PPARg: The in silico screening of PPREs is finished and we obtained for macrophages and adipocytes lists of primary PPAR target genes. Human hepatocytes and beta-cell microarrays are in preparation, while projects with human myocytes have not yet been started. Presently, we are preparing samples for ChIP-Seq of PPAR in macrophages and adipocytes. TCF7L2: The in vitro binding profile of TCF7L2 is nearly finished so that génome-wide in silico screening can soon be started. TCF7L2 microarrays in human beta cells are in preparation. TCF2 and HHEX: Projects with these two transcription factors have not been started yet.

Refereed Scientific Publications:

No publications of the project yet, but the project is based on our following publications:

1. Heinäniemi, M., Uski, J.O., Degenhardt, T. and Carlberg, C. Meta-analysis of primary target genes of peroxisome proliferator-activated receptors. (2007) Genome Biol. 8, R147 (Impact factor2007 6.6).

2. Degenhardt, T., Saramäki, A., Malinen, M., Rieck, M., Huotari, A., Herzig, K.-H., Müller, R. and Carlberg, C. Three members of the human pyruvate dehydrogenase kinase family are direct targets of the peroxisome proliferator-activated receptor b/d. (2007). J. Mol. Biol. 372, 341-355 (Impact factor2007 4.5).

3. Rakhshandehroo, M., Sanderson, L.M, Matilainen, M., Stienstra, R., Carlberg, C., de Groot, P.J., Müller, M. and Kersten, S. Comprehensive analysis of PPARa-dependent regulation of hepatic metabolism by expression profiling. (2007) PPAR Res. 2007, 26839 (doi:10.1155/2007/26839), no impact factor yet.

4. Campbell, M.J., Carlberg, C. and Koeffler, H.P. A role for PPARg in cancer therapy. (2008) PPAR Res. 2008, 314974 (doi:10.1155/2008/314974), no impact factor yet.

5. Heinäniemi, M. and Carlberg, C. Screening for PPAR responsive regulatory modules in cancer. (2008) PPAR Res. 2008, 749073 (doi:10.1155/2008/749073), no impact factor yet.

6. Degenhardt, T., Väisänen, S. Rakhshandehroo, M., Kersten, S. and Carlberg, C. PPARa controls hepatic heme biosynthesis through ALAS1. (2009) J. Mol. Biol. 388, 225-238 (Impact factor2008 4.1). (Retracted in November 2010)

7. Degenhardt, T., Rybakova, K.N., Tomaszewska, A., Mone, M.J., Westerhoff, H.V., Bruggeman, F.J. and Carlberg, C. Population-level transcription cycles derive from stochastic timing of single-cell transcription. (2009) Cell 138, 489-501 (Impact factor2008 31.3). (Retracted in November 2010)

Other publications: none
Project Websites