Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ

We have developed a method for reconstructing gene association networks and have applied this method to gene profiles from 3T3-L1 cells. Priorization of the candidate genes pinpointed a transcript annotated as APMAP (adipocyte plasma membrane-associated protein). Functional studies showed that APMAP is upregulated in murine and human adipogenic cell models as well as in a genetic mouse model of obesity. Silencing APMAP in 3T3-L1 cells strongly impaired the differentiation into adipocytes. Moreover, APMAP expression was strongly induced by the PPARγ ligand rosiglitazone in adipocytes in vitro and in vivo in adipose tissue. Using ChIP-qPCR and luciferase reporter assays, we show a functional PPARγ binding site. In addition, we provide evidence that the extracellular C-terminal domain of APMAP is required for the function of APMAP in adipocyte differentiation. Finally, we demonstrate that APMAP translocates from the endoplasmatic reticulum to the plasma membrane during adipocyte differentiation.

[1]  Jonathan Schug,et al.  PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. , 2008, Genes & development.

[2]  C. Dani,et al.  Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis , 2008, BMC Genomics.

[3]  Sun Tian,et al.  Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases , 2006, BMC Bioinformatics.

[4]  Kazutaka Katoh,et al.  Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..

[5]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[6]  S Fuhrman,et al.  Reveal, a general reverse engineering algorithm for inference of genetic network architectures. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[7]  J. Friedman,et al.  Transcriptional regulation of adipogenesis by KLF4. , 2008, Cell metabolism.

[8]  J. Clausen,et al.  Identification of a novel integral plasma membrane protein induced during adipocyte differentiation. , 2001, The Biochemical journal.

[9]  H. Stunnenberg,et al.  Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. , 2008, Genes & development.

[10]  O. Majdic,et al.  Localization and characterization of the novel protein encoded by C20orf3. , 2008, The Biochemical journal.

[11]  B. Spiegelman,et al.  Stimulation of adipogenesis in fibroblasts by PPARγ2, a lipid-activated transcription factor , 1994, Cell.

[12]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[13]  M. Lazar,et al.  New developments in adipogenesis , 2009, Trends in Endocrinology & Metabolism.

[14]  Gerhard G. Thallinger,et al.  QPCR: Application for real-time PCR data management and analysis , 2009, BMC Bioinformatics.

[15]  Alexander E. Kel,et al.  TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..

[16]  Robert Castelo,et al.  Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs , 2009, J. Comput. Biol..

[17]  M. Lazar,et al.  Adipocyte-specific Expression of Murine Resistin Is Mediated by Synergism between Peroxisome Proliferator-activated Receptor γ and CCAAT/Enhancer-binding Proteins* , 2009, Journal of Biological Chemistry.

[18]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[19]  S. Farmer.  Transcriptional control of adipocyte formation. , 2006, Cell metabolism.

[20]  Claudio Cobelli,et al.  A quantization method based on threshold optimization for microarray short time series , 2005, BMC Bioinformatics.

[21]  H. Green,et al.  An established preadipose cell line and its differentiation in culture II. Factors affecting the adipose conversion , 1975, Cell.

[22]  Ole Winther,et al.  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..

[23]  J. Flier,et al.  PPARgamma regulates adipose triglyceride lipase in adipocytes in vitro and in vivo. , 2007, American journal of physiology. Endocrinology and metabolism.

[24]  B. Spiegelman,et al.  Stimulation of adipogenesis in fibroblasts by PPAR gamma 2, a lipid-activated transcription factor. , 1994, Cell.

[25]  Korbinian Strimmer,et al.  An empirical Bayes approach to inferring large-scale gene association networks , 2005, Bioinform..

[26]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[28]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[29]  Q. Tong,et al.  Function of GATA transcription factors in preadipocyte-adipocyte transition. , 2000, Science.

[30]  S. Panjikar,et al.  3D-Structure and function of strictosidine synthase--the key enzyme of monoterpenoid indole alkaloid biosynthesis. , 2008, Plant physiology and biochemistry : PPB.

[31]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[32]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[33]  Georg Schneider,et al.  ANNIE: integrated de novo protein sequence annotation , 2009, Nucleic Acids Res..

[34]  G. Fritzsch,et al.  Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. , 2001, Structure.

[35]  B. Spiegelman,et al.  Krox20 stimulates adipogenesis via C/EBPbeta-dependent and -independent mechanisms. , 2005, Cell metabolism.

[36]  Barbara D. Saatkamp,et al.  Distinct Transcriptional Profiles of Adipogenesisin Vivo and in Vitro * , 2001, The Journal of Biological Chemistry.

[37]  Sun Tian,et al.  Molecular processes during fat cell development revealed by gene expression profiling and functional annotation , 2005, Genome Biology.

[38]  J. Flier,et al.  PPARγ regulates adipose triglyceride lipase in adipocytes in vitro and in vivo , 2007 .

[39]  T. Werner,et al.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. , 1995, Nucleic acids research.

[40]  I. Tanaka,et al.  Structural and Mutational Analyses of Drp35 from Staphylococcus aureus , 2007, Journal of Biological Chemistry.

[41]  Tim J. P. Hubbard,et al.  Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..

[42]  Adam A. Margolin,et al.  Reverse engineering of regulatory networks in human B cells , 2005, Nature Genetics.

[43]  Dan S. Tawfik,et al.  Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes , 2004, Nature Structural &Molecular Biology.