Cellular and Molecular Life Sciences

, Volume 67, Issue 23, pp 4049–4064 | Cite as

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

  • Juliane G. Bogner-Strauss
  • Andreas Prokesch
  • Fatima Sanchez-Cabo
  • Dietmar Rieder
  • Hubert Hackl
  • Kalina Duszka
  • Anne Krogsdam
  • Barbara Di Camillo
  • Evelyn Walenta
  • Ariane Klatzer
  • Achim Lass
  • Montserrat Pinent
  • Wing-Cheong Wong
  • Frank Eisenhaber
  • Zlatko Trajanoski
Research Article


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.


Adipogenesis APMAP PPARγ Transcriptional regulation Gene expression Gene networks 



This work was supported by the Austrian Ministry for Science and Research (GEN-AU projects GOLD and BIN) and the Austrian Science Fund SFB (Project Lipotoxicity). PPARγ-MEFs were a gift from Dr. E. Rosen. OP9 cells were kindly provided by B. Pickel and SGBS cells by Novo Department of Pediatrics and Adolescent Medicine, University of Ulm. We thank David J. Steger and Mitch A. Lazar for providing ChIP material. The authors acknowledge the technical assistance provided by Stephan Seifriedsberger, Florian Stoeger, Martina Schweiger and Marie Loh.

Supplementary material

18_2010_424_MOESM1_ESM.doc (42 kb)
Supplementary material 1 (DOC 41 kb)
18_2010_424_MOESM2_ESM.xls (1.8 mb)
Supplementary material 2 (XLS 1832 kb)
18_2010_424_MOESM3_ESM.xls (1.4 mb)
Supplementary material 3 (XLS 1384 kb)
18_2010_424_MOESM4_ESM.doc (46 kb)
Supplementary material 4 (DOC 46 kb)
18_2010_424_MOESM5_ESM.xls (10 kb)
Supplementary material 5 (XLS 9 kb)
18_2010_424_MOESM6_ESM.xls (20 kb)
Supplementary material 6 (XLS 19 kb)


  1. 1.
    Green H, Kehinde O (1975) An established preadipose cell line and its differentiation in culture II. Factors affecting the adipose conversion. Cell 5:19–27CrossRefPubMedGoogle Scholar
  2. 2.
    Farmer SR (2006) Transcriptional control of adipocyte formation. Cell Metab 4:263–273CrossRefPubMedGoogle Scholar
  3. 3.
    Tontonoz P, Hu E, Spiegelman BM (1994) Stimulation of adipogenesis in fibroblasts by PPAR gamma 2, a lipid-activated transcription factor. Cell 79:1147–1156CrossRefPubMedGoogle Scholar
  4. 4.
    Lefterova MI, Lazar MA (2009) New developments in adipogenesis. Trends Endocrinol Metab 20:107–114CrossRefPubMedGoogle Scholar
  5. 5.
    Birsoy K, Chen Z, Friedman J (2008) Transcriptional regulation of adipogenesis by KLF4. Cell Metab 7:339–347CrossRefPubMedGoogle Scholar
  6. 6.
    Chen Z, Torrens JI, Anand A, Spiegelman BM, Friedman JM (2005) Krox20 stimulates adipogenesis via C/EBPbeta-dependent and -independent mechanisms. Cell Metab 1:93–106CrossRefPubMedGoogle Scholar
  7. 7.
    Tong Q, Dalgin G, Xu H, Ting CN, Leiden JM, Hotamisligil GS (2000) Function of GATA transcription factors in preadipocyte–adipocyte transition. Science 290:134–138CrossRefPubMedGoogle Scholar
  8. 8.
    Ross SE, Hemati N, Longo KA, Bennett CN, Lucas PC, Erickson RL, MacDougald OA (2000) Inhibition of adipogenesis by Wnt signaling. Science 289:950–953CrossRefPubMedGoogle Scholar
  9. 9.
    Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ Jr, Liu XS, Lazar MA (2008) PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 22:2941–2952CrossRefPubMedGoogle Scholar
  10. 10.
    Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, Denissov S, Borgesen M, Francoijs KJ, Mandrup S, Stunnenberg HG (2008) 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. Genes Dev 22:2953–2967CrossRefPubMedGoogle Scholar
  11. 11.
    Hackl H, Burkard TR, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, Trajanoski Z (2005) Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol 6:R108CrossRefPubMedGoogle Scholar
  12. 12.
    Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair SK, Trajanoski Z, Cobelli C (2005) A quantization method based on threshold optimization for microarray short time series. BMC Bioinformatics 6(Suppl 4):S11CrossRefPubMedGoogle Scholar
  13. 13.
    Liang S, Fuhrman S, Somogyi R (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 18–29Google Scholar
  14. 14.
    Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504CrossRefPubMedGoogle Scholar
  15. 15.
    Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34:D108–D110CrossRefPubMedGoogle Scholar
  16. 16.
    Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 36:D102–D106CrossRefPubMedGoogle Scholar
  17. 17.
    Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002) The human genome browser at UCSC. Genome Res 12:996–1006PubMedGoogle Scholar
  18. 18.
    Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33:D501–D504CrossRefPubMedGoogle Scholar
  19. 19.
    Quandt K, Frech K, Karas H, Wingender E, Werner T (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 23:4878–4884CrossRefPubMedGoogle Scholar
  20. 20.
    Soukas A, Socci ND, Saatkamp BD, Novelli S, Friedman JM (2001) Distinct transcriptional profiles of adipogenesis in vivo and in vitro. J Biol Chem 276:34167–34174CrossRefPubMedGoogle Scholar
  21. 21.
    Pabinger S, Thallinger GG, Snajder R, Eichhorn H, Rader R, Trajanoski Z (2009) QPCR: application for real-time PCR data management and analysis. BMC Bioinformatics 10:268CrossRefPubMedGoogle Scholar
  22. 22.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedGoogle Scholar
  23. 23.
    Kershaw EE, Schupp M, Guan HP, Gardner NP, Lazar MA, Flier JS (2007) PPARgamma regulates adipose triglyceride lipase in adipocytes in vitro and in vivo. Am J Physiol Endocrinol Metab 293:E1736–E1745CrossRefPubMedGoogle Scholar
  24. 24.
    Albrektsen T, Richter HE, Clausen JT, Fleckner J (2001) Identification of a novel integral plasma membrane protein induced during adipocyte differentiation. Biochem J 359:393–402CrossRefPubMedGoogle Scholar
  25. 25.
    Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, Eisenhaber F (2006) Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics 7:164CrossRefPubMedGoogle Scholar
  26. 26.
    Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G (2009) ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res 37:W435–W440CrossRefPubMedGoogle Scholar
  27. 27.
    Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29:2994–3005CrossRefPubMedGoogle Scholar
  28. 28.
    Stockigt J, Barleben L, Panjikar S, Loris EA (2008) 3D-Structure and function of strictosidine synthase–the key enzyme of monoterpenoid indole alkaloid biosynthesis. Plant Physiol Biochem 46:340–355CrossRefPubMedGoogle Scholar
  29. 29.
    Harel M, Aharoni A, Gaidukov L, Brumshtein B, Khersonsky O, Meged R, Dvir H, Ravelli RB, McCarthy A, Toker L, Silman I, Sussman JL, Tawfik DS (2004) Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat Struct Mol Biol 11:412–419CrossRefPubMedGoogle Scholar
  30. 30.
    Scharff EI, Koepke J, Fritzsch G, Lucke C, Ruterjans H (2001) Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Structure 9:493–502CrossRefPubMedGoogle Scholar
  31. 31.
    Tanaka Y, Morikawa K, Ohki Y, Yao M, Tsumoto K, Watanabe N, Ohta T, Tanaka I (2007) Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity. J Biol Chem 282:5770–5780CrossRefPubMedGoogle Scholar
  32. 32.
    Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36:D419–D425CrossRefPubMedGoogle Scholar
  33. 33.
    Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36:W197–W201CrossRefPubMedGoogle Scholar
  34. 34.
    Ilhan A, Gartner W, Nabokikh A, Daneva T, Majdic O, Cohen G, Bohmig GA, Base W, Horl WH, Wagner L (2008) Localization and characterization of the novel protein encoded by C20orf3. Biochem J 414:485–495CrossRefPubMedGoogle Scholar
  35. 35.
    Scheideler M, Elabd C, Zaragosi LE, Chiellini C, Hackl H, Sanchez-Cabo F, Yadav S, Duszka K, Friedl G, Papak C, Prokesch A, Windhager R, Ailhaud G, Dani C, Amri EZ, Trajanoski Z (2008) Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. BMC Genomics 9:340CrossRefPubMedGoogle Scholar
  36. 36.
    Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062–6067CrossRefPubMedGoogle Scholar
  37. 37.
    Tomaru T, Steger DJ, Lefterova MI, Schupp M, Lazar MA (2009) Adipocyte-specific expression of murine resistin is mediated by synergism between peroxisome proliferator-activated receptor gamma and CCAAT/enhancer-binding proteins. J Biol Chem 284:6116–6125CrossRefPubMedGoogle Scholar
  38. 38.
    Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37:382–390CrossRefPubMedGoogle Scholar
  39. 39.
    Schafer J, Strimmer K (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21:754–764CrossRefPubMedGoogle Scholar
  40. 40.
    Castelo R, Roverato A (2009) Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J Comput Biol 16:213–227CrossRefPubMedGoogle Scholar
  41. 41.
    Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298CrossRefPubMedGoogle Scholar

Copyright information

© Springer Basel AG 2010

Authors and Affiliations

  • Juliane G. Bogner-Strauss
    • 1
  • Andreas Prokesch
    • 1
  • Fatima Sanchez-Cabo
    • 2
  • Dietmar Rieder
    • 1
  • Hubert Hackl
    • 1
  • Kalina Duszka
    • 1
  • Anne Krogsdam
    • 1
  • Barbara Di Camillo
    • 3
  • Evelyn Walenta
    • 1
  • Ariane Klatzer
    • 1
  • Achim Lass
    • 4
  • Montserrat Pinent
    • 1
  • Wing-Cheong Wong
    • 5
  • Frank Eisenhaber
    • 5
    • 6
    • 7
  • Zlatko Trajanoski
    • 8
  1. 1.Institute for Genomics and BioinformaticsGraz University of TechnologyGrazAustria
  2. 2.Genomics UnitCentro Nacional de Investigaciones Cardiovasculares (CNIC)MadridSpain
  3. 3.Information Engineering DepartmentUniversity of PadovaPadovaItaly
  4. 4.Institute for Molecular BiosciencesKarl-Franzens University GrazGrazAustria
  5. 5.Bioinformatics Institute (BII)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
  6. 6.Department of Biological Sciences (DBS)National University of Singapore (NUS)SingaporeSingapore
  7. 7.School of Computer Engineering (SCE)Nanyang Technological University (NTU)SingaporeSingapore
  8. 8.Biocenter, Section for BioinformaticsInnsbruck Medical UniversityInnsbruckAustria

Personalised recommendations