Reverse Differentiation as a Gene Filtering Tool in Genome Expression Profiling of Adipogenesis for Fat Marker Gene Selection and Their Analysis

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Ullah, Mujib ^a   Stich, Stefan ^a   Häupl, Thomas ^a   Eucker, Jan ^a   Sittinger, Michael ^a   Ringe, Jochen ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADIPONECTIN; CCAAT ENHANCER BINDING PROTEIN; FATTY ACID BINDING PROTEIN 4; LIPOPROTEIN LIPASE; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA;

ADIPOGENESIS; ADIPOQ GENE; APCDD1 GENE; ARTICLE; BINDING SITE; BIOLOGICAL FUNCTIONS; C/EBPA GENE; CELL DEDIFFERENTIATION; CELL DIFFERENTIATION; CHI3L1 GENE; CLUSTER ANALYSIS; CONTROLLED STUDY; FABP4 GENE; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SELECTION; HUMAN; HUMAN CELL; LPL GENE; MARKER GENE; MESENCHYMAL STEM CELL; NUCLEOTIDE SEQUENCE; PPARG GENE; RARRES1 GENE; SEMA3G GENE; SIGNAL TRANSDUCTION;

ADIPOGENESIS; ADIPOSITY; AGED; BINDING SITES; BIOLOGICAL MARKERS; CELL DEDIFFERENTIATION; CELL DIFFERENTIATION; CELL SEPARATION; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; MESENCHYMAL STROMAL CELLS; MIDDLE AGED; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 84880795333     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0069754     Document Type: Article

References (65)

1. Dominici M, Le Blanc K, Mueller I, Slaper-Cortenbach I, Marini F, et al. (2006) Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement. Cytotherapy 8: 315-317.
2. Pittenger MF, Mackay AM, Beck SC, Jaiswal RK, Douglas R, et al. (1999) Multilineage potential of adult human mesenchymal stem cells. Science 284: 143-147.
3. Wang S, Qu X, Zhao RC, (2011) Mesenchymal stem cells hold promise for regenerative medicine. Front Med 5: 372-378.
4. Greenberg AS, Obin MS, (2006) Obesity and the role of adipose tissue in inflammation and metabolism. Am J Clin Nutr 83: 461S-465S.
5. Trayhurn P, Beattie JH, (2001) Physiological role of adipose tissue: white adipose tissue as an endocrine and secretory organ. Proc Nutr Soc 60: 329-339.
6. Waki H, Tontonoz P, (2007) Endocrine functions of adipose tissue. Annu Rev Pathol 2: 31-56.
7. Philips BJ, Marra KG, Rubin JP, (2012) Adipose stem cell-based soft tissue regeneration. Expert Opin Biol Ther 12: 155-163.
8. Feve B, (2005) Adipogenesis: cellular and molecular aspects. Best Pract Res Clin Endocrinol Metab 19: 483-499.
9. Balachandran A, Guan H, Sellan M, van Uum S, Yang K, (2008) Insulin and dexamethasone dynamically regulate adipocyte 11beta-hydroxysteroid dehydrogenase type 1. Endocrinology 149: 4069-4079.
10. Lizcano JM, Alessi DR, (2002) The insulin signalling pathway. Curr Biol 12: R236-238.
11. Takada I, Kouzmenko AP, Kato S, (2010) PPAR-gamma Signaling Crosstalk in Mesenchymal Stem Cells. PPAR Res 2010.
12. Menssen A, Haupl T, Sittinger M, Delorme B, Charbord P, et al. (2011) Differential gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenic development. BMC Genomics 12: 461.
13. Schilling T, Kuffner R, Klein-Hitpass L, Zimmer R, Jakob F, et al. (2008) Microarray analyses of transdifferentiated mesenchymal stem cells. J Cell Biochem 103: 413-433.
14. Monaco E, Bionaz M, Rodriguez-Zas S, Hurley WL, Wheeler MB, (2012) Transcriptomics comparison between porcine adipose and bone marrow mesenchymal stem cells during in vitro osteogenic and adipogenic differentiation. PLoS One 7: e32481.
15. Armani A, Mammi C, Marzolla V, Calanchini M, Antelmi A, et al. (2010) Cellular models for understanding adipogenesis, adipose dysfunction, and obesity. J Cell Biochem 110: 564-572.
16. Scott MA, Nguyen VT, Levi B, James AW, (2011) Current methods of adipogenic differentiation of mesenchymal stem cells. Stem Cells Dev 20: 1793-1804.
17. Vater C, Kasten P, Stiehler M, (2011) Culture media for the differentiation of mesenchymal stromal cells. Acta Biomater 7: 463-477.
18. Grimaldi PA, (2001) The roles of PPARs in adipocyte differentiation. Prog Lipid Res 40: 269-281.
19. Styner M, Sen B, Xie Z, Case N, Rubin J, (2010) Indomethacin promotes adipogenesis of mesenchymal stem cells through a cyclooxygenase independent mechanism. J Cell Biochem 111: 1042-1050.
20. Yang DC, Tsay HJ, Lin SY, Chiou SH, Li MJ, et al. (2008) cAMP/PKA regulates osteogenesis, adipogenesis and ratio of RANKL/OPG mRNA expression in mesenchymal stem cells by suppressing leptin. PLoS One 3: e1540.
21. Weinberger-Ohana P, Goldschmit D, Mizrachi L, Orly J, (1984) Cyclic nucleotide phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine, induces cytodifferentiation of follicular granulosa cells cultured in serum-free medium. Endocrinology 115: 2160-2169.
22. Brzozowski T, Konturek PC, Pajdo R, Kwiecien SN, Konturek S, et al. (2005) Agonist of peroxisome proliferator-activated receptor gamma (PPAR-gamma): a new compound with potent gastroprotective and ulcer healing properties. Inflammopharmacology 13: 317-330.
23. Ullah M, Stich S, Notter M, Eucker J, Sittinger M, et al. (2013) Transdifferentiation of mesenchymal stem cells-derived adipogenic-differentiated cells into osteogenic- or chondrogenic-differentiated cells proceeds via dedifferentiation and have a correlation with cell cycle arresting and driving genes. Differentiation 85: 78-90.
24. Pfaffl MW, (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
25. Sturn A, Quackenbush J, Trajanoski Z, (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: 207-208.
26. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
27. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
28. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
29. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
30. Hoffmann R, Valencia A, (2004) A gene network for navigating the literature. Nat Genet 36: 664.
31. Hoffmann R, (2008) A wiki for the life sciences where authorship matters. Nat Genet 40: 1047-1051.
32. Engeli S, Utz W, Haufe S, Lamounier-Zepter V, Pofahl M, et al. (2013) Fatty acid binding protein 4 predicts left ventricular mass and longitudinal function in overweight and obese women. Heart.
33. Siitonen N, Pulkkinen L, Lindstrom J, Kolehmainen M, Eriksson JG, et al. (2011) Association of ADIPOQ gene variants with body weight, type 2 diabetes and serum adiponectin concentrations: the Finnish Diabetes Prevention Study. BMC Med Genet 12: 5.
34. Rouleau M, Patel A, Hendzel MJ, Kaufmann SH, Poirier GG, (2010) PARP inhibition: PARP1 and beyond. Nat Rev Cancer 10: 293-301.
35. Shi H, Tzameli I, Bjorbaek C, Flier JS, (2004) Suppressor of cytokine signaling 3 is a physiological regulator of adipocyte insulin signaling. J Biol Chem 279: 34733-34740.
36. Hoffmann R, Valencia A, (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 Suppl 2: ii252-258.
37. Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, et al. (2005) Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE 2005: pe21.
38. Hoffmann R, (2007) Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds. Curr Protoc Bioinformatics Chapter 1: Unit1 16.
39. Cho HS, Hayami S, Toyokawa G, Maejima K, Yamane Y, et al. (2012) RB1 Methylation by SMYD2 Enhances Cell Cycle Progression through an Increase of RB1 Phosphorylation. Neoplasia 14: 476-486.
40. Giannini G, Ambrosini MI, Di Marcotullio L, Cerignoli F, Zani M, et al. (2003) EGF- and cell-cycle-regulated STAG1/PMEPA1/ERG1.2 belongs to a conserved gene family and is overexpressed and amplified in breast and ovarian cancer. Mol Carcinog 38: 188-200.
41. Chua YS, Boh BK, Ponyeam W, Hagen T, (2011) Regulation of cullin RING E3 ubiquitin ligases by CAND1 in vivo. PLoS One 6: e16071.
42. Rosen ED, Walkey CJ, Puigserver P, Spiegelman BM, (2000) Transcriptional regulation of adipogenesis. Genes Dev 14: 1293-1307.
43. Latchman DS, (1997) Transcription factors: an overview. Int J Biochem Cell Biol 29: 1305-1312.
44. van Nimwegen E, (2003) Scaling laws in the functional content of genomes. Trends Genet 19: 479-484.
45. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108-110.
46. Schmidt SF, Jorgensen M, Chen Y, Nielsen R, Sandelin A, et al. (2011) Cross species comparison of C/EBPalpha and PPARgamma profiles in mouse and human adipocytes reveals interdependent retention of binding sites. BMC Genomics 12: 152.
47. Ito T, Tsuruta S, Tomita K, Kikuchi K, Yokoi T, et al. (2011) Genes that integrate multiple adipogenic signaling pathways in human mesenchymal stem cells. Biochem Biophys Res Commun 409: 786-791.
48. Zhang JD, Wiemann S, (2009) KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics 25: 1470-1471.
49. Liu Y, Liu F, Grundke-Iqbal I, Iqbal K, Gong CX, (2011) Deficient brain insulin signalling pathway in Alzheimer's disease and diabetes. J Pathol 225: 54-62.
50. Zhang HH, Huang JX, Duvel K, Boback B, Wu SL, et al. (2009) Insulin Stimulates Adipogenesis through the Akt-TSC2-mTORC1 Pathway. PLoS One 4.
51. Takada I, Kouzmenko AP, Kato S, (2010) PPAR-gamma Signaling Crosstalk in Mesenchymal Stem Cells. Ppar Research.
52. Tomlin CJ, Axelrod JD, (2005) Understanding biology by reverse engineering the control. Proc Natl Acad Sci U S A 102: 4219-4220.
53. Takahashi M, Fujita M, Furukawa Y, Hamamoto R, Shimokawa T, et al. (2002) Isolation of a novel human gene, APCDD1, as a direct target of the beta-catenin/T-cell factor 4 complex with probable involvement in colorectal carcinogenesis. Cancer Research 62: 5651-5656.
54. Shimomura Y, Agalliu D, Vonica A, Luria V, Wajid M, et al. (2010) APCDD1 is a novel Wnt inhibitor mutated in hereditary hypotrichosis simplex. Nature 464: 1043-1047.
55. Christodoulides C, Lagathu C, Sethi JK, Vidal-Puig A, (2009) Adipogenesis and WNT signalling. Trends in Endocrinology and Metabolism 20: 16-24.
56. Laudes M, (2011) Role of WNT signalling in the determination of human mesenchymal stem cells into preadipocytes. J Mol Endocrinol 46: R65-72.
57. Kigel B, Varshavsky A, Kessler O, Neufeld G, (2008) Successful inhibition of tumor development by specific class-3 semaphorins is associated with expression of appropriate semaphorin receptors by tumor cells. PLoS One 3: e3287.
58. Kutschera S, Weber H, Weick A, De Smet F, Genove G, et al. (2011) Differential endothelial transcriptomics identifies semaphorin 3G as a vascular class 3 semaphorin. Arterioscler Thromb Vasc Biol 31: 151-159.
59. Rehli M, Krause SW, Andreesen R, (1997) Molecular characterization of the gene for human cartilage gp-39 (CHI3L1), a member of the chitinase protein family and marker for late stages of macrophage differentiation. Genomics 43: 221-225.
60. Srivastava SK, Antal P, Gal J, Hullam G, Semsei AF, et al. (2011) Lack of evidence for association of two functional SNPs of CHI3L1 gene (HC-gp39) with rheumatoid arthritis. Rheumatol Int 31: 1003-1007.
61. Sahab ZJ, Hall MD, Zhang L, Cheema AK, Byers SW, (2010) Tumor Suppressor RARRES1 Regulates DLG2, PP2A, VCP, EB1, and Ankrd26. J Cancer 1: 14-22.
62. Sahab ZJ, Hall MD, Me Sung Y, Dakshanamurthy S, Ji Y, et al. (2011) Tumor suppressor RARRES1 interacts with cytoplasmic carboxypeptidase AGBL2 to regulate the alpha-tubulin tyrosination cycle. Cancer Res 71: 1219-1228.
63. Kwok WK, Pang JC, Lo KW, Ng HK, (2009) Role of the RARRES1 gene in nasopharyngeal carcinoma. Cancer Genet Cytogenet 194: 58-64.
64. Berry DC, DeSantis D, Soltanian H, Croniger CM, Noy N, (2012) Retinoic acid upregulates preadipocyte genes to block adipogenesis and suppress diet-induced obesity. Diabetes 61: 1112-1121.
65. Harel A, Inger A, Stelzer G, Strichman-Almashanu L, Dalah I, et al. (2009) GIFtS: annotation landscape analysis with GeneCards. BMC Bioinformatics 10: 348.