Dissecting spatio-temporal protein networks driving human heart development and related disorders

Molecular Systems Biology

Volumn 6, Issue , 2010, Pages

  Lage, Kasper ^a,b,c,d,e   Møllgård, Kjeld ^e   Greenway, Steven ^b   Wakimoto, Hiroko ^b   Gorham, Joshua M ^b   Workman, Christopher T ^d   Bendsen, Eske ^f   Hansen, Niclas T ^d   Rigina, Olga ^d   Roque, Francisco S ^d,e   Wiese, Cornelia ^g   Christoffels, Vincent M ^g   Roberts, Amy E ^h,i   Smoot, Leslie B ⁱ   Pu, William T ^i,j   Donahoe, Patricia K ^a,b,c   Tommerup, Niels ^e   Brunak, Søren ^d,e   Seidman, Christine E ^b   Seidman, Jonathan G ^b   Larsen, Lars A ^e   more..

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^e UNIVERSITY OF COPENHAGEN   (Denmark)

^f ODENSE UNIVERSITY HOSPITAL   (Denmark)

^g ACADEMIC MEDICAL CENTER   (Netherlands)

^h LABORATORY FOR MOLECULAR MEDICINE   (United States)

ⁱ BOSTON CHILDREN S HOSPITAL   (United States)

^j HARVARD STEM CELL INSTITUTE   (United States)

more..

Author keywords

genetics; organ developmental networks; polygenic common disorders; proteomics; systems biology

Indexed keywords

ARTICLE; CONTROLLED STUDY; EMBRYO; FETUS; GENE MUTATION; HEART DEVELOPMENT; HEART DISEASE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MORPHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; CARDIOVASCULAR DISEASE; HEART; HISTOLOGY; METABOLISM; PRENATAL DEVELOPMENT; REPRODUCIBILITY; SIGNAL TRANSDUCTION; TIME;

PROTEIN;

CARDIOVASCULAR DISEASES; HEART; HUMANS; PROTEINS; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; TIME FACTORS;

EID: 77954016586     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2010.36     Document Type: Article

References (37)

1. Basson CT, Bachinsky DR, Lin RC, Levi T, Elkins JA, Soults J, Grayzel D, Kroumpouzou E, Traill TA, Leblanc-Straceski J, Renault B, Kucherlapati R, Seidman JG, Seidman CE (1997) Mutations in human TBX5 [corrected] cause limb and cardiac malformation in Holt-Oram syndrome. Nat Genet 15: 30-35
2. Benson DW, Silberbach GM, Kavanaugh-McHugh A, Cottrill C, Zhang Y, Riggs S, Smalls O, Johnson MC, Watson MS, Seidman JG, Seidman CE, Plowden J, Kugler JD (1999) Mutations in the cardiac transcription factor NKX2.5 affect diverse cardiac developmental pathways. J Clin Invest 104: 1567-1573
3. Bergholdt R, Storling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F (2007) Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biol 8: R253
4. BergstromDA, Penn BH, Strand A, Perry RL, Rudnicki MA, Tapscott SJ (2002) Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression. Mol Cell 9: 587-600
5. Bruneau BG (2008) The developmental genetics of congenital heart disease. Nature 451: 943-948
6. Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36: D724-D728
7. Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2: e383
8. Chien KR, Domian IJ, Parker KK (2008) Cardiogenesis and the complex biology of regenerative cardiovascular medicine. Science (New York, NY) 322: 1494-1497
9. D'Hertog W, Overbergh L, Lage K, Ferreira GB, Maris M, Gysemans C, Flamez D, Cardozo AK, Van den Bergh G, Schoofs L, Arckens L, Moreau Y, Hansen DA, Eizirik DL, Waelkens E, Mathieu C (2007) Proteomics analysis of cytokine-induced dysfunction and death in insulin-producing INS-1E cells: new insights into the pathways involved. Mol Cell Proteomics 6: 2180-2199
10. Fishman MC, Olson EN (1997) Parsing the heart: genetic modules for organ assembly. Cell 91: 153-156
11. Garg V, Kathiriya IS, Barnes R, Schluterman MK, King IN, Butler CA, Rothrock CR, Eapen RS, Hirayama-Yamada K, Joo K, Matsuoka R, Cohen JC, Srivastava D (2003) GATA4 mutations cause human congenital heart defects and reveal an interaction with TBX5. Nature 424: 443-447
12. Garg V, Muth AN, Ransom JF, Schluterman MK, Barnes R, King IN, Grossfeld PD, Srivastava D (2005) Mutations in NOTCH1 cause aortic valve disease. Nature 437: 270-274
13. Gaudet J, Mango SE (2002) Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science (New York, NY) 295: 821-825
14. Gaudet J, Muttumu S, Horner M, Mango SE (2004) Whole-genome analysis of temporal gene expression during foregut development. PLoS Biol 2: e352
15. Grego-Bessa J, Luna-Zurita L, del Monte G, Bolos V, Melgar P, Arandilla A, Garratt AN, Zang H, Mukouyama YS, Chen H, ShouW, Ballestar E, Esteller M, Rojas A, Perez-Pomares JM, de la Pompa JL (2007) Notch signaling is essential for ventricular chamber development. Dev Cell 12: 415-429
16. Hulsen T, Huynen MA, de Vlieg J, Groenen PM (2006) Benchmarking ortholog identification methods using functional genomics data. Genome Biol 7: R31
17. Kashtan N, Alon U (2005) Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci USA 102: 13773-13778
18. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, Stuart JM, Eizinger A, Wylie BN, Davidson GS (2001) A gene expression map for Caenorhabditis elegans. Science (New York, NY) 293: 2087-2092
19. Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM, Seidman CE, Seidman JG (2007) Polony multiplex analysis of gene expression (PMAGE) inmouse hypertrophic cardiomyopathy. Science 316: 1481-1484.
20. Kornberg TB, Tabata T (1993) Segmentation of the Drosophila embryo. Curr Opin Genet Dev 3: 585-594
21. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S (2008) A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci USA 105: 20870-20875
22. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotech 25: 309-316
23. Lang JE, Magbanua MJ, Scott JH, Makrigiorgos GM, Wang G, Federman S, Esserman LJ, Park JW, Haqq CM (2009) A comparison of RNA amplification techniques at sub-nanogram input concentration. BMC Genomics 10: 326
24. Lipson H, Pollack JB, Suh NP (2002) On the origin of modular variation. Evolution 56: 1549-1556
25. Maduro MF, Rothman JH (2002) Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm. Dev Biol 246: 68-85
26. Moorman AF, Christoffels VM (2003) Cardiac chamber formation: development, genes, and evolution. Physiol Rev 83:1223-1267.
27. O'Brien KP, Remm M, Sonnhammer EL (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33 Database Issue: D476.
28. Olson EN (2004) A decade of discoveries in cardiac biology. Nat Med 10: 467-474.
29. Olson EN (2006) Gene regulatory networks in the evolution and development of the heart. Science 313:1922-1927.
30. Pourquie O (2003) The segmentation clock: converting embryonic time into spatial pattern. Science (New York, NY) 301: 328-330
31. Satou Y, SatohN (2006) Gene regulatory networks for the development and evolution of the chordate heart. Genes Dev 20: 2634-2638
32. Schott JJ, Benson DW, Basson CT, Pease W, Silberbach GM, Moak JP, Maron BJ, Seidman CE, Seidman JG (1998) Congenital heart disease caused by mutations in the transcription factor NKX2-5. Science (New York, NY) 281: 108-111
33. Skeath JB, Thor S (2003) Genetic control of Drosophila nerve cord development. Curr Opin Neurobiol 13: 8-15
34. Srivastava D (2006) Making or breaking the heart: from lineage determination to morphogenesis. Cell 126: 1037-1048
35. Wagner GP, Pavlicev M, Cheverud JM (2007) The road to modularity. Nat Rev Genet 8: 921-931
36. Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, KusendaM,Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N et al (2008) Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science (New York, NY) 320: 539-543
37. Weatherbee SD, Halder G, Kim J, Hudson A, Carroll S (1998) Ultrabithorax regulates genes at several levels of the wingpatterning hierarchy to shape the development of the Drosophila haltere. Genes Dev 12: 1474-1482