Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Schechter, Matthew A ^a   Hsieh, Michael K H ^a   Njoroge, Linda W ^a   Thompson, J Will ^a   Soderblom, Erik J ^a   Feger, Bryan J ^a   Troupes, Constantine D ^a   Hershberger, Kathleen A ^a   Ilkayeva, Olga R ^a   Nagel, Whitney L ^a   Landinez, Gina P ^a   Shah, Kishan M ^a   Burns, Virginia A ^b   Santacruz, Lucia ^a   Hirschey, Matthew D ^a   Foster, Matthew W ^a   Milano, Carmelo A ^a   Moseley, M Arthur ^a   Piacentino III, Valentino ^a   Bowles, Dawn E ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOPEPTIDE; PHOSPHOPROTEIN; PROTEOME;

AGED; BIOLOGY; CLUSTER ANALYSIS; COMPLICATION; DIFFERENTIAL DIAGNOSIS; GENE EXPRESSION PROFILING; HEART FAILURE; HEART MUSCLE; HEART MUSCLE ISCHEMIA; HEART VENTRICLE; HUMAN; MALE; METABOLISM; METABOLOME; METABOLOMICS; MIDDLE AGED; PROCEDURES; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REPRODUCIBILITY;

AGED; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DIAGNOSIS, DIFFERENTIAL; GENE EXPRESSION PROFILING; HEART FAILURE; HEART VENTRICLES; HUMANS; MALE; METABOLOME; METABOLOMICS; MIDDLE AGED; MYOCARDIAL ISCHEMIA; MYOCARDIUM; PHOSPHOPEPTIDES; PHOSPHOPROTEINS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84905909188     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104157     Document Type: Article

References (55)

1. Roger VL, Go AS, Lloyd-Jones DM, Benjamin EJ, Berry JD, et al. (2012) Heart disease and stroke statistics-2012 update: a report from the American Heart Association. Circulation 125: e2-e220.
2. Lloyd-Jones DM, Larson MG, Leip EP, Beiser A, D'Agostino RB, et al. (2002) Lifetime risk for developing congestive heart failure: the Framingham Heart Study. Circulation 106: 3068-3072. (Pubitemid 35440290)
3. Levy D, Kenchaiah S, Larson MG, Benjamin EJ, Kupka MJ, et al. (2002) Long-term trends in the incidence of and survival with heart failure. N Engl J Med 347: 1397-1402. (Pubitemid 35239711)
4. Roger VL, Go AS, Lloyd-Jones DM, Benjamin EJ, Berry JD, et al. (2012) Executive summary: heart disease and stroke statistics-2012 update: a report from the American Heart Association. Circulation 125: 188-197.
5. Margulies KB, Bednarik DP, Dries DL (2009) Genomics, transcriptional profiling, and heart failure. J Am Coll Cardiol 53: 1752-1759.
6. Sharma P, Cosme J, Gramolini AO (2012) Recent advances in cardiovascular proteomics. J Proteomics.
7. Gonzalez A, Lopez B, Beaumont J, Ravassa S, Arias T, et al. (2009) Cardiovascular translational medicine (III). Genomics and proteomics in heart failure research. Rev Esp Cardiol 62: 305-313.
8. Klawitter J, Klawitter J, Agardi E, Corby K, Leibfritz D, et al. (2013) Association of DJ-1/PTEN/AKT- and ASK1/p38-mediated cell signalling with ischaemic cardiomyopathy. Cardiovasc Res 97: 66-76.
9. Soderblom EJ, Philipp M, Thompson JW, Caron MG, Moseley MA (2011) Quantitative label-free phosphoproteomics strategy for multifaceted experimental designs. Anal Chem 83: 3758-3764.
10. Weng L, Dai H, Zhan Y, He Y, Stepaniants SB, et al. (2006) Rosetta error model for gene expression analysis. Bioinformatics 22: 1111-1121.
11. Piacentino V, 3rd, Milano CA, Bolanos M, Schroder J, Messina E, et al. (2012) X-linked inhibitor of apoptosis protein-mediated attenuation of apoptosis, using a novel cardiac-enhanced adeno-associated viral vector. Hum Gene Ther 23: 635-646.
12. Jensen MV, Joseph JW, Ilkayeva O, Burgess S, Lu D, et al. (2006) Compensatory responses to pyruvate carboxylase suppression in islet beta-cells. Preservation of glucose-stimulated insulin secretion. J Biol Chem 281: 22342-22351. (Pubitemid 44181936)
13. Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, et al. (2007) KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res 35: W588-594.
14. Jourdan-Lesaux C, Zhang J, Lindsey ML (2010) Extracellular matrix roles during cardiac repair. Life Sci 87: 391-400.
15. Vilahur G, Cubedo J, Casani L, Padro T, Sabate-Tenas M, et al. (2012) Reperfusion-triggered stress protein response in the myocardium is blocked by post-conditioning. Systems biology pathway analysis highlights the key role of the canonical aryl-hydrocarbon receptor pathway. Eur Heart J.
16. Bujak M, Ren G, Kweon HJ, Dobaczewski M, Reddy A, et al. (2007) Essential role of Smad3 in infarct healing and in the pathogenesis of cardiac remodeling. Circulation 116: 2127-2138. (Pubitemid 350060350)
17. Chaanine AH, Hajjar RJ (2011) AKT signalling in the failing heart. Eur J Heart Fail 13: 825-829.
18. Rosello-Lleti E, Alonso J, Cortes R, Almenar L, Martinez-Dolz L, et al. (2012) Cardiac protein changes in ischaemic and dilated cardiomyopathy: a proteomic study of human left ventricular tissue. J Cell Mol Med 16: 2471-2486.
19. Barallobre-Barreiro J, Didangelos A, Schoendube FA, Drozdov I, Yin X, et al. (2012) Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury. Circulation 125: 789-802.
20. de Vega S, Iwamoto T, Yamada Y (2009) Fibulins: multiple roles in matrix structures and tissue functions. Cell Mol Life Sci 66: 1890-1902.
21. Argraves WS, Greene LM, Cooley MA, Gallagher WM (2003) Fibulins: physiological and disease perspectives. EMBO Rep 4: 1127-1131. (Pubitemid 38088406)
22. Argraves WS, Tanaka A, Smith EP, Twal WO, Argraves KM, et al. (2009) Fibulin-1 and fibrinogen in human atherosclerotic lesions. Histochem Cell Biol 132: 559-565.
23. Hu B, Thirtamara-Rajamani KK, Sim H, Viapiano MS (2009) Fibulin-3 is uniquely upregulated in malignant gliomas and promotes tumor cell motility and invasion. Mol Cancer Res 7: 1756-1770.
24. Sottrup-Jensen L (1989) Alpha-macroglobulins: structure, shape, and mechanism of proteinase complex formation. J Biol Chem 264: 11539-11542.
25. French K, Yerbury JJ, Wilson MR (2008) Protease activation of alpha2-macroglobulin modulates a chaperone-like action with broad specificity. Biochemistry 47: 1176-1185. (Pubitemid 351161874)
26. Zhang N, Wang X, Huo Q, Li X, Wang H, et al. (2013) The oncogene metadherin modulates the apoptotic pathway based on the tumor necrosis factor superfamily member TRAIL (Tumor Necrosis Factor-related Apoptosisinducing Ligand) in breast cancer. J Biol Chem 288: 9396-9407.
27. Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, et al. (2013) Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci U S A 110: 12414-12419.
28. Kostyukova AS (2007) Leiomodin/tropomyosin interactions are isoform specific. Arch Biochem Biophys 465: 227-230.
29. Clark R, Nosie A, Walker T, Faralli JA, Filla MS, et al. (2013) Comparative genomic and proteomic analysis of cytoskeletal changes in dexamethasonetreated trabecular meshwork cells. Mol Cell Proteomics 12: 194-206.
30. Huet E, Gabison EE, Mourah S, Menashi S (2008) Role of emmprin/CD147 in tissue remodeling. Connect Tissue Res 49: 175-179.
31. Wilson MC, Meredith D, Fox JE, Manoharan C, Davies AJ, et al. (2005) Basigin (CD147) is the target for organomercurial inhibition of monocarboxylate transporter isoforms 1 and 4: the ancillary protein for the insensitive MCT2 is EMBIGIN (gp70). J Biol Chem 280: 27213-27221. (Pubitemid 41040760)
32. Wilson MC, Meredith D, Halestrap AP (2002) Fluorescence resonance energy transfer studies on the interaction between the lactate transporter MCT1 and CD147 provide information on the topology and stoichiometry of the complex in situ. J Biol Chem 277: 3666-3672. (Pubitemid 34953240)
33. Cui HY, Guo T, Wang SJ, Zhao P, Dong ZS, et al. (2012) Dimerization is essential for HAb18G/CD147 promoting tumor invasion via MAPK pathway. Biochem Biophys Res Commun 419: 517-522.
34. Hager HA, Bader DM (2009) Bves: ten years after. Histol Histopathol 24: 777-787.
35. Froese A, Breher SS, Waldeyer C, Schindler RF, Nikolaev VO, et al. (2012) Popeye domain containing proteins are essential for stress-mediated modulation of cardiac pacemaking in mice. J Clin Invest 122: 1119-1130.
36. Gingold-Belfer R, Bergman M, Alcalay Y, Schlesinger H, Aravot D, et al. (2011) Popeye domain-containing 1 is down-regulated in failing human hearts. Int J Mol Med 27: 25-31.
37. Russ PK, Kupperman AI, Presley SH, Haselton FR, Chang MS (2010) Inhibition of RhoA signaling with increased Bves in trabecular meshwork cells. Invest Ophthalmol Vis Sci 51: 223-230.
38. Warren SA, Briggs LE, Zeng H, Chuang J, Chang EI, et al. (2012) Myosin light chain phosphorylation is critical for adaptation to cardiac stress. Circulation 126: 2575-2588.
39. Sanger JM, Wang J, Gleason LM, Chowrashi P, Dube DK, et al. (2010) Arg/Abl-binding protein, a Z-body and Z-band protein, binds sarcomeric, costameric, and signaling molecules. Cytoskeleton (Hoboken) 67: 808-823.
40. Kakimoto Y, Ito S, Abiru H, Kotani H, Ozeki M, et al. (2013) Sorbin and SH3 domain-containing protein 2 is released from infarcted heart in the very early phase: proteomic analysis of cardiac tissues from patients. J Am Heart Assoc 2: e000565.
41. Soubeyran P, Barac A, Szymkiewicz I, Dikic I (2003) Cbl-ArgBP2 complex mediates ubiquitination and degradation of c-Abl. Biochem J 370: 29-34. (Pubitemid 36259416)
42. Frank D, Kuhn C, Katus HA, Frey N (2006) The sarcomeric Z-disc: a nodal point in signalling and disease. J Mol Med (Berl) 84: 446-468. (Pubitemid 43801324)
43. Korotchkina LG, Patel MS (1995) Mutagenesis studies of the phosphorylation sites of recombinant human pyruvate dehydrogenase. Site-specific regulation. J Biol Chem 270: 14297-14304.
44. Karpova T, Danchuk S, Kolobova E, Popov KM (2003) Characterization of the isozymes of pyruvate dehydrogenase phosphatase: implications for the regulation of pyruvate dehydrogenase activity. Biochim Biophys Acta 1652: 126-135. (Pubitemid 38224417)
45. Lopaschuk GD, Ussher JR, Folmes CD, Jaswal JS, Stanley WC (2010) Myocardial fatty acid metabolism in health and disease. Physiol Rev 90: 207-258.
46. Bolanos-Garcia VM, Fernandez-Recio J, Allende JE, Blundell TL (2006) Identifying interaction motifs in CK2beta-a ubiquitous kinase regulatory subunit. Trends Biochem Sci 31: 654-661. (Pubitemid 44802992)
47. Veis A, Sfeir C, Wu CB (1997) Phosphorylation of the proteins of the extracellular matrix of mineralized tissues by casein kinase-like activity. Crit Rev Oral Biol Med 8: 360-379. (Pubitemid 28123813)
48. Tan WQ, Wang JX, Lin ZQ, Li YR, Lin Y, et al. (2008) Novel cardiac apoptotic pathway: the dephosphorylation of apoptosis repressor with caspase recruitment domain by calcineurin. Circulation 118: 2268-2276.
49. Li PF, Li J, Muller EC, Otto A, Dietz R, et al. (2002) Phosphorylation by protein kinase CK2: a signaling switch for the caspase-inhibiting protein ARC. Mol Cell 10: 247-258. (Pubitemid 35007340)
50. Eom GH, Cho YK, Ko JH, Shin S, Choe N, et al. (2011) Casein kinase-2alpha1 induces hypertrophic response by phosphorylation of histone deacetylase 2 S394 and its activation in the heart. Circulation 123: 2392-2403.
51. Murtaza I, Wang HX, Feng X, Alenina N, Bader M, et al. (2008) Down-regulation of catalase and oxidative modification of protein kinase CK2 lead to the failure of apoptosis repressor with caspase recruitment domain to inhibit cardiomyocyte hypertrophy. J Biol Chem 283: 5996-6004.
52. Hauck L, Harms C, An J, Rohne J, Gertz K, et al. (2008) Protein kinase CK2 links extracellular growth factor signaling with the control of p27(Kip1) stability in the heart. Nat Med 14: 315-324. (Pubitemid 351347917)
53. Kim SO, Baines CP, Critz SD, Pelech SL, Katz S, et al. (1999) Ischemia induced activation of heat shock protein 27 kinases and casein kinase 2 in the preconditioned rabbit heart. Biochem Cell Biol 77: 559-567. (Pubitemid 30074750)
54. Konecny F, Zou J, Husain M, von Harsdorf R (2012) Post-myocardial infarct p27 fusion protein intravenous delivery averts adverse remodelling and improves heart function and survival in rodents. Cardiovasc Res 94: 492-500.
55. Liebler DC, Zimmerman LJ (2013) Targeted quantitation of proteins by mass spectrometry. Biochemistry 52: 3797-3806.