Transcriptomic and proteomic analysis in the cardiovascular setting: Unravelling the disease?

Journal of Cardiovascular Medicine

Volumn 10, Issue 5, 2009, Pages 433-442

  Marziliano, Nicola ^a   Grasso, Maurizia ^a   Pilotto, Andrea ^a   Porcu, Emanuele ^a   Tagliani, Marilena ^a   Disabella, Eliana ^a   Diegoli, Marta ^a,b   Pasotti, Michele ^a   Favalli, Valentina ^a   Serio, Alessandra ^a   Gambarin, Fabiana ^a   Tavazzi, Luigi ^a   Klersy, Catherine ^a   Arbustini, Eloisa ^a  

^a FONDAZIONE IRCCS POLICLINICO SAN MATTEO   (Italy)

^b UNIVERSITY OF PAVIA   (Italy)

Author keywords

Cardiovascular disease; Genomics; Heart failure; Microarrays; Proteomics; Transcriptomics

Indexed keywords

BRAIN NATRIURETIC PEPTIDE; CELECOXIB; TROPONIN; BIOLOGICAL MARKER;

ADENOMATOUS POLYP; CHRONIC LYMPHATIC LEUKEMIA; CLINICAL EVALUATION; CLINICAL TRIAL; CONGESTIVE CARDIOMYOPATHY; DNA MICROARRAY; DOWNSTREAM PROCESSING; FAMILIAL ADENOMATOUS POLYPOSIS; FAMILIAL DISEASE; GENE EXPRESSION; GENE MAPPING; GENE MUTATION; GENETIC PREDISPOSITION; GENETIC VARIABILITY; HEART FAILURE; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METABOLOMICS; MOLECULAR CLONING; ONCOLOGY; PATHOGENESIS; PREDICTION; PROGNOSIS; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEOMICS; REVIEW; TRANSCRIPTOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS; ARTICLE; CARDIOVASCULAR DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETICS; METABOLISM; METHODOLOGY; PHENOTYPE;

BIOLOGICAL MARKERS; CARDIOVASCULAR DISEASES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PROTEIN ARRAY ANALYSIS; PROTEOMICS;

EID: 66349127121     PISSN: 15582027     EISSN: None     Source Type: Journal    
DOI: 10.2459/JCM.0b013e328324e972     Document Type: Review

References (65)

1. Liu P. The path to cardiomyopathy: cycles of injury, repair and maladaptation. Curr Opin Cardiol 1996; 11:291-292. (Pubitemid 26238076)
2. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, et al. Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci USA 1998; 95:3752-3757. (Pubitemid 28173201)
3. Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 2002; 8:68-74. (Pubitemid 34101731)
4. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001; 291:1304-1351.
5. Schulze A, Downward J. Navigating gene expression using microarrays: a technology review. Nat Cell Biol 2001; 3:E190-E195. (Pubitemid 32734244)
6. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995; 270:467-470.
7. Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 1997; 15:1359-1367. (Pubitemid 28022729)
8. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acid Res 2000; 28:4552-4557. (Pubitemid 30838254)
9. Luo L, Diamandis EP. Amplification of human genomic DNA sequences with polymerase chain reaction using a single oligonucleotide primer. J Clin Lab Anal 1999; 13:69-77. (Pubitemid 29104627)
10. Brady G. Expression profiling of single mammalian cells: small is beautiful. Yeast 2000; 17:211-217.
11. Stears RL, Getts RC, Gullans SR. A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol Genomics 2000; 3:93-99.
12. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, et al. Molecular portraits of human breast tumours. Nature 2000; 406:474-752.
13. Bridgewater J, van Laar R, Floore A, Van't Veer L. Gene expression profiling may improve diagnosis in patients with carcinoma of unknown primary. Br J Cancer 2008; 98:1425-1430. (Pubitemid 351543580)
14. Adami HO, Malker B, Holmberg L, Persson I, Stone B. The relation between survival and age at diagnosis in breast cancer. N Engl J Med 1986; 315:559-563. (Pubitemid 16052469)
15. El Saghir NS, Seoud M, Khalil MK, Charafeddine M, Salem ZK, Geara FB, et al. Effects of young age at presentation on survival in breast cancer. BMC Cancer 2006; 6:194. (Pubitemid 44321302)
16. Nixon AJ, Neuberg D, Hayes DF, Gelman R, Connolly JL, Schnitt S, et al. Relationship of patient age to pathologic features of the tumor and prognosis for patients with stage I or II breast cancer. J Clin Oncol 1994; 12:888-894. (Pubitemid 24145313)
17. Kollias J, Elston CW, Ellis IO, Robertson JF, Blamey RW. Early-onset breast cancer: histopathological and prognostic considerations. Br J Cancer 1997; 75:1318-1323. (Pubitemid 27179822)
18. Aebi S, Gelber S, Castiglione-Gertsch M, Gelber RD, Collins J, Thürlimann B, et al. Is chemotherapy alone adequate for young women with oestrogenreceptor positive breast cancer? Lancet 2000; 355:1869-1874.
19. Acharya CR, Hsu DS, Anders CK, Anguiano A, Salter KH, Walters KS, et al. Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer. JAMA 2008; 299:1574-1587.
20. Jemal A, Siegel R, Ward E, Murray T, Xu J, Thun MJ. Cancer statistic 2007. Cancer J Clin 2007; 57:43-66.
21. Mountain CF. Revisions in the international system for staging lung cancer. Chest 1997; 111:1710-1717. (Pubitemid 27260107)
22. D'Amico TA. Molecular staging of lung cancer. Ann Thorac Surg 2008; 85:S737-S742.
23. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999; 286:531-537.
24. Ma S, Huang J. Additive risk survival model with microarray data. BMC Bioinform 2008; 8:192.
25. Natkunam Y, Farinha P, Hsi ED, Hans CP, Tibshirani R, Sehn LH, et al. LMO2 protein expression predicts survival in patients with diffuse large B-cell lymphoma treated with anthracycline-based chemotherapy with and without rituximab. J Clin Oncol 2008; 26:447-454. (Pubitemid 351171698)
26. Winter SS, Jiang Z, Khawaja HM, Griffin T, Devidas M, Asselin BL, et al. Identification of genomic classifiers that distinguish induction failure in T-lineage acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood 2007; 110:1429-1438. (Pubitemid 47443957)
27. Barth AS, Kuner R, Buness A, Ruschhaupt M, Merk S, Zwermann L, et al. Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies. J Am Coll Cardiol 2006; 48:1610-1617. (Pubitemid 44528176)
28. Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV, et al. Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation 2004; 110:3444-3451. (Pubitemid 39610504)
29. Bullinger L, Dohner K, Bair E, Frohling S, Schlenk RF, Tibshirani R, et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med 2004; 350:1605-1616. (Pubitemid 38501163)
30. Allessie M, Ausma J, Schotten U. Electrical, contractile and structural remodeling during atrial fibrillation. Cardiovasc Res 2002; 54:230-246. (Pubitemid 34327903)
31. Fedak PW, Smookler DS, Kassiri Z, Ohno N, Leco KJ, Verma S, et al. TIMP- 3 deficiency leads to dilated cardiomyopathy. Circulation 2004; 110:2401-2409. (Pubitemid 39407346)
32. Storey KB. Mammalian hibernation: transcriptional and translational controls. Adv Exp Med Biol 2003; 543:21-38.
33. Nef HM, Möllmann H, Troidl C, Kostin S, Böttger T, Voss S, et al. Expression profiling of cardiac genes in Tako-Tsubo cardiomyopathy: insight into a new cardiac entity. J Mol Cell Cardiol 2008; 44:395-404.
34. Wittstein IS, Thiemann DR, Lima JAC, Baughman KL, Schulman SP, Gerstenblith G, et al. Neurohumoral features of myocardial stunning due to sudden emotional stress. New Engl J Med 2005; 352:539-548. (Pubitemid 40204667)
35. Damas JK, Gullestad L, Aass H, Simonsen S, Fjeld JG, Wikeby L, et al. Enhanced gene expression of chemokines and their corresponding receptors in mononuclear blood cells in chronic heart failure - modulatory effect of intravenous immunoglobulin. J Am Coll Cardiol 2001; 28: 187-193.
36. Horwitz PA, Tsai EJ, Putt ME, Gilmore JM, Lepore JJ, Parmacek MS, et al. Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression. Circulation 2004; 110:3815-3821.
37. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL. Progress with proteome project: why all protein expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 1996; 13:19-50. (Pubitemid 126665348)
38. O'Farrell PH. High resolution two-dimensional electro-phoresis of proteins. J Biol Chem 1975; 250:4007-4021.
39. Scherl A, Coute Y, Deon C, Callé A, Kindbeiter K, Sanchez JC, et al. Functional proteomic analysis of human nucleolus. Mol Biol Cell 2002; 13:4100-4109. (Pubitemid 35398573)
40. Yates JR 3rd. Mass spectrometry and the age of the proteome. J Mass Spectrom 1998; 33:1-19.
41. Fey SJ, Larsen PM. 2D or not 2D. Two-dimensional gel electrophoresis. Curr Opin Chem Biol 2001; 5:26-33.
42. Merchant M, Weinberger SR. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 2000; 21:1164-1177. (Pubitemid 30230781)
43. Celis JE, Gromov P. Proteomics in translational cancer research: toward an integrated approach. Cancer Cell 2003; 3:9-15. (Pubitemid 37448548)
44. Celis JE,Ostergaard M, Jensen NA, Gromova I, Rasmussen HH, Gromov P. Human and mouse proteomic databases: novel resources in the protein universe. FEBS Lett 1998; 430:64-72. (Pubitemid 28307033)
45. Alaiya AA, Franzen B, Auer G, Linder S. Cancer proteomics: from identification of novel markers to creation of artificial learning models for tumor classification. Electrophoresis 2000; 21:1210-1217. (Pubitemid 30230785)
46. Srinivas PR, Srivastava S, Hanash S, Wright GL Jr. Proteomics in early detection of cancer. Clin Chem 2001; 47:1901-1911.
47. Verrills NM, Kavallaris M. Drug resistance mechanisms in cancer cells: a proteomics perspective. Curr Opin Mol Ther 2003; 5:258-265. (Pubitemid 37185344)
48. Jones MB, Krutzsch H, Shu H, Zhao Y, Liotta LA, Kohn EC, et al. Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer. Proteomics 2002; 2:76-84. (Pubitemid 34273101)
49. Celis JE, Celis P, Palsdottir H, Østergaard M, Gromov P, Primdahl H, et al. Proteomic strategies to reveal tumor heterogeneity among urothelial papillomas. Mol Cell Proteomics 2002; 1:269-279.
50. Voss T, Ahorn H, Haberl P, Dohner H, Wilgenbus K. Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocytic leukemia. Int J Cancer 2001; 91:180-186. (Pubitemid 32041737)
51. Xiao Z, Luke BT, Izmirlian G, Umar A, Lynch PM, Phillips RK, et al. Serum proteomic profiles suggest celecoxib-modulated targets and response predictors. Cancer Res 2004; 64:2904-2909. (Pubitemid 38500632)
52. Steinbach G, Lynch PM, Phillips RK, Wallace MH, Hawk E, Gordon GB, et al. The effect of celecoxib, a cyclooxygenase-2 inhibitor, in familial adenomatous polyposis. N Engl J Med 2000; 342:1946-1952. (Pubitemid 30419089)
53. Pang RT, Poon TC, Chan KC, Lee NL, Chiu RW, Tong YK, et al. Serum proteomic fingerprints of adult patients with severe acute respiratory syndrome. Clin Chem 2006; 52:421-429. (Pubitemid 43306465)
54. Knecht M, Regitz-Zagrosek V, Pleissner KP, Jungblut P, Steffen C, Hildebrandt A, Fleck E. Characterization of myocardial protein composition in dilated cardiomyopathy by two-dimensional gel electrophoresis. Eur Heart J 1994; 15 (Suppl D):37-44.
55. Pleissner KP, Söding P, Sander S, Oswald H, Neuss M, Regitz-Zagrosek V, Fleck E. Dilated cardiomyopathy-associated proteins and their presentation in a www-accessible two-dimensional gel protein database. Electrophoresis 1997; 18:802-808.
56. Scheler C, Li XP, Salnikow J, Dunn MJ, Jungblut PR. Comparison of two-dimensional electrophoresis patterns of heat shock protein Hsp27 species in normal and cardiomyopathic hearts. Electrophoresis 1999; 20:3623-3628. (Pubitemid 30007260)
57. Pohlner K, Portig I, Pankuweit S, Lottspeich F, Maisch B. Identification of mitochondrial antigens recognized by antibodies in sera of patients with idiopathic dilated cardiomyopathy by two-dimensional gel electrophoresis and protein sequencing. Am J Cardiol 1997; 80:1040-1045. (Pubitemid 27459205)
58. Pankuweit S, Portig I, Lottspeich F, Maisch B. Autoantibodies in sera of patients with myocarditis: characterization of the corresponding proteins by isoelectric focusing and N-terminal sequence analysis. J Mol Cell Cardiol 1997; 29:77-84. (Pubitemid 27129132)
59. Wheeler CH, Collins A, Dunn MJ, Crisp SJ, Yacoub MH, Rose ML. Characterization of endothelial antigens associated with transplantassociated coronary artery disease. J Heart Lung Transplant 1995; 14:S188-S197. (Pubitemid 26011263)
60. Latif N, Rose ML, Yacoub MH, Dunn MJ. Association of pretransplantation antiheart antibodies with clinical course after heart transplantation. J Heart Lung Transplant 1995; 14:119-126.
61. Mendelsohn AR, Brent R. Protein interaction methods: toward an endgame. Science 1999; 284:1948-1950. (Pubitemid 29309435)
62. Faivre L, Collod-Beroud G, Loeys BL, Child A, Binquet C, Gautier E, et al. Effect of mutation type and location on clinical outcome in 1013 probands with Marfan syndrome or related phenotypes with FBN1 mutations: an international study. Am J Hum Mut 2007; 81:454-466. (Pubitemid 47330205)
63. Arbustini E, Marziliano N, Magrassi L, Loeys BL, Dietz HC. Aneurysm syndromes and TGFb receptor mutations. N Engl J Med 2006; 355:2155-2156. (Pubitemid 44749332)
64. Pasotti M, Klersy C, Pilotto A, Marziliano N, Rapezzi C, Serio A, et al. Longterm outcome and risk stratification in dilated cardiolaminopathies. J Am Coll Cardiol 2008; 52:1250-1260.
65. Elliott P, Andersson B, Arbustini E, Bilinska Z, Cecchi F, Charron P, et al. Classification of the cardiomyopathies: a position statement from the European Society Of Cardiology Working Group on Myocardial and Pericardial Diseases. Eur Heart J 2008; 29:270-276.