Global approach to perinatal medicine: Functional genomics and proteomics

Journal of Perinatal Medicine

Volumn 33, Issue 1, 2005, Pages 5-16

  Kralj, Marijeta ^a   Kraljević, Sandra ^a   Sedić, Mirela ^a   Kurjak, Asim ^b   Pavelić, Krešimir ^a  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b Croatian Academy of Medical Sciences   (Croatia)

Author keywords

Biomarkers; DNA microarrays; Functional genomics; Mass spectrometry; Perinatal medicine; Preeclampsia; Preterm labor; Proteomics; Transcriptomics; Two dimensional electrophoresis

Indexed keywords

BIOLOGICAL MARKER;

COMPUTER PROGRAM; DNA MICROARRAY; FUNCTIONAL GENOMICS; FUNCTIONAL PROTEOMICS; GENE CONTROL; HIGH THROUGHPUT SCREENING; HUMAN; MASS SPECTROMETRY; PERINATAL CARE; PREECLAMPSIA; PREMATURE LABOR; PRIORITY JOURNAL; REVIEW; TRANSCRIPTOMICS; TROPHOBLASTIC TUMOR; TWO DIMENSIONAL GEL ELECTROPHORESIS;

FEMALE; GENOME, HUMAN; GENOMICS; HUMANS; OBSTETRIC LABOR, PREMATURE; PERINATOLOGY; PREGNANCY; PROTEOMICS;

EID: 13844267323     PISSN: 03005577     EISSN: None     Source Type: Journal    
DOI: 10.1515/JPM.2005.001     Document Type: Review

References (71)

1. Aguan K, JA Carvajal, LP Thompson, CP Weiner: Application of a functional genomics approach to identify differentially expressed genes in human myometrium during pregnancy and labour. Mol Hum Reprod 6 (2000) 1141
2. Al Moustafa AE, MA Alaoui-Jamali, G Batist, M Hernandez-Perez, C Serruya, L Alpert, MJ Black, R Sladek, WD Foulkes: Identification of genes associated with head and neck carcinogenesis by cDNA microarray comparison between matched primary normal epithelial and squamous carcinoma cells. Oncogene 21 (2002) 2634
3. Arcellana-Panlilio M, SM Robbins: Cutting-edge technology. I. Global gene expression profiling using DNA microarrays. Am J Physiol Gastr L 282 (2002) G397
4. Batorfi J, B Ye, SC Mok, I Cseh, RS Berkowitz, V Fulop: Protein profiling of complete mole and normal placenta using ProteinChip analysis on laser capture microdissected cells. Gynecol Oncol 88 (2003) 424
5. Beranova-Giorgianni S: Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strengths and limitations. Trends Anal Chem 22 (2003) 273
6. Bethin KE, Y Nagai, R Sladek, M Asada, Y Sadovsky, TJ Hudson, LJ Muglia: Microarray analysis of uterine gene expression in mouse and human pregnancy. Mol Endocrinol 17 (2003) 1454
7. Bilban M, S Head, G Desoye, V Quarante: DNA microarrays: a novel approach to investigate genomics in trophoblast invasion - A review. Placenta 21 (2000) S99
8. Bogusky MS, MW McIntosh: Biomedical informatics for proteomics. Nature 422 (2003) 233
9. Butte A: The use and analysis of microarray data. Nat Rev Drug Discovery 1 (2004) 951
10. Cargill M, D Altshuler, J Ireland, P Sklar, K Ardlie, N Patil, CR Lane, EP Lim, N Kalyanaraman, J Nemesh, L Ziaugra, L Friedland, A Rolfe, J Warrington, R Lipshutz, GQ Daley, ES Lander: Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22 (1999) 231
11. Celis JE, P Gromov: 2D protein electrophoresis: can it be perfected? Curr Opin Biotechnol 10 (1999) 16
12. Celis JE, M Kruhoffer, I Gromova, C Frederiksen, M Ostergaard, T Thykjaer, P Gromov, J Yu, H Palsdottir, N Magnusson, TF Orntoft: Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics. FEBS Lett 480 (2000) 2
13. Chaiwarapongsa T, R Gomez, S Edwin, G Mor, T Barder, R Romero: A proteomic approach for the identification of biological markers of preeclampsia. Am J Obstet Gynecol 189 (2003) S95
14. Chakravarti A: Single nucleotide polymorphisms: ... to a future of genetic medicine. Nature 409 (2001) 822
15. Chan EC, S Fraser, S Yin, G Yeo, K Kwek, RJ Fairclough, R Smith: Human myometrial genes are differentially expressed in labor: a suppression subtractive hybridization study. J Clin Endocrinol Metab 87 (2002) 2435
16. Chmait R, D Woelkers, A Hull, T Moore, I Labat, M Arterburn, S Andramani, B Stache-Crain, J Lee, W Funk, L Bogic: Analysis of placental transcriptome in patients with preeclampsia at preterm labor. Am J Obstet Gynecol 189 (2003) S116
17. Choe LH, KH Lee: Quantitative and qualitative measure of intralaboratory two-dimensional protein gel reproducibility and the effects of sample preparation, sample load and image analysis. Electrophoresis 24 (2003) 3500
18. Crosbie D: Protection of genetic information: an international comparison report to the human genetics commission. www.hgc.gov.uk/ business_publications_international_regulations.rtf
19. De Wit NCJ, M Vatish, AJR Heck, S Thornton: The application of proteomics to fetal and maternal medicine. Fetal Matern Med Rev 14 (2003) 47
20. Debruyne PR, SJ Vermeulen, G Berx, M Pocard, ASC Da Rocha, XD Li, L Cirnes, MF Poupon, FM Van Roy, MM Mareel: Functional and molecular characterization of the epithelioid to round transition in human colorectal cancer LoVo cells. Oncogene 22 (2003) 7199
21. Delpuech O, JB Trabut, F Carnot, J Feuillard, C Brechet, D Kremsdorf: Identification, using cDNA macroarray analysis, of distinct gene expression profiles associated with pathological and virological features of hepatocellular carcinoma. Oncogene 21 (2002) 2926
22. Diehn M, AA Alizadeh, PO Brown: Examining the living genome in health and disease with DNA microarrays. J Am Med Assoc 283 (2000) 2298
23. Dietl J: The pathogenesis of pre-eclampsia: new aspects. J Perinat Med 28 (2000) 464
24. Dudda-Subramanya R, G Lucchese, D Kanduc, AA Sinha: Clinical applications of DNA microarrays analysis. J Exp Ther Oncol 3 (2003) 297
25. Elliott CL, JA Loudon, N Brown, DM Slater, PR Bennett, MH Sullivan: IL-1beta and IL-8 in human fetal membranes: changes with gestational age, labor, and culture conditions. Am J Reprod Immunol Microbiol 46 (2001) 260
26. Esplin M, CD Thulin, K Southwick, RM Silver, MW Varner, D Whiting, SW Graves: The use of proteomic analysis for the discrimination of term and preterm labor. Am J Obstet Gynecol 189 (2003) S207
27. Figeys D, D Pinto: Proteomics on a chip: promising developments. Electrophoresis 22 (2001) 208
28. Fung ET, V Thulasiraman, SR Weinberger, EA Dalmasso: Protein biochips for differential profiling. Curr Opin Biotechnol 12 (2001) 65
29. Garfin DE: Two-dimensional gel electrophoresis: an overview. Trends Anal Chem 22 (2003) 263
30. Gevaert K, J Vandekerckhove: Protein identification methods in proteomics. Electrophoresis 21 (2000) 1145
31. Godovac-Zimmermann J, LR Brown: Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 20 (2001) 1
32. Goodman, N: Biological data becomes computer literate: new advances in bioinformatics. Curr Opin Biotechnol 13 (2002) 68
33. Graves PR, TAJ Haystead: Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 66 (2002) 39
34. Hoang VM, R Foulk, K Clauser, A Burlingame, BW Gibson, SJ Fisher: Functional proteomics: examining the effects of hypoxia on the cytotrophoblast protein repertoire. Biochemistry 40 (2001) 4077
35. Hunter TC, NL Andon, A Koller, JR Yates, PA Haynes: The functional proteomics toolbox: methods and applications. J Chromatogr B 782 (2002) 165
36. Kalionis B, E Moses: Advanced molecular techniques in pregnancy research: proteomics and genomics - A workshop report. Placenta 24 (2003) S119
37. Keelan JA, KW Marvin, TA Sato, M Coleman, LM McCowan, MD Mitchell: Cytokine abundance in placental tissues: evidence of inflammatory activation in gestational membranes with term and preterm parturition. Am J Obstet Gynecol 181 (1999) 1530
38. King HC, AA Sinha: Gene expression profile analysis by DNA microarrays: promise and pitfalls. J Am Med Assoc 286 (2001) 2280
39. Kraljevic S, PJ Stambrook, K Pavelic: Accelerating drug discovery. EMBO Rep (2004) in press
40. Krishna RG, F Wold: Post-translational modification of proteins. Adv Enzymol Relat Areas Mol Biol 67 (1993) 265
41. Lennon GG: High-throughput gene expression analysis for drug discovery. Drug Discovery Today 5 (2000) 59
42. Lockhart DJ, EA Winzeler: Genomics, gene expression and DNA arrays. Nature 405 (2000) 827
43. Lopez MF, MG Pluskal: Protein micro- and macroarrays: digitizing the proteome. J Chromatogr B 787 (2003) 19
44. March R, K Cheeseman, M Doherty. Pharmacogenetics - legal, ethical and regulatory considerations. Pharmacogenomics 2 (2001) 317
45. Marvin KW, JA Keelan, RL Eykholt, TA Sato, MD Mitchell: Use of cDNA arrays to generate differential expression profiles for inflammatory genes in human gestational membranes delivered at term and preterm. Mol Hum Reprod 8 (2002) 399
46. Maynard SE, JY Min, J Merchan, KH Lim, JY Li, S Mondal, TA Libermann, LP Morgan, FW Sellke, IE Stillman, FH Epstein, VP Sukhatme, SA Karumanchi: Excess placental soluble fms-like tyrosine kinase 1 (sFlt1) may contribute to endothelial dysfunction, hypertension, and proteinuria in preeclampsia. J Clin Invest 111 (2003) 649
47. Mounier-Vehier C, O Equine, AS Valat-Rigot, P Devos, A Carre: Hypertensive syndromes during pregnancy - Pathophysiology, definitions and maternofetal complications. Presse Med 28 (1999) 880
48. Orr MS, U Schert Large-scale gene expression analysis in molecular target discovery. Leukemia 16 (2002) 473
49. Page NM, RJ Woods, SM Gardiner, K Lomthaisong, RT Gladwell, DJ Butlin, IT Manyonda, PJ Lowry: Excessive placental secretion of neurokinin B during the third trimester causes pre-eclampsia. Nature 405 (2000) 797
50. Pang ZJ, FQ Xing: Comparative study on the expression of cytokine-receptor genes in normal and preeclamptic human placentas using DNA microarrays. J Perinat Med 31 (2003) 153
51. Patterson SD, RH Aebersold: Proteomics: the first decade and beyond. Nat Genet 33 (2003) 311
52. Persson B, U Hanson: Neonatal morbidities in gestational diabetes mellitus. Diabetes Care 21 (1998) B79
53. Ramaswamy S: DNA microarrays in clinical oncology. J Clin Oncol 20 (2002) 1932
54. Reif DM, BC White, JH Moore: Integrated analysis of genetic, genomic and proteomic data. Expert Rev Proteomics 1 (2004) 67
55. Reimer T, D Koczan, B Gerber, D Richter, HJ Thiesen, K Friese: Microarray analysis of differentially expressed genes in placental tissue of pre-eclampsia: up-regulation of obesity-related genes. Mol Hum Reprod 8 (2002) 674
56. Romero R, T Chaiwarapongsa, R Gomez, YM Kim, S Edwin, E Bujold, B Yoon: Proteomic profiling of premature labor: a method to identify clinical biomarkers and mechanisms of disease. Am J Obstet Gynecol 189 (2003) S63
57. Romero R, H Kuivaniemi, G Tromp: Editorial: Functional genomics and proteomics in term and preterm parturition. J Clin Endocrinol Metab 87 (2002) 2431
58. Romijn EP, J Krijgsveld, AJR Heck: Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics. J Chromatogr A 1000 (2003) 589
59. Saudan P, MA Brown, ML Buddle, M Jones: Does gestational hypertension become pre-eclampsia? Br J Obstet Gynaecol 105 (1998) 1177
60. Sawicki G, J Dakour, DW Morrish: Functional proteomics of neurokinin B in the placenta indicates a novel role in regulating cytotrophoblast antioxidant defences. Proteomics 3 (2003) 2044
61. Shaw MM, BM Riederer: Sample preparation for two-dimensional gel electrophoresis. Proteomics 3 (2003) 1408
62. Sibai BM, M Lindheimer, J Hauth, S Caritis, P Vandorsten, M Klebanoff, C MacPherson, M Landon, M Miodovnik, R Paul, P Meis, M Dombrowski: Risk factors for preeclampsia, abruptio placentae, and adverse neonatal outcomes among women with chronic hypertension. National Institute of Child Health and Human Development Network of Maternal-Fetal Medicine Units. N Engl J Med 339 (1998) 667
63. Snyder M, M Gerstein: Genomics - Defining genes in the genomics era. Science 300 (2003) 258
64. Tashima LS, LK Millar, GD Bryant-Greenwood: Genes upregulated in human fetal membranes by infection or labor. Obstet Gynecol 94 (1999) 441
65. Tauer CA: Central ethical dilemmas in research involving children. Ace Res 9 (2002) 127
66. Vegh GL, V Fulop, Y Liu, SW Ng, ZS Tuncer, DR Genest, P Paldi-Haris, J Foldi, SC Mok, RS Berkowitz: Differential gene expression pattern between normal human trophoblast and choriocarcinoma cell lines: downregulation of heat shock protein-27 in choriocarcinoma in vitro and in vivo. Gynecol Oncol 75 (1999) 391
67. Vuadens F, C Benay, D Crettaz, D Gallot, V Sapin, P Schneider, WV Bienvenut, D Lemery, M Quadroni, B Dastugue, JD Tissot: Identification of biologic markers of the premature rupture of fetal membranes: proteomic approach. Proteomics 3 (2003) 1521
68. Wasinger VC, GL Corthals: Proteomic tools for biomedicine. J Chromatogr B 771 (2002) 33
69. Watanabe H, H Hamada, N Yamada, S Sohda, K Yamakawa-Kobayashi, H Yoshikawa, T Arinami: Proteome analysis reveals elevated serum levels of clusterin in patients with preeclampsia. Proteomics 4 (2004) 537
70. Wilkins MR, JC Sanchez, KL Williams, DF Hochstrasser: Current challenges and future applications for protein maps and post-translational vector maps in proteome projects. Electrophoresis 17 (1996) 830
71. Zhu H, JF Klemic, S Chang, P Bertone, A Casamayor, KG Klemic, D Smith, M Gerstein, MA Reed, M Snyder: Analysis of yeast protein kinases using protein chips. Nat Genet 26 (2000) 283