In arrayed ranks array technology in the study of mesothelioma steven

Journal of Thoracic Oncology

Volumn 4, Issue 3, 2009, Pages 411-425

  Gray, Steven G ^a   Fennell, Dean A ^b   Mutti, Luciano ^c   O'Byrne, Kenneth J ^a  

^a ST JAMES S HOSPITAL   (Ireland)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c Local Health Unit   (Italy)

Author keywords

Array; Mesothelioma; Proteome; Transcription

Indexed keywords

ASBESTOS; BIOLOGICAL MARKER; DNA;

CANCER INCIDENCE; CELL DIFFERENTIATION; CELL LINE; CLINICAL FEATURE; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOGENETICS; GENE EXPRESSION; GENOTYPE; HUMAN; JAPAN; MESOTHELIOMA; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROGNOSIS; PROTEOMICS; SHORT SURVEY; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNOLOGY; TRANSCRIPTOMICS; CANCER STAGING; COMPARATIVE STUDY; DNA MICROARRAY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION; GENETICS; MALE; MICRODISSECTION; PATHOLOGY; PLEURA TUMOR; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SENSITIVITY AND SPECIFICITY;

DNA, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; MESOTHELIOMA; MICRODISSECTION; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLEURAL NEOPLASMS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 67049162829     PISSN: 15560864     EISSN: 15561380     Source Type: Journal    
DOI: 10.1097/JTO.0b013e3181951ce8     Document Type: Review

References (157)

1. Ismail-Khan R, Robinson LA, Williams CC Jr, Garrett CR, Bepler G, Simon GR. Malignant pleural mesothelioma: a comprehensive review. Cancer Control 2006;13:255-263. (Pubitemid 44600936)
2. Robinson BW, Lake RA. Advances in malignant mesothelioma. N Engl J Med 2005;353:1591-1603.
3. Murayama T, Takahashi K, Natori Y, Kurumatani N. Estimation of future mortality from pleural malignant mesothelioma in Japan based on an age-cohort model. Am J Ind Med 2006;49:1-7. (Pubitemid 43083291)
4. Edwards JG, Abrams KR, Leverment JN, Spyt TJ, Waller DA, O'Byrne KJ. Prognostic factors for malignant mesothelioma in 142 patients: validation of CALGB and EORTC prognostic scoring systems. Thorax 2000;55:731-735.
5. Zucali PA, Giaccone G. Biology and management of malignant pleural mesothelioma. Eur J Cancer 2006;42:2706-2714. (Pubitemid 44584672)
6. Fennell DA, Gaudino G, O'Byrne KJ, Mutti L, van Meerbeeck J. Advances in the systemic therapy of malignant pleural mesothelioma. Nat Clin Pract Oncol 2008;5:136-147. (Pubitemid 351330666)
7. Stahel RA. Malignant pleural mesothelioma: a new standard of care. Lung Cancer 2006;54(Suppl 2):S9-S14. (Pubitemid 44692851)
8. Zervos MD, Bizekis C, Pass HI. Malignant mesothelioma 2008. Curr Opin Pulm Med 2008;14:303-309. (Pubitemid 351786540)
9. Draghici S, Khatri P, Eklund AC, Szallasi Z. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 2006; 22:101-109. (Pubitemid 43152029)
10. Sladek R, Rocheleau G, Rung J, et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007;445: 881-885. (Pubitemid 46309843)
11. Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nat Rev Genet 2006;7:632-644.
12. Mantripragada KK, Buckley PG, de Stahl TD, Dumanski JP. Genomic microarrays in the spotlight. Trends Genet 2004;20:87-94.
13. Hudson ME, Snyder M. High-throughput methods of regulatory element discovery. Biotechniques 2006;41:673, 675, 677 passim. (Pubitemid 46534848)
14. Wu J, Smith LT, Plass C, Huang TH. ChIP-chip comes of age for genome-wide functional analysis. Cancer Res 2006;66:6899-6902. (Pubitemid 44197662)
15. Kondo Y, Shen L, Yan PS, Huang TH, Issa JP. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc Natl Acad Sci USA 2004;101:7398-7403. (Pubitemid 38638044)
16. Ballestar E, Paz MF, Valle L, et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. Embo J 2003;22:6335-6345. (Pubitemid 37522590)
17. Chiba T, Yokosuka O, Arai M, et al. Identification of genes upregulated by histone deacetylase inhibition with cDNA microarray and exploration of epigenetic alterations on hepatoma cells. J Hepatol 2004;41:436-445. (Pubitemid 39158753)
18. Shames DS, Girard L, Gao B, et al. A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med 2006;3:e486. (Pubitemid 46028510)
19. van de Vijver MJ, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999-2009. (Pubitemid 35461656)
20. van 't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415: 530-536. (Pubitemid 34130608)
21. Onda M, Emi M, Nagai H, et al. Gene expression patterns as marker for 5-year postoperative prognosis of primary breast cancers. J Cancer Res Clin Oncol 2004;130:537-545. (Pubitemid 39149885)
22. Nagahata T, Onda M, Emi M, et al. Expression profiling to predict postoperative prognosis for estrogen receptor-negative breast cancers by analysis of 25,344 genes on a cDNA microarray. Cancer Sci 2004;95:218-225. (Pubitemid 38489087)
23. Robison JE, Perreard L, Bernard PS. State of the science: molecular classifications of breast cancer for clinical diagnostics. Clin Biochem 2004;37:572-578. (Pubitemid 38845020)
24. Lee CH, Macgregor PF. Using microarrays to predict resistance to chemotherapy in cancer patients. Pharmacogenomics 2004;5:611-625. (Pubitemid 39236577)
25. Villeneuve DJ, Parissenti AM. The use of DNA microarrays to investigate the pharmacogenomics of drug response in living systems. Curr Top Med Chem 2004;4:1329-1345.
26. Wulfkuhle J, Espina V, Liotta L, Petricoin E. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer 2004;40:2623-2632. (Pubitemid 39487084)
27. Player A, Barrett JC, Kawasaki ES. Laser capture microdissection, microarrays and the precise definition of a cancer cell. Expert Rev Mol Diagn 2004;4:831-840. (Pubitemid 39487587)
28. Shi L, Tong W, Goodsaid F, et al. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn 2004;4:761-777. (Pubitemid 39487581)
29. Olson JA Jr. Application of microarray profiling to clinical trials in cancer. Surgery 2004;136:519-523. (Pubitemid 39186562)
30. Orr MS, Goodsaid F, Amur S, Rudman A, Frueh FW. The experience with voluntary genomic data submissions at the FDA and a vision for the future of the voluntary data submission program. Clin Pharmacol Ther 2007;81:294-297. (Pubitemid 46174828)
31. Frueh FW. Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 2006;24:1105-1107.
32. Shi L, Reid LH, Jones WD, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006;24:1151-1161. (Pubitemid 44359727)
33. Strauss E. Arrays of hope. Cell 2006;127:657-659. (Pubitemid 44716262)
34. Rihn BH, Mohr S, McDowell SA, et al. Differential gene expression in mesothelioma. FEBS Lett 2000;480:95-100. (Pubitemid 30682482)
35. Kettunen E, Nissen AM, Ollikainen T, et al. Gene expression profiling of malignant mesothelioma cell lines: cDNA array study. Int J Cancer 2001;91:492-496. (Pubitemid 32115103)
36. Kim JY, Harvard C, You L, et al. Stathmin is overexpressed in malignant mesothelioma. Anticancer Res 2007;27:39-44. (Pubitemid 46363314)
37. Ramos-Nino ME, Scapoli L, Martinelli M, Land S, Mossman BT. Microarray analysis and RNA silencing link fra-1 to cd44 and c-met expression in mesothelioma. Cancer Res 2003;63:3539-3545. (Pubitemid 36793033)
38. Nymark P, Lindholm PM, Korpela MV, et al. Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines. BMC Genomics 2007;8:62. (Pubitemid 46443812)
39. Swain WA, Mossman BT. Carcinogenic mechanisms in mesothelioma: effects of asbestos on cell signalling events, transcription factors, and inflammatory cytokines. In O'Byrne KJ, Rusch V. (Eds.), Malignant Pleural Mesotheliomaed. Oxford: Oxford University Press, 2006. Pp. 129-146.
40. Swain WA, Sander LS, Gant TW, et al. Microarray analysis of mesothelial cells treated with crocidolite, erionite, IL-1beta and TNFalpha. Lung Cancer 2003;41:S25-S26.
41. Hegmans JP, Hemmes A, Hammad H, Boon L, Hoogsteden HC, Lambrecht BN. Mesothelioma environment comprises cytokines and T-regulatory cells that suppress immune responses. Eur Respir J 2006;27:1086-1095. (Pubitemid 44914290)
42. Kettunen E, Nicholson AG, Nagy B, et al. L1CAM, INP10, P-cadherin, tPA and ITGB4 over-expression in malignant pleural mesotheliomas revealed by combined use of cDNA and tissue microarray. Carcinogenesis 2005;26:17-25. (Pubitemid 40207695)
43. Usami N, Fukui T, Kondo M, et al. Establishment and characterization of four malignant pleural mesothelioma cell lines from Japanese patients. Cancer Sci 2006;97:387-394.
44. Minn AJ, Gupta GP, Siegel PM, et al. Genes that mediate breast cancer metastasis to lung. Nature 2005;436:518-524.
45. Yang G, Rosen DG, Zhang Z, et al. The chemokine growth-regulated oncogene 1 (Gro-1) links RAS signaling to the senescence of stromal fibroblasts and ovarian tumorigenesis. Proc Natl Acad Sci USA 2006; 103:16472-16477. (Pubitemid 44715220)
46. Ruffini PA, Morandi P, Cabioglu N, Altundag K, Cristofanilli M. Manipulating the chemokine-chemokine receptor network to treat cancer. Cancer 2007;109:2392-2404. (Pubitemid 46906457)
47. Antony V.B, Hott JW, Godbey SW, Holm K. Angiogenesis in mesotheliomas. Role of mesothelial cell derived IL-8. Chest 1996; 109:21S-22S. (Pubitemid 26086979)
48. Yuan A, Chen JJ, Yao PL, Yang PC. The role of interleukin-8 in cancer cells and microenvironment interaction. Front Biosci 2005;10:853-865.
49. Galffy G, Mohammed KA, Nasreen N, Ward MJ, Antony VB. Inhibition of interleukin-8 reduces human malignant pleural mesothelioma propagation in nude mouse model. Oncol Res 1999;11:187-194.
50. Galffy G, Mohammed KA, Dowling PA, Nasreen N, Ward MJ, Antony VB. Interleukin 8: an autocrine growth factor for malignant mesothelioma. Cancer Res 1999;59:367-371. (Pubitemid 29048869)
51. He W, Liu Q, Wang L, Chen W, Li N, Cao X. TLR4 signaling promotes immune escape of human lung cancer cells by inducing immunosuppressive cytokines and apoptosis resistance. Mol Immunol 2007;44:2850-2859. (Pubitemid 46412506)
52. Wang L, Liu Q, Sun Q, Zhang C, Chen T, Cao X. TLR4 signaling in cancer cells promotes chemoattraction of immature dendritic cells via autocrine CCL20. Biochem Biophys Res Commun 2008;366:852-856.
53. Sun X, Wei L, Liden J, et al. Molecular characterization of tumour heterogeneity and malignant mesothelioma cell differentiation by gene profiling. J Pathol 2005;207:91-101. (Pubitemid 41200718)
54. Ruco LP, de Laat PA, Matteucci C, et al. Expression of ICAM-1 and VCAM-1 in human malignant mesothelioma. J Pathol 1996;179:266-271. (Pubitemid 26266404)
55. Chang CH, Huang Y, Anderson R. Activation of vascular endothelial cells by IL-1alpha released by epithelial cells infected with respiratory syncytial virus. Cell Immunol 2003;221:37-41. (Pubitemid 36555392)
56. Chirivi RG, Chiodoni C, Musiani P, et al. IL-1alpha gene-transfected human melanoma cells increase tumor-cell adhesion to endothelial cells and their retention in the lung of nude mice. Int J Cancer 1996;67:856-863. (Pubitemid 26348816)
57. St-Pierre MV, Hagenbuch B, Ugele B, Meier PJ, Stallmach T. Characterization of an organic anion-transporting polypeptide (OATP-B) in human placenta. J Clin Endocrinol Metab 2002;87:1856-1863. (Pubitemid 34615280)
58. Nagase T, Ishikawa K, Suyama M, et al. Prediction of the codingsequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res 1998;5:355-364. (Pubitemid 128670156)
59. Gordon GJ, Jensen RV, Hsiao LL, et al. Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. Cancer Res 2002;62:4963-4967.
60. Gordon GJ, Jensen RV, Hsiao LL, et al. Using gene expression ratios to predict outcome among patients with mesothelioma. J Natl Cancer Inst 2003;95:598-605. (Pubitemid 36553506)
61. Gordon GJ, Rockwell GN, Godfrey PA, et al. Validation of genomicsbased prognostic tests in malignant pleural mesothelioma. Clin Cancer Res 2005;11:4406-4414.
62. Pass HI, Liu Z, Wali A, et al. Gene expression profiles predict survival and progression of pleural mesothelioma. Clin Cancer Res 2004;10: 849-859. (Pubitemid 38198883)
63. Khatri P, Voichita C, Kattan K, et al. Onto-Tools: new additions and improvements in 2006. Nucleic Acids Res 2007;35:W206-W211.
64. Lopez-Rios F, Chuai S, Flores R, et al. Global gene expression profiling of pleural mesotheliomas: overexpression of aurora kinases and P16/CDKN2A deletion as prognostic factors and critical evaluation of microarray-based prognostic prediction. Cancer Res 2006;66:2970-2979.
65. Glinsky GV, Berezovska O, Glinskii AB. Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. J Clin Invest 2005;115:1503-1521. (Pubitemid 40814659)
66. Hoang CD, D'Cunha J, Kratzke MG, et al. Gene expression profiling identifies matriptase overexpression in malignant mesothelioma. Chest 2004;125:1843-1852. (Pubitemid 38648420)
67. Singhal S, Wiewrodt R, Malden LD, et al. Gene expression profiling of malignant mesothelioma. Clin Cancer Res 2003;9:3080-3097. (Pubitemid 36993271)
68. Mohr S, Bottin MC, Lannes B, et al. Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells. Biochimie 2004;86:13-19. (Pubitemid 38264274)
69. Mohr S, Keith G, Galateau-Salle F, Icard P, Rihn BH. Cell protection, resistance and invasiveness of two malignant mesotheliomas as assessed by 10K-microarray. Biochim Biophys Acta 2004;1688:43-60. (Pubitemid 38366304)
70. Gordon GJ, Rockwell GN, Jensen RV, et al. Identification of novel candidate oncogenes and tumor suppressors in malignant pleural mesothelioma using large-scale transcriptional profiling. Am J Pathol 2005;166:1827-1840.
71. Yamada T, Endo R, Gotoh M, Hirohashi S. Identification of semaphorin E as a non-MDR drug resistance gene of human cancers. Proc Natl Acad Sci USA 1997;94:14713-14718. (Pubitemid 28041439)
72. Mazieres J, You L, He B, et al. Wnt2 as a new therapeutic target in malignant pleural mesothelioma. Int J Cancer 2005;117:326-332. (Pubitemid 41377454)
73. Gordon GJ, Appasani K, Parcells JP, et al. Inhibitor of apoptosis protein-1 promotes tumor cell survival in mesothelioma. Carcinogenesis 2002;23:1017-1024. (Pubitemid 34752958)
74. Gordon G, Mani M, Mukhopadhyay L, et al. Expression patterns of inhibitor of apoptosis proteins in malignant pleural mesothelioma. J Pathol 2007;211:447-454. (Pubitemid 46332556)
75. Schrump DS, Fischette MR, Nguyen DM, et al. Phase I study of decitabine-mediated gene expression in patients with cancers involving the lungs, esophagus, or pleura. Clin Cancer Res 2006;12:5777-5785.
76. Musti M, Kettunen E, Dragonieri S, et al. Cytogenetic and molecular genetic changes in malignant mesothelioma. Cancer Genet Cytogenet 2006;170:9-15. (Pubitemid 44349011)
77. Lockwood WW, Chari R, Chi B, Lam WL. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 2006;14:139-148. (Pubitemid 43135854)
78. Bignell GR, Huang J, Greshock J, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004;14:287-295. (Pubitemid 38219842)
79. Zhao X, Weir BA, LaFramboise T, et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 2005;65: 5561-5570. (Pubitemid 40911156)
80. Pei J, Kruger WD, Testa JR. High-resolution analysis of 9p loss in human cancer cells using single nucleotide polymorphism-based mapping arrays. Cancer Genet Cytogenet 2006;170:65-68. (Pubitemid 44332558)
81. Szlosarek PW, Klabatsa A, Pallaska A, et al. In vivo loss of expression of argininosuccinate synthetase in malignant pleural mesothelioma is a biomarker for susceptibility to arginine depletion. Clin Cancer Res 2006;12:7126-7131. (Pubitemid 44974513)
82. Taniguchi T, Karnan S, Fukui T, et al. Genomic profiling of malignant pleural mesothelioma with array-based comparative genomic hybridization shows frequent non-random chromosomal alteration regions including JUN amplification on 1p32. Cancer Sci 2007;98:438-446. (Pubitemid 46195618)
83. Zanazzi C, Hersmus R, Veltman IM, et al. Gene expression profiling and gene copy-number changes in malignant mesothelioma cell lines. Genes Chromosomes Cancer 2007;46:895-908. (Pubitemid 47435019)
84. Aguilar-Mahecha A, Hassan S, Ferrario C, Basik M. Microarrays as validation strategies in clinical samples: tissue and protein microarrays. OMICS 2006;10:311-326. (Pubitemid 44736317)
85. Simon R, Mirlacher M, Sauter G. Tissue microarrays. Biotechniques 2004;36:98-105. (Pubitemid 38076386)
86. Simon R, Sauter G. Tissue microarray (TMA) applications: implications for molecular medicine. Expert Rev Mol Med 2003;5:1-12.
87. Braunschweig T, Chung JY, Hewitt SM. Tissue microarrays: bridging the gap between research and the clinic. Expert Rev Proteomics 2005;2:325-336. (Pubitemid 40839744)
88. Eguiluz C, Viguera E, Millan L, Pérez J. Multitissue array review: a chronological description of tissue array techniques, applications and procedures. Pathol Res Pract 2006;202:561-568. (Pubitemid 44057769)
89. Gordon G, Mani M, Mukhopadhyay L, et al. Inhibitor of apoptosis proteins are regulated by tumour necrosis factor-alpha in malignant pleural mesothelioma. J Pathol 2007;211:439-446. (Pubitemid 46332555)
90. Pass HI, Lott D, Lonardo F, et al. Asbestos exposure, pleural mesothelioma, and serum osteopontin levels. N Engl J Med 2005;353:1564-1573. (Pubitemid 41434635)
91. Jagadeeswaran R, Ma PC, Seiwert TY, et al. Functional analysis of c-Met/hepatocyte growth factor pathway in malignant pleural mesothelioma. Cancer Res 2006;66:352-361. (Pubitemid 43166042)
92. Opitz I, Soltermann A, Abaecherli M, et al. PTEN expression is a strong predictor of survival in mesothelioma patients. Eur J Cardiothorac Surg 2008;33:502-506.
93. Posadas EM, Simpkins F, Liotta LA, MacDonald C, Kohn EC. Proteomic analysis for the early detection and rational treatment of cancer- realistic hope? Ann Oncol 2005;16:16-22. (Pubitemid 40124471)
94. Borrebaeck CA. Antibody microarray-based oncoproteomics. Expert Opin Biol Ther 2006;6:833-838.
95. Sanchez-Carbayo M. Antibody arrays: technical considerations and clinical applications in cancer. Clin Chem 2006;52:1651-1659. (Pubitemid 44330697)
96. Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006;5:310-320.
97. Haab BB. Applications of antibody array platforms. Curr Opin Biotechnology 2006;17:415-421.
98. Casiano CA, Mediavilla-Varela M, Tan EM. Tumor-associated antigen arrays for the serological diagnosis of cancer. Mol Cell Proteomics 2006;5:1745-1759. (Pubitemid 44688185)
99. Hegmans JP, Bard MP, Hemmes A, et al. Proteomic analysis of exosomes secreted by human mesothelioma cells. Am J Pathol 2004; 164:1807-1815. (Pubitemid 38529783)
100. Bard MP, Hegmans JP, Hemmes A, et al. Proteomic analysis of exosomes isolated from human malignant pleural effusions. Am J Respir Cell Mol Biol 2004;31:114-121. (Pubitemid 38888047)
101. Maeda M, Hino O. Molecular tumor markers for asbestos-related mesothelioma: serum diagnostic markers. Pathol Int 2006;56:649-654. (Pubitemid 44570013)
102. Robinson BW, Creaney J, Lake R, et al. Mesothelin-family proteins and diagnosis of mesothelioma. Lancet 2003;362:1612-1616. (Pubitemid 37443528)
103. Robinson BW, Creaney J, Lake R, et al. Soluble mesothelin-related protein-a blood test for mesothelioma. Lung Cancer 2005;49(Suppl 1): S109-S111. (Pubitemid 40798859)
104. Hassan R, Remaley AT, Sampson ML, et al. Detection and quantitation of serum mesothelin, a tumor marker for patients with mesothelioma and ovarian cancer. Clin Cancer Res 2006;12:447-453. (Pubitemid 43166134)
105. Scherpereel A, Grigoriu B, Conti M, et al. Soluble mesothelin-related peptides in the diagnosis of malignant pleural mesothelioma. Am J Respir Crit Care Med 2006;173:1155-1160. (Pubitemid 43726897)
106. Cristaudo A, Foddis R, Vivaldi A, et al. Clinical significance of serummesothelin in patients with mesothelioma and lung cancer. Clin Cancer Res 2007;13:5076-5081. (Pubitemid 47502073)
107. Shiomi K, Hagiwara Y, Sonoue K, et al. Sensitive and Specific New Enzyme-Linked Immunosorbent Assay for N-ERC/Mesothelin Increases its Potential as a Useful Serum Tumor Marker for Mesothelioma. Clin Cancer Res 2008;14:1431-1437.
108. Park EK, Sandrini A, Yates DH, et al. Soluble Mesothelin-Related Protein (SMRP) in an asbestos exposed population the dust diseases board cohort study. Am J Respir Crit Care Med. 2008;178:832-837.
109. Shiomi K, Miyamoto H, Segawa T, et al. Novel ELISA system for detection of N-ERC/mesothelin in the sera of mesothelioma patients. Cancer Sci 2006;97:928-932. (Pubitemid 44151275)
110. Beyer HL, Geschwindt RD, Glover CL, et al. MESOMARK: a potential test for malignant pleural mesothelioma. Clin Chem 2007;53:666-672. (Pubitemid 46580236)
111. Pass HI, Wali A, Tang N, Ivanova A, et al. Soluble mesothelin-related peptide level elevation in mesothelioma serum and pleural effusions. Ann Thorac Surg 2008;85:265-272; discussion 272. (Pubitemid 350265805)
112. Hassan R, Bullock S, Premkumar A, et al. Phase I study of SS1P, a recombinant anti-mesothelin immunotoxin given as a bolus i.v. infusion to patients with mesothelin-expressing mesothelioma, ovarian, and pancreatic cancers. Clin Cancer Res 2007;13:5144-5149. (Pubitemid 47502082)
113. Hassan R, Ho M. Mesothelin targeted cancer immunotherapy. Eur J Cancer 2008;44:46-53. (Pubitemid 350262830)
114. Ramos-Nino ME, Testa JR, Altomare DA, et al. Cellular and molecular parameters of mesothelioma. J Cell Biochem 2006;98:723-734.
115. Vordermark D, Said HM, Katzer A, et al. Plasma osteopontin levels in patients with head and neck cancer and cervix cancer are critically dependent on the choice of ELISA system. BMC Cancer 2006;6:207. (Pubitemid 44390023)
116. Amati M, Tomasetti M, Scartozzi M, et al. Profiling tumor-associated markers for early detection of malignant mesothelioma: an epidemiologic study. Cancer Epidemiol Biomarkers Prev 2008;17:163-170. (Pubitemid 351196287)
117. Carbone M, Pass HI. Evolving aspects of mesothelioma carcinogenesis: SV40 and genetic predisposition. J Thorac Oncol 2006;1:169-171. (Pubitemid 47164006)
118. Shah KV. SV40 and human cancer: a review of recent data. Int J Cancer 2007;120:215-223. (Pubitemid 44956830)
119. Cacciotti P, Barbone D, Porta C, et al. SV40-dependent AKT activity drives mesothelial cell transformation after asbestos exposure. Cancer Res 2005;65:5256-5262. (Pubitemid 40827336)
120. Cristaudo A, Foddis R, Vivaldi A, et al. SV40 enhances the risk of malignant mesothelioma among people exposed to asbestos: a molecular epidemiologic case-control study. Cancer Res 2005;65:3049-3052. (Pubitemid 40524583)
121. Aoe K, Hiraki A, Murakami T, et al. Infrequent existence of simian virus 40 large T antigen DNA in malignant mesothelioma in Japan. Cancer Sci 2006;97:292-295.
122. Manfredi JJ, Dong J, Liu WJ, et al. Evidence against a role for SV40 in human mesothelioma. Cancer Res 2005;65:2602-2609. (Pubitemid 40490058)
123. Lopez-Rios F, Illei PB, Rusch V, Ladanyi M. Evidence against a role for SV40 infection in human mesotheliomas and high risk of falsepositive PCR results owing to presence of SV40 sequences in common laboratory plasmids. Lancet 2004;364:1157-1166. (Pubitemid 39296603)
124. Kjaerheim K, Roe OD, Waterboer T, et al. Absence of SV40 antibodies or DNA fragments in prediagnostic mesothelioma serum samples. Int J Cancer 2007;120:2459-2465. (Pubitemid 46642135)
125. Elmishad AG, Bocchetta M, Pass HI, Carbone M. Polio vaccines, SV40 and human tumours, an update on false positive and false negative results. Dev Biol (Basel) 2006;123:109 -117; discussion 119-132. (Pubitemid 43207155)
126. Carbone M, Rdzanek MA, Rudzinski JJ, et al. SV40 detection in human tumor specimens. Cancer Res 2005;65:10120-10121. (Pubitemid 41541495)
127. Comar M, Rizzardi C, de Zotti R, et al. SV40 multiple tissue infection and asbestos exposure in a hyperendemic area for malignant mesothelioma. Cancer Res 2007;67:8456-8459. (Pubitemid 47437418)
128. Robinson C, van Bruggen I, Segal A, et al. A novel SV40 TAg transgenic model of asbestos-induced mesothelioma: malignant transformation is dose dependent. Cancer Res 2006;66:10786-10794. (Pubitemid 44876974)
129. Pietruska JR, Kane AB. SV40 oncoproteins enhance asbestos-induced DNA double-strand breaks and abrogate senescence in murine mesothelial cells. Cancer Res 2007;67:3637-3645.
130. Kroczynska B, Cutrone R, Bocchetta M, et al. Crocidolite asbestos and SV40 are cocarcinogens in human mesothelial cells and in causing mesothelioma in hamsters. Proc Natl Acad Sci USA 2006;103:14128-14133. (Pubitemid 44452991)
131. Takahashi M, Rhodes DR, Furge KA, et al. Gene expression profiling of clear cell renal cell carcinoma: gene identification and prognostic classification. Proc Natl Acad Sci USA 2001;98:9754-9759. (Pubitemid 32769376)
132. Lee TC, Zhang Y, Aston C, et al. Normal human mesothelial cells and mesothelioma cell lines express insulin-like growth factor I and associated molecules. Cancer Res 1993;53:2858-2864. (Pubitemid 23180528)
133. Kettunen E, Vivo C, Gattacceca F, Knuutila S, Jaurand MC. Gene expression profiles in human mesothelioma cell lines in response to interferon-gamma treatment. Cancer Genet Cytogenet 2004;152:42-51. (Pubitemid 38757376)
134. Hoang CD, Zhang X, Scott PD, et al. Selective activation of insulin receptor substrate-1 and -2 in pleural mesothelioma cells: association with distinct malignant phenotypes. Cancer Res 2004;64:7479-7485. (Pubitemid 39372091)
135. Nguyen DM, Schrump WD, Chen GA, et al. Abrogation of p21 expression by flavopiridol enhances depsipeptide-mediated apoptosis in malignant pleural mesothelioma cells. Clin Cancer Res 2004;10: 1813-1825.
136. Neuzil J, Swettenham E, Gellert N. Sensitization of mesothelioma to TRAIL apoptosis by inhibition of histone deacetylase: role of Bcl-xL down-regulation. Biochem Biophys Res Commun 2004;314:186-191. (Pubitemid 38058387)
137. Cao XX, Mohuiddin I, Ece F, McConkey DJ, Smythe WR. Histone deacetylase inhibitor downregulation of bcl-xl gene expression leads to apoptotic cell death in mesothelioma. Am J Respir Cell Mol Biol 2001;25:562-568. (Pubitemid 33087106)
138. Weiser TS, Guo ZS, Ohnmacht GA, et al. Sequential 5-Aza-2 deoxycytidine- depsipeptide FR901228 treatment induces apoptosis preferentially in cancer cells and facilitates their recognition by cytolytic T lymphocytes specific for NY-ESO-1. J Immunother 2001;24:151-161.
139. Kelly WK, O'Connor OA, Krug LM, et al. Phase I study of an oral histone deacetylase inhibitor, suberoylanilide hydroxamic acid, in patients with advanced cancer. J Clin Oncol 2005;23:3923-3931. (Pubitemid 46218695)
140. Kelly WK, Richon VM, O'Connor O, et al. Phase I clinical trial of histone deacetylase inhibitor: suberoylanilide hydroxamic acid administered intravenously. Clin Cancer Res 2003;9:3578-3588. (Pubitemid 37169221)
141. Krug LM, Curley T, Schwartz L, et al. Potential role of histone deacetylase inhibitors in mesothelioma: clinical experience with suberoylanilide hydroxamic acid. Clin Lung Cancer 2006;7:257-261. (Pubitemid 43280028)
142. Fischer JR, Ohnmacht U, Rieger N, et al. Promoter methylation of RASSF1A, RARbeta and DAPK predict poor prognosis of patients with malignant mesothelioma. Lung Cancer 2006;54:109-116.
143. Batra S, Shi Y, Kuchenbecker KM, et al. Wnt inhibitory factor-1, a Wnt antagonist, is silenced by promoter hypermethylation in malignant pleural mesothelioma. Biochem Biophys Res Commun 2006;342:1228-1232.
144. Tsou JA, Shen LY, Siegmund KD, et al. Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and nontumor lung. Lung Cancer 2005;47:193-204.
145. Wong L, Zhou J, Anderson D, Kratzke RA. Inactivation of p16INK4a expression in malignant mesothelioma by methylation. Lung Cancer 2002;38:131-136. (Pubitemid 35154376)
146. Christensen BC, Godleski JJ, Marsit CJ, et al. Asbestos exposure predicts cell cycle control gene promoter methylation in pleural mesothelioma. Carcinogenesis 2008;29:1555-1559.
147. Falleni M, Pellegrini C, Marchetti A, et al. Quantitative evaluation of the apoptosis regulating genes Survivin, Bcl-2 and Bax in inflammatory and malignant pleural lesions. Lung Cancer 2005;48:211-216. (Pubitemid 40501809)
148. Butcher EC, Berg EL, Kunkel EJ. Systems biology in drug discovery. Nat Biotechnol 2004;22:1253-1259.
149. Amin W, Parwani AV, Schmandt L, et al. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC Cancer 2008;8:236.
150. Mohanty SK, Mistry AT, Amin W, et al. The development and deployment of Common Data Elements for tissue banks for translational research in cancer - an emerging standard based approach for the Mesothelioma Virtual Tissue Bank. BMC Cancer 2008;8:91. (Pubitemid 351587051)
151. Xia C, Xu Z, Yuan X, et al. Induction of apoptosis in mesothelioma cells by antisurvivin oligonucleotides. Mol Cancer Ther 2002;1:687-694.
152. Rishikof DC, Ricupero DA, Liu H, Goldstein RH. Phenylbutyrate decreases type I collagen production in human lung fibroblasts. J Cell Biochem 2004;91:740-748.
153. Bali P, Pranpat M, Swaby R, et al. Activity of suberoylanilide hydroxamic Acid against human breast cancer cells with amplification of her-2. Clin Cancer Res 2005;11:6382-6389. (Pubitemid 41262970)
154. De Schepper S, Bruwiere H, Verhulst T, et al. Inhibition of histone deacetylases by chlamydocin induces apoptosis and proteasome-mediated degradation of survivin. J Pharmacol Exp Ther 2003;304:881-888. (Pubitemid 36152369)
155. Thangaraju M, Gopal E, Martin PM, et al. SLC5A8 triggers tumor cell apoptosis through pyruvate-dependent inhibition of histone deacetylases. Cancer Res 2006;66:11560-11564. (Pubitemid 46094162)
156. Sasakawa Y, Naoe Y, Noto T, et al. Antitumor efficacy of FK228, a novel histone deacetylase inhibitor, depends on the effect on expression of angiogenesis factors. Biochem Pharmacol 2003;66:897-906. (Pubitemid 37083586)
157. Ryu JK, Lee WJ, Lee KH, et al. SK-7041, a new histone deacetylase inhibitor, induces G2-M cell cycle arrest and apoptosis in pancreatic cancer cell lines. Cancer Lett 2006;237:143-154.