Bioinformatics approach for the validation of non-small cell lung cancer biomarkers

Frontiers in Bioscience - Elite

Volumn 3 E, Issue 1, 2011, Pages 46-50

  Muller, Carolina Beatriz ^a   De Barros, Rafael Longhi Sampaio ^a   Moreira, Jose Claudio Fonseca ^a   Klamt, Fabio ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Bioinformatic approach; Non Small Cell Lung Cancer; Prognostic biomarkers

Indexed keywords

ADVANCED GLYCATION END PRODUCT; ADVANCED GLYCOSYLATION END PRODUCT RECEPTOR; ALKB ALKYLATION REPAIR HOMOLOG 1; ALKB ALKYLATION REPAIR HOMOLOG 5; ALKB ALKYLATION REPAIR HOMOLOG 7; ALKB ALKYLATION REPAIR HOMOLOG 8; ATP BINDING CASSETTE SUBFAMILY C MEMBER 1; AUTOCRINE MOTILITY FACTOR RECEPTOR; BACULOVIRA IAP REPEAT CONTAINING 5; BCL2 LIKE 1; BRCA1 PROTEIN; CALBINDIN; CATHEPSIN B; CAVEOLIN 1; CD9 ANTIGEN; CYCLIN B2; CYCLIN D1; CYCLIN DEPENDENT KINASE 8; EPIDERMAL GROWTH FACTOR RECEPTOR; FIBROBLAST GROWTH FACTOR RECEPTOR 1; FOLATE RECEPTOR 1; GLUTATHIONE TRANSFERASE ALPHA; HEAT SHOCK PROTEIN; KINESIN; LEUCINE TRANSFER RNA LIGASE; PROTEIN BCL 2; PROTEIN TYROSINE KINASE; RETINOIC ACID BINDING PROTEIN; TUMOR MARKER; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ARTICLE; BIOINFORMATICS; CANCER MORTALITY; CANCER PATIENT; CANCER PROGNOSIS; CANCER SURVIVAL; EARLY DIAGNOSIS; GENE EXPRESSION; HUMAN; HUMAN TISSUE; LUNG NON SMALL CELL CANCER; OUTCOME ASSESSMENT; SURVIVAL RATE; TUMOR BIOPSY; VALIDATION STUDY; BIOLOGY; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENETICS; MEDLINE; META ANALYSIS; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; MORTALITY; PROGNOSIS; SURVIVAL;

CARCINOMA, NON-SMALL-CELL LUNG; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, NEOPLASTIC; MEDLINE; MICROARRAY ANALYSIS; PROGNOSIS; SURVIVAL ANALYSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 79957864833     PISSN: 19450494     EISSN: 19450508     Source Type: Journal    
DOI: None     Document Type: Article

References (68)

1. DC Ihde: Chemotherapy of lung cancer. N Engl J Med 327, 1434-1441 (1992)
2. A Spira, DS Ettinger: Multidisciplinary management of lung cancer - Reply. N Engl J Med 350, 2009-2010 (2004)
3. HJ Sung, JY Cho: Biomarkers for the lung cancer diagnosis and their advances in proteomics. BMP Rep 41, 615-625 (2008)
4. CL Sawyers: The cancer biomarker problem. Nature 452, 548-552 (2008) (Pubitemid 351483368)
5. CW Chi-Shing: Potentially useful biomarkers for the diagnosis, treatment and prognosis of lung cancer. Biomed Pharmacother 61, 515-519 (2007)
6. J Niklinski, W Niklinska, J Laudanski, E Chyczewska, L Chyczewski: Prognostic molecular markers in non-small cell lung cancer. Lung Cancer 34, 53-58 (2001)
7. B Kim, HJ Lee, HY Choi, Y Shin, S Nam, G Seo, D Son, J Jo, J Kim, J Lee, J Kim, K Kim, S Lee: Clinical validity of the lung cancer biomarkers identified by bioinformatics analysis of public expression data. Cancer Res 67, 7431-7438 (2007) (Pubitemid 47206573)
8. AH Bild, G Yao, JT Chang, Q Wang, A Potti, D Chasse, M Joshi, D Harpole, J M Lancaster, A Berchuck, J A Olson Jr, J R Marks, H K Dressman, M West, J R Nevin: Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 439, 353-357 (2006) (Pubitemid 43128862)
9. WG Deng, G Jayachandran, G Wu, K Xu, JA Roth, L Ji: Tumor-specific activation of human telomerase reverses transcriptase promoter activity by activating enhancerbinding protein-2beta in human lung cancer cells. J Biol Chem 282, 26460-70 (2007) (Pubitemid 47443763)
10. D Vallbohmer, J Brabender, DY Yang, K Danenberg, PM Schneider, R Metzger, AH Holscher, PV Danenberg: Sex differences in the predictive power of the molecular prognostic factor HER2/neu in patients with non-small-cell lung cancer. Clin Lung Cancer 7, 332-337 (2006) (Pubitemid 43950981)
11. SV Sharma, DW Bell, J Settleman, DA Haber: Epidermal growth factor receptor mutations in lung cancer. Nature Rev. Cancer 7, 169-181 (2007)
12. W Pao, TY Wang, GJ Riely, VA Miller, Q Pan, M Ladanyi, MF Zakowski, RT Heelan, MG Kris, HE Varmus: KRAS mutations and primary resistance of lung adenocarcinomas to gefitinib or erlotinib. PLoS Med 2, e17 (2005)
13. MR Muller, J Thomale, MF Rajewsky, S Seeber: Drug Resistance and DNA repair in Leukaemia. Cytotechnology 27, 175-185 (1998) (Pubitemid 29025468)
14. E Felip, R Rosell: Testing for excision repair crosscomplementing 1 in patients with non-small-cell lung cancer for chemotherapy response. Expert Rev Mol Diagn 7, 261-268 (2007) (Pubitemid 46798616)
15. G Damia, M D'Incalci: Mechanisms of resistance to alkylating agents. Cytotechnology 27, 165-173 (1998) (Pubitemid 129748760)
16. F Drabløs, E Feyzi, PA Aas, CB Vaagbø, B Kavli, MS Bratlie, J Pena-Diaz, M Otterlei, G Slupphaug, HE Krokan: Alkylation damage in DNA and RNA - repair mechanisms and medical significance. DNA Repair (Amst) 3, 1389-1407 (2004) (Pubitemid 39221738)
17. C Schettino, MA Bareschino, P Maione, A Rossi, F Ciardiello, C Gridelli: The potential role of pharmacogenomic and genomic in the adjuvant treatment of early stage non small cell lung cancer. Curr Genomics 9, 252-262 (2008) (Pubitemid 351864251)
18. R Rosell, RV Lord, M Taron, N Reguart: DNA repair and cisplatin resistance in non-small-cell lung cancer. Lung Cancer 38, 217-227 (2002) (Pubitemid 35341796)
19. R Rosell, M Taron, V Alberola, B Massuti, E Felip: Genetic testing for chemotherapy in non-small cell lung cancer. Lung Cancer 41, 97-102 (2003)
20. M Miyake, M Adachi, C Huang, M Higashiyama, K Kodama, T Taki: A novel molecular staging protocol for non-small cell lung cancer. Oncogene 18, 2397-2404 (1999) (Pubitemid 29192718)
21. C McNeil: New NSCLC staging raises treatment issues. J Natl Cancer Inst 99, 1748-1749 (2007)
22. B Karczmarek-Borowska, A Filip, J Wojcierowski, A Smolen, E Korobowicz, I Korszen-Pilecka, M Zdunek: Estimation of prognostic value of Bcl-xL gene expression in non-small cell lung cancer. Lung Cancer 51, 61-69 (2006) (Pubitemid 43088625)
23. M Campioni, V Ambrogi, E Pompeo, G Citro, M Castelli, EP Spugnini, A Gatti, P Cardelli, L Lorenzon, A Baldi, TC Mineo: Identification of genes down-regulated during lung cancer progression: a cDNA array study. J Exp Clin Cancer Res 27:38 (2008)
24. S Ramaswamy, T R Golub: DNA microarrays in clinical oncology. J. Clin. Oncol. 20, 1932-1941 (2002) (Pubitemid 34273286)
25. MA Castro, JL Filho, RJ Damolin, M Sinigaglia, JC Moreira, JC Mombach, RM de Almeida: ViaComplex: software for landscape analysis of gene expression networks in genomic context. Bioinformatics 25, 1468-1469 (2009)
26. M Adachi, T Taki, T Konishi, CI Huang, M Higashiyama, M Miyake: Novel staging protocol for nonsmall- cell lung cancers according to MRP-1/CD9 and KAI1/CD82 gene expression. J Clin Oncol 16, 1397-1406 (1998) (Pubitemid 28175757)
27. Y Lu, W Lemon, PY Liu, Y Yi, C Morrison, P Yang, Z Sun, J Szoke, WL Gerald, M Watson, R Govindan, M You: A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med 3, e467 (2006)
28. D Stav, I Bar, J Sandbank: Usefulness of CDK5RAP3, CCNB2, and RAGE genes for the diagnosis of lung adenocarcinoma. Int J Biol Markers 22, 108-113 (2007) (Pubitemid 47062215)
29. F Oshita, A Sekiyama, H Saito, K Yamada, K Noda, Y Miyagi: Genome-wide cDNA microarray screening of genes related to the benefits of paclitaxel and irinotecan chemotherapy in patients with advanced non-small cell lung cancer. J Exp Ther Oncol 6, 49-53 (2006) (Pubitemid 46068193)
30. I Takanami, K Takeuchi: Autocrine motility factorreceptor gene expression in lung cancer. Jpn J Thorac Cardiovasc Surg 51, 368-373 (2003) (Pubitemid 38166250)
31. I Takanami, K Takeuchi, H Watanabe, T Yanagawa, K Takagishi, A Raz: Significance of autocrine motility factor receptor gene expression as a prognostic factor in nonsmall- cell lung cancer. Int J Cancer 95, 384-387 (2001) (Pubitemid 33015110)
32. B Karczmarek-Borowska, A Filip, J Wojcierowski, Smolen A, I Pilecka, A Jablonka: Survivin antiapoptotic gene expression as a prognostic factor in non-small cell lung cancer: in situ hybridization study. Folia Histochem Cytobiol 43, 237-242 (2005) (Pubitemid 41582146)
33. M Monzo, R Rosell, E Felip, J Astudillo, JJ Sanchez, J Maestre, C Martin, A Font, A Barnadas, A Abad: A novel antiapoptosis gene: Re-expression of survivin messenger RNA as a prognosis marker in non-small-cell lung cancers. J Clin Oncol 17, 2100-2104 (1999) (Pubitemid 29318841)
34. R Rosell, M Skrzypski, E Jassem, M Taron, R Bartolucci, JJ Sanchez, P Mendez, I Chaib, L Perez-Roca, A Szymanowska, W Rzyman, F Puma, G Kobierska-Gulida, R Farabi, J Jassem: BRCA1: a novel prognostic factor in resected non-small-cell lung cancer. PLoS ONE 2, e1129 (2007)
35. NL Guo, YW Wan, K Tosun, H Lin, Z Msiska, DC Flynn, SC Remick, V Vallyathan, A Dowlati, X Shi, V Castranova, DG Beer, Y Qian: Confirmation of Gene Expression-Based Prediction of Survival in Non-Small Cell Lung Cancer. Clin Cancer Res 14, 8213-8220 (2008)
36. CC Ho, SH Kuo, PH Huang, HY Huang, CH Yang, PC Yang: Caveolin-1 expression is significantly associated with drug resistance and poor prognosis in advanced non-small cell lung cancer patients treated with gemcitabine-based chemotherapy. Lung Cancer 59, 105-110 (2008)
37. R Li, SJ An, ZH Chen, GC Zhang, JQ Zhu, Q Nie, Z Xie, AL Guo, TS Mok, YL Wu: Expression of cyclin D1 splice variants is differentially associated with outcome in non-small cell lung cancer patients. Human Pathology 39, 1792-1801 (2008)
38. F Oshita, A Sekiyama, H Ito, Y Kameda, Y Miyagi: Genome-wide cDNA microarray screening of genes related to survival in patients after curative resection of non-small cell lung cancer. Oncol Rep 16, 817-821 (2006)
39. DJ Raz, MR Ray, JY Kim, B He, M Taron, M Skrzypski, M Segal, DR Gandara, R Rosell, DM Jablons: A Multigene Assay Is Prognostic of Survival in Patients with Early-Stage Lung Adenocarcinoma. Clin Cancer Res 14, 5565-5570 (2008)
40. MF Tsai, CC Wang, GC Chang, CY Chen, HY Chen, CL Cheng, YP Yang, CY Wu, FY Shih, CC Liu, HP Lin, YS Jou, SC Lin, CW Lin, WJ Chen, WK Chan, JJ Chen, PC Yang: A new tumor suppressor DnaJ-like heat shock protein, HLJ1, and survival of patients with non-small-cell lung carcinoma. J Natl Cancer Inst 98, 825-838 (2006) (Pubitemid 43923440)
41. HY Chen, SL Yu, CH Chen, GC Chang, CY Chen, A Yuan, CL Cheng, CH Wang, HJ Terng, SF Kao, WK Chan, HN Li, CC Liu, S Singh, WJ Chen, JJ Chen, PC Yang: A fivegene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med 356, 11-20 (2007) (Pubitemid 46041749)
42. T Shibata, S Hanada, A Kokubu, Y Matsuno, H Asamura, T Ohta, M Sakamoto, S Hirohashi: Gene expression profiling of epidermal growth factor receptor/KRAS pathway activation in lung adenocarcinoma. Cancer Sci 98, 985-991 (2007) (Pubitemid 46865381)
43. P Ceppi, M Volante, S Novello, I Rapa, KD Danenberg, PV Danenberg, A Cambieri, G Selvaggi, S Saviozzi, R Calogero, M Papotti, GV Scagliotti ERCC1 and RRM1 gene expressions but not EGFR are predictive of shorter survival in advanced non-small-cell lung cancer treated with cisplatin and gemcitabine. Ann Oncol 17, 1818-1825 (2006) (Pubitemid 44884058)
44. H Tang, E Goldberg: Homo Sapiens Lactate Dehydrogenase c (Ldhc) Gene Expression in Cancer Cells is Regulated by Transcription Factor Sp1, CREB and CpG Island Methylation. J Androl 30, 157-167 (2008)
45. Z Zheng, T Chen, X Li, E Haura, A Sharma, G Bepler: DNA synthesis and repair genes RRM1 and ERCC1 in lung cancer. N Engl J Med 356, 800-808 (2007) (Pubitemid 46294612)
46. L Tian, M Suzuki, T Nakajima, R Kubo, Y Sekine, K Shibuya, K Hiroshima, Y Nakatani, T Fujisawa, I Yoshino: Clinical significance of aberrant methylation of prostaglandin E receptor 2 (PTGER2) in nonsmall cell lung cancer: association with prognosis, PTGER2 expression, and epidermal growth factor receptor mutation. Cancer 113, 1396-1403 (2008)
47. Y Mano, K Takahashi, N Ishikawa, A Takano, W Yasui, K Inai, H Nishimura, E Tsuchiya, Y Nakamura, Y Daigo Fibroblast growth factor receptor 1 oncogene partner as a novel prognostic biomarker and therapeutic target for lung cancer. Cancer Sci 98, 1902-1913 (2007) (Pubitemid 350002196)
48. S Iwakiri, M Sonobe, S Nagai, T Hirata, H Wada, R Miyahara: Expression status of folate receptor alpha is significantly correlated with prognosis in non-small-cell lung cancers. Ann Surg Oncol 15, 889-899 (2008)
49. B Meyer, S Loeschke, A Schultze, T Weigel, M Sandkamp, T Goldmann, E Vollmer, J Bullerdiek: HMGA2 overexpression in non-small cell lung cancer. Mol Carcinog 46, 503-511 (2007) (Pubitemid 47068069)
50. MI Gallegos Ruiz, K Floor, P Roepman, JA Rodriguez, GA Meijer, WJ Mooi, E Jassem, J Niklinski, T Muley, N van Zandwijk, EF Smit, K Beebe, L Neckers, B Ylstra, G Giaccone: Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target. PLoS ONE 3, e0001722 (2008)
51. ES Lee, DS Son, SH Kim, J Lee, J Jo, J Han, H Kim, HJ Lee, HY Choi, Y Jung, M Park, YS Lim, K Kim, YM Shim, BC Kim, K Lee, N Huh, C Ko, K Park, JW Lee, YS Choi, J Kim: Prediction of Recurrence-Free Survival in Postoperative Non-Small Cell Lung Cancer Patients by Using an Integrated Model of Clinical Information and Gene Expression. Clin Cancer Res 14, 7397-7404 (2008)
52. T Kato, S Hayama, T Yamabuki, I Nshikawa, M Miyamoto, T Ito, E Tsuchiya, S Kondo, Y Nakamura, Y Daigo: Increased expression of insulin-like growth factor-II messenger RNA-binding protein 1 is associated with tumor progression in patients with lung cancer. Clin Cancer Res 13, 434-442 (2007) (Pubitemid 46225347)
53. TW Corson, CQ Zhu, SK Lau, FA Shepherd, MS Tsao, BL Gallie: KIF14 messenger RNA expression is independently prognostic for outcome in lung cancer. Clin Cancer Res 13, 3229-3234 (2007) (Pubitemid 46944906)
54. T Shibata, S Hanada, A Kokubu, Y Matsuno, H Asamura, T Ohta, M Sakamoto, S Hirohashi: Gene expression profiling of epidermal growth factor receptor/KRAS pathway activation in lung adenocarcinoma. Cancer Sci 98, 985-991 (2007) (Pubitemid 46865381)
55. J Xing, DJ Stewart, J Gu, C Lu, MR Spitz, X Wu: Expression of methylation-related genes is associated with overall survival in patients with non-small cell lung cancer. Br J Cancer 98, 1716-1722 (2008) (Pubitemid 351684678)
56. Z Sun, P Yang, MC Aubry, F Kosari, C Endo, J Molina, G Vasmatzis: Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung? Mol Cancer 3, 35 (2004)
57. S Tomida, K Koshikawa, Y Yatabe, T Harano, N Ogura, T Mitsudomi, M Some, K Yanagisawa, T Takahashi, H Osada, T Takahashi: Gene expression-based, individualized outcome prediction for surgically treated lung cancer patients. Oncogene 23, 5360-5370 (2004) (Pubitemid 39005811)
58. SI Yamashita, Y Masuda, N Yoshida, H Matsuzaki, T Kurizaki, Y Haga, S Ikei, M Miyawaki, Y Kawano, M Chujyo, K Kawahara: p53AIP1 expression can be a prognostic marker in non-small cell lung cancer. Clin Oncol (R Coll Radiol ) 20, 148-151 (2008) (Pubitemid 351194284)
59. B Angulo, A Suarez-Gauthier, F Lopez-Rios, PP Medina, E Conde, M Tang, G Soler, A Lopez-Encuentra, JC Cigudosa, M Sanchez-Cespedes: Expression signatures in lung cancer reveal a profile for EGFR-mutant tumours and identify selective PIK3CA overexpression by gene amplification. J Pathol 214, 347-356 (2008) (Pubitemid 351212390)
60. HS Hofmann, B Bartling, A Simm, R Murray, N Aziz, G Hansen, RE Silber, S Burdach: Identification and classification of differentially expressed genes in non-small cell lung cancer by expression profiling on a global human 59.620-element oligonucleotide array. Oncol Rep 16, 587-595 (2006)
61. JH Kim, PN Bogner, SH Baek, N Ramnath, P Liang, HR Kim, C Andrews, YM Park: Up-regulation of peroxiredoxin 1 in lung cancer and its implication as a prognostic and therapeutic target. Clin Cancer Res 14, 2326-2333 (2008) (Pubitemid 351551064)
62. S Diederichs, E Bulk, B Steffen, P Ji, L Tickenbrock, K Lang, KS Zanker, R Metzger, PM Schneider, V Gerke, M Thomas, WE Berdel, H Serve, C Muller-Tidow: S100 family members and trypsinogens are predictors of distant metastasis and survival in early-stage non-small cell lung cancer. Cancer Res 64, 5564-5569 (2004) (Pubitemid 39095550)
63. T Amachika, D Kobayashi, R Moriai, N Tsuji, N Watanabe: Diagnostic relevance of overexpressed mRNA of novel oncogene with kinase-domain (NOK) in lung cancers. Lung Cancer 56, 337-340 (2007) (Pubitemid 46679075)
64. X Lin, J Gu, C Lu, MR Spitz, X Wu: Expression of telomere-associated genes as prognostic markers for overall survival in patients with non-small cell lung cancer. Clin Cancer Res 12, 5720-5725 (2006) (Pubitemid 44629601)
65. N Miura, H Nakamura, R Sato, T Tsukamoto, T Harada, S Takahashi, Y Adachi, K Shomori, A Sano, Y Kishimoto, H Ito, J Hasegawa, G Shiota: Clinical usefulness of serum telomerase reverse transcriptase (hTERT) mRNA and epidermal growth factor receptor (EGFR) mRNA as a novel tumor marker for lung cancer. Cancer Sci 97, 1366-1373 (2006) (Pubitemid 44614989)
66. P Ceppi, M Longo, M Volante, S Novello, S Cappia, E Bacillo, G Selvaggi, S Saviozzi, R Calogero, M Papotti, GV Scagliotti: Excision repair cross complementing-1 and topoisomerase IIalpha gene expression in small-cell lung cancer patients treated with platinum and etoposide: a retrospective study. J Thorac Oncol 3, 583-589 (2008) (Pubitemid 351787300)
67. Y Shintani, M Ohta, H Hirabayashi, H Tanaka, K Iuchi, K Nakagawa, H Maeda, T Kido, S Miyoshi, H Matsuda: Thymidylate synthase and dihydropyrimidine dehydrogenase mRNA levels in tumor tissues and the efficacy of 5-fluorouracil in patients with non-small-cell lung cancer. Lung Cancer 45, 189-196 (2004) (Pubitemid 38891481)
68. Y Shintani, M Ohta, H Hirabayashi, H Tanaka, K Iuchi, K Nakagawa, H Maeda, T Kido, S Miyoshi, H Matsuda: New prognostic indicator for non-small-cell lung cancer, quantitation of thymidylate synthase by real-time reverse transcription polymerase chain reaction. Int J Cancer 104, 790-795 (2003) (Pubitemid 36418519)