Expression profiling-based subtyping identifies novel non-small cell lung cancer subgroups and implicates putative resistance to pemetrexed therapy

Journal of Thoracic Oncology

Volumn 7, Issue 1, 2012, Pages 105-114

  Hou, Jun ^a   Lambers, Margaretha ^a   Den Hamer, Bianca ^a   Den Bakker, Michael A ^a   Hoogsteden, Henk C ^a   Grosveld, Frank ^a   Hegmans, Joost ^a   Aerts, Joachim ^a   Philipsen, Sjaak ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Carcinoma; Expression profiling; Non small cell lung cancer; Pemetrexed

Indexed keywords

CDC A7; CELL CYCLE PROTEIN; CHEMOKINE RECEPTOR CXCR6; MINICHROMOSOME MAINTENANCE PROTEIN 6; NEUROGENIC DIFFERENTIATION FACTOR; PEMETREXED; TRANSCRIPTION FACTOR MASH1; UNCLASSIFIED DRUG;

ARTICLE; CANCER PATIENT; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE CLASSIFICATION; DRUG EFFICACY; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; IC 50; LUNG NON SMALL CELL CANCER; LUNG SQUAMOUS CELL CARCINOMA; MAJOR CLINICAL STUDY; PHENOTYPE; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN EXPRESSION; SENSITIVITY ANALYSIS; TISSUE MICROARRAY; TREATMENT RESPONSE;

EID: 84655164992     PISSN: 15560864     EISSN: 15561380     Source Type: Journal    
DOI: 10.1097/JTO.0b013e3182352a45     Document Type: Article

References (44)

1. Travis WD, Gal AA, Colby TV, et al. Reproducibility of neuroendocrine lung tumor classification. Hum Pathol 1998;29:272-279. (Pubitemid 28123925)
2. Takeuchi T, Tomida S, Yatabe Y, et al. Expression profile-defined classification of lung adenocarcinoma shows close relationship with underlying major genetic changes and clinicopathologic behaviors. J Clin Oncol 2006;24:1679-1688. (Pubitemid 46622139)
3. Bhattacharjee A, Richards WG, Staunton J, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 2001;98:13790-13795. (Pubitemid 33115977)
4. Anbazhagan R, Tihan T, Bornman DM, et al. Classification of small cell lung cancer and pulmonary carcinoid by gene expression profiles. Cancer Res 1999;59:5119-5122. (Pubitemid 29503970)
5. Hanauske AR, Chen V, Paoletti P, et al. Pemetrexed disodium: a novel antifolate clinically active against multiple solid tumors. Oncologist 2001;6:363-373. (Pubitemid 32816541)
6. Hanauske AR, Eismann U, Oberschmidt O, et al. In vitro chemosensitivity of freshly explanted tumor cells to pemetrexed is correlated with target gene expression. Invest New Drugs 2007;25:417-423. (Pubitemid 47222911)
7. Esteban E, Casillas M, Cassinello A. Pemetrexed in first-line treatment of non-small cell lung cancer. Cancer Treat Rev 2009;35:364-373.
8. Longo-Sorbello GS, Chen B, Budak-Alpdogan T, et al. Role of pemetrexed in non-small cell lung cancer. Cancer Invest 2007;25:59-66. (Pubitemid 46423593)
9. Bepler G, Sommers KE, Cantor A, et al. Clinical efficacy and predictive molecular markers of neoadjuvant gemcitabine and pemetrexed in resectable non-small cell lung cancer. J Thorac Oncol 2008;3:1112-1118.
10. Ciuleanu T, Brodowicz T, Zielinski C, et al. Maintenance pemetrexed plus best supportive care versus placebo plus best supportive care for non-small-cell lung cancer: a randomised, double-blind, phase 3 study. Lancet 2009;374:1432-1440.
11. Scagliotti G, Hanna N, Fossella F, et al. The differential efficacy of pemetrexed according to NSCLC histology: a review of two Phase III studies. Oncologist 2009;14:253-263.
12. Scagliotti GV, Parikh P, von Pawel J, et al. Phase III study comparing cisplatin plus gemcitabine with cisplatin plus pemetrexed in chemother-apy-naive patients with advanced-stage non-small-cell lung cancer. J Clin Oncol 2008;26:3543-3551.
13. Ceppi P, Volante M, Saviozzi S, et al. Squamous cell carcinoma of the lung compared with other histotypes shows higher messenger RNA and protein levels for thymidylate synthase. Cancer 2006;107:1589-1596. (Pubitemid 44546920)
14. Monica V, Scagliotti GV, Ceppi P, et al. Differential Thymidylate Synthase Expression in Different Variants of Large-Cell Carcinoma of the Lung. Clin Cancer Res 2009;15:7547-7552.
15. Hou J, Aerts J, den Hamer B, et al. Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One; 5:e10312.
16. Li T, Ling YH, Goldman ID, et al. Schedule-dependent cytotoxic synergism of pemetrexed and erlotinib in human non-small cell lung cancer cells. Clin Cancer Res 2007;13:3413-3422. (Pubitemid 46944930)
17. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001;98:5116-5121. (Pubitemid 32397092)
18. Tibshirani R, Hastie T, Narasimhan B, et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 2002;99:6567-6572. (Pubitemid 34526173)
19. Golub T, Slonim D, Tamayo P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286:531-536.
20. Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102:15545-15550. (Pubitemid 41528093)
21. Borczuk AC, Gorenstein L, Walter KL, et al. Non-small-cell lung cancer molecular signatures recapitulate lung developmental pathways. Am J Pathol 2003;163:1949-1960. (Pubitemid 37310025)
22. Righi L, Volante M, Rapa I, et al. Neuro-endocrine tumours of the lung. A review of relevant pathological and molecular data. Virchows Arch 2007;51(Suppl 1):S51-S59. (Pubitemid 47283377)
23. Gustafsson BI, Kidd M, Chan A, et al. Bronchopulmonary neuroendocrine tumors. Cancer 2008;113:5-21. (Pubitemid 351976381)
24. Giovannetti E, Mey V, Nannizzi S, et al. Cellular and pharmacogenetics foundation of synergistic interaction of pemetrexed and gemcitabine in human non-small-cell lung cancer cells. Mol Pharmacol 2005;68:110-118. (Pubitemid 41002949)
25. Tubbs RR, Pettay JD, Roche PC, et al. Discrepancies in clinical laboratory testing of eligibility for trastuzumab therapy: apparent immunohistochemical false-positives do not get the message. J Clin Oncol 2001;19:2714-2721. (Pubitemid 32441377)
26. Rosell R, Felip E, Garcia-Campelo R, et al. The biology of non-smallcell lung cancer: identifying new targets for rational therapy. Lung Cancer 2004;46:135-148. (Pubitemid 39330407)
27. Jackman DM, Miller VA, Cioffredi LA, et al. Impact of epidermal growth factor receptor and KRAS mutations on clinical outcomes in previously untreated non-small cell lung cancer patients: results of an online tumor registry of clinical trials. Clin Cancer Res 2009;15:5267-5273.
28. Shukuya T, Takahashi T, Kaira R, et al. Efficacy of gefitinib for non-adenocarcinoma non-small-cell lung cancer patients harboring epidermal growth factor receptor mutations: a pooled analysis of published reports. Cancer Sci 2011;102:1032-1037.
29. Raponi M, Zhang Y, Yu J, et al. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 2006;66:7466-7472. (Pubitemid 44289200)
30. Inamura K, Fujiwara T, Hoshida Y, et al. Two subclasses of lung squamous cell carcinoma with different gene expression profiles and prognosis identified by hierarchical clustering and non-negative matrix factorization. Oncogene 2005;24:7105-7113. (Pubitemid 41573639)
31. Garber ME, Troyanskaya OG, Schluens K, et al. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A 2001;98:13784-13789. (Pubitemid 33115976)
32. Wigle DA, Jurisica I, Radulovich N, et al. Molecular profiling of non-small cell lung cancer and correlation with disease-free survival. Cancer Res 2002;62:3005-3008. (Pubitemid 34602385)
33. Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353-357. (Pubitemid 43128862)
34. Gronberg BH, Bremnes RM, Flotten O, et al. Phase III study by the Norwegian lung cancer study group: pemetrexed plus carboplatin compared with gemcitabine plus carboplatin as first-line chemotherapy in advanced non-small-cell lung cancer. J Clin Oncol 2009;27:3217-3224.
35. Scagliotti G, Brodowicz T, Shepherd FA, et al. Treatment-by-histology interaction analyses in three phase III trials show superiority of pemetrexed in nonsquamous non-small cell lung cancer. J Thorac Oncol 2011;6:64-70.
36. Bertino EM, Confer PD, Colonna JE, et al. Pulmonary neuroendocrine/ carcinoid tumors: a review article. Cancer 2009;115:4434-4441.
37. Ceppi P, Volante M, Ferrero A, et al. Thymidylate synthase expression in gastroenteropancreatic and pulmonary neuroendocrine tumors. Clin Cancer Res 2008;14:1059-1064. (Pubitemid 351302551)
38. Moreira LR, Schenka AA, Latuff Filho P, et al. Correlation between thymidylate synthase protein expression and gene polymorphism with clinicopathological parameters in colorectal carcinoma. Int J Surg Pathol 2009;17:181-186.
39. Koscielny S. Why most gene expression signatures of tumors have not been useful in the clinic. Sci Transl Med 2010;2:14ps12.
40. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747-752.
41. Parker JS, Mullins M, Cheang MC, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 2009;27:1160-1167.
42. Fan C, Oh DS, Wessels L, et al. Concordance among gene-expressionbased predictors for breast cancer. N Engl J Med 2006;355:560-569. (Pubitemid 44200649)
43. Finnegan TJ, Carey LA. Gene-expression analysis and the basal-like breast cancer subtype. Future Oncol 2007;3:55-63.
44. Sun JM, Han J, Ahn JS, et al. Significance of thymidylate synthase and thyroid transcription factor 1 expression in patients with nonsquamous non-small cell lung cancer treated with pemetrexed-based chemotherapy. J Thorac Oncol 2011;6:1392-1399.