ASCL1-coexpression profiling but not single gene expression profiling defines lung adenocarcinomas of neuroendocrine nature with poor prognosis

Lung Cancer

Volumn 75, Issue 1, 2012, Pages 119-125

  Fujiwara, Takeshi ^a   Hiramatsu, Miyako ^b   Isagawa, Takayuki ^a   Ninomiya, Hironori ^b   Inamura, Kentaro ^b   Ishikawa, Shumpei ^a   Ushijima, Masaru ^c   Matsuura, Masaaki ^c   Jones, Michael H ^a,d   Shimane, Miyuki ^a,d   Nomura, Hitoshi ^a,d   Ishikawa, Yuichi ^b   Aburatani, Hiroyuki ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b CANCER INSTITUTE   (Japan)

^c CANCER CHEMOTHERAPY CENTER   (Japan)

^d CHUGAI PHARMACEUTICAL CO LTD   (Japan)

Author keywords

Adenocarcinoma; Gene expression; Lung; Neuroendocrine; Prognosis; Subtype

Indexed keywords

COMPLEMENTARY DNA; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR MASH1;

ARTICLE; CANCER SURVIVAL; CELL DIFFERENTIATION; CLINICAL FEATURE; DNA MICROARRAY; DOWN REGULATION; FEMALE; GENE EXPRESSION PROFILING; HISTOPATHOLOGY; HUMAN; LUNG ADENOCARCINOMA; LUNG ALVEOLUS CELL; MAJOR CLINICAL STUDY; MALE; NEUROENDOCRINE TUMOR; PRIORITY JOURNAL; PROGNOSIS; SQUAMOUS CELL CARCINOMA; TUMOR CLASSIFICATION;

ADENOCARCINOMA; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CARCINOMA, NEUROENDOCRINE; CARCINOMA, SQUAMOUS CELL; CELL LINE, TUMOR; COHORT STUDIES; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; MULTIVARIATE ANALYSIS; NEUROENDOCRINE CELLS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; RNA, SMALL INTERFERING; SURVIVAL RATE;

EID: 83555165134     PISSN: 01695002     EISSN: 18728332     Source Type: Journal    
DOI: 10.1016/j.lungcan.2011.05.028     Document Type: Article

References (26)

1. Travis W.D., Brambilla E., Müller-Hermelink H.K., et al. Pathology and Genetics: Tumours of the Lung, Pleura, Thymus and Heart 2004, IARC, Lyon.
2. Bhattacharjee A., Richards W.G., Staunton J., Li C., Monti S., Vasa P., et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001, 98:13790-13795.
3. Ionescu D.N., Treaba D., Gilks C.B., Leung S., Renouf D., Laskin J., et al. Nonsmall cell lung carcinoma with neuroendocrine differentiation-an entity of no clinical or prognostic significance. Am J Surg Pathol 2007, 31:26-32.
4. Jiang S.X., Kameya T., Asamura H., Umezawa A., Sato Y., Shinada J., et al. hASH1 expression is closely correlated with endocrine phenotype and differentiation extent in pulmonary neuroendocrine tumors. Mod Pathol 2004, 17:222-229.
5. Jiang T., Collins B.J., Jin N., Watkins D.N., Brock M.V., Matsui W., et al. Achaete-scute complex homologue 1 regulates tumor-initiating capacity in human small cell lung cancer. Cancer Res 2009, 69:845-854.
6. Sippel R.S., Carpenter J.E., Kunnimalaiyaan M., Chen H. The role of human achaete-scute homolog-1 in medullary thyroid cancer cells. Surgery 2003, 134:866-871.
7. Borges M., Linnoila R.I., van de Velde H.J., Chen H., Nelkin B.D., Mabry M., et al. An achaete-scute homologue essential for neuroendocrine differentiation in the lung. Nature 1997, 386:852-855.
8. Lee H.K., Hsu A.K., Sajdak J., Qin J., Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14:1085-1094.
9. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
10. Ge H., Liu Z., Church G.M., Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29:482-486.
11. Hashimoto T., Tokuchi Y., Hayashi M., Kobayashi Y., Nishida K., Hayashi S., et al. Different subtypes of human lung adenocarcinoma caused by different etiological factors. Am J Pathol 2000, 157:2133-2141.
12. Virtanen C., Ishikawa Y., Honjoh D., Kimura M., Shimane M., Miyoshi M., et al. Integrated classification of lung tumors and cell lines by expression profiling. Proc Natl Acad Sci USA 2002, 99:12357-12362.
13. Jones M.H., Virtanen C., Honjoh D., Miyoshi T., Satoh Y., Okumura S., et al. Two prognostically significant subtypes of high-grade lung neuroendocrine tumours independent of small-cell and large-cell neuroendocrine carcinomas identified by gene expression profiles. Lancet 2004, 363:775-781.
14. Inamura K., Fujiwara T., Hoshida Y., Isagawa T., Jones M.H., Virtanen C., 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.
15. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.
16. Brunet J.P., Tamayo P., Golub T.R., Mesirov J.P. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci USA 2004, 101:4164-4169.
17. Kim P.M., Tidor B., Keating A.E. Subsystem identification through dimensionality reduction of large-scale gene expression data. Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Genome Res 2003, 13:1706-1718.
18. Hosack D.A., Dennis G., Sherman B.T., Lane H.C., Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70.
19. Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma, Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008;14(8):822-7.
20. Lee D.D., Seung H.S. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401:788-791.
21. Hoshida Y., Nijman S.M., Kobayashi M., Chan J.A., Brunet J.P., Chiang D.Y., et al. Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res 2009, 69(18):7385-7392.
22. Hayes D.N., Monti S., Parmigiani G., Gilks C.B., Naoki K., Bhattacharjee A., et al. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol 2006, 24(31):5079-5090.
23. Shelton S.B., Johnson G.V. Cyclin-dependent kinase-5 in neurodegeneration. J Neurochem 2004, 88:1313-1326.
24. Parish J.L., Rosa J., Wang X., Lahti J.M., Doxsey S.J., Androphy E.J. The DNA helicase ChlR1 is required for sister chromatid cohesion in mammalian cells. J Cell Sci 2006, 119:4857-4865.
25. Ariani F., Hayek G., Rondinella D., Artuso R., Mencarelli M.A., Spanhol-Rosseto A., et al. FOXG1 is responsible for the congenital variant of Rett syndrome. Am J Hum Genet 2008, 83:89-93.
26. International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, et al. International Cancer Genome Consortium International network of cancer genome projects. Nature 2010;464(7291):993-8.