Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: Comparison to human non-small cell lung cancer

Toxicologic Pathology

Volumn 40, Issue 8, 2012, Pages 1141-1159

  Pandiri, Arun R ^a,b   Sills, Robert C ^a   Ziglioli, Vincent ^c   Ton, Thai Vu T ^a   Hong, Hue Hua L ^a   Lahousse, Stephanie A ^a   Gerrish, Kevin E ^a   Auerbach, Scott S ^a   Shockley, Keith R ^a   Bushel, Pierre R ^a   Peddada, Shyamal D ^a   Hoenerhoff, Mark J ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b EXPERIMENTAL PATHOLOGY LABORATORIES INC   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

B6C3F1 mouse; comparative genomics; gene expression analysis; lung cancer; microarray

Indexed keywords

CHEMOKINE RECEPTOR CXCR4; GENOMIC DNA; INITIATION FACTOR 2; INOSITOL PHOSPHATE; INTERLEUKIN 8; MAMMALIAN TARGET OF RAPAMYCIN INHIBITOR; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; RHOA GUANINE NUCLEOTIDE BINDING PROTEIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CARCINOGENICITY; CONTROLLED STUDY; ENDOCYTOSIS; FEMALE; HUMAN; HUMAN TISSUE; IMMUNE RESPONSE; IMMUNOHISTOCHEMISTRY; LUNG NON SMALL CELL CANCER; LUNG PARENCHYMA; LUNG TUMOR; MALE; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHAGOCYTOSIS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN METABOLISM; PURINE METABOLISM; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; SPONTANEOUS LUNG TUMOR; TRANSCRIPTOMICS;

ANIMALS; CARCINOMA, NON-SMALL-CELL LUNG; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MICE; MICE, INBRED STRAINS; NEOPLASM PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SPECIES SPECIFICITY; TUMOR MARKERS, BIOLOGICAL;

ANIMALIA; EUKARYOTA; MAMMALIA; MURINAE; MUS;

EID: 84869990474     PISSN: 01926233     EISSN: 15331601     Source Type: Journal    
DOI: 10.1177/0192623312447543     Document Type: Article

References (133)

1. Ackerstaff E., Glunde K., Bhujwalla Z. M.. Choline phospholipid metabolism: A target in cancer cells?. J Cell Biochem. 2003 ; 90: 525-33
2. Adida C., Crotty P. L., McGrath J., Berrebi D., Diebold J., Altieri D. C.. Developmentally regulated expression of the novel cancer anti-apoptosis gene survivin in human and mouse differentiation. Am J Pathol. 1998 ; 152: 43-9
3. Ai J., Maturu A., Johnson W., Wang Y., Marsh C. B., Tridandapani S.. The inositol phosphatase SHIP-2 down-regulates FcgammaR-mediated phagocytosis in murine macrophages independently of SHIP-1. Blood. 2006 ; 107: 813-20
4. Aiello A., Pandini G., Sarfstein R., Werner H., Manfioletti G., Vigneri R., Belfiore A.. HMGA1 protein is a positive regulator of the insulin-like growth factor-I receptor gene. Eur J Cancer. 2010 ; 46: 1919-26
5. Akpinar P., Kuwajima S., Krutzfeldt J., Stoffel M.. Tmem27: A cleaved and shed plasma membrane protein that stimulates pancreatic beta cell proliferation. Cell Metab. 2005 ; 2: 385-97
6. Aksoy-Sagirli P., Cakmakoglu B., Isbir T., Kaytan-Saglam E., Kizir A., Topuz E., Berkkan H.. Paraoxonase-1 192/55 polymorphisms and the risk of lung cancer in a Turkish population. Anticancer Res. 2011 ; 31: 2225-9
7. Amatschek S., Koenig U., Auer H., Steinlein P., Pacher M., Gruenfelder A., Dekan G., Vogl S., Kubista E., Heider K. H., Stratowa C., Schreiber M., Sommergruber W.. Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes. Cancer Res. 2004 ; 64: 844-56
8. Ambrosini G., Adida C., Altieri D. C.. A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma. Nat Med. 1997 ; 3: 917-21
9. Ames B. N., Shigenaga M. K.. Oxidants are a major contributor to aging. Ann N Y Acad Sci. 1992 ; 663: 85-96
10. Ando K., Kikuchi M., Eimoto T., Shirakusa T.. Involucrin in well-differentiated adenocarcinoma of the lung. Comparison with adenocarcinomas of different organs. Pathol Res Pract. 1991 ; 187: 50-54
11. Backman K. A., Guyre P. M.. Gamma-interferon inhibits Fc receptor II-mediated phagocytosis of tumor cells by human macrophages. Cancer Res. 1994 ; 54: 2456-61
12. Balatoni C. E., Dawson D. W., Suh J., Sherman M. H., Sanders G., Hong J. S., Frank M. J., Malone C. S., Said J. W., Teitell M. A.. Epigenetic silencing of Stk39 in B-cell lymphoma inhibits apoptosis from genotoxic stress. Am J Pathol. 2009 ; 175: 1653-61
13. Balsara B. R., Pei J., Mitsuuchi Y., Page R., Klein-Szanto A., Wang H., Unger M., Testa J. R.. Frequent activation of AKT in non-small cell lung carcinomas and preneoplastic bronchial lesions. Carcinogenesis. 2004 ; 25: 2053-9
14. Basile J. R., Castilho R. M., Williams V. P., Gutkind J. S.. Semaphorin 4D provides a link between axon guidance processes and tumor-induced angiogenesis. Proc Natl Acad Sci U S A. 2006 ; 103: 9017-22
15. Benjamin J. T., Gaston D. C., Halloran B. A., Schnapp L. M., Zent R., Prince L. S.. The role of integrin alpha8beta1 in fetal lung morphogenesis and injury. Dev Biol. 2009 ; 335: 407-17
16. Benjamini Y., Hochberg Y.. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc Ser B Stat Methodol. 1995 ; 57: 289-300
17. Cai L. Y., Abe M., Izumi S., Imura M., Yasugi T., Ushijima T.. Identification of PRTFDC1 silencing and aberrant promoter methylation of GPR150 ITGA8 and HOXD11 in ovarian cancers. Life Sci. 2007 ; 80: 1458-65
18. Carlson H., Ota S., Song Y., Chen Y., Hurlin P. J.. Tbx3 impinges on the p53 pathway to suppress apoptosis, facilitate cell transformation and block myogenic differentiation. Oncogene. 2002 ; 21: 3827-35
19. Chapman D. L., Garvey N., Hancock S., Alexiou M., Agulnik S. I., Gibson-Brown J. J., Cebra-Thomas J., Bollag R. J., Silver L. M., Papaioannou V. E.. Expression of the T-box family genes, Tbx1-Tbx5, during early mouse development. Dev Dyn. 1996 ; 206: 379-90
20. Charfi C., Voisin V., Levros L. C., Edouard E., Rassart E.. Gene profiling of Graffi murine leukemia virus-induced lymphoid leukemias: identification of leukemia markers and Fmn2 as a potential oncogene. Blood. 2011 ; 117: 1899-1910
21. Choi K., Creighton C. J., Stivers D., Fujimoto N., Kurie J. M.. Transcriptional profiling of non-small cell lung cancer cells with activating EGFR somatic mutations. PLoS One. 2007 ; 2: e1226
22. Czerwinski M., McLemore T. L., Gelboin H. V., Gonzalez F. J.. Quantification of CYP2B7, CYP4B1, and CYPOR messenger RNAs in normal human lung and lung tumors. Cancer Res. 1994 ; 54: 1085-1091
23. Danilczyk U., Sarao R., Remy C., Benabbas C., Stange G., Richter A., Arya S., Pospisilik J. A., Singer D., Camargo S. M., Makrides V., Ramadan T., Verrey F., Wagner C. A., Penninger J. M.. Essential role for collectrin in renal amino acid transport. Nature. 2006 ; 444: 1088-91
24. Darsigny M., Babeu J. P., Seidman E. G., Gendron F. P., Levy E., Carrier J., Perreault N., Boudreau F.. Hepatocyte nuclear factor-4alpha promotes gut neoplasia in mice and protects against the production of reactive oxygen species. Cancer Res. 2010 ; 70: 9423-33
25. Delloye-Bourgeois C., Brambilla E., Coissieux M. M., Guenebeaud C., Pedeux R., Firlej V., Cabon F., Brambilla C., Mehlen P., Bernet A.. Interference with netrin-1 and tumor cell death in non-small cell lung cancer. J Natl Cancer Inst. 2009 ; 101: 237-247
26. de Seranno S., Meuwissen R.. Progress and applications of mouse models for human lung cancer. Eur Respir J. 2010 ; 35: 426-443
27. Dietrich D., Krispin M., Dietrich J., Fassbender A., Lewin J., Harbeck N., Schmitt M., Eppenberger-Castori S., Vuaroqueaux V., Spyratos F., Foekens J. A., Lesche R., Martens J. W.. CDO1 promoter methylation is a biomarker for outcome prediction of anthracycline treated, estrogen receptor-positive, lymph node-positive breast cancer patients. BMC Cancer. 2010 ; 10: 247
28. Dixon D., Herbert R. A., Sills R. C., Boorman G. A. Lungs, Pleura, and Mediatinum. Cache River Press: St. Louis, MO ; 1999 :
29. Doll S. R.. Smoking and lung cancer. Am J Respir Crit Care Med. 2000 ; 162: 4-6
30. Farrar C., Houser C. R., Clarke S.. Activation of the PI3K/Akt signal transduction pathway and increased levels of insulin receptor in protein repair-deficient mice. Aging Cell. 2005 ; 4: 1-12
31. Fernando R. I., Castillo M. D., Litzinger M., Hamilton D. H., Palena C.. IL-8 signaling plays a critical role in the epithelial-mesenchymal transition of human carcinoma cells. Cancer Res. 2011 ; 71: 5296-306
32. Futamura M., Kamino H., Miyamoto Y., Kitamura N., Nakamura Y., Ohnishi S., Masuda Y., Arakawa H.. Possible role of semaphorin 3F, a candidate tumor suppressor gene at 3p21.3, in p53-regulated tumor angiogenesis suppression. Cancer Res. 2007 ; 67: 1451-60
33. Gingras A. C., Raught B., Sonenberg N. eIF4 initiation factors: Effectors of mRNA recruitment to ribosomes and regulators of translation. Annu Rev Biochem. 1999 ; 68: 913-63
34. Gogvadze V., Orrenius S., Zhivotovsky B.. Mitochondria in cancer cells: What is so special about them?. Trends Cell Biol. 2008 ; 18: 165-73
35. Gu J., Tamura M., Yamada K. M.. Tumor suppressor PTEN inhibits integrin- and growth factor-mediated mitogen-activated protein (MAP) kinase signaling pathways. J Cell Biol. 1998 ; 143: 1375-83
36. Guo W., Sarkar S. K., Peddada S. D.. Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories. Biometrics. 2010 ; 66: 485-92
37. Guyton K. Z., Liu Y., Gorospe M., Xu Q., Holbrook N. J.. Activation of mitogen-activated protein kinase by H2O2. Role in cell survival following oxidant injury. J Biol Chem. 1996 ; 271: 4138-42
38. Hanahan D., Weinberg R. A.. Hallmarks of cancer: The next generation. Cell. 2011 ; 144: 646-74
39. Hatzivassiliou G., Zhao F., Bauer D. E., Andreadis C., Shaw A. N., Dhanak D., Hingorani S. R., Tuveson D. A., Thompson C. B.. ATP citrate lyase inhibition can suppress tumor cell growth. Cancer Cell. 2005 ; 8: 311-21
40. Hendriksen P. J., Dits N. F., Kokame K., Veldhoven A., van Weerden W. M., Bangma C. H., Trapman J., Jenster G.. Evolution of the androgen receptor pathway during progression of prostate cancer. Cancer Res. 2006 ; 66: 5012-20
41. Hoenerhoff M. J., Pandiri A. R., Lahousse S. A., Hong H. H., Ton T. V., Masinde T., Auerbach S. S., Gerrish K., Bushel P. R., Shockley K. R., Peddada S. D., Sills R. C.. Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: Similarities in the molecular landscape with human liver cancer. Toxicol Pathol. 2011 ; 39: 678-99
42. Hofmann H. S., Hansen G., Richter G., Taege C., Simm A., Silber R. E., Burdach S.. Matrix metalloproteinase-12 expression correlates with local recurrence and metastatic disease in non-small cell lung cancer patients. Clin Cancer Res. 2005 ; 11: 1086-92
43. Hoffman W. H., Biade S., Zilfou J. T., Chen J., Murphy M.. Transcriptional repression of the anti-apoptotic survivin gene by wild type p53. J Biol Chem. 2002 ; 277: 3247-57
44. Huang Y. T., Heist R. S., Chirieac L. R., Lin X., Skaug V., Zienolddiny S., Haugen A., Wu M. C., Wang Z., Su L., Asomaning K., Christiani D. C.. Genome-wide analysis of survival in early-stage non-small-cell lung cancer. J Clin Oncol. 2009 ; 27: 2660-7
45. Hudson C. C., Liu M., Chiang G. G., Otterness D. M., Loomis D. C., Kaper F., Giaccia A. J., Abraham R. T.. Regulation of hypoxia-inducible factor 1alpha expression and function by the mammalian target of rapamycin. Mol Cell Biol. 2002 ; 22: 7004-14
46. Iavarone A., Garg P., Lasorella A., Hsu J., Israel M. A.. The helix-loop-helix protein Id-2 enhances cell proliferation and binds to the retinoblastoma protein. Genes Dev. 1994 ; 8: 1270-84
47. Inoki K., Zhu T., Guan K. L.. TSC2 mediates cellular energy response to control cell growth and survival. Cell. 2003 ; 115: 577-90
48. Irizarry R. A., Hobbs B., Collin F., Beazer-Barclay Y. D., Antonellis K. J., Scherf U., Speed T. P.. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 ; 4: 249-64
49. Isik B., Ceylan A., Isik R.. Oxidative stress in smokers and non-smokers. Inhal Toxicol. 2007 ; 19: 767-9
50. Jozwiak J., Jozwiak S., Grzela T., Lazarczyk M.. Positive and negative regulation of TSC2 activity and its effects on downstream effectors of the mTOR pathway. Neuromolecular Med. 2005 ; 7: 287-96
51. Kamata H., Hirata H.. Redox regulation of cellular signalling. Cell Signal. 1999 ; 11: 1-14
52. Kim J. W., Tchernyshyov I., Semenza G. L., Dang C. V.. HIF-1-mediated expression of pyruvate dehydrogenase kinase: a metabolic switch required for cellular adaptation to hypoxia. Cell Metab. 2006 ; 3: 177-85
53. Kojima K., Kishimoto T., Nagai Y., Tanizawa T., Nakatani Y., Miyazaki M., Ishikura H.. The expression of hepatocyte nuclear factor-4alpha, a developmental regulator of visceral endoderm, correlates with the intestinal phenotype of gastric adenocarcinomas. Pathology. 2006 ; 38: 548-54
54. Kopantzev E. P., Monastyrskaya G. S., Vinogradova T. V., Zinovyeva M. V., Kostina M. B., Filyukova O. B., Tonevitsky A. G., Sukhikh G. T., Sverdlov E. D.. Differences in gene expression levels between early and later stages of human lung development are opposite to those between normal lung tissue and non-small lung cell carcinoma. Lung Cancer. 2008 ; 62: 23-34
55. Koumenis C., Naczki C., Koritzinsky M., Rastani S., Diehl A., Sonenberg N., Koromilas A., Wouters B. G.. Regulation of protein synthesis by hypoxia via activation of the endoplasmic reticulum kinase PERK and phosphorylation of the translation initiation factor eIF2alpha. Mol Cell Biol. 2002 ; 22: 7405-16
56. Kraunz K. S., Nelson H. H., Liu M., Wiencke J. K., Kelsey K. T.. Interaction between the bone morphogenetic proteins and Ras/MAP-kinase signalling pathways in lung cancer. Br J Cancer. 2005 ; 93: 949-52
57. Kupershmidt I., Su Q. J., Grewal A., Sundaresh S., Halperin I., Flynn J., Shekar M., Wang H., Park J., Cui W., Wall G. D., Wisotzkey R., Alag S., Akhtari S., Ronaghi M.. Ontology-based meta-analysis of AQ16 global collections of high-throughput public data. PLoS One. 2010 ; 5: e13066
58. Kwon Y. J., Lee S. J., Koh J. S., Kim S. H., Lee H. W., Kang M. C., Bae J. B., Kim Y. J., Park J. H. Genome-wide analysis of DNA methylation and the gene expression change in lung cancer. J Thorac Oncol. 2012 ; 7: 20-33
59. Langenfeld E. M., Kong Y., Langenfeld J.. Bone morphogenetic protein 2 stimulation of tumor growth involves the activation of Smad-1/5. Oncogene. 2006 ; 25: 685-92
60. Lasorella A., Noseda M., Beyna M., Yokota Y., Iavarone A.. Id2 is a retinoblastoma protein target and mediates signalling by Myc oncoproteins. Nature. 2000 ; 407: 592-8
61. Lasorella A., Rothschild G., Yokota Y., Russell R. G., Iavarone A.. Id2 mediates tumor initiation, proliferation, and angiogenesis in Rb mutant mice. Mol Cell Biol. 2005 ; 25: 3563-74
62. Lausen M., Lynch N., Schlosser A., Tornoe I., Saekmose S. G., Teisner B., Willis A. C., Crouch E., Schwaeble W., Holmskov U.. Microfibril-associated protein 4 is present in lung washings and binds to the collagen region of lung surfactant protein D. J Biol Chem. 1999 ; 274: 32234-40
63. Lazarevich N. L., Cheremnova O. A., Varga E. V., Ovchinnikov D. A., Kudrjavtseva E. I., Morozova O. V., Fleishman D. I., Engelhardt N. V., Duncan S. A.. Progression of HCC in mice is associated with a downregulation in the expression of hepatocyte nuclear factors. Hepatology. 2004 ; 39: 1038-47
64. Leclerc J., Tournel G., Courcot-Ngoubo Ngangue E., Pottier N., Lafitte J. J., Jaillard S., Mensier E., Lhermitte M., Broly F., Lo-Guidice J. M.. Profiling gene expression of whole cytochrome P450 superfamily in human bronchial and peripheral lung tissues: Differential expression in non-small cell lung cancers. Biochimie. 2010 ; 92: 292-306
65. Lewis B. P., Burge C. B., Bartel D. P.. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 ; 120: 15-20
66. Li Y., Du H., Qin Y., Roberts J., Cummings O. W., Yan C.. Activation of the signal transducers and activators of the transcription 3 pathway in alveolar epithelial cells induces inflammation and adenocarcinomas in mouse lung. Cancer Res. 2007 ; 67: 8494-503
67. Lingbeek M. E., Jacobs J. J., van Lohuizen M.. The T-box repressors TBX2 and TBX3 specifically regulate the tumor suppressor gene p14ARF via a variant T-site in the initiator. J Biol Chem. 2002 ; 277: 26120-7
68. Lu J., Getz G., Miska E. A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B. L., Mak R. H., Ferrando A. A., Downing J. R., Jacks T., Horvitz H. R., Golub T. R.. MicroRNA expression profiles classify human cancers. Nature. 2005 ; 435: 834-8
69. Lu J., Sharma L. K., Bai Y.. Implications of mitochondrial DNA mutations and mitochondrial dysfunction in tumorigenesis. Cell Res. 2009 ; 19: 802-15
70. Lu T. P., Tsai M. H., Lee J. M., Hsu C. P., Chen P. C., Lin C. W., Shih J. Y., Yang P. C., Hsiao C. K., Lai L. C., Chuang E. Y.. Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev. 2010 ; 19: 2590-7
71. Lucas B., Grigo K., Erdmann S., Lausen J., Klein-Hitpass L., Ryffel G. U.. HNF4alpha reduces proliferation of kidney cells and affects genes deregulated in renal cell carcinoma. Oncogene. 2005 ; 24: 6418-31
72. Malkinson A. M.. Genetic studies on lung tumor susceptibility and histogenesis in mice. Environ Health Perspect. 1991 ; 93: 149-59
73. Marxsen J. H., Stengel P., Doege K., Heikkinen P., Jokilehto T., Wagner T., Jelkmann W., Jaakkola P., Metzen E.. Hypoxia-inducible factor-1 (HIF-1) promotes its degradation by induction of HIF-alpha-prolyl-4-hydroxylases. Biochem J. 2004 ; 381: 761-7
74. Matsubara J., Honda K., Ono M., Tanaka Y., Kobayashi M., Jung G., Yanagisawa K., Sakuma T., Nakamori S., Sata N., Nagai H., Ioka T., Okusaka T., Kosuge T., Tsuchida A., Shimahara M., Yasunami Y., Chiba T., Hirohashi S., Yamada T.. Reduced plasma level of CXC chemokine ligand 7 in patients with pancreatic cancer. Cancer Epidemiol Biomarkers Prev. 2011 ; 20: 160-71
75. Matsumoto T., Wang P. Y., Ma W., Sung H. J., Matoba S., Hwang P. M.. Polo-like kinases mediate cell survival in mitochondrial dysfunction. Proc Natl Acad Sci U S A. 2009 ; 106: 14542-6
76. Mattingly R. R., Stephens L. R., Irvine R. F., Garrison J. C.. Effects of transformation with the v-src oncogene on inositol phosphate metabolism in rat-1 fibroblasts. D-myo-inositol 1,4,5,6-tetrakisphosphate is increased in v-src-transformed rat-1 fibroblasts and can be synthesized from D-myo-inositol 1,3,4-trisphosphate in cytosolic extracts. J Biol Chem. 1991 ; 266: 15144-53
77. Meuwissen R., Berns A.. Mouse models for human lung cancer. Genes Dev. 2005 ; 19: 643-64
78. Michibata H., Okuno T., Konishi N., Wakimoto K., Kyono K., Aoki K., Kondo Y., Takata K., Kitamura Y., Taniguchi T.. Inhibition of mouse GPM6A expression leads to decreased differentiation of neurons derived from mouse embryonic stem cells. Stem Cells Dev. 2008 ; 17: 641-51
79. Miyamori H., Takino T., Kobayashi Y., Tokai H., Itoh Y., Seiki M., Sato H.. Claudin promotes activation of pro-matrix metalloproteinase-2 mediated by membrane-type matrix metalloproteinases. J Biol Chem. 2001 ; 276: 28204-11
80. Moldvay J., Jackel M., Paska C., Soltesz I., Schaff Z., Kiss A.. Distinct claudin expression profile in histologic subtypes of lung cancer. Lung Cancer. 2007 ; 57: 159-67
81. Monzo M., Rosell R., Felip E., Astudillo J., Sanchez J. J., Maestre J., Martin C., Font A., Barnadas A., Abad A.. A novel anti-apoptosis gene: Re-expression of survivin messenger RNA as a prognosis marker in non-small-cell lung cancers. J Clin Oncol. 1999 ; 17: 2100-4
82. Moon E. H., Kim M. J., Ko K. S., Kim Y. S., Seo J., Oh S. P., Lee Y. J.. Generation of mice with a conditional and reporter allele for Tmem100. Genesis. 2010 ; 48: 673-8
83. Morey J. S., Ryan J. C., Van Dolah F. M.. Microarray validation: Factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online. 2006 ; 8: 175-93
84. Nacht M., Martin T. B., Byrne A., Klinger K. W., Teicher B. A., Madden S. L., Jiang Y.. Netrin-4 regulates angiogenic responses and tumor cell growth. Exp Cell Res. 2009 ; 315: 784-94
85. Nagai H., Sugito N., Matsubara H., Tatematsu Y., Hida T., Sekido Y., Nagino M., Nimura Y., Takahashi T., Osada H.. CLCP1 interacts with semaphorin 4B and regulates motility of lung cancer cells. Oncogene. 2007 ; 26: 4025-31
86. Navon R., Wang H., Steinfeld I., Tsalenko A., Ben-Dor A., Yakhini Z.. Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PLoS One. 2009 ; 4: e8003
87. Nikitin A. Y., Alcaraz A., Anver M. R., Bronson R. T., Cardiff R. D., Dixon D., Fraire A. E., Gabrielson E. W., Gunning W. T., Haines D. C., Kaufman M. H., Linnoila R. I., Maronpot R. R., Rabson A. S., Reddick R. L., Rehm S., Rozengurt N., Schuller H. M., Shmidt E. N., Travis W. D., Ward J. M., Jacks T.. Classification of proliferative pulmonary lesions of the mouse: recommendations of the mouse models of human cancers consortium. Cancer Res. 2004 ; 64: 2307-16
88. Northcott P. A., Korshunov A., Witt H., Hielscher T., Eberhart C. G., Mack S., Bouffet E., Clifford S. C., Hawkins C. E., French P., Rutka J. T., Pfister S., Taylor M. D.. Medulloblastoma comprises four distinct molecular variants. J Clin Oncol. 2011 ; 29: 1408-14
89. Ochi K., Mori T., Toyama Y., Nakamura Y., Arakawa H.. Identification of semaphorin3B as a direct target of p53. Neoplasia. 2002 ; 4: 82-87
90. Olie R. A., Simoes-Wust A. P., Baumann B., Leech S. H., Fabbro D., Stahel R. A., Zangemeister-Wittke U.. A novel antisense oligonucleotide targeting survivin expression induces apoptosis and sensitizes lung cancer cells to chemotherapy. Cancer Res. 2000 ; 60: 2805-9
91. Papandreou I., Cairns R. A., Fontana L., Lim A. L., Denko N. C.. HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption. Cell Metab. 2006 ; 3: 187-97
92. Paschoud S., Bongiovanni M., Pache J. C., Citi S.. Claudin-1 and claudin-5 expression patterns differentiate lung squamous cell carcinomas from adenocarcinomas. Mod Pathol. 2007 ; 20: 947-54
93. Pasquale E. B.. Eph receptors and ephrins in cancer: Bidirectional signalling and beyond. Nat Rev Cancer. 2010 ; 10: 165-80
94. Pestova T. V., Kolupaeva V. G., Lomakin I. B., Pilipenko E. V., Shatsky I. N., Agol V. I., Hellen C. U.. Molecular mechanisms of translation initiation in eukaryotes. Proc Natl Acad Sci U S A. 2001 ; 98: 7029-36
95. Polek T. C., Talpaz M., Spivak-Kroizman T. R.. TRAIL-induced cleavage and inactivation of SPAK sensitizes cells to apoptosis. Biochem Biophys Res Commun. 2006 ; 349: 1016-24
96. Potiron V. A., Roche J., Drabkin H. A.. Semaphorins and their receptors in lung cancer. Cancer Lett. 2009 ; 273: 1-14
97. Preston T. J., Abadi A., Wilson L., Singh G.. Mitochondrial contributions to cancer cell physiology: Potential for drug development. Adv Drug Deliv Rev. 2001 ; 49: 45-61
98. Qu P., Du H., Wang X., Yan C.. Matrix metalloproteinase 12 overexpression in lung epithelial cells plays a key role in emphysema to lung bronchioalveolar adenocarcinoma transition. Cancer Res. 2009a ; 69: 7252-61
99. Qu P., Roberts J., Li Y., Albrecht M., Cummings O. W., Eble J. N., Du H., Yan C.. Stat3 downstream genes serve as biomarkers in human lung carcinomas and chronic obstructive pulmonary disease. Lung Cancer. 2009b ; 63: 341-7
100. Rao G. N.. Protein tyrosine kinase activity is required for oxidant-induced extracellular signal-regulated protein kinase activation and c-fos and c-jun expression. Cell Signal. 1997 ; 9: 181-7
101. Rawlins E. L., Clark C. P., Xue Y., Hogan B. L.. The Id2 + distal tip lung epithelium contains individual multipotent embryonic progenitor cells. Development. 2009 ; 136: 3741-5
102. Rollin J., Blechet C., Regina S., Tenenhaus A., Guyetant S., Gidrol X.. The intracellular localization of ID2 expression has a predictive value in non small cell lung cancer. PLoS One. 2009 ; 4: e4158
103. Rosenwald I. B.. The role of translation in neoplastic transformation from a pathologist's point of view. Oncogene. 2004 ; 23: 3230-47
104. Rotondo R., Barisione G., Mastracci L., Grossi F., Orengo A. M., Costa R., Truini M., Fabbi M., Ferrini S., Barbieri O.. IL-8 induces exocytosis of arginase 1 by neutrophil polymorphonuclears in nonsmall cell lung cancer. Int J Cancer. 2009 ; 125: 887-93
105. Schlosser A., Thomsen T., Shipley J. M., Hein P. W., Brasch F., Tornoe I., Nielsen O., Skjodt K., Palaniyar N., Steinhilber W., McCormack F. X., Holmskov U.. Microfibril-associated protein 4 binds to surfactant protein A (SP-A) and colocalizes with SP-A in the extracellular matrix of the lung. Scand J Immunol. 2006 ; 64: 104-16
106. Smith L. T., Lin M., Brena R. M., Lang J. C., Schuller D. E., Otterson G. A., Morrison C. D., Smiraglia D. J., Plass C.. Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer. Proc Natl Acad Sci U S A. 2006 ; 103: 982-7
107. Soini Y.. Claudins in lung diseases. Respir Res. 2011 ; 12: 70
108. Spano J. P., Andre F., Morat L., Sabatier L., Besse B., Combadiere C., Deterre P., Martin A., Azorin J., Valeyre D., Khayat D., Le Chevalier T., Soria J. C.. Chemokine receptor CXCR4 and early-stage non-small cell lung cancer: pattern of expression and correlation with outcome. Ann Oncol. 2004 ; 15: 613-7
109. Spataro V., Norbury C., Harris A. L.. The ubiquitin-proteasome pathway in cancer. Br J Cancer. 1998 ; 77: 448-55
110. Steger D. J., Haswell E. S., Miller A. L., Wente S. R., O'Shea E. K.. Regulation of chromatin remodeling by inositol polyphosphates. Science. 2003 ; 299: 114-6
111. Subramanian A., Tamayo P., Mootha V. K., Mukherjee S., Ebert B. L., Gillette M. A., Paulovich A., Pomeroy S. L., Golub T. R., Lander E. S., Mesirov J. P.. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 ; 102: 15545-50
112. Sunaga N., Miyajima K., Suzuki M., Sato M., White M. A., Ramirez R. D., Shay J. W., Gazdar A. F., Minna J. D.. Different roles for caveolin-1 in the development of non-small cell lung cancer versus small cell lung cancer. Cancer Res. 2004 ; 64: 4277-85
113. Surawska H., Ma P. C., Salgia R.. The role of ephrins and Eph receptors in cancer. Cytokine Growth Factor Rev. 2004 ; 15: 419-33
114. Takatani T., Takahashi K., Uozumi Y., Shikata E., Yamamoto Y., Ito T., Matsuda T., Schaffer S. W., Fujio Y., Azuma J.. Taurine inhibits apoptosis by preventing formation of the Apaf-1/caspase-9 apoptosome. Am J Physiol Cell Physiol. 2004 ; 287: C949-53
115. Tanaka T., Jiang S., Hotta H., Takano K., Iwanari H., Sumi K., Daigo K., Ohashi R., Sugai M., Ikegame C., Umezu H., Hirayama Y., Midorikawa Y., Hippo Y., Watanabe A., Uchiyama Y., Hasegawa G., Reid P., Aburatani H., Hamakubo T., Sakai J., Naito M., Kodama T.. Dysregulated expression of P1 and P2 promoter-driven hepatocyte nuclear factor-4alpha in the pathogenesis of human cancer. J Pathol. 2006 ; 208: 662-72
116. Tasheva E. S., Koester A., Paulsen A. Q., Garrett A. S., Boyle D. L., Davidson H. J., Song M., Fox N., Conrad G. W.. Mimecan/osteoglycin-deficient mice have collagen fibril abnormalities. Mol Vis. 2002 ; 8: 407-15
117. Tasheva E. S., Maki C. G., Conrad A. H., Conrad G. W.. Transcriptional activation of bovine mimecan by p53 through an intronic DNA-binding site. Biochim Biophys Acta. 2001 ; 1517: 333-8
118. Teng D. H., Hu R., Lin H., Davis T., Iliev D., Frye C., Swedlund B., Hansen K. L., Vinson V. L., Gumpper K. L., Ellis L., El-Naggar A., Frazier M., Jasser S., Langford L. A., Lee J., Mills G. B., Pershouse M. A., Pollack R. E., Tornos C., Troncoso P., Yung W. K., Fujii G., Berson A., Steck P. A., et al. MMAC1/PTEN mutations in primary tumor specimens and tumor cell lines. Cancer Res. 1997 ; 57: 5221-5
119. Tessema M., Belinsky S. A.. Mining the epigenome for methylated genes in lung cancer. Proc Am Thorac Soc. 2008 ; 5: 806-10
120. Tomizawa Y., Sekido Y., Kondo M., Gao B., Yokota J., Roche J., Drabkin H., Lerman M. I., Gazdar A. F., Minna J. D.. Inhibition of lung cancer cell growth and induction of apoptosis after reexpression of 3p21.3 candidate tumor suppressor gene SEMA3B. Proc Natl Acad Sci U S A. 2001 ; 98: 13954-9
121. Viallet J., Sausville E. A.. Involvement of signal transduction pathways in lung cancer biology. J Cell Biochem Suppl. 1996 ; 24: 228-36
122. Ward J. H.. Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association. 1963 ; 58: 236-44
123. Waugh D. J., Wilson C.. The interleukin-8 pathway in cancer. Clin Cancer Res. 2008 ; 14: 6735-41
124. Williams T. M., Lisanti M. P.. Caveolin-1 in oncogenic transformation, cancer, and metastasis. Am J Physiol Cell Physiol. 2005 ; 288: C494-506
125. Woenckhaus M., Klein-Hitpass L., Grepmeier U., Merk J., Pfeifer M., Wild P., Bettstetter M., Wuensch P., Blaszyk H., Hartmann A., Hofstaedter F., Dietmaier W.. Smoking and cancer-related gene expression in bronchial epithelium and non-small-cell lung cancers. J Pathol. 2006 ; 210: 192-204
126. Wullschleger S., Loewith R., Hall M. N.. TOR signaling in growth and metabolism. Cell. 2006 ; 124: 471-84
127. Yamashita S., Tsujino Y., Moriguchi K., Tatematsu M., Ushijima T.. Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-aza-2'-deoxycytidine treatment and oligonucleotide microarray. Cancer Sci. 2006 ; 97: 64-71
128. Yanagi S., Kishimoto H., Kawahara K., Sasaki T., Sasaki M., Nishio M., Yajima N., Hamada K., Horie Y., Kubo H., Whitsett J. A., Mak T. W., Nakano T., Nakazato M., Suzuki A.. Pten controls lung morphogenesis, bronchioalveolar stem cells, and onset of lung adenocarcinomas in mice. J Clin Invest. 2007 ; 117: 2929-40
129. Yu L., Todd N. W., Xing L., Xie Y., Zhang H., Liu Z., Fang H., Zhang J., Katz R. L., Jiang F. Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers. Int J Cancer. 2010 ; 127: 2870-2878
130. Zaravinos A., Lambrou G. I., Boulalas I., Delakas D., Spandidos D. A.. Identification of common differentially expressed genes in urinary bladder cancer. PLoS One. 2011 ; 6: e18135
131. Zhang Y., Gao X., Saucedo L. J., Ru B., Edgar B. A., Pan D.. Rheb is a direct target of the tuberous sclerosis tumour suppressor proteins. Nat Cell Biol. 2003 ; 5: 578-81
132. Zhong H., De Marzo A. M., Laughner E., Lim M., Hilton D. A., Zagzag D., Buechler P., Isaacs W. B., Semenza G. L., Simons J. W.. Overexpression of hypoxia-inducible factor 1 alpha in common human cancers and their metastases. Cancer Res. 1999 ; 59: 5830-5
133. Zhu Y. M., Webster S. J., Flower D., Woll P. J.. Interleukin-8/CXCL8 is a growth factor for human lung cancer cells. Br J Cancer. 2004 ; 91: 1970-6