Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis

Cancer Prevention Research

Volumn 7, Issue 5, 2014, Pages 487-495

  Ooi, Aik T ^a   Gower, Adam C ^e   Zhang, Kelvin X ^c   Vick, Jessica L ^e   Hong, Longsheng ^c   Nagao, Brian ^c   Wallace, W Dean ^c   Elashoff, David A ^b,d   Walser, Tonya C ^b   Dubinett, Steven M ^b,c   Pellegrini, Matteo ^d   Lenburg, Marc E ^e   Spira, Avrum ^e   Gomperts, Brigitte N ^a,b,d  

^a MATTEL CHILDREN S HOSPITAL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE TRANSPORTER 1; PROTEIN; PROTEIN CEACAM5; PROTEIN PTBP3; UNCLASSIFIED DRUG;

ARTICLE; CARCINOMA CELL; CASE REPORT; CEACAM5 GENE; CELL POPULATION; CHROMOSOME 3P; CHROMOSOME GAIN; CHROMOSOME LOSS; CONTROLLED STUDY; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; IMMUNOFLUORESCENCE TEST; LASER CAPTURE MICRODISSECTION; LUNG CARCINOGENESIS; LUNG SQUAMOUS CELL CARCINOMA; NUMERICAL CHROMOSOME ABERRATION; ONCOGENE MYC; PRECANCER; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PTBP3 GENE; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SLC2A1 GENE; TRANSCRIPTOMICS; CANCER STAGING; CARCINOGENESIS; CHROMOSOME ABERRATION; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETICS; LUNG TUMOR; MICROARRAY ANALYSIS; PATHOLOGY; SEQUENCE ALIGNMENT; SQUAMOUS CELL CARCINOMA; TUMOR GENE;

CARCINOGENESIS; CARCINOMA, SQUAMOUS CELL; CHROMOSOME ABERRATIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; GENETIC ASSOCIATION STUDIES; HUMANS; LUNG NEOPLASMS; MICROARRAY ANALYSIS; NEOPLASM STAGING; PRECANCEROUS CONDITIONS; SEQUENCE ALIGNMENT;

EID: 84900804116     PISSN: 19406207     EISSN: 19406215     Source Type: Journal    
DOI: 10.1158/1940-6207.CAPR-13-0372     Document Type: Article

References (35)

1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2012. CA Cancer J Clin 2012;62:10-29.
2. Stat bite: mortality from lung and bronchus cancer by race/ethnicity, 1998-2002. J Natl Cancer Inst 2006;98:158.
3. Ettinger DS, Akerley W, Borghaei H, Chang AC, Cheney RT, Chirieac LR, et al. Non-small cell lung cancer. J Natl Compr Canc Netw 2012;10:1236-71.
4. Colby TV, Wistuba II, Gazdar A. Precursors to pulmonary neoplasia. Adv Anat Pathol 1998;5:205-15.
5. Kerr KM. Pulmonary preinvasive neoplasia. J Clin Pathol 2001;54:257-71. (Pubitemid 32270007)
6. Peebles KA, Lee JM, Mao JT, Hazra S, Reckamp KL, Krysan K, et al. In flammation and lung carcinogenesis: applying findings in prevention and treatment. Expert Rev Anticancer Ther 2007;7:1405-21. (Pubitemid 351826907)
7. Kettunen E, Anttila S, Seppanen JK, Karjalainen A, Edgren H, Lindstrom I, et al. Differentially expressed genes in nonsmall cell lung cancer: expression profiling of cancer-related genes in squamous cell lung cancer. Cancer Genet Cytogenet 2004;149:98-106. (Pubitemid 38293026)
8. Seo JS, Ju YS, Lee WC, Shin JY, Lee JK, Bleazard T, et al. The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res 2012;22:2109-19.
9. Xi L, Feber A, Gupta V, Wu M, Bergemann AD, Landreneau RJ, et al. Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer. Nucleic Acids Res 2008;36:6535-47.
10. Hong KU, Reynolds SD, Watkins S, Fuchs E, Stripp BR. Basal cells are a multipotent progenitor capable of renewing the bronchial epithelium. Am J Pathol 2004;164:577-88. (Pubitemid 38364673)
11. Ooi AT, Mah V, Nickerson DW, Gilbert JL, Ha VL, Hegab AE, et al. Presence of a putative tumor-initiating progenitor cell population predicts poor prognosis in smokers with non -small cell lung cancer. Cancer Res 2010;70:6639-48.
12. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25.
13. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-2.
14. Mortazavi A, WilliamsBA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8. (Pubitemid 351911867)
15. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, 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- 50.
16. Greenbaum D, Colangelo C, Williams K, Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003;4:117.
17. Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, et al. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010;329:533-8.
18. Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein andmRNAabundance in yeast. Mol Cell Biol 1999;19:1720-30.
19. Wachi S, Yoneda K, Wu R. Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics 2005;21:4205-8. (Pubitemid 41724298)
20. Kuner R, Muley T, Meister M, Ruschhaupt M, Buness A, Xu EC, et al. Global gene expression analysis reveals specific patterns of cell junctions in non-small cell lung cancer subtypes. Lung Cancer 2009;63:32-8.
21. Spira A, Beane J, Shah V, Liu G, Schembri F, Yang X, et al. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci U S A 2004;101:10143-8. (Pubitemid 38891209)
22. Brunelli M, Bria E, Nottegar A, Cingarlini S, Simionato F, Calio A, et al. True 3q chromosomal amplification in squamous cell lung carcinoma by FISH and aCGH molecular analysis: impact on targeted drugs. PLoS ONE 2012;7:e49689.
23. Partridge M, Kiguwa S, Langdon JD. Frequent deletion of chromosome 3p in oral squamous cell carcinoma. Eur J Cancer B Oral Oncol 1994;30B:248-51. (Pubitemid 24257735)
24. Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, et al. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet 2009;41:1238-42.
25. Pignatelli M, Durbin H, Bodmer WF. Carcinoembryonic antigen functions as an accessory adhesion molecule mediating colon epithelial cell-collagen interactions. Proc Natl Acad Sci U S A 1990;87:1541-5.
26. Amann T, Maegdefrau U, Hartmann A, Agaimy A, Marienhagen J, Weiss TS, et al. GLUT1 expression is increased in hepatocellular carcinoma and promotes tumorigenesis. Am J Pathol 2009;174:1544-52.
27. Heikkinen PT, Nummela M, Jokilehto T, Grenman R, Kahari VM, Jaakkola PM. Hypoxic conversion of SMAD7 function from an inhibitor into a promoter of cell invasion. Cancer Res 2010;70:5984-93.
28. Sadvakassova G, Dobocan MC, Difalco MR, Congote LF. Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity. J Cell Physiol 2009;220:672-9.
29. Yamamoto H, Tsukahara K, Kanaoka Y, Jinno S, Okayama H. Isolation of a mammalian homologue of a fission yeast differentiation regulator. Mol Cell Biol 1999;19:3829-41. (Pubitemid 29193842)
30. Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol 2007;8:R201.
31. Massion PP, Zou Y, Uner H, Kiatsimkul P, Wolf HJ, Baron AE, et al. Recurrent genomic gains in preinvasive lesions as a biomarker of risk for lung cancer. PLoS ONE 2009;4:e5611.
32. Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, et al. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway. Cancer Res 2002;62:3636-40. (Pubitemid 34728838)
33. van Boerdonk RA, Sutedja TG, Snijders PJ, Reinen E, Wilting SM, van de Wiel MA, et al. DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer. Am J Respir Crit Care Med 2011;184:948-56.
34. Ling H, Sylvestre JR, Jolicoeur P. Notch1-induced mammary tumor development is cyclin D1-dependent and correlates with expansion of premalignant multipotent duct-limited progenitors. Oncogene 2010;29:4543-54.
35. Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 2007;13:361-6. (Pubitemid 46376687)