Whole Transcriptome Analysis of Pre-invasive and Invasive Early Squamous Lung Carcinoma in Archival Laser Microdissected Samples

Respiratory Research

Volumn 18, Issue 1, 2017, Pages

  Koper, Andre ^a   Zeef, Leo A H ^b   Joseph, Leena ^c   Kerr, Keith ^d   Gosney, John ^e   Lindsay, Mark A ^f   Booton, Richard ^c  

^a QIAGEN GMBH   (Germany)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c MANCHESTER UNIVERSITY NHS FOUNDATION TRUST   (United Kingdom)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

^e ROYAL LIVERPOOL UNIVERSITY HOSPITAL   (United Kingdom)

^f University of Bath   (United Kingdom)

Author keywords

Exon arrays; Gene expression profiling; Invasive squamous cell cancer; Microdissection; Preinvasive squamous cell cancer

Indexed keywords

TRANSCRIPTOME; TRANSCRIPTION FACTOR; TUMOR PROTEIN;

ADULT; AGED; ARTICLE; BRONCHUS EPITHELIUM; CANCER CELL; CANCER GRADING; CARCINOMA IN SITU; CLINICAL ARTICLE; CONTROLLED STUDY; DNA DAMAGE RESPONSE; DNA METABOLISM; EARLY CANCER; FEMALE; GENE CONTROL; GENE EXPRESSION; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; INFLAMMATION; INVASIVE CARCINOMA; LASER MICRODISSECTION; MALE; MALIGNANT TRANSFORMATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA METABOLISM; SQUAMOUS CELL LUNG CARCINOMA; TUMOR BIOPSY; TUMOR GROWTH; UPREGULATION; CELL CULTURE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LASER CAPTURE MICRODISSECTION; LUNG TUMOR; METABOLISM; MIDDLE AGED; PATHOLOGY; SQUAMOUS CELL CARCINOMA; TUMOR CELL CULTURE; TUMOR INVASION;

AGED; CARCINOMA, SQUAMOUS CELL; CELLS, CULTURED; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LASER CAPTURE MICRODISSECTION; LUNG NEOPLASMS; MALE; MIDDLE AGED; NEOPLASM INVASIVENESS; NEOPLASM PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTOME; TUMOR CELLS, CULTURED;

EID: 85008698230     PISSN: 14659921     EISSN: 1465993X     Source Type: Journal    
DOI: 10.1186/s12931-016-0496-3     Document Type: Article

References (40)

1. Dela Cruz CS, Tanoue LT, Matthay RA. Lung cancer: epidemiology, etiology, and prevention. Clin Chest Med. 2011;32(4):605-44. Pubmed Central PMCID: 3864624.
2. National Lung Screening Trial Research T, Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011;365(5):395-409.
3. William D. Travis MD, Cancer TIAfRo, Pathology IAo. Pathology & Genetics: Tumours of the Lung, Pleura, Thymus, and Heart: IARC Press, World Health Organisation; 2004. ISBN 9789283224181.
4. Wistuba II. Genetics of preneoplasia: lessons from lung cancer. Curr Mol Med. 2007;7(1):3-14.
5. Klebe S, Henderson DW. Facts and fiction: premalignant lesions of lung tissues. Pathology. 2013;45(3):305-15.
6. Ishizumi T, McWilliams A, MacAulay C, Gazdar A, Lam S. Natural history of bronchial preinvasive lesions. Cancer Metastasis Rev. 2010;29(1):5-14. http://www.ncbi.nlm.nih.gov/pubmed/20112052.
7. Banerjee AK. Preinvasive lesions of the bronchus. J Thorac Oncol. 2009;4(4):545-51. %U http://www.ncbi.nlm.nih.gov/pubmed/19279508.
8. Nicholson AG, Perry LJ, Cury PM, Jackson P, McCormick CM, Corrin B, et al. Reproducibility of the WHO/IASLC grading system for pre-invasive squamous lesions of the bronchus: a study of inter-observer and intra-observer variation. Histopathology. 2001;38(3):202-8.
9. Breuer RH, Pasic A, Smit EF, van Vliet E, Vonk Noordegraaf A, Risse EJ, et al. The natural course of preneoplastic lesions in bronchial epithelium. Clin Cancer Res. 2005;11(2 Pt 1):537-43. Epub 2005/02/11. eng.
10. Thiberville L, Payne P, Vielkinds J, LeRiche J, Horsman D, Nouvet G, et al. Evidence of cumulative gene losses with progression of premalignant epithelial lesions to carcinoma of the bronchus. Cancer Res. 1995;55(22):5133-9.
11. Wistuba II, Behrens C, Milchgrub S, Bryant D, Hung J, Minna JD, et al. Sequential molecular abnormalities are involved in the multistage development of squamous cell lung carcinoma. Oncogene. 1999;18(3):643-50.
12. 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(8):948-56.
13. McCaughan F, Pole JC, Bankier AT, Konfortov BA, Carroll B, Falzon M, et al. Progressive 3q amplification consistently targets SOX2 in preinvasive squamous lung cancer. Am J Respir Crit Care Med. 2010;182(1):83-91. Pubmed Central PMCID: 2902760.
14. 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. Nature Genet. 2009;41(11):1238-42. Pubmed Central PMCID: 2783775.
15. Farragher SM, Tanney A, Kennedy RD, Paul Harkin D. RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol. 2008;130(3):435-45.
16. Hall JS, Leong HS, Armenoult LS, Newton GE, Valentine HR, Irlam JJ, et al. Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples. Br J Cancer. 2011;104(6):971-81. Pubmed Central PMCID: 3065290.
17. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101-8.
18. Roberts L, Bowers J, Sensinger K, Lisowski A, Getts R, Anderson MG. Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling. Genomics. 2009;94(5):341-8. %U http://linkinghub.elsevier.com/retrieve/pii/S088875430900175X.
19. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001;98(1):31-6. Pubmed Central PMCID: 14539.
20. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.
21. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100(16):9440-5. Pubmed Central PMCID: 170937.
22. Ooi AT, Gower AC, Zhang KX, Vick JL, Hong L, Nagao B, et al. Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis. Cancer Prev Res. 2014;7(5):487-95.
23. Zhang H, Meltzer P, Davis S. RCircos: an R package for Circos 2D track plots. BMC Bioinformatics. 2013;14:244. Pubmed Central PMCID: 3765848.
24. 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(43):15545-50. Pubmed Central PMCID: 1239896, Epub 2005/10/04. eng.
25. Liebermann DA, Hoffman B. Gadd45 in stress signaling. J Molec Signal. 2008;3:15. Pubmed Central PMCID: 2563007.
26. Lobrich M, Jeggo PA. The impact of a negligent G2/M checkpoint on genomic instability and cancer induction. Nat Rev Cancer. 2007;7(11):861-9.
27. Meek DW. Regulation of the p53 response and its relationship to cancer. Biochem J. 2015;469(3):325-46.
28. Sever R, Brugge JS. Signal transduction in cancer. Cold Spring Harb Perspect Med. 2015;5:4.
29. Salehi F, Kovacs K, Scheithauer BW, Lloyd RV, Cusimano M. Pituitary tumor-transforming gene in endocrine and other neoplasms: a review and update. Endocr Relat Cancer. 2008;15(3):721-43.
30. Wistuba II. Histologic evaluation of bronchial squamous lesions: any role in lung cancer risk assessment? Clin Cancer Res. 2005;11(4):1358-60.
31. Hait WN, Levine AJ. Genomic complexity: a call to action. Sci Transl Med. 2014;6(255):255cm10.
32. Giam M, Rancati G. Aneuploidy and chromosomal instability in cancer: a jackpot to chaos. Cell Div. 2015;10:3. Pubmed Central PMCID: 4443636.
33. Lonergan KM, Chari R, Coe BP, Wilson IM, Tsao MS, Ng RT, et al. Transcriptome profiles of carcinoma-in-situ and invasive non-small cell lung cancer as revealed by SAGE. PloS One. 2010;5(2):e9162. Pubmed Central PMCID: 2820080, Epub 2010/02/18. eng.
34. Khuder SA. Effect of cigarette smoking on major histological types of lung cancer: a meta-analysis. Lung Cancer. 2001;31(2-3):139-48.
35. Hecht SS. Lung carcinogenesis by tobacco smoke. Int J Cancer. 2012;131(12):2724-32. Pubmed Central PMCID: 3479369.
36. Hyun SY, Hwang HI, Jang YJ. Polo-like kinase-1 in DNA damage response. BMB Rep. 2014;47(5):249-55. Pubmed Central PMCID: 4163859.
37. Oyama T, Uramoto H, Kagawa N, Yoshimatsu T, Osaki T, Nakanishi R, et al. Cytochrome P450 in non-small cell lung cancer related to exogenous chemical metabolism. Front Biosci. 2012;4:1539-46.
38. Wierinckx A, Auger C, Devauchelle P, Reynaud A, Chevallier P, Jan M, et al. A diagnostic marker set for invasion, proliferation, and aggressiveness of prolactin pituitary tumors. Endocr Relat Cancer. 2007;14(3):887-900.
39. Gales D, Clark C, Manne U, Samuel T. The Chemokine CXCL8 in Carcinogenesis and Drug Response. ISRN Oncol. 2013;2013:859154. Pubmed Central PMCID: 3810054.
40. Trinchieri G. Cancer and inflammation: an old intuition with rapidly evolving new concepts. Annu Rev Immunol. 2012;30:677-706.