Gene expression profile of A549 cells from tissue of 4D model predicts poor prognosis in lung cancer patients

International Journal of Cancer

Volumn 134, Issue 4, 2014, Pages 789-798

  Mishra, Dhruva K ^a   Creighton, Chad J ^b,c   Zhang, Yiqun ^b   Gibbons, Don L ^c   Kurie, Jonathan M ^c   Kim, Min P ^a,d  

^a HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^d HOUSTON METHODIST HOSPITAL   (United States)

Author keywords

ex vivo 4D model; gene expression profile; lung cancer; matrigel; survival

Indexed keywords

PROTEINASE;

ARTICLE; CANCER MODEL; CANCER PATIENT; CANCER PROGNOSIS; CANCER SURVIVAL; CELL FATE; CELL GROWTH; CELL POLARITY; CELL STRAIN; CELL STRAIN A549; CONTROLLED STUDY; CULTURE TECHNIQUE; ENZYME RELEASE; EX VIVO STUDY; EXTRACELLULAR MATRIX; GENE CONTROL; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENETIC MARKER; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; LUNG CANCER; LUNG NODULE; MAJOR CLINICAL STUDY; PREDICTION; PRIORITY JOURNAL; UPREGULATION;

EID: 84890123818     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.28428     Document Type: Article

References (38)

1. Siegel R, Naishadham D, Jemal A,. Cancer statistics, 2012. CA Cancer J Clin 2012; 62: 10-29.
2. Goldstraw P, International Association for the Study of Lung Cancer. Staging manual in thoracic oncologyed. Orange Park, FL: Editorial Rx Press, 2009.
3. Mishra DK, Thrall MJ, Baird BN, et al. Human lung cancer cells grown on acellular rat lung matrix create perfusable tumor nodules. Ann Thorac Surg 2012; 93: 1075-81.
4. Kuttan R, Spall RD, Duhamel RC, et al. Preparation and composition of alveolar extracellular matrix and incorporated basement membrane. Lung 1981; 159: 333-45.
5. Ott HC, Clippinger B, Conrad C, et al. Regeneration and orthotopic transplantation of a bioartificial lung. Nat Med 2010; 16: 927-33.
6. Mishra DK, Sakamoto JH, Thrall MJ, et al. Human lung cancer cells grown in an ex vivo 3D lung model produce matrix metalloproteinases not produced in 2D culture. PLoS One 2012; 7: e45308.
7. Kovacs G, Berghold A, Scheidl S, et al. Pulmonary arterial pressure during rest and exercise in healthy subjects: a systematic review. Eur Respir J 2009; 34: 888-94.
8. Kiernan J,. Histological and histochemical methods: theory and practice, 3rd edn. Oxford [UK]: Scion Publishing Ltd., 2008: 502.
9. Ohira T,. WNT7a induces E-cadherin in lung cancer cells. Proc Natl Acad Sci 2003; 100: 10429-34.
10. Untergasser A, Nijveen H, Rao X, et al. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 2007; 35: W71-4.
11. Zhang Y, Taveggia C, Melendez-Vasquez C, et al. Interleukin-11 potentiates oligodendrocyte survival and maturation, and myelin formation. J Neurosci 2006; 26: 12174-85.
12. Storey JD, Tibshirani R,. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003; 100: 9440-5.
13. Creighton CJ, Nagaraja AK, Hanash SM, et al. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA 2008; 14: 2290-6.
14. Saldanha AJ,. Java Treeview-extensible visualization of microarray data. Bioinformatics 2004; 20: 3246-8.
15. Zschenker O, Streichert T, Hehlgans S, et al. Genome-wide gene expression analysis in cancer cells reveals 3D growth to affect ECM and processes associated with cell adhesion but not DNA repair. PloS One 2012; 7: e34279.
16. Tomida S, Takeuchi T, Shimada Y, et al. Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis. J Clin Oncol 2009; 27: 2793-9.
17. Chitale D, Gong Y, Taylor BS, et al. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 2009; 28: 2773-83.
18. Shedden K, Taylor JM, Enkemann SA, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008; 14: 822-7.
19. 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 USA 2001; 98: 13790-5.
20. Beer DG, Kardia SL, Huang CC, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002; 8: 816-24.
21. Zhu CQ, Ding K, Strumpf D, et al. Prognostic and predictive gene signature for adjuvant chemotherapy in resected non-small-cell lung cancer. J Clin Oncol 2010; 28: 4417-24.
22. Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006; 439: 353-7.
23. Tang H, Xiao G, Behrens C, et al. A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients. Clin Cancer Res 2013; 19: 1577-86.
24. Okayama H, Kohno T, Ishii Y, et al. Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res 2012; 72: 100-11.
25. Botling J, Edlund K, Lohr M, et al. Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clin Cancer Res 2013; 19: 194-204.
26. Hou J, Aerts J, den Hamer B, et al. Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PloS One 2010; 5: e10312.
27. Gibbons DL, Lin W, Creighton CJ, et al. Expression signatures of metastatic capacity in a genetic mouse model of lung adenocarcinoma. PLoS One 2009; 4: e5401.
28. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-15.
29. Cukierman E, Pankov R, Stevens DR, et al. Taking cell-matrix adhesions to the third dimension. Science 2001; 294: 1708-12.
30. Pampaloni F, Reynaud EG, Stelzer EH,. The third dimension bridges the gap between cell culture and live tissue. Nat Rev Mol Cell Biol 2007; 8: 839-45.
31. Thiery JP,. Epithelial-mesenchymal transitions in tumour progression. Nature reviews. Cancer 2002; 2: 442-54.
32. Gibbons DL, Lin W, Creighton CJ, et al. Contextual extracellular cues promote tumor cell EMT and metastasis by regulating miR-200 family expression. Genes Dev 2009; 23: 2140-51.
33. Al-Batran SE, Astner ST, Supthut M, et al. Three-dimensional in vitro cocultivation of lung carcinoma cells with human bronchial organ culture as a model for bronchial carcinoma. Am J Respir Cell Mol Biol 1999; 21: 200-8.
34. Cichon MA, Gainullin VG, Zhang Y, et al. Growth of lung cancer cells in three-dimensional microenvironments reveals key features of tumor malignancy. Integr Biol (Camb) 2012; 4: 440-8.
35. Hughes CS, Postovit LM, Lajoie GA,. Matrigel: a complex protein mixture required for optimal growth of cell culture. Proteomics 2010; 10: 1886-90.
36. Wallis JM, Borg ZD, Daly AB, et al. Comparative assessment of detergent-based protocols for mouse lung de-cellularization and re-cellularization. Tissue Eng Part C Methods 2012; 18: 420-32.
37. Zhou J, Mochizuki T, Smeets H, et al. Deletion of the paired alpha 5(IV) and alpha 6(IV) collagen genes in inherited smooth muscle tumors. Science 1993; 261: 1167-9.
38. Yajnik V, Paulding C, Sordella R, et al. DOCK4, a GTPase activator, is disrupted during tumorigenesis. Cell 2003; 112: 673-84.