Integrative analysis of microRNA, mRNA and aCGH data reveals asbestos- and histology-related changes in lung cancer

Genes Chromosomes and Cancer

Volumn 50, Issue 8, 2011, Pages 585-597

  Nymark, Penny ^a,b   Guled, Mohamed ^a   Borze, Ioana ^a   Faisal, Ali ^c   Lahti, Leo ^b,c   Salmenkivi, Kaisa ^a   Kettunen, Eeva ^b   Anttila, Sisko ^a,b   Knuutila, Sakari ^a  

^a HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^b FINNISH INSTITUTE OF OCCUPATIONAL HEALTH   (Finland)

^c AALTO UNIVERSITY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

AKR1C1 PROTEIN; AP1S1 PROTEIN; ASBESTOS; CACNA2D2 PROTEIN; CYP2B7P1 PROTEIN; EPB41L3 PROTEIN; EXCITATORY AMINO ACID TRANSPORTER 3; F13A1 PROTEIN; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; HBEGF PROTEIN; IGF2BP3 PROTEIN; LTBP1 PROTEIN; MESSENGER RNA; MICRORNA; MICRORNA 148B; MICRORNA 202; MICRORNA 96; MTSS1 PROTEIN; MYO1D PROTEIN; NCALD PROTEIN; NDRG1 PROTEIN; PC PROTEIN; PLAGL1 PROTEIN; PROTEIN; RNA; SLC35A1 PROTEIN; TAOK1 PROTEIN; TRANSCRIPTION FACTOR FOSB; UNCLASSIFIED DRUG; UNINDEXED DRUG; VAV3 PROTEIN;

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DOWN REGULATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE TARGETING; HISTOLOGY; HUMAN; HUMAN TISSUE; LUNG ADENOCARCINOMA; LUNG CANCER; LUNG PARENCHYMA; LUNG SMALL CELL CANCER; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ADULT; AGED; ASBESTOS; COMPARATIVE GENOMIC HYBRIDIZATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; MALE; MICRORNAS; MIDDLE AGED; RNA, MESSENGER;

EID: 79958027909     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20880     Document Type: Article

References (58)

1. Amornsiripanitch N, Hong S, Campa M, Frank M, Gottlin E, Patz EJ. 2010. Complement factor H autoantibodies are associated with early stage NSCLC. Clin Cancer Res 16: 3226-3231.
2. Andersen CL, Christensen LL, Thorsen K, Schepeler T, Sorensen FB, Verspaget HW, Simon R, Kruhoffer M, Aaltonen LA, Laurberg S, Orntoft TF. 2009. Dysregulation of the transcription factors SOX4, CBFB and SMARCC1 correlates with outcome of colorectal cancer. Cancer Res 100: 511-523.
3. Bishop J, Benjamin H, Cholakh H, Chajut A, Clark D, Westra W. 2010. Accurate classification of non-small cell lung carcinoma using a novel microRNA-based approach. Clin Cancer Res 16: 610-619.
4. Braunewell K-H, Szanto A. 2009. Visinin-like proteins (VSNLs): interaction partners and emerging functions in signal transduction of a subfamily of neuronal Ca2+-sensor proteins. Cell Tiss Res 335: 301-316.
5. Busacca S, Germano S, De Cecco L, Rinaldi M, Comoglio F, Favero F, Murer B, Mutti L, Pierotti M, Gaudino G. 2010. MicroRNA signature of malignant mesothelioma with potential diagnostic and prognostic implications. Am J Resp Cell Mol Biol 42: 312-319.
6. Carboni GL, Gao B, Nishizaki M, Xu K, Minna JD, Roth JA, Ji L. 2003. CACNA2D2-mediated apoptosis in NSCLC cells is associated with alterations of the intracellular calcium signaling and disruption of mitochondria membrane integrity. Oncogene 22: 615-626.
7. Churg A. 1997. Mineral analysis of the lung parenchyma. In: Crystal RG WJWE, Barnes PJ, editors. The Lung: Scientific Foundations. Philadelphia: Lippincott-Raven Pub. pp 2325-2338.
8. Collins CS, Hong J, Sapinoso L, Zhou Y, Liu Z, Micklash K, Schultz PG, Hampton GM. 2006. A small interfering RNA screen for modulators of tumor cell motility identifies MAP4K4 as a promigratory kinase. Proc Natl Sci USA 103: 3775-3780.
9. Consensus Report. 1997. Asbestos, asbestosis, and cancer: The Helsinki criteria for diagnosis and attribution. Scand J Work Environ Health 23: 311-316.
10. Dacic S, Kelly L, Shuai Y, Nikiforova MN. 2010. miRNA expression profiling of lung adenocarcinomas: Correlation with mutational status. Mod Pathol 23: 1577-1582.
11. Dafou D, Grun B, Sinclair J, Lawrenson K, Benjamin E, Hogdall E, Kruger-Kjaer S, Christensen L, Sowter H, Al-Attar A, Edmondson R, Darby S, Berchuck A, Laird PW, Pearce CL, Ramus SJ, Jacobs IJ, Gayther SA. 2010. Microcell-mediated chromosome transfer identifies EPB41L3 as a functional suppressor of epithelial ovarian cancers. Neoplasia 2: 579-589.
12. Gao W, Yu Y, Cao H, Shen H, Li X, Pan S, Shu Y. Deregulated expression of miR-21, miR-143 and miR-181a in non small cell lung cancer is related to clinicopathologic characteristics or patient prognosis. Biomed Pharmacother 64: 399-408.
13. Gray S, Al-Sarraf N, Baird A, Gately K, McGovern E, O'Byrne K. 2008. Transcriptional regulation of IRS5/DOK4 expression in non-small-cell lung cancer cells. Clin Lung Cancer 9: 367-374.
14. Guled M, Lahti L, Lindholm PM, Salmenkivi K, Bagwan I, Nicholson AG, Knuutila S. 2009. CDKN2A, NF2, and JUN are dysregulated among other genes by miRNAs in malignant mesotheliomaâ€"A miRNA microarray analysis. Genes Chromosomes Cancer 48: 615-623.
15. Han C, Cho J, Moon J, Kim H, Kim S, Shin D, Chang J, Ahn C, Kim S, Chang Y. 2006. Clinical significance of insulin receptor substrate-I down-regulation in non-small cell lung cancer. Oncol Rep 16: 1205-1210.
16. Husgafvel-Pursiainen K, Karjalainen A, Kannio A, Anttila S, Partanen T, Ojajärvi A, Vainio H. 1999. Lung cancer and past occupational exposure to asbestos. Role of p53 and K-ras mutations. Am J Respir Cell Mol Biol 20: 667-674.
17. Inamura K, Togashi Y, Nomura K, Ninomiya H, Hiramatsu M, Satoh Y, Okumura S, Nakagawa K, Ishikawa Y. 2007. let-7 microRNA expression is reduced in bronchioloalveolar carcinoma, a non-invasive carcinoma, and is not correlated with prognosis. Lung Cancer 58: 392-396.
18. Karjalainen A, Anttila S, Heikkila L, Karhunen P, Vainio H. 1993. Asbestos exposure among Finnish lung cancer patients: Occupational history and fiber concentration in lung tissue. Am J Ind Med 23: 461-471.
19. Karjalainen A, Anttila S, Vanhala E, Vainio H. 1994. Asbestos exposure and the risk of lung cancer in a general urban population. Scand J Work Environ Health 20: 243-250.
20. Kettunen E, Aavikko M, Nymark P, Ruosaari S, Wikman H, Vanhala E, Salmenkivi K, Pirinen R, Karjalainen A, Kuosma E, Anttila, S. 2009. DNA copy number loss and allelic imbalance at 2p16 in lung cancer associated with asbestos exposure. Br J Cancer 100: 1336-1342.
21. Kim J, Lee J, Lee K, Lee J, Lee K, Jang K, Heo J, Choi S, Rhee J. 2010. RGS16 and FosB underexpressed in pancreatic cancer with lymph node metastasis promote tumor progression. Tumour Biol 31: 541-548.
22. Komiya T, Coxon A, Park Y, Chen W-D, Zajac-Kaye M, Meltzer P, Karpova T, Kaye FJ. 2010. Enhanced activity of the CREB co-activator Crtc1 in LKB1 null lung cancer. Oncogene 29: 1672-1680.
23. LaDou J. 2004. The asbestos cancer epidemic. Environ Health Perspect 112: 285-290.
24. Lahti L, Myllykangas S, Knuutila S, Kaski S. 2009. Dependency detection with similarity constraints. In: Adali T, Chanussot J, Jutten C, Larsen J, editors. Proceedings of the 2009 IEEE International Workshop on Machine Learning for Signal Processing XIX; Piscataway, NJ. pp. 89-94.
25. Lebanony D, Benjamin H, Gilad S, Ezagouri M, Dov A, Ashkenazi K, Gefen N, Izraeli S, Rechavi G, Pass H, Nonaka D, Li J, Spector Y, Rosenfeld N, Chajut A, Cohen D, Aharonov R, Mansukhani M. 2009. Diagnostic assay based on hsa-miR-205 expression distinguishes squamous from nonsquamous non-small-cell lung carcinoma. J Clin Oncol 27: 2030-2037.
26. Levin N, Brzoska P, Gupta N, Minna J, Gray J, Christman M. 1994. Identification of frequent novel genetic alterations in small cell lung carcinoma. Cancer Res 54: 5086-5091.
27. Liu K, Wang G, Ding H, Chen Y, Yu G, Wang J. 2010. Downregulation of metastasis suppressor 1(MTSS1) is associated with nodal metastasis and poor outcome in Chinese patients with gastric cancer. BMC Cancer 10: 428a.
28. Liu T, Tang H, Lang Y, Liu M, Li X. 2009. MicroRNA-27a functions as an oncogene in gastric adenocarcinoma by targeting prohibitin. Cancer Lett 273: 233-242.
29. Liu X, Sempere LF, Ouyang H, Memoli VA, Andrew AS, Luo Y, Demidenko E, Korc M, Shi W, Preis M, Dragnev KH, Li H, DiRenzo J, Bak M, Freemantle SJ, Kauppinen S, Dmitrovsky E. 2010. MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest 120: 1298-1309b.
30. Lopez-Romero P, Gonzalez M, Callejas S, Dopazo A, Irizarry R. 2010. Processing of Agilent microRNA array data. BMC Res Notes 3: 18.
31. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. 2005. MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
32. Marsit CJ, Hasegawa M, Hirao T, Kim D-H, Aldape K, Hinds PW, Wiencke JK, Nelson HH, Kelsey KT. 2004. Loss of heterozygosity of chromosome 3p21 is associated with mutant TP53 and better patient survival in non-small-cell lung cancer. Cancer Res 64: 8702-8707.
33. Mascaux C, Laes JF, Anthoine G, Haller A, Ninane V, Burny A, Sculier JP. 2009. Evolution of microRNA expression during human bronchial squamous carcinogenesis. Eur Respir J 33: 352-359.
34. Matsushima K, Isomoto H, Kohno S, Nakao K. 2010. MicroRNAs and esophageal squamous cell carcinoma. Digestion 82: 138-144.
35. Medina P, Castillo S, Blanco S, Sanz-Garcia M, Largo C, Alvarez S, Yokota J, Gonzalez-Neira A, Benitez J, Clevers H, Cigudosa JC, Lazo PA, Sanchez- Cespedes M. 2009. The SRY-HMG box gene, SOX4, is a target of gene amplification at chromosome 6p in lung cancer. Hum Mol Gen 18: 1343-1352.
36. Myllarniemi M, Lindholm P, Ryynanen MJ, Kliment CR, Salmenkivi K, Keski-Oja J, Kinnula VL, Oury TD, Koli K. 2008. Gremlin-mediated decrease in bone morphogenetic protein signaling promotes pulmonary fibrosis. Am J Respir Crit Care Med 177: 321-329.
37. Navon R, Wang H, Steinfeld I, Tsalenko A, Ben-Dor A, Yakhini Z. 2009. Novel rank-based statistical methods reveal MicroRNAs with differential expression in multiple cancer types. PLoS ONE 4: e8003.
38. Neri M, Ugolini D, Dianzani I, Gemignani F, Landi S, Cesario A, Magnani C, Mutti L, Puntoni R, Bonassi S. 2008. Genetic susceptibility to malignant pleural mesothelioma and other asbestos-associated diseases. Mutat Res/Rev Mutat Res/Proc 5th Int Conf Environ Mutagens Hum Populations (ICEMHP) 659: 126-136.
39. Nymark P, Wikman H, Ruosaari S, Hollmen J, Vanhala E, Karjalainen A, Anttila S, Knuutila S. 2006. Identification of specific gene copy number changes in asbestos-related lung cancer. Cancer Res 66: 5737-5743.
40. Nymark P, Wikman H, Hienonen-Kempas T, Anttila S. 2008. Molecular and genetic changes in asbestos-related lung cancer. Cancer Lett 265: 1-15.
41. Nymark P, Kettunen E, Aavikko M, Ruosaari S, Kuosma E, Vanhala E, Salmenkivi K, Pirinen R, Karjalainen A, Knuutila S, Wikman H, Anttila S. 2009. Molecular alterations at 9q33.1 and polyploidy in asbestos-related lung cancer. Clin Canc Res 15: 468-475.
42. Parr C, Jiang WG. 2009. Metastasis suppressor 1 (MTSS1) demonstrates prognostic value and anti-metastatic properties in breast cancer. Eur J Cancer 45: 1673-1683.
43. Pizzimenti S, Ferracin M, Sabbioni S, Toaldo C, Pettazzoni P, Dianzani MU, Negrini M, Barrera G. 2009. MicroRNA expression changes during human leukemic HL-60 cell differentiation induced by 4-hydroxynonenal, a product of lipid peroxidation. Free Radic Biol Med 46: 282-288.
44. Poli G, Schaur R, Siems W, Leonarduzzi G. 2008. 4-Hydroxynonenal: A membrane lipid oxidation product of medicinal interest. Med Res Rev 28: 569-631.
45. Pradervand S, Weber J, Thomas Jrm, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. 2009. Impact of normalization on miRNA microarray expression profiling. RNA 15: 493-501.
46. Ruosaari S, Nymark P, Aavikko M, Kettunen E, Knuutila S, Hollmen J, Norppa H, Anttila S. 2008. Aberrations of chromosome 19 in asbestos-associated lung cancer and in asbestos-induced micronuclei of bronchial epithelial cells in vitro. Carcinogenesis 29: 913-917.
47. Rydzanicz M, Giefing M, Ziolkowski A, Kasprzyk M, Gabriel A, Dyszkiewicz W, Szyfter K. 2008. Nonrandom DNA copy number changes related to lymph node metastases in squamous cell carcinoma of the lung. Neoplasma 55: 493-500.
48. Sanchez-Cespedes M, Ahrendt SA, Piantadosi S, Rosell R, Monzo M, Wu L, Westra WH, Yang SC, Jen J, Sidransky D. 2001. Chromosomal Alterations in Lung Adenocarcinoma from Smokers and Nonsmokers. Cancer Res 61: 1309-1313.
49. Shukla A, Ramos-Nino M, Mossman B. 2003. Cell signaling and transcription factor activation by asbestos in lung injury and disease. Int J Biochem. Cell Biol 35: 1198-1209.
50. Suda K, Tomizawa K, Mitsudomi T. 2010. Biological and clinical significance of KRAS mutations in lung cancer: An oncogenic driver that contrasts with EGFR mutation. Cancer Metas Rev 29: 49-60.
51. Tam CW, Liu VWS, Leung WY, Yao K-M, Shiu SYW. 2008. The autocrine human secreted PDZ domain-containing protein 2 (sPDZD2) induces senescence or quiescence of prostate, breast and liver cancer cells via transcriptional activation of p53. Cancer Lett 271: 64-80.
52. Vainio H, Boffetta P. 1994. Mechanisms of the combined effect of asbestos and smoking in the etiology of lung cancer. Scand J Work Environ Health 20: 235-242.
53. Wang Q, Xu W, Habib N, Xu R. 2009. Potential uses of microRNA in lung cancer diagnosis, prognosis, and therapy. Curr Cancer Drug Targ 9: 572-594.
54. Venkatraman E, Olshen A. 2007. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
55. Wikman H, Ruosaari S, Nymark P, Sarhadi V, Saharinen J, Vanhala E, Karjalainen A, Hollmén J, Knuutila S, Anttila S. 2007. Gene expression and copy number profiling suggests the importance of allelic imbalance in 19p in asbestos-associated lung cancer. Oncogene 26: 4730-4737.
56. Wu X, Piper-Hunter MG, Crawford M, Nuovo GJ, Marsh CB, Otterson GA, Nana-Sinkam SP. 2009. MicroRNAs in the pathogenesis of lung cancer. J Thorac Oncol 4: 1028-1034.
57. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, Calin GA, Liu C-G, Croce CM, Harris CC. 2006. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9: 189-198.
58. Zerbini L, Libermann T. 2005. GADD45 deregulation in cancer: frequently methylated tumor suppressors and potential therapeutic targets. Clin Cancer Res 11: 6409-6413.