Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Fontaine, Jean Fred ^a,b,c   Mirebeau Prunier, Delphine ^b,c,d   Raharijona, Mahatsangy ^e,f   Franc, Brigitte ^g   Triau, Stephane ^d   Rodien, Patrice ^b,c,d   Goëau Brissonniére, Olivier ^g   Karayan Tapon, Lucie ^h   Mello, Marielle ^b   Houlgatte, Rémi ^e,f   Malthiery, Yves ^b,c,d   Savagner, Frédérique ^b,c,d,e  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b INSERM   (France)

^c UNIVERSITÉ D'ANGERS   (France)

^d ANGERS UNIVERSITY HOSPITAL   (France)

^e L INSTITUT DU THORAX   (France)

^f UNIVERSITÉ DE NANTES   (France)

^g HÔPITAL AMBROISE PARÉ   (France)

^h UNIVERSITÉ DE POITIERS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN D; APOLIPOPROTEIN E; CASPASE 10; HIGH MOBILITY GROUP B2 PROTEIN; ONCOPROTEIN; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PROTEIN ADAMTS2; PROTEIN ALDH1A3; PROTEIN CABIN1; PROTEIN CDH16; PROTEIN CLGN; PROTEIN CRABP1; PROTEIN KRTHB5; PROTEIN NR2F2; PROTEIN SDHA; PROTEIN USP13; THYROTROPIN RECEPTOR; TISSUE INHIBITOR OF METALLOPROTEINASE 1; TRANSCRIPTION FACTOR PAX8; TUMOR MARKER; UNCLASSIFIED DRUG; PAIRED BOX TRANSCRIPTION FACTOR; PAX8 PROTEIN, HUMAN; PRIMER DNA;

ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC VALUE; DOWN REGULATION; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE MUTATION; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; MUTATIONAL ANALYSIS; PREDICTION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; THYROID CANCER; THYROID FOLLICULAR CARCINOMA; BIOSYNTHESIS; CHEMISTRY; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETIC MARKER; METABOLISM; METHODOLOGY; MUTATION; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; THYROID GLAND; THYROID TUMOR;

CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; DNA PRIMERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC MARKERS; HUMANS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAIRED BOX TRANSCRIPTION FACTORS; PPAR GAMMA; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; THYROID GLAND; THYROID NEOPLASMS;

EID: 70449589689     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007632     Document Type: Article

References (52)

1. Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, et al. (2004) Largescale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 101: 9309-9314.
2. Hundahl SA, Fleming ID, Fremgen AM, Menck HR (1998) A National Cancer Data Base report on 53,856 cases of thyroid carcinoma treated in the U.S., 1985-1995. Cancer 83: 2638-2648.
3. Yeh MW, Demircan O, Ituarte P, Clark OH (2004) False-negative fine-needle aspiration cytology results delay treatment and adversely affect outcome in patients with thyroid carcinoma. Thyroid 14: 207-215.
4. Lacroix L, Lazar V, Michiels S, Ripoche H, Dessen P, et al. (2005) Follicular thyroid tumors with the PAX8-PPARgamma1 rearrangement display characteristic genetic alterations. Am J Pathol 167: 223-231.
5. Giordano TJ, Au AY, Kuick R, Thomas DG, Rhodes DR, et al. (2006) Delineation, functional validation, and bioinformatic evaluation of gene expression in thyroid follicular carcinomas with the PAX8-PPARG translocation. Clin Cancer Res 12: 1983-1993.
6. Barden CB, Shister KW, Zhu B, Guiter G, Greenblatt DY, et al. (2003) Classification of follicular thyroid tumors by molecular signature: results of gene profiling. Clin Cancer Res 9: 1792-1800.
7. Nikiforova MN, Lynch RA, Biddinger PW, Alexander EK, Dorn GW, et al. (2003) RAS point mutations and PAX8-PPAR gamma rearrangement in thyroid tumors: evidence for distinct molecular pathways in thyroid follicular carcinoma. J Clin Endocrinol Metab 88: 2318-2326.
8. Aldred MA, Huang Y, Liyanarachchi S, Pellegata NS, Gimm O, et al. (2004) Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol 22: 3531-3539.
9. Huang Y, Prasad M, Lemon WJ, Hampel H, Wright FA, et al. (2001) Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. Proc Natl Acad Sci U S A 98: 15044-15049.
10. Jarzab B, Wiench M, Fujarewicz K, Simek K, Jarzab M, et al. (2005) Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res 65: 1587-1597.
11. Weber F, Shen L, Aldred MA, Morrison CD, Frilling A, et al. (2005) Genetic classification of benign and malignant thyroid follicular neoplasia based on a three-gene combination. J Clin Endocrinol Metab 90: 2512-2521.
12. Eszlinger M, Wiench M, Jarzab B, Krohn K, Beck M, et al. (2006) Meta- and reanalysis of gene expression profiles of hot and cold thyroid nodules and papillary thyroid carcinoma for gene groups. J Clin Endocrinol Metab 91: 1934-1942.
13. Griffith OL, Melck A, Jones SJ, Wiseman SM (2006) Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol 24: 5043-5051.
14. Finley DJ, Zhu B, Fahey TJ, III (2004) Molecular analysis of Hurthle cell neoplasms by gene profiling. Surgery 136: 1160-1168.
15. Fontaine JF, Mirebeau-Prunier D, Franc B, Triau S, Rodien P, et al. (2008) Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy. Oncogene 27: 2228-2236.
16. Stolf BS, Abreu CM, Mahler-Araujo MB, Dellamano M, Martins WK, et al. (2005) Expression profile of malignant and non-malignant diseases of the thyroid gland reveals altered expression of a common set of genes in goiter and papillary carcinomas. Cancer Lett 227: 59-73.
17. Yukinawa N, Oba S, Kato K, Taniguchi K, Iwao-Koizumi K, et al. (2006) A multi-class predictor based on a probabilistic model: application to gene expression profiling-based diagnosis of thyroid tumors. BMC Genomics 7: 190.
18. Eszlinger M, Krohn K, Hauptmann S, Dralle H, Giordano TJ, et al. (2008) Perspectives for improved and more accurate classification of thyroid epithelial tumors. J Clin Endocrinol Metab 93: 3286-3294.
19. Corvilain B, Van SJ, Dumont JE, Vassart G (2001) Somatic and germline mutations of the TSH receptor and thyroid diseases. Clin Endocrinol (Oxf) 55: 143-158.
20. Baris O, Savagner F, Nasser V, Loriod B, Granjeaud S, et al. (2004) Transcriptional profiling reveals coordinated up-regulation of oxidative metabolism genes in thyroid oncocytic tumors. J Clin Endocrinol Metab 89: 994-1005.
21. Wasenius VM, Hemmer S, Kettunen E, Knuutila S, Franssila K, et al. (2003) Hepatocyte growth factor receptor, matrix metalloproteinase-11, tissue inhibitor of metalloproteinase-1, and fibronectin are up-regulated in papillary thyroid carcinoma: a cDNA and tissue microarray study. Clin Cancer Res 9: 68-75.
22. Franc B, de la SP, Lange F, Hoang C, Louvel A, et al. (2003) Interobserver and intraobserver reproducibility in the histopathology of follicular thyroid carcinoma. Hum Pathol 34: 1092-1100.
23. Lloyd RV, Erickson LA, Casey MB, Lam KY, Lohse CM, et al. (2004) Observer variation in the diagnosis of follicular variant of papillary thyroid carcinoma. Am J Surg Pathol 28: 1336-1340.
24. Ao A, Wang H, Kamarajugadda S, Lu J (2008) Involvement of estrogen-related receptors in transcriptional response to hypoxia and growth of solid tumors. Proc Natl Acad Sci U S A 105: 7821-7826.
25. Sierra JR, Corso S, Caione L, Cepero V, Conrotto P, et al. (2008) Tumor angiogenesis and progression are enhanced by Sema4D produced by tumor-associated macrophages. J Exp Med 205: 1673-1685.
26. Taylor KL, Leaman DW, Grane R, Mechti N, Borden EC, et al. (2008) Identification of interferon-beta-stimulated genes that inhibit angiogenesis in vitro. J Interferon Cytokine Res 28: 733-740.
27. Nikiforova MN, Tseng GC, Steward D, Diorio D, Nikiforov YE (2008) MicroRNA expression profiling of thyroid tumors: biological significance and diagnostic utility. J Clin Endocrinol Metab 93: 1600-1608.
28. Nucera C, Mazzon E, Caillou B, Violi MA, Moleti M, et al. (2005) Human galectin-3 immunoexpression in thyroid follicular adenomas with cell atypia. J Endocrinol Invest 28: 106-112.
29. Fukumori T, Oka N, Takenaka Y, Nangia-Makker P, Elsamman E, et al. (2006) Galectin-3 regulates mitochondrial stability and antiapoptotic function in response to anticancer drug in prostate cancer. Cancer Res 66: 3114-3119.
30. Savin S, Cvejic D, Isic T, Paunovic I, Tatic S, et al. (2008) Thyroid peroxidase and galectin-3 immunostaining in differentiated thyroid carcinoma with clinicopathologic correlation. Hum Pathol in press.
31. Schmid KW, Farid NR (2006) How to define follicular thyroid carcinoma?. Virchows Arch 448: 385-393.
32. Wattel S, Mircescu H, Venet D, Burniat A, Franc B, et al. (2005) Gene expression in thyroid autonomous adenomas provides insight into their physiopathology. Oncogene 24: 6902-6916.
33. Carinci F, Lo ML, Piattelli A, Rubini C, Chiesa F, et al. (2005) Potential markers of tongue tumor progression selected by cDNA microarray. Int J Immunopathol Pharmacol 18: 513-524.
34. Porter S, Scott SD, Sassoon EM, Williams MR, Jones JL, et al. (2004) Dysregulated expression of adamalysin-thrombospondin genes in human breast carcinoma. Clin Cancer Res 10: 2429-2440.
35. Watanabe T, Kobunai T, Sakamoto E, Yamamoto Y, Konishi T, et al. (2009) Gene expression signature for recurrence in stage III colorectal cancers. Cancer 115: 283-292.
36. Soiland H, Soreide K, Janssen EA, Korner H, Baak JP, et al. (2007) Emerging concepts of apolipoprotein D with possible implications for breast cancer. Cell Oncol 29: 195-209.
37. Netea-Maier RT, Hunsucker SW, Hoevenaars BM, Helmke SM, Slootweg PJ, et al. (2008) Discovery and validation of protein abundance differences between follicular thyroid neoplasms. Cancer Res 68: 1572-1580.
38. Delys L, Detours V, Franc B, Thomas G, Bogdanova T, et al. (2007) Gene expression and the biological phenotype of papillary thyroid carcinomas. Oncogene 26: 7894-7903.
39. Hawthorn L, Stein L, Varma R, Wiseman S, Loree T, et al. (2004) TIMP1 and SERPIN-A overexpression and TFF3 and CRABP1 underexpression as biomarkers for papillary thyroid carcinoma. Head Neck 26: 1069-1083.
40. Huang Y, de la CA, Pellegata NS (2003) Hypermethylation, but not LOH, is associated with the low expression of MT1G and CRABP1 in papillary thyroid carcinoma. Int J Cancer 104: 735-744.
41. Eszlinger M, Krohn K, Berger K, Lauter J, Kropf S, et al. (2005) Gene expression analysis reveals evidence for increased expression of cell cycleassociated genes and Gq-protein-protein kinase C signaling in cold thyroid nodules. J Clin Endocrinol Metab 90: 1163-1170.
42. Barroeta JE, Baloch ZW, Lal P, Pasha TL, Zhang PJ, et al. (2006) Diagnostic value of differential expression of CK19, Galectin-3, HBME-1, ERK, RET, and p16 in benign and malignant follicular-derived lesions of the thyroid: an immunohistochemical tissue microarray analysis. Endocr Pathol 17: 225-234.
43. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 102: 19075-19080.
44. Jarzab B, Wiench M, Fujarewicz K, Simek K, Jarzab M, et al. (2005) Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res 65: 1587-1597.
45. Weber F, Shen L, Aldred MA, Morrison CD, Frilling A, et al. (2005) Genetic classification of benign and malignant thyroid follicular neoplasia based on a three-gene combination. J Clin Endocrinol Metab 90: 2512-2521.
46. Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J (2005) BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res 33: W460-W464.
47. Dudoit S, Fridlyand J (2002) A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol 3: 1-21.
48. Efron B, Tibshirani R (1997) Improvments of cross-validation: the.632+ bootstrap method. 92: 548-560.
49. Kubat M (1998) Decision trees can initialize radial-basis function networks. IEEE Trans Neural Netw 9: 813-821.
50. Vasko V, Ferrand M, Di CJ, Carayon P, Henry JF, et al. (2003) Specific pattern of RAS oncogene mutations in follicular thyroid tumors. J Clin Endocrinol Metab 88: 2745-2752.
51. Bourasseau I, Savagner F, Rodien P, Duquenne M, Reynier P, et al. (2000) No evidence of thyrotropin receptor and G(s alpha) gene mutation in high iodine uptake thyroid carcinoma. Thyroid 10: 761-765.
52. Kroll TG, Sarraf P, Pecciarini L, Chen CJ, Mueller E, et al. (2000) PAX8-PPARgamma1 fusion oncogene in human thyroid carcinoma. Science 289: 1357-1360.