Integrated genomic characterization of adrenocortical carcinoma

Nature Genetics

Volumn 46, Issue 6, 2014, Pages 607-612

  Assié, Guillaume ^a,d   Letouzé, Eric ^e   Fassnacht, Martin ^f,g,h   Jouinot, Anne ^a,b,c   Luscap, Windy ^a,b,c   Barreau, Olivia ^a,b,c,d   Omeiri, Hanin ^a,b,c   Rodriguez, Stéphanie ^a,b,c   Perlemoine, Karine ^a,b,c   René Corail, Fernande ^a,b,c   Elarouci, Nabila ^e   Sbiera, Silviu ^f,g   Kroiss, Matthias ^h   Allolio, Bruno ^g   Waldmann, Jens ⁱ   Quinkler, Marcus ^j   Mannelli, Massimo ^k   Mantero, Franco ^l   Papathomas, Thomas ^m   De Krijger, Ronald ^m   Tabarin, Antoine ^n,o   Kerlan, Véronique ^o,p   Baudin, Eric ^o,q   Tissier, Frédérique ^a,b,c,r   Dousset, Bertrand ^a,b,c,d   Groussin, Lionel ^a,b,c,d   Amar, Laurence ^s   Clauser, Eric ^d   Bertagna, Xavier ^a,b,c,d,o   Ragazzon, Bruno ^a,b,c   Beuschlein, Felix ^f   Libé, Rossella ^a,b,c,d,o   De Reyniès, Aurélien ^e   Bertherat, Jérôme ^a,b,c,d,o   more..

^a INSTITUT COCHIN   (France)

^b CNRS   (France)

^c UNIVERSITÉ PARIS DESCARTES   (France)

^d Center for Rare Adrenal Diseases Department of Endocrinology Hôpital Cochin ^*  (France)

^e Programme Cartes d'Identite des Tumeurs CIT   (France)

^f LUDWIG MAXIMILIANS UNIVERSITY   (Germany)

^g UNIVERSITY HOSPITAL WÜRZBURG   (Germany)

^h UNIVERSITY OF WÜRZBURG   (Germany)

ⁱ UNIVERSITY HOSPITAL MARBURG   (Germany)

^j CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^k UNIVERSITY OF FLORENCE   (Italy)

^l UNIVERSITY OF PADOVA   (Italy)

^m JOSEPHINE NEFKENS INSTITUTE   (Netherlands)

ⁿ BORDEAUX UNIVERSITY HOSPITAL   (France)

^o Rare Adrenal Cancer Network   (France)

^p BREST UNIVERSITY HOSPITAL   (France)

^q INSTITUT GUSTAVE ROUSSY   (France)

^r PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^s HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; MICRORNA; UBIQUITIN PROTEIN LIGASE E3;

ADRENAL CORTEX CARCINOMA; ARTICLE; CANCER PROGNOSIS; CDKN2A GENE; CTNNB1 GENE; DAXX GENE; DNA METHYLATION; EXOME; GENE CLUSTER; GENE MUTATION; GENE SEQUENCE; GENOMICS; HUMAN; HUMAN TISSUE; MED12 GENE; MEN1 GENE; ONCOGENE; PRIORITY JOURNAL; RB1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TERT GENE; TP53 GENE; TUMOR SUPPRESSOR GENE; ZNRF3 GENE;

ADOLESCENT; ADRENAL CORTEX NEOPLASMS; ADRENOCORTICAL CARCINOMA; ADULT; AGED; AGED, 80 AND OVER; BETA CATENIN; COHORT STUDIES; DNA METHYLATION; DNA MUTATIONAL ANALYSIS; EXOME; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; LOSS OF HETEROZYGOSITY; MALE; MICRORNAS; MIDDLE AGED; MULTIGENE FAMILY; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGNOSIS; TELOMERE; UBIQUITIN-PROTEIN LIGASES; YOUNG ADULT;

EID: 84901648115     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2953     Document Type: Article

References (75)

1. Schteingart, D.E. et al. Management of patients with adrenal cancer: recommendations of an international consensus conference. Endocr. Relat. Cancer 12, 667-680 (2005).
2. Abiven, G. et al. Clinical and biological features in the prognosis of adrenocortical cancer: poor outcome of cortisol-secreting tumors in a series of 202 consecutive patients. J. Clin. Endocrinol. Metab. 91, 2650-2655 (2006).
3. Fassnacht, M. et al. Limited prognostic value of the 2004 International Union Against Cancer staging classification for adrenocortical carcinoma: proposal for a Revised TNM Classification. Cancer 115, 243-250 (2009).
4. Wandoloski, M., Bussey, K.J. & Demeure, M.J. Adrenocortical cancer. Surg. Clin. North Am. 89, 1255-1267 (2009).
5. Soon, P.S.H. & Sidhu, S.B. Molecular basis of adrenocortical carcinomas. Minerva Endocrinol. 34, 137-147 (2009).
6. Hao, H.-X. et al. ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner. Nature 485, 195-200 (2012).
7. Grumbach, M.M. et al. Management of the clinically inapparent adrenal mass ('incidentaloma'). Ann. Intern. Med. 138, 424-429 (2003).
8. Kebebew, E., Reiff, E., Duh, Q.-Y., Clark, O.H. & McMillan, A. Extent of disease at presentation and outcome for adrenocortical carcinoma: have we made progress? World J. Surg. 30, 872-878 (2006).
9. Kerkhofs, T.M.A. et al. Adrenocortical carcinoma: a population-based study on incidence and survival in the Netherlands since 1993. Eur. J. Cancer 49, 2579-2586 (2013).
10. Luton, J.-P. et al. Clinical features of adrenocortical carcinoma, prognostic factors, and the effect of mitotane therapy. N. Engl. J. Med. 322, 1195-1201 (1990).
11. Icard, P. et al. Adrenocortical carcinomas: surgical trends and results of a 253-patient series from the French Association of Endocrine Surgeons study group. World J. Surg. 25, 891-897 (2001).
12. Allolio, B. & Fassnacht, M. Clinical review: adrenocortical carcinoma: clinical update. J. Clin. Endocrinol. Metab. 91, 2027-2037 (2006).
13. Fassnacht, M. et al. Combination chemotherapy in advanced adrenocortical carcinoma. N. Engl. J. Med. 366, 2189-2197 (2012).
14. Libè, R., Fratticci, A. & Bertherat, J. Adrenocortical cancer: pathophysiology and clinical management. Endocr. Relat. Cancer 14, 13-28 (2007).
15. Tissier, F. et al. Mutations of β-catenin in adrenocortical tumors: activation of the Wnt signaling pathway is a frequent event in both benign and malignant adrenocortical tumors. Cancer Res. 65, 7622-7627 (2005).
16. de Reyniès, A. et al. Gene expression profiling reveals a new classification of adrenocortical tumors and identifies molecular predictors of malignancy and survival. J. Clin. Oncol. 27, 1108-1115 (2009).
17. Giordano, T.J. et al. Molecular classification and prognostication of adrenocortical tumors by transcriptome profiling. Clin. Cancer Res. 15, 668-676 (2009).
18. Laurell, C. et al. Transcriptional profiling enables molecular classification of adrenocortical tumours. Eur. J. Endocrinol. 161, 141-152 (2009).
19. Barreau, O. et al. Clinical and pathophysiological implications of chromosomal alterations in adrenocortical tumors: an integrated genomic approach. J. Clin. Endocrinol. Metab. 97, E301-E311 (2012).
20. Stephan, E.A. et al. Adrenocortical carcinoma survival rates correlated to genomic copy number variants. Mol. Cancer Ther. 7, 425-431 (2008).
21. De Martino, M.C. et al. Molecular screening for a personalized treatment approach in advanced adrenocortical cancer. J. Clin. Endocrinol. Metab. 98, 4080-4088 (2013).
22. Ronchi, C.L. et al. Single nucleotide polymorphism array profiling of adrenocortical tumors-evidence for an adenoma carcinoma sequence? PLoS ONE 8, e73959 (2013).
23. Barreau, O. et al. Identification of a CpG island methylator phenotype in adrenocortical carcinomas. J. Clin. Endocrinol. Metab. 98, E174-E184 (2013).
24. Rechache, N.S. et al. DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors. J. Clin. Endocrinol. Metab. 97, E1004-E1013 (2012).
25. Fonseca, A.L. et al. Comprehensive DNA methylation analysis of benign and malignant adrenocortical tumors. Genes Chromosom. Cancer 51, 949-960 (2012).
26. Soon, P.S.H. et al. miR-195 and miR-483-5p identified as predictors of poor prognosis in adrenocortical cancer. Clin. Cancer Res. 15, 7684-7692 (2009).
27. Tömböl, Z. et al. Integrative molecular bioinformatics study of human adrenocortical tumors: microRNA, tissue-specific target prediction, and pathway analysis. Endocr. Relat. Cancer 16, 895-906 (2009).
28. Patterson, E.E., Holloway, A.K., Weng, J., Fojo, T. & Kebebew, E. MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy. Cancer 117, 1630-1639 (2011).
29. Schmitz, K.J. et al. Differential expression of microRNA-675, microRNA-139-3p and microRNA-335 in benign and malignant adrenocortical tumours. J. Clin. Pathol. 64, 529-535 (2011).
30. Özata, D.M. et al. The role of microRNA deregulation in the pathogenesis of adrenocortical carcinoma. Endocr. Relat. Cancer 18, 643-655 (2011).
31. Chabre, O. et al. Serum miR-483-5p and miR-195 are predictive of recurrence risk in adrenocortical cancer patients. Endocr. Relat. Cancer 20, 579-594 (2013).
32. Guichard, C. et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat. Genet. 44, 694-698 (2012).
33. Gicquel, C. et al. Rearrangements at the 11p15 locus and overexpression of insulin-like growth factor-II gene in sporadic adrenocortical tumors. J. Clin. Endocrinol. Metab. 78, 1444-1453 (1994).
34. Pasic, I. et al. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res. 70, 160-171 (2010).
35. Liu, Q. et al. LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Res. 41, 4976-4987 (2013).
36. Zack, T.I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134-1140 (2013).
37. Du, Z. et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat. Struct. Mol. Biol. 20, 908-913 (2013).
38. Cheetham, S.W., Gruhl, F., Mattick, J.S. & Dinger, M.E. Long noncoding RNAs and the genetics of cancer. Br. J. Cancer 108, 2419-2425 (2013).
39. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158 (2007).
40. Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
41. Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
42. Gonzalez-Perez, A., Jene-Sanz, A. & Lopez-Bigas, N. The mutational landscape of chromatin regulatory factors across 4623 tumor samples. Genome Biol. 14, r106 (2013).
43. Heaphy, C.M. et al. Altered telomeres in tumors with ATRX and DAXX mutations. Science 333, 425 (2011).
44. Mäkinen, N. et al. MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas. Science 334, 252-255 (2011).
45. Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
46. Kim, S., Xu, X., Hecht, A. & Boyer, T.G. Mediator is a transducer of Wnt/β-catenin signaling. J. Biol. Chem. 281, 14066-14075 (2006).
47. Houseman, E.A. et al. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 9, 365 (2008).
48. Streicher, K.L. et al. A novel oncogenic role for the miRNA-506-514 cluster in initiating melanocyte transformation and promoting melanoma growth. Oncogene 31, 1558-1570 (2012).
49. Benetatos, L. et al. The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis. Cell. Mol. Life Sci. 70, 795-814 (2013).
50. Cheunsuchon, P. et al. Silencing of the imprinted DLK1-MEG3 locus in human clinically nonfunctioning pituitary adenomas. Am. J. Pathol. 179, 2120-2130 (2011).
51. Zhang, L. et al. Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proc. Natl. Acad. Sci. USA 105, 7004-7009 (2008).
52. Haga, C.L. & Phinney, D.G. MicroRNAs in the imprinted DLK1-DIO3 region repress the epithelial-to-mesenchymal transition by targeting the TWIST1 protein signaling network. J. Biol. Chem. 287, 42695-42707 (2012).
53. Zhou, Y. et al. Activation of p53 by MEG3 non-coding RNA. J. Biol. Chem. 282, 24731-24742 (2007).
54. Plouin, P.-F., Gimenez-Roqueplo, A.-P. & Bertagna, X. COMETE, a network for the study and management of hypersecreting adrenal tumors. Bull. Acad. Natl. Med. 192, 73-82 (2008).
55. Stell, A. & Sinnott, R. The ENSAT registry: a digital repository supporting adrenal cancer research. Stud. Health Technol. Inform. 178, 207-212 (2012).
56. Bibikova, M. et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 1, 177-200 (2009).
57. Staaf, J. et al. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 9, 409 (2008).
58. Venkatraman, E.S. & Olshen, A.B. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23, 657-663 (2007).
59. Popova, T. et al. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol. 10, R128 (2009).
60. Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
61. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189 (2009).
62. Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24-26 (2011).
63. Chen, C.-L. et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res. 20, 447-457 (2010).
64. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
65. Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
66. Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).
67. Henson, J.D. et al. DNA C-circles are specific and quantifiable markers of alternative-lengthening-of-telomeres activity. Nat. Biotechnol. 27, 1181-1185 (2009).
68. Hinoue, T. et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 22, 271-282 (2012).
69. Monti, S., Tamayo, P., Mesirov, J. & Golub, T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52, 91-118 (2003).
70. Jung, A.C. et al. A poor prognosis subtype of HNSCC is consistently observed across methylome, transcriptome and miRNome analysis. Clin. Cancer Res. 19, 4174-4184 (2013).
71. Vigneault, F. et al. High-throughput multiplex sequencing of miRNA. Curr. Protoc. Hum. Genet. Chapter 11, Unit 11.12.1-10 (2012).
72. Wang, W.-C. et al. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 10, 328 (2009).
73. Hackenberg, M., Rodríguez-Ezpeleta, N. & Aransay, A.M. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res. 39, W132-W138 (2011).
74. Kozomara, A. & Griffiths-Jones, S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157 (2011).
75. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).