Whole exome sequencing identifies somatic ATRX mutations in pheochromocytomas and paragangliomas

Nature Communications

Volumn 6, Issue , 2015, Pages

  Fishbein, Lauren ^a   Khare, Sanika ^a   Wubbenhorst, Bradley ^a   Desloover, Daniel ^a,b   D'Andrea, Kurt ^a   Merrill, Shana ^a   Cho, Nam Woo ^b   Greenberg, Roger A ^a,b   Else, Tobias ^c   Montone, Kathleen ^b   LiVolsi, Virginia ^a,b   Fraker, Douglas ^a,b   Daber, Robert ^b   Cohen, Debbie L ^a   Nathanson, Katherine L ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ATRX PROTEIN, HUMAN; CHROMATIN; DNA HELICASE; NUCLEAR PROTEIN; SDHB PROTEIN, HUMAN; SUCCINATE DEHYDROGENASE;

BRAIN; CELLS AND CELL COMPONENTS; CHROMOSOME; GENETIC ANALYSIS; MUTATION; NEUROLOGY; PROTEIN; TUMOR;

AMPLICON; ARTICLE; ATRX GENE; CARCINOGENESIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; EXOME; EXON; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CODE; GENETIC SUSCEPTIBILITY; GERMLINE MUTATION; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; PARAGANGLIOMA; PHENOTYPE; PHEOCHROMOCYTOMA; SEGMENTAL DUPLICATION; SOMATIC MUTATION; TELOMERE; TELOMERE HOMEOSTASIS; WHOLE EXOME SEQUENCING; X CHROMOSOME; ADRENAL TUMOR; CHEMISTRY; CHROMATIN; GENE EXPRESSION; GENETIC PREDISPOSITION; GENETICS; HEAD AND NECK TUMOR; HIGH THROUGHPUT SEQUENCING; METABOLISM; MUTATION; PATHOLOGY; ULTRASTRUCTURE;

ADRENAL GLAND NEOPLASMS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA HELICASES; EXOME; GENE EXPRESSION; GENETIC PREDISPOSITION TO DISEASE; HEAD AND NECK NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NUCLEAR PROTEINS; PARAGANGLIOMA; PHEOCHROMOCYTOMA; SUCCINATE DEHYDROGENASE; TELOMERE; TELOMERE HOMEOSTASIS;

EID: 84928566914     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7140     Document Type: Article

References (46)

1. Dahia PL. Pheochromocytoma and paraganglioma pathogenesis: learning from genetic heterogeneity. Nat Rev Cancer. 2014;14:108-119. [PubMed: 24442145]
2. Cho NH, et al. Genetic aberrance of sporadic MEN 2A component tumours: analysis of RET. Pathology. 2005;37:10-13. [PubMed: 15875728]
3. Hrascan R, et al. Analysis of selected genes in neuroendocrine tumours: insulinomas and phaeochromocytomas. J Neuroendocrinol. 2008;20:1015-1022. [PubMed: 18510707]
4. Kimura T, Yoshimoto K, Yokogoshi Y, Saito S. Mutations in the cysteine-rich region of the RET proto-oncogene in patients diagnosed as having sporadic medullary thyroid carcinoma. Endocr J. 1995;42:517-525. [PubMed: 8556059]
5. Komminoth P, et al. Detection of RET proto-oncogene point mutations in paraffin-embedded pheochromocytoma specimens by nonradioactive single-strand conformation polymorphism analysis and direct sequencing. Am J Pathol. 1994;145:922-929. [PubMed: 7943181]
6. Van Der Harst E, et al. Prognostic value of RET proto-oncogene point mutations in malignant and benign, sporadic phaeochromocytomas. Int J Cancer. 1998;79:537-540. [PubMed: 9761126]
7. Crona J, et al. Somatic Mutations in H-RAS in Sporadic Pheochromocytoma and Paraganglioma Identified by Exome Sequencing. J Clin Endocrinol Metab. 2013
8. Burnichon N, et al. Somatic NF1 inactivation is a frequent event in sporadic pheochromocytoma. Hum Mol Genet. 2012;21:5397-5405. [PubMed: 22962301]
9. Burnichon N, et al. Integrative Genomic Analysis Reveals Somatic Mutations in Pheochromocytoma and Paraganglioma. Hum Mol Genet. 2011
10. Welander J, et al. Rare germline mutations identified by targeted next-generation sequencing of susceptibility genes in pheochromocytoma and paraganglioma. J Clin Endocrinol Metab. 2014 jc20134375.
11. Welander J, et al. Integrative genomics reveals frequent somatic NF1 mutations in sporadic pheochromocytomas. Hum Mol Genet. 2012;21:5406-5416. [PubMed: 23010473]
12. Gimm O, Armanios M, Dziema H, Neumann HP, Eng C. Somatic and occult germ-line mutations in SDHD, a mitochondrial complex II gene, in nonfamilial pheochromocytoma. Cancer Res. 2000;60:6822-6825. [PubMed: 11156372]
13. Pasini B, Stratakis CA. SDH mutations in tumorigenesis and inherited endocrine tumours: lesson from the phaeochromocytoma-paraganglioma syndromes. J Intern Med. 2009;266:19-42. [PubMed: 19522823]
14. Van Nederveen FH, Korpershoek E, Lenders JW, De Krijger RR, Dinjens WN. Somatic SDHB mutation in an extraadrenal pheochromocytoma. N Engl J Med. 2007;357:306-308. [PubMed: 17634472]
15. DeLellis, RA.; Lloyd, RV.; Heitz, PU.; Eng, C., editors. Pathology and Genetics of Tumours of Endocrine Organs. Lyon, France: IARC Press; 2004. World Health Organization Classification of Tumours.
16. Jimenez C, et al. Current and Future Treatments for Malignant Pheochromocytoma and Sympathetic Paraganglioma. Curr Oncol Rep. 2013
17. Parenti G, et al. Updated and new perspectives on diagnosis, prognosis, and therapy of malignant pheochromocytoma/paraganglioma. J Oncol. 2012;2012:872713. [PubMed: 22851969]
18. Fishbein L, Nathanson KL. Pheochromocytoma and paraganglioma: understanding the complexities of the genetic background. Cancer Genet. 2012;205:1-11. [PubMed: 22429592]
19. Fishbein L, Merrill S, Fraker DL, Cohen DL, Nathanson KL. Inherited mutations in pheochromocytoma and paraganglioma: why all patients should be offered genetic testing. Ann Surg Oncol. 2013;20:1444-1450. [PubMed: 23512077]
20. Jiao Y, et al. DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science. 2011;331:1199-1203. [PubMed: 21252315]
21. Pugh TJ, et al. The genetic landscape of high-risk neuroblastoma. Nat Genet. 2013;45:279-284. [PubMed: 23334666]
22. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812-3814. [PubMed: 12824425]
23. Adzhubei IA, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-249. [PubMed: 20354512]
24. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575-576. [PubMed: 20676075]
25. Cheung NK, et al. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA. 2012;307:1062-1071. [PubMed: 22416102]
26. Kannan K, et al. Whole-exome sequencing identifies ATRX mutation as a key molecular determinant in lower-grade glioma. Oncotarget. 2012;3:1194-1203. [PubMed: 23104868]
27. Schwartzentruber J, et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012;482:226-231. [PubMed: 22286061]
28. Heaphy CM, et al. Altered telomeres in tumors with ATRX and DAXX mutations. Science. 2011;333:425. [PubMed: 21719641]
29. Lovejoy CA, et al. Loss of ATRX, genome instability, and an altered DNA damage response are hallmarks of the alternative lengthening of telomeres pathway. PLoS Genet. 2012;8:e1002772. [PubMed: 22829774]
30. Jiao Y, et al. Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas. Oncotarget. 2012;3:709-722. [PubMed: 22869205]
31. Ratnakumar K, Bernstein E. ATRX: the case of a peculiar chromatin remodeler. Epigenetics. 2013;8:3-9. [PubMed: 23249563]
32. Drane P, Ouararhni K, Depaux A, Shuaib M, Hamiche A. The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev. 2010;24:1253-1265. [PubMed: 20504901]
33. Lewis PW, Elsaesser SJ, Noh KM, Stadler SC, Allis CD. Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres. Proc Natl Acad Sci USA. 2010;107:14075-14080. [PubMed: 20651253]
34. Abedalthagafi M, et al. The alternative lengthening of telomere phenotype is significantly associated with loss of ATRX expression in high-grade pediatric and adult astrocytomas: a multiinstitutional study of 214 astrocytomas. Mod Pathol. 2013;26:1425-1432. [PubMed: 23765250]
35. Ratnakumar K, et al. ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha-globin expression. Genes Dev. 2012;26:433-438. [PubMed: 22391447]
36. Goldberg AD, et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell. 2010;140:678-691. [PubMed: 20211137]
37. Killian JK, et al. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 2013;3:648-657. [PubMed: 23550148]
38. Letouze E, et al. SDH mutations establish a hypermethylator phenotype in paraganglioma. Cancer Cell. 2013;23:739-752. [PubMed: 23707781]
39. Yang M, Pollard PJ. Succinate: a new epigenetic hacker. Cancer Cell. 2013;23:709-711. [PubMed: 23763995]
40. Marinoni I, et al. Loss of DAXX and ATRX are associated with chromosome instability and reduced survival of patients with pancreatic neuroendocrine tumors. Gastroenterology. 2014;146:453-460. e5. [PubMed: 24148618]
41. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-595. [PubMed: 20080505]
42. DePristo MA, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-498. [PubMed: 21478889]
43. Chang X, Wang K. ANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet. 2012;49:433-436. [PubMed: 22717648]
44. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010;20:110-121. [PubMed: 19858363]
45. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat. 2011;32:894-899. [PubMed: 21520341]
46. Daber R, Sukhadia S, Morrissette JJ. Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets. Cancer Genet. 2013;206:441-448. [PubMed: 24528889]