The landscape of fusion transcripts in spitzoid melanoma and biologically indeterminate spitzoid tumors by RNA sequencing

Modern Pathology

Volumn 29, Issue 4, 2016, Pages 359-369

  Wu, Gang ^a   Barnhill, Raymond L ^b   Lee, Seungjae ^a   Li, Yongjin ^a   Shao, Ying ^a   Easton, John ^a   Dalton, James ^a   Zhang, Jinghui ^a   Pappo, Alberto ^a   Bahrami, Armita ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b INSTITUT CURIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; MESSENGER RNA; PARAFFIN; RNA; TELOMERASE; TRANSCRIPTOME; ONCOPROTEIN;

ADOLESCENT; ARTICLE; CHILD; CLINICAL ARTICLE; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; FOLLOW UP; FUSION GENE; GENE FUSION; HUMAN; HUMAN TISSUE; IN SITU HYBRIDIZATION; LANDSCAPE; MALE; MELANOMA; METASTASIS; ONCOGENE N RAS; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; SPITZOID TUMOR; GENETICS; NEVUS; PATHOLOGY; PRESCHOOL CHILD; SEQUENCE ANALYSIS; SKIN TUMOR;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; FEMALE; HUMANS; IN SITU HYBRIDIZATION; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; MELANOMA; NEVUS, EPITHELIOID AND SPINDLE CELL; ONCOGENE PROTEINS, FUSION; RNA; SEQUENCE ANALYSIS, RNA; SKIN NEOPLASMS; TELOMERASE;

EID: 84958818367     PISSN: 08933952     EISSN: 15300285     Source Type: Journal    
DOI: 10.1038/modpathol.2016.37     Document Type: Article

References (42)

1. Reed D, Kudchadkar R, Zager JS et al. Controversies in the evaluation and management of atypical melanocytic proliferations in children, adolescents, and young adults. J Natl Compr Canc Netw 2013;11:679-686
2. Barnhill RL, Argenyi ZB, From L et al. Atypical Spitz nevi/tumors: lack of consensus for diagnosis, discrimination from melanoma, and prediction of outcome. Hum Pathol 1999;30:513-520
3. Gerami P, Busam K, Cochran A et al. Histomorphologic assessment and interobserver diagnostic reproducibility of atypical spitzoid melanocytic neoplasms with long-term follow-up. Am J Surg Pathol 2014;38: 934-940
4. Spatz A, Barnhill RL. The Spitz tumor 50 years later: revisiting a landmark contribution and unresolved controversy. J Am Acad Dermatol 1999;40: 223-228
5. Cerroni L, Barnhill R, Elder D et al. Melanocytic tumors of uncertain malignant potential: results of a tutorial held at the XXIX Symposium of the International Society of Dermatopathology in Graz, October 2008. Am J Surg Pathol 2010;34:314-326
6. Paradela S, Fonseca E, Pita S et al. Spitzoid melanoma in children: clinicopathological study and application of immunohistochemistry as an adjunct diagnostic tool. J Cutan Pathol 2009;36:740-752
7. Berk DR, LaBuz E, Dadras SS et al. Melanoma and melanocytic tumors of uncertain malignant potential in children, adolescents and young adults-the Stanford experience 1995-2008. Pediatr Dermatol 2010;27: 244-254
8. Busam KJ, Pulitzer M. Sentinel lymph node biopsy for patients with diagnostically controversial Spitzoid melanocytic tumors? Adv Anat Pathol 2008;15: 253-262
9. Hung T, Piris A, Lobo A et al. Sentinel lymph node metastasis is not predictive of poor outcome in patients with problematic spitzoid melanocytic tumors. Hum Pathol 2013;44:87-94
10. Ludgate MW, Fullen DR, Lee J et al. The atypical Spitz tumor of uncertain biologic potential: a series of 67 patients from a single institution. Cancer 2009;115: 631-641
11. Lallas A, Kyrgidis A, Ferrara G et al. Atypical Spitz tumours and sentinel lymph node biopsy: a systematic review. Lancet Oncol 2014;15:e178-e183
12. Lee S, Barnhill RL, Dummer R et al. TERT promoter mutations are predictive of aggressive clinical behavior in patients with spitzoid melanocytic neoplasms. Sci Rep 2015;5:11200
13. Busam KJ, Murali R, Pulitzer M et al. Atypical spitzoid melanocytic tumors with positive sentinel lymph nodes in children and teenagers, and comparison with histologically unambiguous and lethal melanomas. Am J Surg Pathol 2009;33:1386-1395
14. Gerami P, Zembowicz A. Update on fluorescence in situ hybridization in melanoma: state of the art. Arch Pathol Lab Med 2011;135:830-837
15. Gerami P, Scolyer RA, Xu X et al. Risk assessment for atypical spitzoid melanocytic neoplasms using FISH to identify chromosomal copy number aberrations. Am J Surg Pathol 2013;37:676-684
16. Bastian BC, Olshen AB, LeBoit PE et al. Classifying melanocytic tumors based on DNA copy number changes. Am J Pathol 2003;163:1765-1770
17. Ali L, Helm T, Cheney R et al. Correlating array comparative genomic hybridization findings with histology and outcome in spitzoid melanocytic neoplasms. Int J Clin Exp Pathol 2010;3:593-599
18. Cancer Genome Atlas Network. Genomic Classification of Cutaneous Melanoma. Cell 2015;161:1681-1696
19. Yazdan P, Cooper C, Sholl LM et al. Comparative analysis of atypical spitz tumors with heterozygous versus homozygous 9p21 deletions for clinical outcomes, histomorphology, BRAF mutation, and p16 expression. Am J Surg Pathol 2014;38:638-645
20. Lu C, Zhang J, Nagahawatte P et al. The genomic landscape of childhood and adolescent melanoma. J Invest Dermatol 2015;135:816-823
21. Wiesner T, He J, Yelensky R et al. Kinase fusions are frequent in Spitz tumours and spitzoid melanomas. Nat Commun 2014;5:3116
22. Hutchinson KE, Lipson D, Stephens PJ et al. BRAF fusions define a distinct molecular subset of melanomas with potential sensitivity to MEK inhibition. Clin Cancer Res 2013;19:6696-6702
23. Botton T, Yeh I, Nelson T et al. Recurrent BRAF kinase fusions in melanocytic tumors offer an opportunity for targeted therapy. Pigment Cell Melanoma Res 2013;26: 845-851
24. Yeh I, Botton T, Talevich E et al. Activating MET kinase rearrangements in melanoma and Spitz tumours. Nat Commun 2015;6:7174
25. Parker M, Mohankumar KM, Punchihewa C et al. C11orf95-RELA fusions drive oncogenic NF-kappaB signalling in ependymoma. Nature 2014;506:451-455
26. Wang F, Flanagan J, Su N et al. RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J Mol Diagn 2012;14: 22-29
27. Jones DT, Kocialkowski S, Liu L et al. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res 2008;68:8673-8677
28. Kwak EL, Bang YJ, Camidge DR et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med 2010;363:1693-1703
29. Takeuchi K, Choi YL, Soda M et al. Multiplex reverse transcription-PCR screening for EML4-ALK fusion transcripts. Clin Cancer Res 2008;14:6618-6624
30. Williams SV, Hurst CD, Knowles MA. Oncogenic FGFR3 gene fusions in bladder cancer. Hum Mol Genet 2013;22:795-803
31. Nakanishi Y, Akiyama N, Tsukaguchi T et al. Mechanism of oncogenic signal activation by the novel fusion kinase FGFR3-BAIAP2L1. Mol Cancer Ther 2015;14: 704-712
32. Shinmura K, Kato H, Matsuura S et al. A novel somatic FGFR3 mutation in primary lung cancer. Oncol Rep 2014;31:1219-1224
33. Yeh I, de la Fouchardiere A, Pissaloux D et al. Clinical, histopathologic, and genomic features of Spitz tumors with ALK fusions. Am J Surg Pathol 2015;39:581-591
34. Busam KJ, Kutzner H, Cerroni L et al. Clinical and pathologic findings of Spitz nevi and atypical Spitz tumors with ALK fusions. Am J Surg Pathol 2014;38: 925-933
35. Lawrence B, Perez-Atayde A, Hibbard MK et al. TPM3- ALK and TPM4-ALK oncogenes in inflammatory myofibroblastic tumors. Am J Pathol 2000;157: 377-384
36. Lamant L, Dastugue N, Pulford K et al. A new fusion gene TPM3-ALK in anaplastic large cell lymphoma created by a (1;2)(q25;p23) translocation. Blood 1999;93:3088-3095
37. Jazii FR, Najafi Z, Malekzadeh R et al. Identification of squamous cell carcinoma associated proteins by proteomics and loss of beta tropomyosin expression in esophageal cancer. World J Gastroenterol 2006;12: 7104-7112
38. Sugawara E, Togashi Y, Kuroda N et al. Identification of anaplastic lymphoma kinase fusions in renal cancer: large-scale immunohistochemical screening by the intercalated antibody-enhanced polymer method. Cancer 2012;118:4427-4436
39. Wiesner T, Lee W, Obenauf AC et al. Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. Nature 2015;526:453-457
40. Ohtsuka M, Arase H, Takeuchi A et al. NFAM1, an immunoreceptor tyrosine-based activation motifbearing molecule that regulates B cell development and signaling. Proc Natl Acad Sci USA 2004;101: 8126-8131
41. Bao ZS, Chen HM, Yang MY et al. RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas. Genome Res 2014;24:1765-1773
42. Hodis E, Watson IR, Kryukov GV et al. A landscape of driver mutations in melanoma. Cell 2012;150:251-263