PMID- 26892443 OWN - NLM STAT- MEDLINE DCOM- 20170105 LR - 20230210 IS - 1530-0285 (Electronic) IS - 0893-3952 (Print) IS - 0893-3952 (Linking) VI - 29 IP - 4 DP - 2016 Apr TI - The landscape of fusion transcripts in spitzoid melanoma and biologically indeterminate spitzoid tumors by RNA sequencing. PG - 359-69 LID - 10.1038/modpathol.2016.37 [doi] AB - Kinase activation by chromosomal translocations is a common mechanism that drives tumorigenesis in spitzoid neoplasms. To explore the landscape of fusion transcripts in these tumors, we performed whole-transcriptome sequencing using formalin-fixed, paraffin-embedded (FFPE) tissues in malignant or biologically indeterminate spitzoid tumors from 7 patients (age 2-14 years). RNA sequence libraries enriched for coding regions were prepared and the sequencing was analyzed by a novel assembly-based algorithm designed for detecting complex fusions. In addition, tumor samples were screened for hotspot TERT promoter mutations, and telomerase expression was assessed by TERT mRNA in situ hybridization (ISH). Two patients had widespread metastasis and subsequently died of disease, and 5 patients had a benign clinical course on limited follow-up (mean: 30 months). RNA sequencing and TERT mRNA ISH were successful in six tumors and unsuccessful in one disseminating tumor because of low RNA quality. RNA sequencing identified a kinase fusion in five of the six sequenced tumors: TPM3-NTRK1 (2 tumors), complex rearrangements involving TPM3, ALK, and IL6R (1 tumor), BAIAP2L1-BRAF (1 tumor), and EML4-BRAF (1 disseminating tumor). All predicted chimeric transcripts were expressed at high levels and contained the intact kinase domain. In addition, two tumors each contained a second fusion gene, ARID1B-SNX9 or PTPRZ1-NFAM1. The detected chimeric genes were validated by home-brew break-apart or fusion fluorescence in situ hybridization (FISH). The two disseminating tumors each harbored the TERT promoter -124C>T (Chr 5:1,295,228 hg19 coordinate) mutation, whereas the remaining five tumors retained the wild-type gene. The presence of the -124C>T mutation correlated with telomerase expression by TERT mRNA ISH. In summary, we demonstrated complex fusion transcripts and novel partner genes for BRAF by RNA sequencing of FFPE samples. The diversity of gene fusions demonstrated by RNA sequencing defines the molecular heterogeneity of spitzoid neoplasms. FAU - Wu, Gang AU - Wu G AUID- ORCID: 0000-0002-1678-5864 AD - Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Barnhill, Raymond L AU - Barnhill RL AD - Department of Pathology, Institute Curie, and Faculty of Medicine, University of Paris Descartes, Paris, France. FAU - Lee, Seungjae AU - Lee S AD - Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Li, Yongjin AU - Li Y AD - Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Shao, Ying AU - Shao Y AD - Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Easton, John AU - Easton J AD - Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Dalton, James AU - Dalton J AD - Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Zhang, Jinghui AU - Zhang J AD - Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Pappo, Alberto AU - Pappo A AD - Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA. FAU - Bahrami, Armita AU - Bahrami A AD - Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA. LA - eng GR - P30 CA021765/CA/NCI NIH HHS/United States GR - P30CA021765/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20160219 PL - United States TA - Mod Pathol JT - Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc JID - 8806605 RN - 0 (Oncogene Proteins, Fusion) RN - 63231-63-0 (RNA) RN - EC 2.7.7.49 (Telomerase) SB - IM MH - Adolescent MH - Child MH - Child, Preschool MH - Female MH - Humans MH - In Situ Hybridization MH - In Situ Hybridization, Fluorescence MH - Male MH - Melanoma/*genetics MH - Nevus, Epithelioid and Spindle Cell/genetics/pathology MH - Oncogene Proteins, Fusion/*genetics MH - RNA/analysis MH - Sequence Analysis, RNA MH - Skin Neoplasms/*genetics MH - Telomerase/genetics PMC - PMC4811687 MID - NIHMS750807 COIS- Disclosure/Conflict of Interest: The authors declare no conflict of interest. EDAT- 2016/02/20 06:00 MHDA- 2017/01/06 06:00 PMCR- 2016/08/19 CRDT- 2016/02/20 06:00 PHST- 2015/10/31 00:00 [received] PHST- 2016/01/09 00:00 [revised] PHST- 2016/01/09 00:00 [accepted] PHST- 2016/02/20 06:00 [entrez] PHST- 2016/02/20 06:00 [pubmed] PHST- 2017/01/06 06:00 [medline] PHST- 2016/08/19 00:00 [pmc-release] AID - S0893-3952(22)02115-9 [pii] AID - 10.1038/modpathol.2016.37 [doi] PST - ppublish SO - Mod Pathol. 2016 Apr;29(4):359-69. doi: 10.1038/modpathol.2016.37. Epub 2016 Feb 19.