title: Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.
abstract: Benign fibrous histiocytomas (FH) can be subdivided into several morphological and clinical subgroups. Recently, gene fusions involving either one of two protein kinase C genes (PRKCB and PRKCD) or the ALK gene were described in FH. We here wanted to evaluate the frequency of PRKCB and PRKCD gene fusions in FH. Using interphase fluorescence in situ hybridization on sections from formalin-fixed paraffin-embedded (FFPE) tumors, 36 cases could be analyzed. PRKCB or PRKCD rearrangements were seen in five tumors: 1/7 regular, 0/3 aneurysmal, 0/6 cellular, 2/7 epithelioid, 0/1 atypical, 2/10 deep, and 0/2 metastatic lesions. We also evaluated the status of the ALK gene in selected cases, finding rearrangements in 3/7 epithelioid and 0/1 atypical lesions. To assess the gene fusion status of FH further, deep sequencing of RNA (RNA-Seq) was performed on FFPE tissue from eight cases with unknown gene fusion status, as well as on two FH and six soft tissue sarcomas with known gene fusions; of the latter eight positive controls, the expected fusion transcript was found in all but one, while 2/8 FH with unknown genetic status showed fusion transcripts, including a novel KIRREL/PRKCA chimera. Thus, also a third member of the PRKC family is involved in FH tumorigenesis. We conclude that gene fusions involving PRKC genes occur in several morphological (regular, cellular, aneurysmal, epithelioid) and clinical (cutaneous, deep) subsets of FH, but they seem to account for only a minority of the cases. In epithelioid lesions, however, rearrangements of PRKC or ALK were seen, as mutually exclusive events, in the majority (5/7) of cases. Finally, the study also shows that RNA-Seq is a promising tool for identifying gene fusions in FFPE tissues.
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Charles
authors.initials: C
authors.lastname: Walther
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Jakob
authors.initials: J
authors.lastname: Hofvander
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Jenny
authors.initials: J
authors.lastname: Nilsson
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Linda
authors.initials: L
authors.lastname: Magnusson
authors.affiliation: Department of Pathology, University and Regional Laboratories, Skåne University Hospital, Lund, Sweden.
authors.forename: Henryk A
authors.initials: HA
authors.lastname: Domanski
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.|Department of Pathology, University and Regional Laboratories, Skåne University Hospital, Lund, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Gisselsson
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Johnbosco
authors.initials: J
authors.lastname: Tayebwa
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Leona A
authors.initials: LA
authors.lastname: Doyle
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Christopher D M
authors.initials: CD
authors.lastname: Fletcher
authors.affiliation: Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Mertens
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D017931:DNA Primers / Q000235:genetics; D005557:Formaldehyde; D050939:Gene Fusion / Q000235:genetics*; D015321:Gene Rearrangement / Q000235:genetics*; D018219:Histiocytoma, Benign Fibrous / Q000235:genetics / Q000473:pathology*; D006652:Histological Techniques; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D064546:Protein Kinase C beta / Q000235:genetics* / Q000378:metabolism; D051745:Protein Kinase C-delta / Q000235:genetics* / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012509:Sarcoma / Q000235:genetics / Q000473:pathology*; D017423:Sequence Analysis, RNA / Q000379:methods; D016707:Tissue Fixation
chemical_list: D017931:DNA Primers; D005557:Formaldehyde; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases; C579054:PRKCB protein, human; C497258:PRKCD protein, human; D064546:Protein Kinase C beta; D051745:Protein Kinase C-delta