Recurrent BRAF Gene Rearrangements in Myxoinflammatory Fibroblastic Sarcomas, but Not Hemosiderotic Fibrolipomatous Tumors

Abstract

Myxoinflammatory fibroblastic sarcoma (MIFS) is a low grade soft tissue sarcoma with a predilection for acral sites, being associated with a high rate of local recurrence but very infrequent distant metastases. Although a t(1;10) translocation resulting in TGFBR3-MGEA5 fusion has been reported as a recurrent genetic event in MIFS, this abnormality is seen only in a subset of cases. As no studies to date have investigated the spectrum of alternative genetic alterations in TGFBR3-MGEA5 fusion negative MIFS, we undertook a genetic analysis of this particular cohort for further molecular classification. Triggered by an index case occurring in the finger of a 37 year-old female and harboring a novel TOM1L2-BRAF fusion by targeted RNA sequencing we investigated potential recurrent BRAF abnormalities by screening a large group of 19 TGFBR3-MGEA5 fusion negative MIFS by FISH. There were 6 (32%) additional MIFS with BRAF genetic abnormalities, including 5 gene rearrangements and one showing BRAF amplification. Interestingly, VGLL3 amplification, a recurrent genetic abnormality coexisting with t(1;10) in some MIFS, was also detected by FISH in 4/6 (67%) BRAF-rearranged MIFS, but not in the BRAF-amplified case. Up-regulated VGLL3 mRNA expression was also demonstrated in the index case by RNAseq. The 7 BRAF-rearranged/amplified MIFS arose in the fingers (n=3), and 1 each in wrist, forearm, foot, and knee, of adult patients (36–74 years; M:F=4:3). The histological spectrum ranged from predominantly solid growth of plump histiocytoid to epithelioid tumor cells with focal myxoid change to a predominantly myxoid background with scattered tumor cells. Varying degree of inflammatory infiltrates and large tumor cells with virocyte-like macronucleoli were observed in most cases. Immunohistochemical stains of phosphorylated ERK, a downstream effector of BRAF activation, were positive in all 4 cases tested (2 diffuse strong, 2 focal strong). Unlike t(1;10), BRAF rearrangements were only found in MIFS but not in 6 hemosiderotic fibrolipomatous tumor (HFLT) lacking TGFBR3-MGEA5 fusions (including 2 pure HFLT, 2 hybrid HFLT-MIFS, and 2 associated with pleomorphic hyalinizing angiectatic tumors).

Deep sequencing of myxoinflammatory fibroblastic sarcoma

“…The French Sarcoma Group found such amplicons in 19/404 (5%) sarcomas analyzed with genomic arrays; amplification‐positive tumors were primarily diagnosed as UPS and dedifferentiated liposarcomas and none as MIFS, HFLT, or PHAT . In addition, array‐ and FISH‐based studies have identified VGLL3 amplification as a recurrent feature (70%‐80% of the cases) in both HFLT and MIFS, including cases with BRAF rearrangement . The present study thus confirms that an amplicon in 3p11‐12, correlating with increased expression of VGLL3 is a highly recurrent feature of MIFS, irrespective of whether a t(1;10) or a BRAF fusion is present or not.…”

“…MIFS with or without the t(1;10) have also been shown to display loss of material from chromosome arm 3p and amplification of a ~1.5 Mb sequence in chromosome bands 3p11‐12; the amplicon includes the genes VGLL3 , CHMP2B , and POU1F1 , of which only the former two showed increased expression . Frequent amplification of VGLL3 in both MIFS and HFLT was confirmed by others using FISH . However, VGLL3 amplicons, and corresponding overexpression, have been detected also in other types of, typically high‐grade, sarcoma (eg, myxofibrosarcoma, undifferentiated pleomorphic sarcoma [UPS], and de‐differentiated liposarcoma), some of which were negative for the t(1;10) and some had an unknown t(1;10) status …”

“…Recently, RNA‐sequencing of a PHAT identified an out‐of‐frame fusion between TGFBR3 and FBXW4 , mapping 11 kb centromeric of OGA . Further complicating the picture, recurrent rearrangements of the serine/threonine kinase‐encoding BRAF gene were described in t(1;10)‐negative cases of MIFS, but not in HFLT or hybrid HFLT/MIFS …”

Malignant melanoma with metaplastic cartilaginous transdifferentiation: A case report

“…In another study done by Movva et al 2539 sarcomas were profiled by IHC, FISH/CISH, NGS and Sanger sequencing and none harbored a BRAF mutation . Notably, BRAF fusions have been detected in few sarcomas (non‐chondrosarcomatous), as reported by Kao et al On the other hand, BRAF mutation has not yet been reported in chondrosarcoma. Therefore, with regards to our patient, BRAF mutation in the cartilaginous component supports the interpretation of melanocytic differentiation.…”

Targeted RNA sequencing: A routine ancillary technique in the diagnosis of bone and soft tissue neoplasms

“…Depending on the breadth of assay coverage, novel fusion partners and completely novel fusion genes will invariably be incidentally identified in the course of routine clinical practice . As our nascent understanding of sarcomagenesis evolves, it is important to take this opportunity to rigorously evaluate cases, and to share this information through the literature and databases.…”