Novel EWSR1-SMAD3 Gene Fusions in a Group of Acral Fibroblastic Spindle Cell Neoplasms

Abstract

Benign/low-grade fibroblastic tumors encompass a broad spectrum of tumors with different morphologies and molecular genetic abnormalities. However, despite significant progress in recent genomic characterization, there are still tumors in this histologic spectrum that are difficult to classify, lacking known molecular characteristics. Triggered by a challenging congenital spindle cell neoplasm arising in the heel of a 1-year-old boy, we applied RNA sequencing for genetic discovery and identified a novel EWSR1-SMAD3 gene fusion. On the basis of the index case superficial acral location and fibroblastic appearance with a nonspecific immunophenotype, we searched our files for similar cases and screened them by fluorescence in situ hybridization for these abnormalities. Thus an identical EWSR1-SMAD3 fusion was identified in 2 additional spindle cell tumors with similar clinicopathologic features. Both cases occurred in the feet of adult women (58 and 61 y old) and were characterized by distinctive nodular growth with zonation pattern of peripheral hypercellular areas arranged in short fascicles, transitioning to hypocellular central areas of hyalinization and infarction. Focal stippled calcification in the collagenous area was present in 1 case. All 3 tumors had similar immunoprofiles, being negative for SMA, CD34, CD31, and S100, but showing consistent ERG positivity of uncertain significance. Follow-up information was available in 2 patients who developed local recurrences after incomplete initial excisions, at 5 and 14 months, respectively. None developed metastatic disease. In summary, we report a group of locally recurrent superficial acral tumors, characterized by bland spindle cell fascicular growth, occasional zonation pattern, ERG positivity, and recurrent EWSR1-SMAD3 gene fusions.

Figure 1. Histologic features of the index case, a heel tumor in a one year-old boy

The tumor presented as a buldging nodule involving the dermis and subcutaneous tissues with infiltrative border (A,B). It is composed of intersecting fascicles of uniform plump spindle cells with fibrillary cytoplasm and bland fusiform nuclei (C,D).

Figure 2

(A) A novel EWSR1-SMAD3 gene fusion, resulting from a t(15;22)(q22.33;q12.2) was identified in the index case by whole transcriptome sequencing. (B) The fusion transcript was composed of exon 7 of EWSR1 fused in-frame to exon 5 of SMAD3. The deduced chimeric protein contains the N-terminal transcriptional activation domain of EWSR1 and the MH2 domain with part of the linker region of SMAD3. (C) The fusion was validated by break-apart FISH assays for EWSR1 and SMAD3, respectively. SMAD3 shows unbalanced rearrangement, with single telomeric (green) signals and deletion of the centromeric (red) signals (arrows). FISH for EWSR1 similarly shows unbalanced pattern with deletion of telomeric signals (not shown). (D) Unsupervised clustering of RNA sequencing data shows the index case (red) clusters with a calcifying aponeurotic fibroma with FN1-EGF fusion (purple), a lipofibromatosis (light blue), and a lipofibromatosis-like neural tumor with TPR-NTRK1 fusion (dark blue), among other soft tissue tumors. (E) Left panel: high FN1 mRNA expression in the index case (red), calcifying aponeurotic fibroma (purple), and lipofibromatosis-like neural tumor (dark blue). Right panel ERG mRNA level is significantly up-regulated in the index case (red), even at higher levels than 3 angiosarcomas in the same dataset (green bars in D, E).

Figure 3. Histologic features of the additional two adult acral spindle cell neoplasms with EWSR1-SMAD3 fusions

(A–E) Case #2, a subcutaneous nodule in the foot of a 61 year-old female showing an infiltrative border (A) and a distinctive zonation pattern with hypercellular periphery (B), transitioning to hypocellular collagenous area (C), and an acellular central zone (D). Focal fine calcifications were also present (E). (F–H) Case #3, a toe lesion in a 58 year-old female, displayed a similar zonation pattern in the primary lesion (F,G) and the cellular component only in the local recurrent lesion 5 months later. (I) All 3 cases show diffuse and strong ERG immunoreactivity.