Undifferentiated small round cell sarcomas with rare EWS gene fusions: identification of a novel EWS-SP3 fusion and of additional cases with the EWS-ETV1 and EWS-FEV fusions

Abstract

Ewing family tumors (EFTs) are prototypical primitive small round blue cell sarcomas arising in bone or extraskeletal soft tissues in children or adolescents. EFTs show fusions of EWS with a gene of the ETS family of transcription factors, either EWS-FLI1 (90 to 95%) or EWS-ERG (5 to 10%). Rare cases with fusions of EWS to other ETS family genes, such as ETV1, E1AF, and FEV, have been identified, but their clinicopathological similarity to classic EFTs remains unclear. We report four new cases of EFT-like tumors with rare EWS fusions, including two with EWS-ETV1, one with EWS-FEV, and a fourth case in which we cloned a novel EWS-SP3 fusion, the first known cancer gene fusion involving a gene of the Sp zinc finger family. Analysis of these three new cases along with data on nine previously reported cases with fusions of EWS to ETV1, E1AF, or FEV suggest a strong predilection for extraskeletal primary sites. EFT-like cases with fusions of EWS to non-ETS translocation partners are also uncommon but involve the same amino-terminal portion of EWS, which in our novel EWS-SP3 fusion is joined to the SP3 zinc-finger DNA-binding domain. As these data further support, these types of EWS fusions are associated with primitive extraskeletal small round cell sarcomas of uncertain lineage arising mainly in the pediatric population.

Figure 1

Patient A. A: H&E-stained section showing characteristic small round blue cell tumor morphology. B: Diffuse and strong positivity for CD99 (O13 antibody). C: Partial karyotype showing a t(7;22) translocation. Arrows indicate the derivative chromosomes.

Figure 2

Patient B. Undifferentiated tumor showing areas of spindling in a specimen obtained after neoadjuvant chemotherapy.

Figure 3

Patient C. A: H&E-stained section showing small round blue cell tumor with crush artifact. B: Immunostain for CD99 showing diffuse and strong staining. C: CAM5.2 immunostain showing dot-like positivity for cytokeratin in the tumor cells.

Figure 4

Patient D. A: H&E-stained section showing small round blue cell tumor with high mitotic rate. B: Immunostain for CD99 showing focal weak staining. C: BCL2 immunostain showing strong diffuse positivity in the tumor cells.

Figure 5

Patient D. A: Partial karyotype showing t(2;22)(q31;q12). Arrows indicate the derivative chromosomes. B: FISH using dual-color, break-apart EWS probe on a metaphase preparation. The small arrow shows the normal fusion signal (red and green signals together) on the intact chromosome 22; the large arrow indicates the der(22)t(2;22) with only red signal (EWS centromeric probe); the midsize arrow indicates the der(2)t(2;22) with the green signal (EWS telomeric probe). C: Same FISH on interphase nuclei showing one normal fusion signal and separation of the other red and green signals.

Figure 6

Patient D. A: Partial sequence of the type I EWS-SP3 fusion transcript is an in-frame junction of EWS exon 7 with SP3 exon 6 (see Results for details). The translated protein sequence is shown below, with the codon at the junction in red. B: Partial sequence of the type II EWS-SP3 transcript. The transcript has a full open reading frame and is a fusion of EWS exon 8 to SP3 exon 6 with an intervening cryptic exon. The arrowhead indicates the extra T (see Results for details). The translated protein sequence is shown below, with the codons at the junctions in red. C: Partial genomic sequence of SP3. The intron sequence is in lower case and the exon sequence is in upper case. The portion of SP3 exon 6 coding for the zinc finger is underlined. The two cryptic splice acceptor sites in SP3 exon 6 are shown in green (used in type I fusion transcript) and red (used type II fusion transcript), respectively.

Figure 7

Patient D: RT-PCR detection of EWS-SP3 fusion. The presence of both type I and type II fusion transcripts was confirmed by RT-PCR using an EWS primer (sequence: 5′-CTGGATCCTACAGCCAAGCTCCAAGTC-3′) and an SP3 reverse primer (sequence: 5′-CAGAATGCCAACGCAGATGA-3′). Lane ptD is the RT-PCR product obtained from tumor RNA. Band A is 120 bp, and band B is 375 bp. Sequencing of A and B confirmed that A represents the type I EWS-SP3 fusion transcript, whereas B represents the type II fusion, both of which are in-frame (see Figure 6). Sequencing of band C revealed an out-of-frame EWS-SP3 fusion transcript (sequence data not shown). Lane neg is the no RNA negative control. Size marker (lane M) is φ X174/HaeIII (Invitrogen).

Figure 8

Schematic diagrams of EWS, SP3, and the predicted EWS-SP3 protein. NTD, amino-terminal domain; AD, transactivation domain; ID, inhibitory domain; zinc finger, zinc finger DNA-binding domain.