Recurrent Fusion Transcripts Detected by Whole-transcriptome Sequencing of 120 Primary Breast Cancer Samples

Abstract

Purpose: Although fusion genes serve as an effective target in hematologic malignancies, recurrent gene fusion events are relatively rare in solid tumors. To detect recurrent novel fusion transcripts we performed whole transcriptome sequencing primary breast cancer samples. Experimental Design: Whole-transcriptome sequencing of 120 fresh-frozen primary breast cancer samples and five adjacent normal breast tissues using the Illumina HiSeq2000 platform was performed. Three different fusion-detecting tools (deFuse, Chimerascan, and TopHat) were used, and the results were compared. Results: These tools detected 3831, 6630 and 516 fusion transcripts (FTs) overall. We primarily focused on the results obtained using the deFuse software. More FTs were identified from HER2 subtype breast cancer samples than from the luminal or triple-negative subtypes (p < 0.05). Seventy fusion candidates were selected for validation, and 32 (45.7%) were confirmed by RT-PCR and Sanger sequencing. Of the validated fusions, six were recurrent (found in 2 or more samples), three were in-frame (PRDX1-AKR1A1, TACSTD2-OMA1 and C2CD2-TFF1) and three were off-frame (CEACAM7-CEACAM6, CYP4X1-CYP4Z2P, and EEF1DP3-FRY). Notably, the novel read-through fusion, EEF1DP3-FRY, was identified and validated in 6.7% (8/120) of the breast cancer samples. This off-frame fusion results in early truncation of the FRY gene, which plays a key role in the structural integrity during mitosis. Three previously reported fusions, PPP1R1B-STARD3, MFGE8-HAPL, and ETV6-NTRK3, were detected in 8.3%, 3.3% and 0.8% of the 120 samples, respectively, by both deFuse and Chimerascan. The recently reported MAGI3-AKT3 fusion was not detected in our analysis. Conclusion: Among the 3800s fusions detected by mRNA Sequencing, 32 fusions were validated using Sanger sequencing, including the novel recurrent read-through fusion, EEF1DP3-FRY. Previously reported FTs, such as PPP1R1B-STARD3, MFGE8-HAPLN3 and ETV6-NTRK3, were also identified. Future work is warranted to elucidate the biological significance of these fusions.