期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 23, 期 19, 页码 -出版社
MDPI
DOI: 10.3390/ijms231911007
关键词
mRNA capture sequencing; RT-qPCR; formalin-fixed paraffin-embedded (FFPE) tissue; fusion gene; fusion transcript; sarcoma; alveolar rhabdomyosarcoma; undifferentiated round cell sarcoma
资金
- Kom op tegen Kanker (Stand up to Cancer, the Flemish cancer society)
- UGent Special Research Fund Concerted Research Actions (GOA) [BOF16-GOA-023]
- Special Research Fund of Ghent University
- Research Foundation-Flanders (FWO) [1224021N]
This study demonstrates that mRNA capture sequencing improves the detection rate of pathognomonic fusions in sarcomas and enables the identification of novel and secondary fusion transcripts.
We assess the performance of mRNA capture sequencing to identify fusion transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR confirmation. To validate our workflow, six positive control tumors with a specific chromosomal rearrangement were analyzed using the TruSight RNA Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. For six patients, a pathognomonic fusion transcript was readily detected, i.e., PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in four URCS patients. For the 11 remaining patients, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this study shows that mRNA capture sequencing enhances the detection rate of pathognomonic fusions and enables the identification of novel and secondary fusion transcripts in sarcomas.
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