Thermo Fisher Scientific Baltics, Vilnius, Lithuania.
National Cancer Institute, Vilnius, Lithuania.
Mol Oncol. 2023 Jun;17(6):993-1006. doi: 10.1002/1878-0261.13428. Epub 2023 Apr 13.
Genetic rearrangements that fuse an androgen-regulated promoter area with a protein-coding portion of an originally androgen-unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) being the most prevalent. Conventional hybridization- or amplification-based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost-prohibitive. Here, we developed an innovative next-generation sequencing (NGS)-based approach for gene fusion analysis termed fusion sequencing via terminator-assisted synthesis (FTAS-seq). FTAS-seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3'-terminal fusion partners. Using this novel semi-targeted RNA-sequencing technique, we were able to identify 11 previously uncharacterized TMPRSS2 fusion partners and capture a range of TMPRSS2-ERG isoforms. We tested the performance of FTAS-seq with well-characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS-seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.
在前列腺癌中，经常发生将雄激素调节启动子区域与原本不受雄激素影响的基因的蛋白质编码部分融合的遗传重排，其中跨膜丝氨酸蛋白酶 2（TMPRSS2）和 ETS 转录因子 ERG（ERG）之间的融合（TMPRSS2-ERG 融合）最为常见。传统的基于杂交或扩增的方法可以检测预期基因融合的存在，但目前未知融合伙伴的探索性分析通常成本过高。在这里，我们开发了一种创新的基于下一代测序（NGS）的基因融合分析方法，称为终止子辅助合成（FTAS-seq）的融合测序。FTAS-seq 可用于富集目标基因，同时同时分析其 3'末端融合伙伴的全谱。使用这种新颖的半靶向 RNA-seq 技术，我们能够鉴定出 11 种以前未表征的 TMPRSS2 融合伙伴，并捕获一系列 TMPRSS2-ERG 同工型。我们用经过充分表征的前列腺癌细胞系测试了 FTAS-seq 的性能，并将该技术用于分析患者的 RNA 样本。FTAS-seq 化学与适当的引物组相结合，具有作为支持个性化癌症治疗开发的生物标志物发现工具的巨大潜力。
