Ukkola Iiris, Nummela Pirjo, Kero Mia, Tammio Hanna, Tuominen Jenni, Kairisto Veli, Kallajoki Markku, Haglund Caj, Peltomäki Päivi, Kytölä Soili, Ristimäki Ari
Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, P.O. Box 400, 00029, HUS, Helsinki, Finland.
Applied Tumor Genomics Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Virchows Arch. 2022 Apr;480(4):807-817. doi: 10.1007/s00428-022-03302-x. Epub 2022 Mar 3.
Gene fusions can act as oncogenic drivers and offer targets for cancer therapy. Since fusions are rare in colorectal cancer (CRC), their universal screening seems impractical. Our aim was to investigate gene fusions in 62 CRC cases with deficient MLH1 (dMLH1) and BRAFV600E wild-type (wt) status from a consecutive real-life series of 2079 CRCs. First, gene fusions were analysed using a novel FusionPlex Lung v2 RNA-based next-generation sequencing (NGS) panel, and these results were compared to a novel Idylla GeneFusion assay and pan-TRK immunohistochemistry (IHC). NGS detected seven (7/62, 11%) NTRK1 fusions (TPM3::NTRK1, PLEKHA6::NTRK1 and LMNA::NTRK1, each in two cases, and IRF2BP2::NTRK1 in one case). In addition, two ALK, four RET and seven BRAF fusions were identified. Idylla detected seven NTRK1 expression imbalances, in line with the NGS results (overall agreement 100%). Furthermore, Idylla detected the two NGS-identified ALK rearrangements as one specific ALK fusion and one ALK expression imbalance, whilst only two of the four RET fusions were discovered. However, Idylla detected several expression imbalances of ALK (n = 7) and RET (n = 1) that were found to be fusion negative with the NGS. Pan-TRK IHC showed clearly detectable, fusion partner-dependent staining patterns in the seven NTRK1 fusion cases. Overall agreement for pan-TRK antibody clone EPR17341 was 98% and for A7H6R 100% when compared to the NGS. Of the 62 CRCs, 43 were MLH1 promoter hypermethylated (MLH1ph) and 39 were RASwt. All fusion cases were both MLH1ph and RASwt. Our results show that kinase fusions (20/30, 67%) and most importantly targetable NTRK1 fusions (7/30, 23%) are frequent in CRCs with dMLH1/BRAFV600Ewt/MLH1ph/RASwt. NGS was the most comprehensive method in finding the fusions, of which a subset can be screened by Idylla or IHC, provided that the result is confirmed by NGS.
基因融合可作为致癌驱动因素，并为癌症治疗提供靶点。由于融合在结直肠癌（CRC）中很少见，对其进行全面筛查似乎不切实际。我们的目的是研究来自连续2079例CRC的现实系列中62例错配修复蛋白1（MLH1）缺陷（dMLH1）且BRAF V600E野生型（wt）状态的CRC病例中的基因融合。首先，使用基于新型FusionPlex Lung v2 RNA的二代测序（NGS）面板分析基因融合，并将这些结果与新型Idylla基因融合检测和泛TRK免疫组化（IHC）进行比较。NGS检测到7例（7/62，11%）神经营养酪氨酸激酶受体1（NTRK1）融合（TPM3::NTRK1、PLEKHA6::NTRK1和核纤层蛋白A/C（LMNA）::NTRK1各2例，干扰素调节因子2结合蛋白2（IRF2BP2）::NTRK1 1例）。此外，还鉴定出2例间变性淋巴瘤激酶（ALK）、4例转染重排（RET）和7例BRAF融合。Idylla检测到7例NTRK1表达失衡，与NGS结果一致（总体一致性100%）。此外，Idylla将NGS鉴定出的2例ALK重排检测为1例特定的ALK融合和1例ALK表达失衡，而4例RET融合中仅发现2例。然而，Idylla检测到几例ALK（n = 7）和RET（n = 1）的表达失衡，经NGS检测发现为融合阴性。泛TRK免疫组化在7例NTRK1融合病例中显示出明显可检测到的、依赖融合伴侣的染色模式。与NGS相比，泛TRK抗体克隆EPR17341的总体一致性为98%，A7H6R为100%。在62例CRC中，43例MLH1启动子高甲基化（MLH1ph），39例RAS野生型（RASwt）。所有融合病例均为MLH1ph和RASwt。我们的结果表明，激酶融合（20/30，67%），最重要的是可靶向的NTRK1融合（7/30，23%）在dMLH1/BRAFV600Ewt/MLH1ph/RASwt的CRC中很常见。NGS是发现融合最全面的方法，其中一部分可以通过Idylla或免疫组化进行筛查，前提是结果经NGS确认。
