Nesic Ksenija, Krais John J, Vandenberg Cassandra J, Wang Yifan, Patel Pooja, Cai Kathy Q, Kwan Tanya, Lieschke Elizabeth, Ho Gwo-Yaw, Barker Holly E, Bedo Justin, Casadei Silvia, Farrell Andrew, Radke Marc, Shield-Artin Kristy, Penington Jocelyn S, Geissler Franziska, Kyran Elizabeth, Zhang Fan, Dobrovic Alexander, Olesen Inger, Kristeleit Rebecca, Oza Amit, Ratnayake Gayanie, Traficante Nadia, DeFazio Anna, Bowtell David D L, Harding Thomas C, Lin Kevin, Swisher Elizabeth M, Kondrashova Olga, Scott Clare L, Johnson Neil, Wakefield Matthew J
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
medRxiv. 2023 Aug 28:2023.03.20.23287465. doi: 10.1101/2023.03.20.23287465.
splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out the mutation-containing exon, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi. exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary splice site mutations (SSMs), predicted to drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots and minigene modelling. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials. We demonstrate that SSMs drive exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.
剪接异构体Δ11和Δ11q可通过剪接去除含突变的外显子，产生截短的、部分功能的蛋白质，从而导致对聚（ADP-核糖）聚合酶抑制剂（PARPi）产生耐药性。然而，外显子跳跃的临床影响和潜在驱动因素仍未确定。我们分析了9个携带外显子11移码突变的卵巢癌和乳腺癌患者来源的异种移植瘤（PDX），以研究外显子跳跃和治疗反应，其中包括一对来自同一患者化疗/ PARPi治疗前后的匹配PDX。在对PARPi耐药的PDX肿瘤中，外显子11跳跃增加。两个独立的PDX模型获得了继发性剪接位点突变（SSM），预计这些突变会导致外显子跳跃。通过定量逆转录聚合酶链反应（qRT-PCR）、RNA测序、蛋白质免疫印迹和微型基因建模证实了这些预测。在ARIEL2和ARIEL4临床试验的PARPi治疗后的卵巢癌患者队列中，SSM也有所富集。我们证明，SSM会导致外显子11跳跃和PARPi耐药，因此应与恢复读框的继发性突变一起进行临床监测。
