高通量基因组学和靶向治疗的最新进展为识别和治疗与癌症相关的不同突变提供了巨大的潜力。然而，迄今为止，大多数靶向疗法用于治疗同一基因内的所有功能突变，无论受影响的密码子或表型如何。在这项研究中，我们开发了功能基因组分析工作流程，其中包含具有两个不同热点的独特等基因细胞系面板PIK3CA 突变、E545K 和 H1047R，可准确识别同一基因内突变之间的可靶向差异。我们进行了 RNA-seq 和 ATAC-seq，并鉴定了与每个 PIK3CA 热点突变相关的不同转录组和表观基因组差异。我们利用这些数据来策划精选的 CRISPR 敲除筛选，以识别突变特异性基因途径的漏洞。这些数据揭示了 AREG 作为 E545K 优先靶点，通过体外分析和公开的患者数据库进一步验证了这一点。使用我们的多模式基因组学框架，我们发现 PIK3CA 热点突变之间的基因组调控存在明显差异，表明 PIK3CA 突变具有不同的差异性。对 PI3K 复合物的功能和下游信号传导的调节作用。我们的结果证明了快速发现突变特异性分子靶点的潜力，特别是 AREG 和近端基因调控区域，这可能提供临床相关的治疗靶点。概述的方法为研究人员提供了一种综合策略，以确定用于治疗同基因系统中其他致癌突变的突变特异性靶标。© 2024。作者。

Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype.In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases.Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.© 2024. The Author(s).