Promoter activity profiling reveals on- and off-target transcriptional responses to drug treatment

Owing to safety concerns or insufficient potential for efficacy, only 0.01% to 0.02% of new drug candidates are approved for marketing. Drugs already on the market may be withdrawn or restricted to certain uses due to adverse effects (AEs) discovered after market introduction. Comprehensively investigating the on-/off-target effects of drugs can help expose AEs during the drug development process. In this study, we developed an integrative framework for systematic identification of on-/off-target pathways and elucidation of the underlying mechanisms, by combining expression profiling after drug treatment with gene perturbation of the primary drug target. Expression profiles from statin-treated cells and HMG-CoA reductase knockdowns were analyzed using the framework, allowing for identification of not only reported adverse effects but also novel candidates of off-target effects from statin treatment. Our findings may provide new insights for finding new usages or potential side effects of drug treatment. Overall design: CAGE profiling in three different cell types after treatment with four different statins and two siRNAs targeting HMG-CoA reductase (HMGCR), including replicates and control samples.

由于安全性顾虑或疗效潜力不足，仅有0.01%至0.02%的新药候选化合物可获批上市。已上市药物亦可能因上市后发现的不良反应（Adverse Effects, AEs）被撤市或限制特定使用场景。全面解析药物的靶标效应与脱靶效应，有助于在药物研发阶段提前甄别不良反应。本研究将药物处理后的表达谱分析与原药靶标的基因扰动实验相结合，构建了一套可系统鉴定药物靶标/脱靶通路并阐明其潜在作用机制的整合分析框架。研究团队利用该框架分析了他汀类药物处理细胞以及羟甲基戊二酰辅酶A还原酶（HMG-CoA reductase, HMGCR）基因敲低后的表达谱，不仅成功鉴定出已报道的他汀类药物不良反应，还筛选出他汀类药物脱靶效应的新型候选靶点。本研究结果可为挖掘药物的新用途或潜在治疗副作用提供全新研究视角。实验设计概况：对三种不同细胞类型分别施以四种他汀类药物与两种靶向羟甲基戊二酰辅酶A还原酶（HMG-CoA reductase, HMGCR）的小干扰RNA（small interfering RNA, siRNA）处理，设置生物学重复与对照样本，随后开展CAGE（Cap Analysis of Gene Expression，基因表达帽分析）谱分析。