Dini Alice, Barker Harlan, Piki Emilia, Sharma Subodh, Raivola Juuli, Murumägi Astrid, Ungureanu Daniela
Disease Networks Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Nat Chem Biol. 2025 Mar;21(3):432-442. doi: 10.1038/s41589-024-01761-8. Epub 2024 Oct 31.
The gene-regulatory dynamics governing drug responses in cancer are yet to be fully understood. Here, we report a pipeline capable of producing high-throughput pharmacotranscriptomic profiling through live-cell barcoding using antibody-oligonucleotide conjugates. This pipeline combines drug screening with 96-plex single-cell RNA sequencing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of phosphatidylinositol 3-OH kinase (PI3K), protein kinase B (AKT) and mammalian target of rapamycin (mTOR) inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this was mediated by the upregulation of caveolin 1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of agents targeting PI3K-AKT-mTOR and EGFR for HGSOC with CAV1 and EGFR expression. Using this workflow could enable the personalized testing of patient-derived tumor samples at single-cell resolution.
癌症中药物反应的基因调控动力学尚未完全了解。在此，我们报告了一种能够通过使用抗体-寡核苷酸偶联物进行活细胞条形码标记来产生高通量药物转录组分析的流程。该流程将药物筛选与96孔单细胞RNA测序相结合。我们通过探索45种药物处理后原发性高级别浆液性卵巢癌（HGSOC）细胞的异质转录图谱，展示了这种方法的潜力，这些药物具有13种不同类别的作用机制。磷脂酰肌醇3-羟基激酶（PI3K）、蛋白激酶B（AKT）和雷帕霉素哺乳动物靶点（mTOR）抑制剂的一个子集诱导了受体酪氨酸激酶的激活，如表皮生长因子受体（EGFR），这是由小窝蛋白1（CAV1）的上调介导的。对于具有CAV1和EGFR表达的HGSOC，靶向PI3K-AKT-mTOR和EGFR的药物的协同作用可以减轻这种耐药性反馈回路。使用这种工作流程可以在单细胞分辨率下对患者来源的肿瘤样本进行个性化测试。
