Calistri Nicholas L, Liby Tiera A, Hu Zhi, Zhang Hongmei, Dane Mark, Gross Sean M, Heiser Laura M
Biomedical Engineering Department, Oregon Health & Science University, Portland Oregon.
Knight Cancer Institute, Oregon Health & Science University, Portland Oregon.
bioRxiv. 2024 Jun 6:2024.06.04.596911. doi: 10.1101/2024.06.04.596911.
Paclitaxel is a standard of care neoadjuvant therapy for patients with triple negative breast cancer (TNBC); however, it shows limited benefit for locally advanced or metastatic disease. Here we used a coordinated experimental-computational approach to explore the influence of paclitaxel on the cellular and molecular responses of TNBC cells. We found that escalating doses of paclitaxel resulted in multinucleation, promotion of senescence, and initiation of DNA damage induced apoptosis. Single-cell RNA sequencing (scRNA-seq) of TNBC cells after paclitaxel treatment revealed upregulation of innate immune programs canonically associated with interferon response and downregulation of cell cycle progression programs. Systematic exploration of transcriptional responses to paclitaxel and cancer-associated microenvironmental factors revealed common gene programs induced by paclitaxel, IFNB, and IFNG. Transcription factor (TF) enrichment analysis identified 13 TFs that were both enriched based on activity of downstream targets and also significantly upregulated after paclitaxel treatment. Functional assessment with siRNA knockdown confirmed that the TFs FOSL1, NFE2L2 and ELF3 mediate cellular proliferation and also regulate nuclear structure. We further explored the influence of these TFs on paclitaxel-induced cell cycle behavior via live cell imaging, which revealed altered progression rates through G1, S/G2 and M phases. We found that ELF3 knockdown synergized with paclitaxel treatment to lock cells in a G1 state and prevent cell cycle progression. Analysis of publicly available breast cancer patient data showed that high ELF3 expression was associated with poor prognosis and enrichment programs associated with cell cycle progression. Together these analyses disentangle the diverse aspects of paclitaxel response and identify ELF3 upregulation as a putative biomarker of paclitaxel resistance in TNBC.
紫杉醇是三阴性乳腺癌（TNBC）患者新辅助治疗的标准方案；然而，它对局部晚期或转移性疾病的疗效有限。在此，我们采用了一种协同的实验-计算方法，以探究紫杉醇对TNBC细胞的细胞和分子反应的影响。我们发现，逐步增加剂量的紫杉醇会导致多核化、促进衰老，并引发DNA损伤诱导的凋亡。对紫杉醇处理后的TNBC细胞进行单细胞RNA测序（scRNA-seq），结果显示，与干扰素反应典型相关的固有免疫程序上调，而细胞周期进程程序下调。对紫杉醇和癌症相关微环境因素的转录反应进行系统探索，发现了由紫杉醇、IFNB和IFNG诱导的共同基因程序。转录因子（TF）富集分析确定了13个TF，它们基于下游靶点的活性而富集，并且在紫杉醇处理后也显著上调。用小干扰RNA（siRNA）敲低进行功能评估证实，TFs FOSL1、NFE2L2和ELF3介导细胞增殖，并调节核结构。我们通过活细胞成像进一步探究了这些TFs对紫杉醇诱导的细胞周期行为的影响，结果显示，细胞在G1期、S/G2期和M期的进展速率发生了改变。我们发现，敲低ELF3与紫杉醇处理协同作用，可将细胞锁定在G1期，阻止细胞周期进程。对公开可用的乳腺癌患者数据进行分析表明，ELF3高表达与预后不良以及与细胞周期进程相关的富集程序有关。这些分析共同解开了紫杉醇反应的不同方面，并确定ELF3上调是TNBC中紫杉醇耐药的一个假定生物标志物。
