论文标题
通过整合SCRNA-SEQ和蛋白质组学数据的生物信息学推断和多尺度建模来揭示DEX治疗对肺癌的动态影响
Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data
论文作者
论文摘要
动机:肺癌是与癌症相关死亡的主要原因之一,五年生存率为18%。我们要理解影响肺癌治疗剂实施和有效性的基本机制是一个优先事项。在这项研究中,我们将生物信息学和系统生物学的功能结合在一起,使用SCRNA-SEQ数据和蛋白质组学数据的生物信息学推断和多尺度建模,全面地发现药物处理的功能和信号传导途径。创新和跨学科的方法可以进一步应用于肿瘤发生和过度疗法中的其他计算研究。结果:分析了DEX处理后肺腺癌衍生的A549细胞的时间序列。 (1)我们首先在这些肺癌细胞中发现了差异表达的基因。然后,通过询问其调节网络,我们确定了包括TGF- \ b {eta},MYC和SMAD3在内的关键集线器基因,并且SMAD3在DEX处理的基础上变化。进一步的富集分析表明,TGF- \ b {eta}信号通路是最大的术语。那些参与TGF- \ b {eta}途径及其与ERBB途径的串扰的基因在临床肺癌样本中具有很强的生存预后。 (2)基于生物学验证和进一步的策划,开发了以TGF- \ b {eta}诱导的和ERBB扩增的信号通路为中心的肿瘤调节的多尺度模型,以表征Dex治疗对肺癌细胞的动力学作用。我们的仿真结果与SMAD2,FOXO3,TGF \ B {ETA} 1和TGF \ B {ETA} R1的可用数据非常匹配。此外,我们提供了不同剂量的预测,以说明DEX治疗的趋势和治疗潜力。
Motivation: Lung cancer is one of the leading causes for cancer-related death, with a five-year survival rate of 18%. It is a priority for us to understand the underlying mechanisms that affect the implementation and effectiveness of lung cancer therapeutics. In this study, we combine the power of Bioinformatics and Systems Biology to comprehensively uncover functional and signaling pathways of drug treatment using bioinformatics inference and multiscale modeling of both scRNA-seq data and proteomics data. The innovative and cross-disciplinary approach can be further applied to other computational studies in tumorigenesis and oncotherapy. Results: A time series of lung adenocarcinoma-derived A549 cells after DEX treatment were analysed. (1) We first discovered the differentially expressed genes in those lung cancer cells. Then through the interrogation of their regulatory network, we identified key hub genes including TGF-\b{eta}, MYC, and SMAD3 varied underlie DEX treatment. Further enrichment analysis revealed the TGF-\b{eta} signaling pathway as the top enriched term. Those genes involved in the TGF-\b{eta} pathway and their crosstalk with the ERBB pathway presented a strong survival prognosis in clinical lung cancer samples. (2) Based on biological validation and further curation, a multiscale model of tumor regulation centered on both TGF-\b{eta}-induced and ERBB-amplified signaling pathways was developed to characterize the dynamics effects of DEX therapy on lung cancer cells. Our simulation results were well matched to available data of SMAD2, FOXO3, TGF\b{eta}1, and TGF\b{eta}R1 over the time course. Moreover, we provided predictions of different doses to illustrate the trend and therapeutic potential of DEX treatment.