Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data

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.