Systematic Analysis Of Lung Tumor Microenvironment And Discovery Of Targeted Traditional Chinese Medicine

A solid tumor is not a group of cancer cells that exist alone,but are embedded in a tumor microenvironment(TME)composed of infiltrating and resident host cells.The tumor microenvironment is not only a silent bystander,but also an active promoter of cancer progression and a crucial target for oncotherapy.Immune checkpoint blockade(ICB)therapy is the most striking innovation,which reinvigorates the effective anti-tumor immune response of immune cells infiltrated in tumors,and induces durable or even curative therapeutic effects in vinous advanced cancers.However,only a small fraction of patients benefits from it.Therefore,new technologies and methods are needed to clarify the interaction between tumors and their tumor microenvironment in order to identify ICB response biomarkers and novel microenvironmental targets and drugs.Here,we take lung cancer,the most frequent human malignant neoplasm,and the highest cause of cancer-related deaths in China,as an example.By integrating high-resolution single-cell RNA sequencing(scRNA-seq)data and large-scale transcriptome data,we have constructed a high-resolution TME cell atlas for lung adenocarcinoma(LUAD)and lung squamous cell carcinoma(LUSC)which shows the abundance of 39 cell types in 1141 samples.In this way,we clarified the associations of infiltration of virous cell types with clinical features and prognosis,analyzed potential immunotherapy targets and immunotherapy response biomarkers,and constructed a tumor prognosis model based on the TME cell atlas.Finally,through the integration of a series of pharmacological analysis techniques,we constructed a novel systems pharmacology strategy to clarify the mechanism of Radix Sophorae Flavescentis(Kushen)targeting the tumor microenvironment to inhibit LUAD.The main findings of this work are summarized as follow:(1)To analyze the correlation between tumor microenvironment,prognosis and other clinical features and immunotherapy at a high-resolution level,we used a state-of-the-art Bayesian model to infer the abundance of 39 cell types from 1141 LUAD and LUSC bulk RNA-seq data using a high-resolution scRNA-seq reference as prior information,which resulted in a comprehensive cell atlas of lung cancer TME.A series of analyses were combined and combined:1)Correlation of different cell types and clinical characteristics of lung cancer;2)Analysis of the reasons for the failure of MAGEA3 vaccine therapy in non-small cell lung cancer and the biomarkers of PD-1/PD-L1 delivery interruption treatment response cell.The results show that the tumor microenvironment atlas we implanted can explain the known knowledge about the microenvironment of lung cancer,and we have also discovered the relationship between a series of new cell types and tumor development and treatment.(1)To correlate lung cancer TME with prognosis and other clinical features and immunotherapy at a high-resolution level,we used a state-of-the-art Bayesian model to infer the abundance of 39 cell types from 1141 LUAD and LUSC bulk RNA-seq data using a high-resolution scRNA-seq reference as prior information,which resulted in a comprehensive TME cell atlas of lung cancer.This led to a series of analyses including:1)Correlating different cell types with the clinical features of lung cancer;2)Analyzing the reasons for the failure of MAGEA3 vaccine therapy in non-small cell lung cancer and the biomarkers for PD-1/PD-L1pathway blockade response.These results show that our TME cell atlas can not only explain the known knowledge about lung cancer microenvironment,but also discover the new association between stromal cells and tumor progression and therapeutic strategies.(2)Based on the TME cell atlas,we constructed a tumor prognosis model(called TME risk score,TMERS),which has a predictive power in LUAD and LUSC.And we demonstrated that the TMERS is independent of classic tumor prognosis factors(tumor staging,age,gender,smoking behavior,gene mutations).These suggest that the TME cell composition is a key factor for patient prognosis predication,and our TMERS could be as an effective supplement for lung cancer prognosis prediction.(3)Finally,by integrating the TME cell atlas with systems biology and pharmacology methods,we designed a novel system pharmacology strategy to discover the chemical components in Traditional Chinese Medicine to enhance efficacy of PD-1/PD-L1 blockade therapy.We have clarified that oxymatrine,the main component of Radix Sophorae Flavescentis,promotes the infiltration of CD8~+T cells in the tumor microenvironment and synergy with the anti-cancer effect of PD-L1 inhibitor.The main contents include:1)Screening the active ingredients of Radix Sophorae Flavescentis through ADME parameter evaluation;2)Predicting the targets of potential active ingredients and clarifying the potential role of the targets in anti-tumor and immunomodulation;3)Based on the correlation of targets with the clinical features and immunophenotypes of LUAD,we found the potential effect of oxymatrine in increasing the infiltration of CD8~+T cells in lung adenocarcinoma;4)Animal experiments verified that oxymatrine can enhance CD8~+T in the tumor microenvironment and synergy with PD-L1 inhibitor to inhibit the growth of lung adenocarcinoma in mice.In summary,this study takes advantage of single-cell sequencing data to understand the TME and its interaction with cancer cells.We constructed a high-resolution lung cancer TME cell atlas,which provides an important resource for guiding the effectiveness of cancer vaccine treatment and immune checkpoint therapy and predicting prognosis and therapeutic drugs for lung cancer.