Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort
单位:[1]China Med Univ, Hosp 1, Dept Pulm & Crit Care Med, Shenyang 110001, Peoples R China[2]China Japan Friendship Hosp, Ctr Resp Med, Dept Pulm & Crit Care Med, Beijing 100029, Peoples R China[3]Chinese Acad Med Sci, Peking Union Med Coll, Grad Sch, Beijing 100029, Peoples R China[4]Natl Ctr Resp Med, Beijing 100029, Peoples R China[5]Chinese Acad Med Sci, Inst Resp Med, Beijing 100029, Peoples R China[6]Natl Clin Res Ctr Resp Dis, Beijing 100029, Peoples R China[7]China Med Univ, Shengjing Hosp, Dept Pathol, Shenyang 110001, Peoples R China中国医科大学附属盛京医院中国医科大学盛京医院[8]Clinical Lab Co Ltd, Shenyang KingMed Ctr, Dept Pathol, Shenyang 110001, Peoples R China
Background: Recent studies have emphasized the close relationship between macrophages and tumor immunity, and the prognosis of lung adenocarcinoma (LUAD) patients is intimately linked to this. Nonetheless, the prog-nostic signature and classification of different immune patterns in LUAD patients based on the macrophages is largely unexplored.Methods: Two sc-RNAseq datasets of LUAD patients were collected and reprocessed. The differentially expressed genes (DEGs) related to macrophages between LUAD tissues and normal lung tissues were then identified. Based upon the above genes, three distinct immune patterns in the TCGA-LUAD cohort were identified. The ssGSEA and CIBERSORT were applied for immune profiling and characterization of different subtypes. A four-gene prog-nostic signature for LUAD patients was established based on the DEGs between the subtypes using stepwise multi-Cox regression. TCGA-LUAD cohort was used as training set. Five GEO-LUAD datasets and an independent cohort containing 112 LUAD samples were used for validation. TIDE (tumor immune dysfunction and exclusion) and drug sensitivity analyses were also performed.Results: Macrophage-related differentially expressed genes were found out using the publicly available scRNA-seq data of LUAD. Three different immune patterns which were proved to have distinct immune infiltration char-acteristics in the TCGA-LUAD cohort were recognized based on the above macrophage-related genes. Thereafter, 174 DEGs among the above three different immune patterns were figured out; on the basis of this, a four-gene prognostic signature was constructed. This signature distinguished the prognosis of LUAD patients well in various GSE datasets as well as our independent cohort. Further analyses revealed that patients which had a higher risk score also accompanied with a lower immune infiltration level and a worse response to several immunotherapy biomarkers.Conclusion: This study highlighted that macrophage were significantly associated with TME diversity and complexity. The four-gene prognostic signature could be used for predicting outcomes and immune landscapes for patients with LUAD.
基金:
National High Level Hospital Clinical Research Funding; Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences; National Natural Science Foundation of China; [2022-NHLHCRF-LX-01]; [81900040]; [81700041]
第一作者单位:[1]China Med Univ, Hosp 1, Dept Pulm & Crit Care Med, Shenyang 110001, Peoples R China
共同第一作者:
通讯作者:
通讯机构:[2]China Japan Friendship Hosp, Ctr Resp Med, Dept Pulm & Crit Care Med, Beijing 100029, Peoples R China[4]Natl Ctr Resp Med, Beijing 100029, Peoples R China[5]Chinese Acad Med Sci, Inst Resp Med, Beijing 100029, Peoples R China[6]Natl Clin Res Ctr Resp Dis, Beijing 100029, Peoples R China[*1]Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China
推荐引用方式(GB/T 7714):
Li Ruixia,Tong Run,Zhang Zhe,et al.Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort[J].GENOMICS.2022,114(6):doi:10.1016/j.ygeno.2022.110520.
APA:
Li, Ruixia,Tong, Run,Zhang, Zhe,Deng, Mingming,Wang, Tao&Hou, Gang.(2022).Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort.GENOMICS,114,(6)
MLA:
Li, Ruixia,et al."Single-cell sequencing analysis and transcriptome analysis constructed the macrophage related gene-related signature in lung adenocarcinoma and verified by an independent cohort".GENOMICS 114..6(2022)