Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations

• Published in: Oncogene 2021-01, Vol.40 (2), p.355-368
• Main Authors: He, Di, Wang, Di, Lu, Ping, Yang, Nan, Xue, Zhigang, Zhu, Xianmin, Zhang, Peng, Fan, Guoping
• Format: Article
• Language: English
• Subjects: 1-Phosphatidylinositol 3-kinase; 13/109; 13/51; 38/89; 38/91; 631/67/1612/1350; 631/67/2329; Adenocarcinoma; Adenocarcinoma of Lung - genetics; Adenocarcinoma of Lung - immunology; Adenocarcinoma of Lung - pathology; Aged; AKT protein; Antigen presentation; Apoptosis; Biomarkers, Tumor - genetics; Care and treatment; CD1c antigen; Cell Biology; Cell cycle; Dendritic cells; Dendritic Cells - immunology; Diagnosis; Epidermal growth factor receptors; ErbB Receptors - genetics; Female; Gene expression; Gene Expression Regulation, Neoplastic; Gene mutations; Genetic aspects; Glycolysis; Health aspects; Human Genetics; Humans; Hypoxia; Inflammation; Interleukin 1; Internal Medicine; Lung cancer; Lung Neoplasms - genetics; Lung Neoplasms - immunology; Lung Neoplasms - pathology; Lymphocytes T; Lymphocytes, Tumor-Infiltrating - immunology; Macrophages; Male; Medicine; Medicine & Public Health; Methods; Middle Aged; Mutation; Myeloid cells; Myeloid Cells - immunology; NF-κB protein; Oncology; Prognosis; Ribonucleic acid; RNA; RNA sequencing; Sequence Analysis, RNA; Single-Cell Analysis - methods; Stromal cells; Translation initiation; Tumor cells; Tumor microenvironment; Tumor Microenvironment - immunology; Tumors
• ISSN: 0950-9232; 1476-5594
• DOI: 10.1038/s41388-020-01528-0

Lung adenocarcinoma (LUAD) harboring EGFR mutations prevails in Asian population. However, the inter-patient and intra-tumor heterogeneity has not been addressed at single-cell resolution. Here we performed single-cell RNA sequencing (scRNA-seq) of total 125,674 cells from seven stage-I/II LUAD samples harboring EGFR mutations and five tumor-adjacent lung tissues. We identified diverse cell types within the tumor microenvironment (TME) in which myeloid cells and T cells were the most abundant stromal cell types in tumors and adjacent lung tissues. Within tumors, accompanied by an increase in CD1C + dendritic cells, the tumor-associated macrophages (TAMs) showed pro-tumoral functions without signature gene expression of defined M1 or M2 polarization. Tumor-infiltrating T cells mainly displayed exhausted and regulatory T-cell features. The adenocarcinoma cells can be categorized into different subtypes based on their gene expression signatures in distinct pathways such as hypoxia, glycolysis, cell metabolism, translation initiation, cell cycle, and antigen presentation. By performing pseudotime trajectory, we found that ELF3 was among the most upregulated genes in more advanced tumor cells. In response to secretion of inflammatory cytokines (e.g., IL1B) from immune infiltrates, ELF3 in tumor cells was upregulated to trigger the activation of PI3K/Akt/NF-κB pathway and elevated expression of proliferation and anti-apoptosis genes such as BCL2L1 and CCND1 . Taken together, our study revealed substantial heterogeneity within early-stage LUAD harboring EGFR mutations, implicating complex interactions among tumor cells, stromal cells and immune infiltrates in the TME.