Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma

Abstract

Recent developments in immuno-oncology demonstrate that not only cancer cells, but also the tumor microenvironment can guide precision medicine. A comprehensive and in-depth characterization of the tumor microenvironment is challenging since its cell populations are diverse and can be important even if scarce. To identify clinically relevant microenvironmental and cancer features, we applied single-cell RNA sequencing to ten human lung adenocarcinomas and ten normal control tissues. Our analyses revealed heterogeneous carcinoma cell transcriptomes reflecting histological grade and oncogenic pathway activities, and two distinct microenvironmental patterns. The immune-activated CP²E microenvironment was composed of cancer-associated myofibroblasts, proinflammatory monocyte-derived macrophages, plasmacytoid dendritic cells and exhausted CD8+ T cells, and was prognostically unfavorable. In contrast, the inert N³MC microenvironment was characterized by normal-like myofibroblasts, non-inflammatory monocyte-derived macrophages, NK cells, myeloid dendritic cells and conventional T cells, and was associated with a favorable prognosis. Microenvironmental marker genes and signatures identified in single-cell profiles had progonostic value in bulk tumor profiles. In summary, single-cell RNA profiling of lung adenocarcinoma provides additional prognostic information based on the microenvironment, and may help to predict therapy response and to reveal possible target cell populations for future therapeutic approaches.

Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment

“…It suggests that TAMs can promote lung cancer progression through inhibiting tumor immunity and promoting of tumor growth and invasion. Among the subtypes of TAMs, M2 macrophages were found high expression of SELENOP, whereas M1 macrophages expressed high levels of pro-inflammatory chemokines, such as CXCL9 and CXCL10, pro-inflammatory cytokine IL1B, and M1 macrophages were also found to be associated with other myeloid cell types such as plasmacytoid DCs in LUAD via scRNA-seq ( 95 ).…”

“…The cluster of fibroblasts was found to be divided into seven known cell types by scRNA-seq in NSCLC ( 43 , 54 ), with COL13A1 + and COL14A1 + fibroblasts being the major fibroblast types in early NSCLC tissues ( 43 ). Moreover, myofibroblasts were found to replace fibroblasts in the TME ( 43 , 95 ), which may promote extensive tissue reconstruction ( 114 ), angiogenesis ( 115 ), and tumor progression ( 116 ). Myofibroblasts were characterized by expression of both fibroblastic marker genes, such as PDGFRA and LUM, and smooth muscle marker genes, such as MYLK and ACTA2 ( 95 ).…”

“…Moreover, myofibroblasts were found to replace fibroblasts in the TME ( 43 , 95 ), which may promote extensive tissue reconstruction ( 114 ), angiogenesis ( 115 ), and tumor progression ( 116 ). Myofibroblasts were characterized by expression of both fibroblastic marker genes, such as PDGFRA and LUM, and smooth muscle marker genes, such as MYLK and ACTA2 ( 95 ). And high expression of genes related to myogenesis (MEF2C, MYH11 or ITGA7), the Notch pathway and angiogenesis were found in the highest ACTA2 expression clusters, indicating that these cells were activated ( 54 ).…”

“…Each of the fibroblast types expresses unique collagen and other extracellular matrix molecules ( 54 ). Fibroblasts in normal tissues express high elastin and low levels of certain collagens (collagen types I, III, V and VIII) but not others (e.g., collagen type VI) ( 54 ), while subpopulations of myofibroblasts exclusively existing in tumor tissues exhibit high expression of collagens such as COL3A1, COL5A1, COL5A2 and COL6A3, other matrix proteins and matrix degrading enzymes ( 95 ), suggesting roles in extracellular matrix remodeling. Via scRNA-seq, Myofibroblasts in tumor tissue also exhibit high activity of transforming growth factor beta (TGF-β) and JAK/STAT signaling as well as hypoxia-induced pathways ( 54 , 95 ).…”

Deciphering the Immune–Tumor Interplay During Early-Stage Lung Cancer Development via Single-Cell Technology

“…Lambrechts et al identified some heterogeneous sub-subpopulations in stromal cells and the transcription factors that regulate their heterogeneity in the early LUAD patients by scRNA-seq (43). ScRNA-seq analysis of 10 normal lung tissues and 10 fresh LUAD tissues found that the TME was composed of cancer-associated myofibroblasts, exhausted CD8 + T cells, proinflammatory monocyte-derived macrophages, plasmacytoid dendritic cells, myeloid dendritic cells, anti-inflammatory monocyte-derived macrophages, normal-like myofibroblasts, NK cells, and conventional T cells (69). Multi-region of five early-stage LUADs and 14 multi-region normal lung tissues found that the Treg + cells are increased in normal tissues with proximity to LUAD and the signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages, and inflammatory dendritic cells were decreased (37).…”