Integration of single-cell and bulk RNA-seq to establish a predictive signature based on the differentiation trajectory of M2 macrophages in lung adenocarcinoma

Abstract

Background: Tumor-associated macrophages as important members of the tumor microenvironment, are highly plastic and heterogeneous. TAMs can be classified into two preliminary subtypes: M1 and M2 macrophages. M2 macrophages are significantly associated with the progression of lung adenocarcinoma. However, no study has investigated the heterogeneity among M2 macrophages and their differentiation-related genes at the single-cell level to guide the clinical treatment of lung adenocarcinoma.Methods: Using the available annotation information from the Tumor Immune Single-cell Hub database, we clustered and annotated 12 lung adenocarcinoma samples using the R package ‘Seurat’. Subsequently, we extracted M2 macrophages for secondary clustering analysis and performed cell trajectory analysis using the R package ‘monocle2’. Based on heterogeneous genes associated with the differentiation trajectory of M2 macrophages, we established a prognostic lung adenocarcinoma model using Lasso-Cox and multivariate stepwise regression. In addition, we also performed immunotherapy and chemotherapy predictions.Results: M2 macrophages exhibit heterogeneity among themselves. M2 macrophages in different differentiation states showed significant differences in pathway activation and immune cell communication. Prognostic signature based on heterogeneous genes can be used to classify the prognostic status and abundance of immune cell infiltration in lung adenocarcinoma patients. In addition, the calculation of the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and the validation of the GSE126044 database indicated that lung adenocarcinoma patients with high-risk scores had poorer treatment outcomes when receiving immune checkpoint inhibitors treatment.Conclusion: Based on scRNA-seq and Bulk-seq data, we identified M2 macrophage-associated prognostic signature with a potential clinical utility to improve precision therapy.

Single-cell and Bulk RNA-Seq reveal angiogenic heterogeneity and microenvironmental features to evaluate prognosis and therapeutic response in lung adenocarcinoma

“…Given that ARS has a good prognostic value, a multifactorial regression model was constructed, and the accuracy of prognostic prediction (3-year AUC of 0.82) was significantly improved with excellent discrimination ( 47 ). The accuracy is comparable to our previously established prognostic models related to sumoylation and M2 macrophages, and ARS can be combined with them in prognostic assessments ( 48 , 49 ). Although the role of angiogenesis in mediating intercellular crosstalk in the TME of LUAD was examined by analyzing angiogenic pathway activation, the underlying mechanisms warrant comprehensive and in-depth investigation.…”

Identification and validation of a novel signature based on cell-cell communication in head and neck squamous cell carcinoma by integrated analysis of single-cell transcriptome and bulk RNA-sequencing

“…T cell data were extracted from cell population, data quality control and calibration were performed again, and T cell population was performed again with reference to T cell gene annotation (19). At the same time, the first 1000 significant genes were used as input of "Monocle2" algorithm for subsequent sequencing to construct developmental tracks of different CD8+ T cell subsets (20).…”

An update to experimental and clinical aspects of tumor-associated macrophages in cancer development: hopes and pitfalls

“…This technology is influential in exploring the mechanisms supporting tumor progression and therapeutic strategies [ 16 ]. Current scRNA-seq investigations predominantly focus on some solid tumors like glioma, breast cancer, and lung cancer [ 17 – 19 ]. In various solid tumor tissues, functional enrichment analysis and gene expression profiling in scRNA-seq data delineate distinct roles for different tumor-associated macrophages (TAMs): FCN1 + TAMs show a proinflammatory influence, SPP1 + TAMs are implicated in metastasis, angiogenesis, and cancer stem cell activation, C1Q + TAMs play a role in immune regulation and suppression, and CCL18 + cells represent terminal immunosuppressive macrophages with potent immunosuppressive abilities and the capacity to promote tumor metastasis[ 20 ].…”