MSR1 characterized by chromatin accessibility mediates M2 macrophage polarization to promote gastric cancer progression

Background: M2 macrophages play an important role in gastric cancer progression and metastasis, but the underlying tumor-promoting mechanisms are largely unknown.

Methods: The TCIA database was used to identify the infiltration profile of macrophages. Integrated ATAC-seq, RNA-seq, and single-cell RNA sequencing (scRNA-seq) data from GC samples were used for the analysis. Using ATAC-seq profiles and RNA-seq datasets, combined with cox univariate survival analysis, we identified prognosis-related differentially expressed genes (DEGs) with chromatin accessibility, which were identified as hub genes. The CIBERSORTx algorithm was utilized to estimate the relative infiltration level of M2 macrophages, and Pearson correlation analysis was performed to investigate the relationship between hub genes and M2 macrophages. Multidimensional database validations were carried out to avoid biases. The expression level and function of hub genes in the clusters of macrophages were evaluated by using scRNA-seq data. The role of hub genes in the alternative activation of macrophages and gastric cancer malignant behaviors, as well as their potential regulatory mechanism in gastric cancer progression, were further explored.

Results: 17,334 genes were acquired with chromatin accessibility in promoter regions by ATAC-seq. 2,714 genes were identified with both chromatin accessibility and differential expression based on the gene expression profiles (RNA-seq). By performing Cox univariate survival analysis, 171 survival-related DEGs with chromatin accessibility were identified as hub genes. Through the CIBERSORTx algorithm and Pearson correlation analysis, the gene MSR1 most associated with M2 macrophages was screened out. According to the scRNA-seq analysis, MSR1 was highly expressed in the clusters of macrophages and may be involved in regulating M2 macrophage polarization. In vitro experiments confirmed that M2 macrophage polarization and its induced malignant behavior of gastric cancer cells were inhibited by knockdown of MSR1. Furthermore, MSR1 mediated M2 macrophage polarization by regulating arginine and proline metabolism, thereby activating the AMPK/mTOR pathway to promote gastric cancer progression.

Conclusion: We identified a gene-MSR1-characterized by chromatin accessibility, associated with poor prognosis in gastric cancer. This gene dictates the progression of gastric cancer by facilitating M2 macrophage polarization.