Differences in microenvironment of lung cancer and pleural effusions by single-cell RNA sequencing

Background: Direct comparison of tumor microenvironment of matched lung cancer biopsies and pleural effusions (PE) from the same patients is critical in understanding tumor biology but has not been performed. This is the first study to compare the lung cancer and PE microenvironment by single-cell RNA sequencing (scRNA-seq). Methods: Matched lung cancer biopsies and PE were obtained prospectively from ten patients. We isolated CD45⁺ cells and performed scRNA-seq to compare the biopsies and PE. Results: PE had a higher proportion of CD4⁺ T cells but lower proportion of CD8⁺ T cells (False detection rate, FDR = 0.0003) compared to biopsies. There was a higher proportion of naïve CD4⁺ T cells (FDR = 0.04) and naïve CD8⁺ T cells (FDR = 0.0008) in PE vs. biopsies. On the other hand, there was a higher proportion of Tregs (FDR = 0.04), effector CD8⁺ (FDR = 0.006), and exhausted CD8⁺ T cells (FDR = 0.01) in biopsies. The expression of inflammatory genes in T cells was increased in biopsies vs. PE, including TNF, IFN-ɣ, IL-1R1, IL-1R2, IL-2, IL-12RB2, IL-18R1, and IL-18RAP (FDR = 0.009, 0.013, 0.029, 0.043, 0.009, 0.013, 0.004, and 0.003, respectively). The gene expression of exhaustion markers in T cells was also increased in tumor biopsies including PDCD1, CTLA4, LAG 3, HAVCR2, TIGIT, and CD160 (FDR = 0.008, 0.003, 0.002, 0.011, 0.006, and 0.049, respectively). Conclusions: There is a higher proportion of naïve T cells and lower proportion of exhausted T cells and Tregs in PE compared to lung cancer biopsies, which can be leveraged for prognostic and therapeutic applications.