Single cell RNA sequencing to reveal immune microenvironment in primary and brain metastatic lesion of non-small cell lung cancer

e21009 Background: Despite immune checkpoint inhibitors (ICIs) have been proven effective in patients with advanced NSCLC, suboptimal therapeutic responses are seen in brain metastatic lesions. The heterogeneous cellular components in the tumor immune microenvironment (TIME) pose a challenge in understanding the low immune response. A comprehensive understanding of the heterogeneous TIME in primary and brain metastatic NSCLC is currently lacking, but crucial for improving ICI therapeutic responses in NSCLC patients with brain metastasis. Therefore, we use single cell RNA sequencing (scRNA-seq) to reveal distinct immune microenvironment in primary and brain metastatic lesion of NSCLC. Methods: Eight primary and nine brain metastatic NSCLC tumor samples were obtained through surgical resection. Immune cells (CD45+) were enriched through fluorescence-activated cell sorting (FACS) and subjected to scRNA-seq using the 10X Genomics platform. Sequencing reads were normalized and analyzed using R/Seurat package. Cellular components of each sample were determined based on known marker genes. Results: In our study, we observed a significant difference in the immune cell composition between primary and brain metastatic tumor samples. We found brain metastatic tumors are marked by an enrichment of TIMP1+ monocytes and PLTP+ tumor-associated macrophages (TAMs), both of which display heightened anti-inflammatory properties. In contrast, primary tumors exhibit an enrichment of FCN1+ monocytes and MARCO+ TAMs. Further analysis has revealed that the enrichment of TIMP1+ monocytes and PLTP+ TAMs is associated with a worse prognosis in patients receiving immunotherapy. Additionally, our examination of the transcriptome profile of CD8+ T cells showed an upregulation of inhibitory and exhausted signatures in brain metastatic tumor samples. Conclusions: Our study provided a comprehensive understanding of the TIME of primary and brain metastatic NSCLC and to gain deeper insights into the immunological mechanisms involved in the response to ICIs. The results of our study could prove valuable for the development of future immunotherapy strategies for NSCLC patients with brain metastasis.