Single-cell landscape of the immune microenvironment of leptomeningeal metastases in non-small cell lung cancer treated with pemetrexed sheath injection.

e20026 Background: The incidence of leptomeningeal metastasis (LM) is increasing in non-small cell lung cancer (NSCLC) and pemetrexed injection is an important treatment for LM. Here, we used single-cell RNA sequencing (scRNA-seq) to define the immune landscape of LM in NSCLC treated with pemetrexed sheath injection. Methods: scRNA-seq was utilized on 27 cerebrospinal fluid (CSF) samples from 20 patients, including 7 pairs of pre- and post-treatment samples. Detailed immune landscapes were mapped, and key results were confirmed by flow cytometry and IHC. Biomarkers for the efficacy of pemetrexed sheath injection was analyzed. Results: The LM microenvironment was characterized by macrophages and cancer cells with decreased significantly after pemetrexed injection. The cancer cells in LM was highly expressed CEACAM6, SFTPB and NAPSA, and chemokines liked CXCL16 in macrophages decreased significantly after receiving pemetrexed sheath treatment than pre- treatment, which was validated by flow cytometry and IHC. In the signal pathway enrichment analysis, significant changes of metabolism and cell cycle genes occurred before and after pemetrexed injection. Moreover, the analysis of tumor cells and immune cells interaction showed that CSF1-CSF1R, AREG/HBEGF-EGFR, FD1-Intergrin_a2B1_complex, CCL5-CCR1, CD55_ADGRE play a key role in tumor cells recruiting monocytes and inhibiting macrophages. Gene set based on the efficacy of pemetrexed sheath injection was enriched, including C15orf48, CCL5, DUSP6, FLNA, TXNIP, TNNT1, was confirmed associating with increased overall survival. Conclusions: Our study characterizes the immune cell landscape of LM from NSCLC, and provided the biomarkers for the efficacy of pemetrexed injection.