Metastases, especially those to the meninges of the brain and spinal cord (leptomeningeal disease, LMD), have particularly poor prognoses. Clinical trials are currently underway to determine if a new immunotherapy will be effective in patients with LMD, but directly identifying critical mechanisms and biomarkers for clinical benefit requires methods that can comprehensively profile the minute quantities of cells found in cerebrospinal fluid where the metastasis occurs. To address this need, we will apply a low-input, high-throughput single-cell RNA-sequencing technology we recently co-developed called Seq-Well to these precious clinical samples. With this tool, we will be able to characterize cancerous and noncancerous cells in pre- and on-treatment spinal fluid, and determine how the tumor and its microenvironment change in response to immunotherapy. Findings from our work could help uncover unique prognostic markers for the disease and provide mechanistic insight into the utility of using immune-boosting agents for treating LMD and other metastases.