Multimodal evaluation of cerebrospinal fluid from breast cancer leptomeningeal metastases using circulating tumor cell detection, single-cell sequencing, and proteomics

Patients with human epidermal growth factor receptor 2 positive (HER2+) or triple-negative breast cancer are at higher risk than those with other breast cancer subtypes for developing brain metastases, including leptomeningeal metastases. Despite advances in the treatment of primary breast tumors, the prognosis of breast cancer patients with brain metastases remains poor. Frequent and sensitive monitoring of response to treatments is crucial to optimize treatments for brain metastases. Multimodal molecular analyses of cells in cerebrospinal fluid (CSF) may provide a less invasive approach than biopsy for monitoring disease in the central nervous system. A 41-year-old female with refractory leptomeningeal metastases from HER2 + breast cancer had serial sampling of cerebrospinal fluid (CSF) from an Ommaya reservoir prior to, and after, the addition of sacituzumab govitecan to her treatment regimen. Cytopathologic clinical analysis, circulating tumor cell enumeration, single-cell RNA sequencing, and cytokine profiling assays were performed on collected samples. A reduction in CSF tumor cells and absence of HER2-expressing cells was observed following treatment, with MRI confirming decreased tumor size. Single-cell RNA sequencing revealed diverse tumor and immune cell populations in CSF, highlighting gene expression signatures associated with breast cancer and triple negative disease and dynamic changes in cellular composition throughout the course of treatment. Cytokine profiling identified increased pro-inflammatory cytokines post-treatment. These findings highlight the potential utility of molecular profiling of CSF as an early indicator of treatment response and an approach for identifying resistance mechanisms and optimal combination therapies.