Detection of actionable mutations in the cerebrospinal fluid and concordance/discordance with extracranial mutations in patients with metastatic breast cancer and leptomeningeal disease

Background: Leptomeningeal disease (LMD) is a devastating complication of metastatic breast cancer (MBC). Metastatic tumors to the central nervous system (CNS) are not routinely assessed for the presence of actionable mutations, hence the frequency and concordance of actionable mutations in the cerebrospinal fluid (CSF) versus extracranial sites are not well characterized. Objective: To evaluate the frequency and concordance of actionable mutations in the CSF versus extracranial sites in patients with MBC and LMD. Methods: In this single-center non-therapeutic prospective observational study, we enrolled 15 patients with MBC and known or suspected LMD from 2020 to 2024 and collected CSF, blood, and archival tumor samples. We enumerated CSF circulating tumor cells (CTCs) and analyzed circulating tumor DNA (ctDNA) via next-generation sequencing (NGS) using the CNSide technology (Biocept). When available, we compared CSF NGS results with available NGS data from matched blood and tumor samples. Results: Of the 15 patients enrolled, 14 were determined to have LMD based on CSF cytology, radiographic, and clinical assessment (7 hormone receptor-positive (HR+)/human epidermal growth factor receptor 2 negative (HER2−), 6 triple negative breast cancer, 1 HER2+). CSF CTC enumeration was performed in a subset of patients and was positive in 5/7 (71.4%), of which 4/5 had negative CSF cytology. Median CTC enumeration was 0.29 CTCs/mL (range 0–136.4). Of the 14 patients with confirmed LMD, analysis of CSF ctDNA detected pathogenic variants in half of the patients (7/14, 50.0%). Comparison of CSF versus blood and/or tissue-based NGS testing was available for 10 patients: 5 patients (50%) had concordant CSF versus extracranial mutations, 3 patients (30%) had discordant CSF versus extracranial mutations, and 2 patients (20%) had both concordant and discordant CSF versus extracranial mutations. Conclusion: CSF CTCs can be detected and enumerated in patients with MBC and LMD, even in patients with negative CSF cytology. We were able to detect pathogenic mutations in the CSF ctDNA in half of the patients. We observed variable concordance and heterogeneity in the detection of actionable mutations between the CSF, blood, and tumor tissue, supporting the value of investigating the CSF to identify novel targets and resistance mechanisms. Larger studies are needed to assess the clinical utility of these observations, particularly with the development of novel targeted CNS-penetrant agents.