Single-Cell RNA Sequencing Reveals Compartment-Specific Immune and Tumor Cell States in a Contiguous Spinal Metastasis

Abstract Background Metastatic disease commonly exhibits differential treatment responses across anatomical sites, including visceral versus osseous lesions and, within the spine, osseous, epidural, and intradural compartments. Intradural spinal metastases, though rare, portend rapid neurologic deterioration and worse outcomes than epidural disease, yet the biological mechanisms underlying this differential behavior remain poorly understood. Methods We report a 61-year-old woman with metastatic ER+/PR+ breast cancer who developed bilateral leg weakness and loss of walking due to severe thoracic spinal cord compression. Imaging showed progressive epidural and intradural tumors where osseous metastases were stable. We performed single-cell RNA sequencing on tumor samples from both compartments after surgical decompression, analyzing cell types, immune subclustering, gene expression, and tumor module scores. Results Sequencing revealed twelve distinct cell populations in both epidural and intradural metastases, including tumor epithelial, neural, glial, macrophages, myeloid, cytotoxic T, NK, and proliferating cells. While major cell types were similar, their composition and gene expression differed. Epidural cytotoxic T and NK cells expressed higher levels of GZMB, PRF1, NKG7, KLRD1, and GNLY. Macrophages split into two groups: a C1QA/C1QB-enriched subset mainly in the intradural compartment, and an activated, inflammatory, antigen-presenting group enriched in the epidural compartment with IL1B, HLA-DRA, CD74, and other genes. Tumor epithelial cells also differed: intradural cells showed increased immune gene expression, antigen presentation, and interferon expression. Conclusion The study shows cellular and transcriptional differences within a single spinal metastasis, influenced by local anatomy. These findings suggest the microenvironment impacts immune and tumor states, guiding future research on metastasis and therapy responses.