Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions

Cancer metastasis in the bone represents an incurable disease. About one-third of patients with advanced renal cell carcinoma (ccRCC) have bone metastasis at the time of diagnosis making it a life-threatening disease. The bone metastatic niche, including immune and stroma microenvironment, has not been defined. Here, we created a human single-cell transcriptome cell-atlas of ccRCC bone metastases, contrasted with normal bone marrow immune cells and stroma. We collected fresh patient samples directly from the operating room and performed single-cell transcriptomic profiling of solid metastatic tissue (Tumor fraction), liquid bone marrow at the vertebral level of spinal cord compression (Involved), as well as liquid bone marrow from a different vertebral body distant from the tumor site but within the surgical field (Distal). In addition, we enriched immune and stroma cells from patients undergoing hip replacement surgery (Benign) as extra control. Bone marrow were disaggregated and profiled by 10X Genomics Single cell 3 gene expression V2.