Single-cell Sequencing Reveals Multi-omics Dynamics During Lymph Node Metastasis in Breast Cancer

Single-cell sequencing and analysis have advanced our understanding of intra-tumoral heterogeneity for breast cancer lymph node metastasis. However, how alterations at multi-omics levels coordinate together in a single tumor cell to drive metastasis remains unclear. Here we performed single-cell multi-omics sequencing of paired primary tumors and metastatic lymph nodes from breast cancer patients. This enabled a comprehensive reconstruction of dynamic molecular landscapes by simultaneously profiling genome, epigenome and transcriptome in the same single tumor cell. During metastasis of patients with higher heterogeneity, clonal evolution analysis based on copy number variations at single-cell resolution showed a specific clone possessing metastatic advantages. Meanwhile, the genome-wide DNA methylation underwent stageable changes. In contrast, gene expression was specifically reprogrammed concentrated at tumor cell transition, suggesting a remodelling by organ microenvironment. By integrative multi-omics analysis, we identified genes that were dysregulated at more than one omics, and showed the importance of SLC39A6, ELP2 and RPL13 genes in breast cancer metastasis or prognosis. Our study traces the genomic, epigenomic and transcriptomic dynamics simultaneously from primary tumors to metastatic lymph nodes in the same single cell, providing new insights into breast cancer metastasis.