The mechanisms underlying the interaction between disseminated tumor cells (DTCs) and their tissue microenvironment during metastasis colonization are poorly understood.

We integrated multimodal single-cell and spatial profiling from liver cancer mouse models and human metastases to track the spatiotemporal dynamics of DTCs and their microenvironments across nine sequential time points from single-cell seeding until overt lung metastasis.

We identified a residual population of quiescent Phgdhhigh DTCs that survive initial innate immune clearance and become transiently enriched in micrometastases. These cells shape an immune-scarce microenvironment through PHGDH-dependent, H3K27me3-mediated epigenetic silencing of chemokine transcription, promoting metastatic expansion. Cx3cr1high interstitial macrophages were also found to be transiently enriched before DTCs expansion, creating an immune-privileged niche for metastatic outgrowth by recruiting immunosuppressive cells. Inactivating the Phgdh-H3K27me3 axis in DTCs or depleting interstitial macrophages restored immune surveillance and inhibited metastatic colonization. These findings provide new therapeutic concepts for developing micrometastasis-targeting regimens.

In summary, an integrated analysis of this atlas coupled with additional multi-omics data from human patients and in vitro, ex vivo, in vivo validation assays identified key cellular programs transiently activated in disseminated tumor cells (DTCs) or in immune cells that promote metastatic seeding by building an immune-compromised microenvironment. Our results shed light on the spatial and temporal complexity of metastatic colonization, laying a foundation for elucidation of the pathogenic mechanisms and therapeutic vulnerabilities of cancer metastases.