Metastasis dramatically reduces survival. While multiple drugs targeting various steps of the metastatic process have been approved, the overall survival remains poor. To metastasize, cancer cells go through multiple steps: local invasion is the spread from their original location to surrounding tissue or lymph nodes. It eventually spreads to distant tissues of the body.
Mechanisms Driving Tumor Migration
One reason for so many drug failures to inhibit cancer dissemination is the intricate biology of the TME, particularly its role in supporting angiogenesis, the formation of new blood vessels that supply tumors with essential oxygen and nutrients. This process is orchestrated through a sophisticated interplay of cellular and molecular signals within the TME.
Stromal cells, key architects of the TME, secrete a variety of growth factors and cytokines —VEGF, EGF and TGFβ—that promote tumor cell proliferation, survival, and a pro-angiogenic milieu.
While angiogenesis enables tumor expansion and vascular access, the ability of tumor cells to migrate is equally crucial for metastasis. A key driver to migration and metastasis is the epithelial-to-mesenchymal transition (EMT), a reversible process through which tumor cells gain motility and invasiveness. EMT reduces epithelial markers like EpCAM and cytokeratins while increasing mesenchymal traits such as vimentin and N-cadherin. Following this transition, cell migration can be grouped in two broader categories, single cell migration and collective migration. Once in the vascular system, cells can circulate individually as “circulating tumor cells” (CTCs), or in an aggregate of circulating microemboli as “circulating tumor microemboli” (CTMs). While there is evidence that CTM is a more dominant form of migration, more literature has focused on CTC biology.
Tumor cells adapt to different organ-specific microenvironments
A characteristic of metastasizing cancer is its ability to escape and colonize another organ and its new environment.
CTC, shed from the primary tumor, must survive in the bloodstream, evade immune destruction, adapt to organ-specific microenvironments, and reprogram local stromal cells to support their growth and survival. They are highly heterogeneous, reflecting diverse genotypic and phenotypic states, and often exist in hybrid epithelial/mesenchymal states that confer apoptosis resistance and enhance metastatic potential.
Single cell sequencing has revealed that CTCs can harbor mutations distinct from the primary tumor, suggesting clonal evolution or therapy-driven selection during dissemination. Their transcriptomic profiles frequently exhibit expression of stemness-associated genes, activation of survival pathways, and drug resistance signatures—underscoring their central role in cancer progression and therapy resistance.
Because CTCs circulate in the bloodstream, they provide a unique opportunity for longitudinal analysis in patients. Detecting and profiling CTCs in real time offers a window into tumor evolution and the potential to guide clinical decision-making.
Tracking Tumor Spread: How Single Cell RNA Sequencing Clarifies the Cellular Programs Driving Angiogenesis and Metastasis
While angiogenesis has long been recognized as a prerequisite for metastatic spread, single-cell RNA sequencing (scRNA-seq) now allows unprecedented resolution of the cellular contributors and molecular signals orchestrating this process within the TME.
Beyond the primary tumor, scRNA-seq captures the remarkable plasticity of CTCs, resolving their dynamic phenotypic states and transcriptional programs over time. Because CTCs are rare, sensitive and scalable scRNA-seq platforms are essential for capturing them alongside other rare but clinically important populations such as cancer stem cells.
Large-scale scRNA-seq with combinatorial barcoding studies across hundreds of patients have uncovered conserved gene programs and master transcriptional regulators that appear to drive metastatic behavior across multiple cancer types. These insights not only deepen our understanding of metastasis biology but also open avenues for therapeutic intervention and real-time monitoring of cancer progression.
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Mechanisms of Local Invasion and Metastasis with scRNA-seq
Metastasis is the main cause of cancer-related mortality. It refers to the spread of tumor cells from the primary site to distant organs, a process that unfolds through three major stages. First, cancer cells migrate through the surrounding extracellular matrix. They then undergo intravasation, penetrating into the lymphatic or vascular circulation. Once in the bloodstream, the cells disseminate throughout the body and eventually colonize new tissues, where they can establish secondary tumors. ScRNA-seq has helped scientists analyze local invasion and metastasis. By comparing primary and metastatic tumors, you can decipher the molecular nature of cancer spread and uncover potential vulnerabilities that may be uniquely targetable in metastatic disease.
Clonal Evolution and Gene Expression Dynamics in Tumor Progression
- How do clones evolve over time during tumor progression or treatment?
- Which genetic alterations correlate with distinct expression programs?
- Are there rare, transient, or intermediate cell states that drive progression?
- How do therapy and selective pressure reshape clonal and transcriptional landscapes?
Mechanisms Underlying Competition Between Expanding Clones Using scRNA-seq
- How do microenvironmental stresses shape competitive outcomes between clones?
- What metabolic states or pathways give certain clones a fitness advantage?
- Do competing clones employ distinct stress-response or survival programs?
- What cell–cell communication networks drive competitive dominance?
TLDR: Metastasis arises through a series of coordinated cellular programs that enable tumor cells to invade surrounding tissues, enter circulation, and colonize distant organs. These processes are shaped by transcriptional plasticity, interactions with stromal and immune cells, and adaptation to new microenvironments. Distinct migratory states and survival programs emerge across tumor cell populations, contributing to dissemination and therapy resistance. Single cell RNA sequencing uncovers the gene expression programs and transitional states that underlie invasion and metastasis, offering insight into the cellular routes that enable tumor spread.
