Deconvolution of tumor evolution and ecosystem through EV-based liquid biopsy

Cancer progression and drug resistance are driven not only by tumor-intrinsic factors but also by complex interactions between tumor cells and their evolving microenvironment. Understanding the longitudinal co-evolution of tumors and their microenvironment is critical for developing personalized therapeutic strategies, including optimizing immunotherapeutic approaches. Liquid biopsies provide a minimally invasive approach for longitudinal monitoring of cancer dynamics. Current methods primarily focus on next-generation sequencing-based analysis of circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs), which track only tumor-specific changes during disease progression. However, other sources, such as extracellular vesicle RNA (EV-RNA) profiling, can capture broader transcriptomic changes in response to therapy. This capability is exemplified by our RExCuE (mRNA Expression in Circulating EVs) platform, an innovative tool that monitors mRNA alterations in circulation. However, RExCuE is currently unable to distinguish tumor-specific changes from systemic effects. To address this gap, I will build upon my expertise in EV-RNA analysis to understand tumor-intrinsic pathways and the activation status of tumor-extrinsic factors, including the tumor stroma and immune ecosystem. In particularly, I will: (1) identify tumor-specific EV-RNA alterations associated with therapy response and disease progression; (2) characterize the impact of ecosystem-derived EVs on tumor evolution and therapy outcomes; and (3) develop a comprehensive tool to deconvolute tumor-intrinsic and extrinsic transcriptomic changes from clinical samples in circulation. This approach intends to provide a deeper understanding of the adaptive responses of both tumors and their ecosystems to treatments, ultimately guiding more effective and personalized therapeutic strategies.