Microfluidics-based High-throughput Circulating Tumor Cell Sorting and Single-cell Sequencing Technology

Circulating tumor cells (CTCs) serve as a promising biomarker for tracking cancer metastasis, progression, and recurrence. Liquid biopsy techniques centered on CTC detection have demonstrated considerable potential due to their non-invasive nature and ability to provide real-time monitoring of tumor dynamics. However, conventional bulk CTC analyses fail to capture the intrinsic heterogeneity among CTC populations, obscuring crucial insights into tumor biology. Single-cell RNA sequencing (scRNA-seq) enables high-resolution characterization of CTC heterogeneity, offering new opportunities for precision oncology and mechanistic studies of tumor progression. Despite these advantages, the existing methodologies for single-CTC sequencing tend to suffer from inefficiencies, including low recovery rates, labor-intensive workflows, and contamination risks associated with multiple manual handling steps. To address these limitations, we present an integrated microfluidic protocol that consolidates CTC enrichment, purification, and single-cell sequencing into a unified workflow. The method employs dynamically controlled magnetic capture within a herringbone-structured chip, where vortex mixing and cumulative immunomagnetic bead binding enable robust, high-throughput CTC isolation with minimal cell damage. Subsequent purification using a leukocyte antibody-coated microfluidic chip effectively removes the non-target cells, further enhancing CTC purity through negative selection. Finally, a high-precision single-cell sequencing chip, designed based on differential flow resistance principles, facilitates efficient single-cell capture and pairing with uniquely barcoded microbeads. This novel platform overcomes the limitations of Poisson distribution-based methods, improving CTC utilization while minimizing microbead consumption and sequencing costs. Our integrated protocol significantly enhances CTC capture efficiency, purity, and single-cell sequencing throughput, making it well-suited for clinical applications and large-scale cancer research. By enabling a more precise and scalable analysis of CTC heterogeneity, this method has the potential to refine early cancer diagnosis, treatment monitoring, and mechanistic studies of metastasis, ultimately advancing the field of precision oncology.