High-Purity Magnetic Fluidic Isolation of Viable Circulating Tumor Cells Enables Single-Cell Multi-Omics Profiling

Abstract Circulating tumor cells (CTCs) provide a minimally invasive window into tumor evolution, yet their rarity, phenotypic heterogeneity, and vulnerability to processing-induced damage impose stringent requirements on upstream enrichment workflows for single-cell molecular analysis. Here, we report a magnetic-fluidic analytical platform for rapid, high-purity isolation of viable CTCs from whole blood and downstream single-cell profiling. The device integrates immunomagnetic labeling with hydrodynamically confined laminar flow, enabling magnetically tagged tumor cells to be laterally deflected into a CTC-enriched outlet, while unlabeled hematologic cells are depleted through waste outlets. After optimization of inlet flow rates, the platform achieved an MCF-7 sorting efficiency of 97.98 ± 0.60% and a white blood cell removal efficiency of 99.96 ± 0.01%. In spiked whole-blood samples, the enriched fraction showed a CTC purity of 99.68 ± 0.08%, while post-sorting viability remained comparable to untreated controls, supporting compatibility with downstream single-cell assays. Application to breast cancer patient blood samples enabled the detection of 3−6 CTCs from 2 mL of blood. Coupling this enrichment workflow with single-cell RNA sequencing generated 56 high-quality single-cell transcriptomes from a HER2-low breast cancer patient and identified epithelial CTC-like and immune cell populations, with negligible ERBB2 transcript levels observed in the epithelial CTC-like population. Exploratory single-cell proteomic analysis further demonstrated measurable intercellular heterogeneity among patient-derived CTCs. This magnetic-fluidic workflow provides a practical analytical route for viability-preserving CTC enrichment and single-cell molecular characterization in liquid biopsy.