A “Space-for-Time” Strategy Based on Single-Cell Dual-Isotope ICP-MS Analysis Enabling High-Throughput and Sensitive Quantification of miRNAs in Breast Cancer Cells for Therapeutic Assessment

miRNAs regulate cancer progression and serve as both biomarkers and therapeutic targets in chemotherapy and gene therapy. Current analytical platforms lack the capacity to concurrently satisfy single-cell resolution and target specificity while maintaining high-throughput performance and cost-effectiveness. This limitation underscores the critical demand for innovative precision detection technologies. In this study, we focused on two key regulatory miRNAs in breast cancer therapeutic assessment and developed a "space-for-time" strategy using dual-isotope ICP-MS for single-cell miRNAs quantification. The spatial expansion of analytes via single hydrogel microbead encapsulation and collision gas utilization significantly prolonged single-particle ion cloud duration, overcoming the limitations of traditional quadrupole mass spectrometry in the precise dual-isotope quantification. A custom-designed microfluidic chip integrating droplet generation and inertial focusing achieved a single-cell encapsulation efficiency of 57%, thereby enabling a high throughput of ∼1000 cells/min in ICP-MS. In-bead rolling circle amplification combined with nanoprobe labeling enabled femtomolar-level sensitivity for miR-21 and miR-10b detection. This platform facilitated high-throughput, quantitative profiling of miRNA expression across various breast cancer subtypes and offered enhanced resolution of therapeutic responses. In chemotherapy monitoring, our approach revealed early molecular signatures of apoptosis/invasion, outperforming traditional viability and invasion assays in sensitivity and timeliness. For gene therapy evaluation, the platform uncovered subtype-specific differences in miRNA inhibition at single-cell resolution, highlighting tumor heterogeneity thus may potentially guiding precision treatment strategies. Overall, our platform represents a powerful tool for miRNA quantification and therapeutic evaluation, offering robust support for personalized oncology and preclinical drug screening.