High-Efficiency Microfluidics for Single Cell Phenotypic and Transcriptomic Analysis of Rare Cancer Cells åç

Abstract:

Cancer is one of the leading causes of death worldwide, with recent research suggesting that small populations of cancer cells, called cancer stem-like cells (CSCs), are responsible for tumor relapse and metastasis. Characterizing these cells at single-cell resolution promises greater insight into the mechanisms of cancer progression and facilitates the development of cancer treatments targeting those CSCs. To overcome the challenges in investigating such rare cancer cells, we developed high-efficiency microfluidic technologies for single cell phenotypic and transcriptomic studies. For phenotypic analysis, we achieved the scaling and automation of high-throughput single-cell-derived tumor sphere assays, which are a strong indicator of disease outcome (e.g. tumor relapse and metastasis). With up to 12,800 single cell chambers per chip, the assay elucidated a controversial hypothesis of the linkage between cell size and tumor-initiating potential. The cell capture scheme was also applied to cell-to-cell interaction and cell differentiation studies, highlighting its versatility in single cell analysis. For transcriptomic analysis, Hydro-Seq, a scalable hydrodynamic bead-cell-pairing technique, was developed to analyze CSCs in circulating tumor cells (CTCs) with high cell capture efficiency, high-throughput, and contamination removal capability. We successfully achieved whole transcriptome sequencing of 666 CTCs from 21 breast cancer patient samples, identifying cellular heterogeneity in critical biomarkers of tumor metastasis and therapy. The presented technology offers the capability to analyze the phenotype and gene signatures of CSCs, ultimately providing better diagnostics and treatment of cancer in the future.