Development of High-Throughput Platforms for Single-Cell Analysis

Abstract

Many important areas of research regarding human health, such as immunology and cancer biology, deal with highly heterogeneous populations of cells where the contributions of individual players cannot be ignored. Single-cell technologies aim to resolve this heterogeneity by analyzing many individual cells in a high-throughput manner. Here we developed two examples of such tools that rely on microfabricated arrays of microwells. The first platform merges fluorescence cytometry with label-free profiling of the small molecule composition of tens of thousands of cells based on matrix assisted laser desorption/ionization (MALDI) mass spectrometry. We evaluated several materials and approaches to chip fabrication suitable for interfacing with a MALDI instrument. We also developed an analytical pipeline for efficient processing of cells on the chip and demonstrated its application to the analysis of brain tumor samples. The second platform provides a new format of microwell arrays for fluorescence cytometry that improves their compatibility with a range of automated equipment and enables more efficient processing of a greater number of samples, while preserving viability and identity of cells for subsequent analyses. We demonstrated its utility for on-chip enrichment and recovery of circulating tumor cells (CTCs) and high-content immuno phenotyping of small clinical samples.