Multiplexed laser particles for spatially resolved single-cell analysis

Biomolecular analysis at the single-cell level is increasingly important in the study of cellular heterogeneity and its consequences, particularly in organismic development and complex diseases such as cancer. Single-cell molecular analyses have led to the identification of new cell types(1) and the discovery of novel targets for diagnosis and therapy(2). While these analyses are performed predominantly on dissociated single cells, emerging techniques seek understanding of cellular state, cellular function and cell–cell interactions within the native tissue environment by combining optical microscopy and single-cell molecular analyses. These techniques include in situ multiplexed imaging of fluorescently labeled proteins and nucleotides, as well as low-throughput ex vivo methods in which specific cells are isolated for downstream molecular analyses. However, these methods are limited in either the number and type of molecular species they can identify or the number of cells that can be analyzed. High-throughput methods are needed for comprehensive profiling of many cells (>1000) to detect rare cell types, discriminate relevant biomarkers from intrinsic population noise, and reduce the time and cost of measurement. Many established, high-throughput single-cell analyses are not directly applicable because they require tissue dissociation, leading to a loss of spatial information(3). No current methods exist that can seamlessly connect spatial mapping to single-cell techniques. In this Perspective, we review current methods for spatially resolved single-cell analysis and discuss the prospect of novel multiplexed imaging probes, called laser particles, which allow individual cells to be tagged in tissue and analyzed subsequently using high-throughput, comprehensive single-cell techniques.