High-resolution interrogation of biological systems via mass cytometry

Most complex organisms have hundreds of coexisting cell types undergoing temporal changes and homeostatic adaptations. Understanding each cell type’s response to treatment or external stimuli is of paramount importance to cell biology and biomedicine, but heterogeneity within cell types often adds complexity to such systems. Single-cell analysis technologies are essential resources to tease apart differing responses within cell types to understand the role that such cellular diversity plays in biological systems and disease. Mass cytometry is a recently developed single-cell technology in which cellular targets are immunolabeled with lanthanide isotopes. Single cells are sequentially delivered in a high-throughput manner to an inductively coupled plasma torch, which releases the lanthanide species that are finally detected via a time-of-flight mass spectrometer, which provides a series of elemental mass spectra for each cell. Due to the mass range of the instrumentation and the number of lanthanide isotopes available, the technique is truly multiparametric, capable of simultaneous analysis of more than 40 cellular targets. This chapter begins with a general overview of mass cytometry, making allusion to related technologies such as flow cytometry. Instrumentation design and function are key to the current capabilities of the technology so one section is dedicated to the three main instrument features: sample injection, mass spectrometric filtering of reporter ions, and analysis of reporter ions. Another section is dedicated to sample preparation, emphasizing the types of reagents used to incorporate reporter ions into cells, brief protocols for labeling both cell surface and intracellular markers, and the instrumental conditions required for sample analysis. Another section is dedicated to the options currently available to analyze and visualize mass cytometry data. Emphasis is placed on the algorithms SPADE, viSNE, Wanderlust, and Citrus, which have been used more frequently. The chapter concludes with three selected applications of mass cytometry: immunology, cancer biology, and vaccine development, which highlight the power and revolutionary nature of this technology.