Titration of Mass Cytometry Reagents

Mass cytometry immunostaining protocol for multiplexing clinical samples

This is a cytometry by time-of-flight (CyTOF) staining protocol for hematopoietic-derived cells, that leverages live-cell barcoding using receptor-type tyrosine-protein phosphatase C (CD45) antibodies conjugated to metal isotopes in combination with DNA-based palladium barcoding to multiplex up to 40 samples. In this protocol, DNA-based barcoding is performed before surface and intracellular immunostaining, which reduces the batch effects that result from day-to-day variations in staining and instrument sensitivity. This protocol also reduces antibody consumption and eliminates the need for repeated instrument adjustment.

•

Mass cytometry immunostaining for 40+ samples to reduce batch-to-batch variation

•

Barcoding samples before immunostaining ensures consistency across all samples

•

Reduction in antibody volume consumption and data acquisition time

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

CyTOF® for the Masses

Mass cytometry has revolutionized immunophenotyping, particularly in exploratory settings where simultaneous breadth and depth of characterization of immune populations is needed with limited samples such as in preclinical and clinical tumor immunotherapy. Mass cytometry is also a powerful tool for single-cell immunological assays, especially for complex and simultaneous characterization of diverse intratumoral immune subsets or immunotherapeutic cell populations. Through the elimination of spectral overlap seen in optical flow cytometry by replacement of fluorescent labels with metal isotopes, mass cytometry allows, on average, robust analysis of 60 individual parameters simultaneously. This is, however, associated with significantly increased complexity in the design, execution, and interpretation of mass cytometry experiments. To address the key pitfalls associated with the fragmentation, complexity, and analysis of data in mass cytometry for immunologists who are novices to these techniques, we have developed a comprehensive resource guide. Included in this review are experiment and panel design, antibody conjugations, sample staining, sample acquisition, and data pre-processing and analysis. Where feasible multiple resources for the same process are compared, allowing researchers experienced in flow cytometry but with minimal mass cytometry expertise to develop a data-driven and streamlined project workflow. It is our hope that this manuscript will prove a useful resource for both beginning and advanced users of mass cytometry.

Improving oligo-conjugated antibody signal in multimodal single-cell analysis

Simultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high-resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. We investigated the response of oligo-conjugated antibodies towards four variables: concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations causes unnecessarily high background and amount of antibody used can be drastically reduced without loss of biological information. Reducing staining volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background, and reduces costs. Background signal can account for a major fraction of total sequencing and is primarily derived from antibodies used at high concentrations. This study provides new insight into titration response and background of oligo-conjugated antibodies and offers concrete guidelines to improve such panels.

Phenotyping of tumor infiltrating immune cells using mass-cytometry (CyTOF)

The anti-tumor immune response plays a crucial role in cancer patient outcome as well as in response to the growing family of immunotherapeutic treatments. Improving patient prognostic and therapeutic management requires a better knowledge of the tumor microenvironment, for which a deep characterization of tumor-infiltrating immune populations is instrumental. Mass cytometry represents an excellent tool in tumor Immunology, as it allows the simultaneous analysis of >40 markers on single cells. In this chapter, we review challenging technical aspects of the mass cytometry phenotyping of tumor infiltrating immune cells, focusing on fresh human solid tumor samples. We first explain how to design mass cytometry experiments, then provide detailed protocols to isolate mononuclear immune cells from solid tissues and to stain them for an acquisition on a mass cytometer. We also discuss how to optimize the preparation of single immune cell samples, and how to ensure the reproducibility of data generated from distinct fresh human samples. Finally, we provide troubleshooting suggestions for difficult sample acquisitions on a mass cytometer.