Sample Preparation for Mass Cytometry Analysis

Summary

This article describes the collection and processing of samples for mass cytometry analysis.

Abstract

Mass cytometry utilizes antibodies conjugated with heavy metal labels, an approach that has greatly increased the number of parameters and opportunities for deep analysis well beyond what is possible with conventional fluorescence-based flow cytometry. As with any new technology, there are critical steps that help ensure the reliable generation of high-quality data. Presented here is an optimized protocol that incorporates multiple techniques for the processing of cell samples for mass cytometry analysis. The methods described here will help the user avoid common pitfalls and achieve consistent results by minimizing variability, which can lead to inaccurate data. To inform experimental design, the rationale behind optional or alternative steps in the protocol and their efficacy in uncovering new findings in the biology of the system being investigated is covered. Lastly, representative data is presented to illustrate expected results from the techniques presented here.

Introduction

Cytometry enables the simultaneous measurement of multiple antibody targets at a single cell level across large populations of cells. In traditional fluorescence-based flow cytometry, the number of parameters that can be quantified is limited by spectral overlap between the emission spectrum of multiple fluorophores, which requires increasingly complex compensation calculations as the number of parameters increases. These limitations are addressed by mass cytometry, where heavy metal-conjugated antibodies are detected and quantified by time of flight (TOF) mass spectrometry to greatly expand the number of parameters collected simultaneously and yield a high dimensiona....

Protocol

1. Cell Harvesting

1. Harvesting cells from primary tissue
   NOTE: The process described for harvesting cells from primary tissue is specifically applicable to mouse breast tumor tissue and may not be applicable as is to primary tissues from other sources.
   1. Prepare digestion buffer by dissolving 5 mg hyaluronidase and 30 mg collagenase in 10 mL DMEM/F12 media per gram of tissue to be processed. Filter sterilize digestion buffer.
   2. Isolate primary mammary gland tumor from mouse and record tumor weight.
   3. Mince tissue with #10 scalpel for at least 5 min.
   4. Add minced tissue to appropriate volume of dig....

Results

The protocol presented here can be broadly applied to a wide variety of cultured and primary cell samples with only minor modifications. Depending upon the requirements of the experiment, it can be performed in a modular manner when certain elements, such as barcoding or cell surface staining, are not necessary. Utilized in its entirety this protocol enables the preparation of multiplexed mass cytometry samples labeled for dead cell exclusion, S-phase population identification and stained.......

Discussion

The protocol presented here has been successfully employed for the processing of various cultured cell lines (H1 and H9 hESCs, mESCs, MCF7, HEK 293, KBM5, HMEC, MCF10a) and primary tissue samples (mouse bone marrow, mouse embryonic liver, mouse adult liver, mouse tumor). Irrespective of the source, any tissue that can be dissociated into single cells while preserving the cellular state should be amenable to analysis by mass cytometry, but may require some protocol optimization. It is important to note that some epitopes .......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
mTeSR1 medium kit	Stem Cell technologies	05850	Warm at room temperature before use
DMEM F-12	ThermoFisher	11330-032	Warm at 37 °C before use
Accutase	Stem Cell technologies	07920	Warm at 37 °C before use
Bovine serum albumin	Equitech	BAH62
phosphate buffered saline	Hyclone	SH30256.01
Saponin	Sigma-Aldrich	47036
Cell ID Pt194	Fluidigm		Provided at 1 mM
Cell ID Pt195	Fluidigm		Provided at 1 mM
Cell ID Pt196	Fluidigm		Provided at 1 mM
Cisplatin	Enzo Life Sciences	ALX-400-040-M250	Soluble to 25 mg/mL in DMSO
Cell-ID 20-plex Pd Barcoding Kit	Fluidigm	201060
5-Iodo-2'-deoxyuridine	Sigma-Aldrich	I7125	Soluble to 74 mg/mL in 0.2 N NaOH
Rhodium 103 intercelating agent	Fluidigm	201103A
Methanol	Fisher	BP1105-4	Chill at -20 °C before use
Sodium Azide	Sigma-Aldrich	S2002
5 mL round bottom tubes	Falcon	352058
5 mL 35 μm filter cap tubes	Falcon	352235
EQ four element calibration beads	Fluidigm	201078
Hyaluronidase Type I-S	Sigma-Aldrich	H3506
Collagenase from Clostridium histolyticum	Sigma-Aldrich	C9891
Disposable Scalpel #10	Sigma-Aldrich	Z69239