Tantalum Oxide Nanoparticle-Based Mass Tag for Mass Cytometry

Harmonized analysis of PBMC by mass cytometry

Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.

Recent developments in ionization techniques for single-cell mass spectrometry

The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.

All-in-One Microfluidic Chip for Online Labeling, Separating, and Focusing Rare Circulating Tumor Cells from Blood Samples Followed by Inductively Coupled Plasma Mass Spectrometry Detection

Circulating tumor cell (CTC) detection is essential for early cancer diagnosis and evaluating treatment efficacy. Despite the growing interest in isolating CTCs and further quantifying surface biomarkers at the single-cell level, highly efficient separation of rare CTCs from massive blood cells is still a big challenge. Here, we developed an all-in-one microfluidic chip system for the immunolabeling, magnetic separation, and focusing of HepG2 cells (as a CTC model) and online combined it with single cell-inductively coupled plasma mass spectrometry (SC-ICP-MS) for quantitative analysis of the asialoglycoprotein receptor (ASGPR) on single HepG2 cells. Lanthanide-labeled anti-ASGPR monoclonal antibody and antiepithelial cell adhesion molecule-modified magnetic beads were prepared as signal and magnetic probes, respectively. Target cells were highly efficiently labeled with signal and magnetic probes in the mixing zone of the microfluidic chip and then focused and sorted in the separation zone by specific magnetic separation techniques to avoid matrix contamination. The average cell recovery of HepG2 cells was derived to be 94.1 ± 5.7% with high separation efficiency and purity. The sorted cells with signal probes were detected for enumeration and quantification of ASGPR on their surface by SC-ICP-MS. The developed method showed good specificity and high sensitivity, detecting an average of (1.0 ± 0.2) × 105 ASGPR molecules per cell surface. This method can be used for absolute quantitative analysis of ASGPR on the surface of single hepatocellular carcinoma cells in real-world samples, providing a highly efficient analytical platform for studying targeted drug delivery in cancer therapy.

A universal mass tag based on polystyrene nanoparticles for single-cell multiplexing with mass cytometry

Mass cytometry (MC) is an emerging bioanalytical technique for high-dimensional biomarkers interrogation simultaneously on individual cells. However, the sensitivity and multiplexed analysis ability of MC was highly restricted by the current metal chelating polymer (MCP) mass tags. Herein, a new design strategy for MC mass tags by using a commercial available and low cost classical material, polystyrene nanoparticle (PS-NP) to carry metals was reported. Unlike inorganic materials, sub-micron-grade metal-loaded polystyrene can be easily detected by MC, thus it is not essential to pursue extremely small particle size in this mass tag design strategy. An altered cell staining buffer can significantly lower the nonspecific binding (NSB) of non-functionalized PS-NPs, revealing another method to lower NSB beside surface modification. The metal doped PS-NP_Abs mass tags showed high compatibility with MCP mass tags and 5-fold higher sensitivity. By using Hf doped PS-NP_Abs as mass tags, four new MC detection channels (¹⁷⁷Hf, ¹⁷⁸Hf, ¹⁷⁹Hf and ¹⁸⁰Hf) were developed. In general, this work provides a new strategy in designing MC mass tags and lowering NSB, opening up possibility of introducing more potential MC mass tag candidates.

Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules

Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.

Reagents for Mass Cytometry

Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm² spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.

Combining Isoprenoid Probes with Antibody Markers for Mass Cytometric Analysis of Prenylation in Single Cells

Protein prenylation is an essential post-translational modification that plays a key role in facilitating protein localization. Aberrations in protein prenylation have been indicated in multiple disease pathologies including progeria, some forms of cancer, and Alzheimer's disease. While there are single-cell methods to study prenylation, these methods cannot simultaneously assess prenylation and other cellular changes in the complex cell environment. Here, we report a novel method to monitor, at the single-cell level, prenylation and expression of autophagy markers. An isoprenoid analogue containing a terminal alkyne, substrate of prenylation enzymes, was metabolically incorporated into cells in culture. Treatment with a terbium reporter containing an azide functional group, followed by copper-catalyzed azide-alkyne cycloaddition, covalently attached terbium ions to prenylated proteins within cells. In addition, simultaneous treatment with a holmium-containing analogue of the reporter, without an azide functional group, was used to correct for non-specific retention at the single-cell level. This procedure was compatible with other mass cytometric sample preparation steps that use metal-tagged antibodies. We demonstrate that this method reports changes in levels of prenylation in competitive and inhibitor assays, while tracking autophagy molecular markers with metal-tagged antibodies. The method reported here makes it possible to track prenylation along with other molecular pathways in single cells of complex systems, which is essential to elucidate the role of this post-translational modification in disease, cell response to pharmacological treatments, and aging.

Hybrid Fluorescent Mass-Tag Nanotrackers as Universal Reagents for Long-Term Live-Cell Barcoding

Barcoding and pooling cells for processing as a composite sample are critical to minimize technical variability in multiplex technologies. Fluorescent cell barcoding has been established as a standard method for multiplexing in flow cytometry analysis. In parallel, mass-tag barcoding is routinely used to label cells for mass cytometry. Barcode reagents currently used label intracellular proteins in fixed and permeabilized cells and, therefore, are not suitable for studies with live cells in long-term culture prior to analysis. In this study, we report the development of fluorescent palladium-based hybrid-tag nanotrackers to barcode live cells for flow and mass cytometry dual-modal readout. We describe the preparation, physicochemical characterization, efficiency of cell internalization, and durability of these nanotrackers in live cells cultured over time. In addition, we demonstrate their compatibility with standardized cytometry reagents and protocols. Finally, we validated these nanotrackers for drug response assays during a long-term coculture experiment with two barcoded cell lines. This method represents a new and widely applicable advance for fluorescent and mass-tag barcoding that is independent of protein expression levels and can be used to label cells before long-term drug studies.

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.

Biotinylated Lipid-Coated NaLnF4 Nanoparticles: Demonstrating the Use of Lanthanide Nanoparticle-Based Reporters in Suspension and Imaging Mass Cytometry

Lanthanide nanoparticles (LnNPs) have the potential to be used as high-sensitivity mass tag reporters in mass cytometry immunoassays. For this application, however, the LnNPs must be made colloidally stable in aqueous buffers, demonstrate minimal non-specific binding to cells, and have functional groups to attach antibodies or other targeting agents. One possible approach to address these requirements is by using lipid coating to modify the surface of the LnNPs. In this work, 39 nm diameter NaYF₄:Yb, Er NPs (LnNPs) were coated with a lipid formulation consisting of egg sphingomyelin, 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1,2-dioleoyl-3-trimethylammonium propane, cholesterol-(polyethylene glycol-600), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[biotinyl(polyethylene glycol)-2000]. The resulting biotinylated lipid-coated LnNPs were characterized by dynamic light scattering to determine the hydrodynamic size and stability in phosphate buffered saline, and the composition of the lipid coatings was quantified by liquid chromatography-tandem mass spectrometry. The specific and non-specific binding of the biotinylated lipid-coated LnNPs to a model system of functionalized polystyrene microbeads were then tested by both suspension and imaging mass cytometry. We found that targeted binding with minimal non-specific binding can be achieved with the lipid-coated LnNPs and that the lipid composition of the coating has an impact on the performance of the LnNPs as mass cytometry reporters. These results additionally establish the importance of quantifying the composition of lipid-coated nanomaterials to optimize them more effectively for their desired application.

Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications

Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.

New Structure Mass Tag based on Zr-NMOF for Multiparameter and Sensitive Single-Cell Interrogating in Mass Cytometry

Mass cytometry, also called cytometry by time-of-flight (CyTOF), is an emerging powerful proteomic analysis technique that utilizes metal chelated polymer (MCP) as mass tags for interrogating high-dimensional biomarkers simultaneously on millions of individual cells. However, under the typical polymer-based mass tag system, the sensitivity and multiplexing detection ability has been highly restricted. Herein, a new structure mass tag based on a nanometal organic framework (NMOF) is reported for multiparameter and sensitive single-cell biomarker interrogating in CyTOF. A uniform-sized Zr-NMOF (33 nm) carrying 10⁵ metal ions is synthesized under modulator/reaction time coregulation, which is monodispersed and colloidally stable in water for over one-year storage. On functionalization with an antibody, the Zr mass tag exhibits specific molecular recognition properties and minimal cross-reaction toward nontargeted cells. In addition, the Zr-mass tag is compatible with MCP mass tags in a multiparameter assay for mouse spleen cells staining, which exploits four additional channels, m/z = 90, 91, 92, 94, for single-cell immunoassays in CyTOF. Compared to the MCP mass tag, the Zr-mass tag provides an additional fivefold signal amplification. This work provides the fundamental technical capability for exploiting NMOF-based mass tags for CyTOF application, which opens up possibility of high-dimensional single-cell immune profiling, low abundant antigen detection, and development of new barcoding systems.

Mass Cytometry, Imaging Mass Cytometry, and Multiplexed Ion Beam Imaging Use in a Clinical Setting

Mass cytometry (MC), imaging mass cytometry (IMC), and multiplexed ion beam imaging (MIBI) represent a new generation of tools to understand increasingly complex systems. Although these technologies differ in their intended applications, with MC being most similar to flow cytometry, and IMC/MIBI being similar to immunohistochemistry, they all share a time of flight mass spectrometry (TOF MS) platform. These TOF MS platforms use metal conjugated antibodies as opposed to fluorophores, increasing the measurable parameters up to approximately 50 with a theoretic limit approximately 100 parameters. These tools are being adapted to understand highly complex systems in basic and clinical research.

Mass Cytometry Tags: Where Chemistry Meets Single-Cell Analysis

Mass cytometry is a highly multiparametric proteomic technology that allows the measurement and quantification of nearly 50 markers with single-cell resolution. Mass cytometry reagents are probes tagged with metal isotopes of defined mass and act as reporters. Metals are detected using inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS). Many different types of mass-tag reagents have been developed to afford myriad applications. We have classified these compounds into polymer-based mass-tag reagents, nonpolymer-based mass-tag reagents, and inorganic nanoparticles. Metal-chelating polymers (MCPs) are widely used to profile and quantify cellular biomarkers; however, both the range of metals that can be detected and the metal signals have to be improved. Several strategies such as the inclusion of chelating agents or highly branched polymers may overcome these issues. Biocompatible materials such as polystyrene and inorganic nanoparticles are also of profound interest in mass cytometry. While polystyrene allows the inclusion of a wide variety of metals, the high metal content of inorganic nanoparticles offers an excellent opportunity to increase the signal from the metals to detect low-abundance biomarkers. Nonpolymer-based mass-tag reagents offer multiple applications: cell detection, cell cycle property determination, biomarker detection, and mass-tag cellular barcoding (MCB). Recent developments have been achieved in live cell barcoding by targeting proteins (CD45, b2m, and CD298), by using small and nonpolar probes or by ratiometric barcoding. From this perspective, the principal applications, strengths, and shortcomings of mass-tag reagents are highlighted, summarized, and discussed, with special emphasis on mass-tag reagents for MCB. Thereafter, the future perspectives of mass-tag reagents are discussed considering the current state-of-the-art technologies.

An Iodinated DAPI-Based Reagent for Mass Cytometry

Multiparametric single-cell analysis has seen dramatic improvements with the introduction of mass cytometry (MC) and imaging mass cytometry (IMC^™ ). These technologies expanded the number of biomarkers that can be identified simultaneously by using heavy-isotope-tagged antibody reagents. Small-molecule probes bearing heavy isotopes are emerging as additional useful functional reporters of cellular features. Realizing this, we explored the iodination of DAPI to produce a heavy-atom-substituted derivative of the commonly used fluorescent DNA stain. Although exhibiting a drastically reduced fluorescence emission profile, I-DAPI retains strong binding affinity for DNA. I-DAPI was used to detect cellular DNA in MC and IMC™ assays with comparable efficiency to known Ir-containing DNA intercalators. This work suggests repurposing well-known colorimetric stains through simple reactions could be an effective strategy to develop new, functional MC and IMC™ reagents.