scholarly journals Mass Cytometry Study on the Heterogeneity in Cellular Association and Cytotoxicity of Silver Nanoparticles in Human Immune Cells

2019 ◽  
Author(s):  
My Kieu Ha ◽  
Jang-Sik Choi ◽  
Zayakhuu Gerelkhuu ◽  
Sook Jin Kwon ◽  
Jaewoo Song ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Adverse Effects ◽  
Single Cell ◽  
Dose Response ◽  
Immune Cells ◽  
Intracellular Signaling ◽  
Single Cell Level ◽  
Mass Cytometry ◽  
Cell Level ◽  
Human Immune

AbstractThere have been many reports about the adverse effects of nanoparticles (NPs) on the environment and human health. Conventional toxicity assessments of NPs frequently assume uniform distribution of monodisperse NPs in homogeneous cell populations, and provide information on the relationships between the administered dose of NPs and cellular responses averaged for a large number of cells. They may have limitations in describing the wide heterogeneity of cell-NP interactions, caused by cell-to-cell and NP-to-NP variances. To achieve more detailed insight into the heterogeneity of cell-NP interactions, it is essential to understand the cellular association and adverse effects of NPs at single-cell level. In this study, we applied mass cytometry to investigate the interactions between silver nanoparticles (AgNPs) and primary human immune cells. High dimensionality of mass cytometry allowed us to identify various immune cell types and observe the cellular association and toxicity of AgNPs in each population. Our findings showed that AgNPs had higher affinity with phagocytic cells like monocytes and dendritic cells and caused more severe toxic effects than with T cells, B cells and NK cells. Multi-element detection capability of mass cytometry also enabled us to simultaneously monitor cellular AgNP dose and intracellular signaling of individual cells, and subsequently investigate the dose-response relationships of each immune population at single-cell level, which are often hidden in conventional toxicity assays at bulk-cell level. Our study will assist future development of single-cell dose-response models for various NPs and will provide key information for the safe use of nanomaterials for biomedical applications.

scholarly journals CyTOFmerge: integrating mass cytometry data across multiple panels

2019 ◽  
Vol 35 (20) ◽  
pp. 4063-4071 ◽  
Author(s):  
Tamim Abdelaal ◽  
Thomas Höllt ◽  
Vincent van Unen ◽  
Boudewijn P F Lelieveldt ◽  
Frits Koning ◽  
...  
Keyword(s):  
Single Cell ◽  
Biological Sample ◽  
Supplementary Information ◽  
High Dimensional ◽  
Single Cell Level ◽  
Supplementary Data ◽  
Mass Cytometry ◽  
Cell Level ◽  
Cellular Markers

Abstract Motivation High-dimensional mass cytometry (CyTOF) allows the simultaneous measurement of multiple cellular markers at single-cell level, providing a comprehensive view of cell compositions. However, the power of CyTOF to explore the full heterogeneity of a biological sample at the single-cell level is currently limited by the number of markers measured simultaneously on a single panel. Results To extend the number of markers per cell, we propose an in silico method to integrate CyTOF datasets measured using multiple panels that share a set of markers. Additionally, we present an approach to select the most informative markers from an existing CyTOF dataset to be used as a shared marker set between panels. We demonstrate the feasibility of our methods by evaluating the quality of clustering and neighborhood preservation of the integrated dataset, on two public CyTOF datasets. We illustrate that by computationally extending the number of markers we can further untangle the heterogeneity of mass cytometry data, including rare cell-population detection. Availability and implementation Implementation is available on GitHub (https://github.com/tabdelaal/CyTOFmerge). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Mass-Ratiometry-Based CD45 Barcoding Method for Mass Cytometry Detection

2019 ◽  
Vol 24 (4) ◽  
pp. 408-419
Author(s):  
Hongu Meng ◽  
Antony Warden ◽  
Lulu Zhang ◽  
Ting Zhang ◽  
Yiyang Li ◽  
...  
Keyword(s):  
Data Acquisition ◽  
Sample Size ◽  
Single Cell ◽  
Large Sample Size ◽  
Single Cell Level ◽  
Mass Cytometry ◽  
Cell Level ◽  
Large Sample ◽  
Antibody Staining ◽  
Instrument Sensitivity

Mass cytometry (CyTOF) is a critical cell profiling tool in acquiring multiparameter proteome data at the single-cell level. A major challenge in CyTOF analysis is sample-to-sample variance arising from the pipetting process, staining variation, and instrument sensitivity. To reduce such variations, cell barcoding strategies that enable the combination of individual samples prior to antibody staining and data acquisition on CyTOF are often utilized. The most prevalent barcoding strategy is based on a binary scheme that cross-examines the existence or nonexistence of certain mass signals; however, it is limited by low barcoding efficiency and high cost, especially for large sample size. Herein, we present a novel barcoding method for CyTOF application based on mass ratiometry. Different mass tags with specific fixed ratios are used to label CD45 antibody to achieve sample barcoding. The presented method exponentially increases the number of possible barcoded samples with the same amount of mass tags compared with conventional methods. It also reduces the overall time for the labeling process to 40 min and avoids the need for expensive commercial barcoding buffer reagents. Moreover, unlike the conventional barcoding process, this strategy does not pre-permeabilize cells before the barcoding procedure, which offers additional benefits in preserving surface biomarker signals.

Single Cell Level Quantification of Nanoparticle–Cell Interactions Using Mass Cytometry

2017 ◽  
Vol 89 (16) ◽  
pp. 8228-8232 ◽  
Author(s):  
Angela Ivask ◽  
Andrew J. Mitchell ◽  
Christopher M. Hope ◽  
Simon C. Barry ◽  
Enzo Lombi ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Single Cell Level ◽  
Mass Cytometry ◽  
Cell Level

scholarly journals LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5’-single cell RNA-Seq

2021 ◽  
Author(s):  
Wilson McKerrow ◽  
Shane A. Evans ◽  
Azucena Rocha ◽  
John Sedivy ◽  
Nicola Neretti ◽  
...  
Keyword(s):  
Single Cell ◽  
Cancer Cells ◽  
Early Development ◽  
Immune Cells ◽  
Copy Number ◽  
Single Cells ◽  
Single Cell Level ◽  
Rna Seq ◽  
Cell Level ◽  
Mouse Hippocampus

AbstractLINE-1 retrotransposons are known to be expressed in early development, in tumors and in the germline. Less is known about LINE-1 expression at the single cell level, especially outside the context of cancer. Because LINE-1 elements are present at a high copy number, many transcripts that are not driven by the LINE-1 promoter nevertheless terminate at the LINE-1 3’ UTR. Thus, 3’ targeted single cell RNA-seq datasets are not appropriate for studying LINE-1. However, 5’ targeted single cell datasets provide an opportunity to analyze LINE-1 expression at the single cell level. Most LINE-1 copies are 5’ truncated, and a transcript that contains the LINE-1 5’ UTR as its 5’ end is likely to have been transcribed from its promoter. We developed a method, L1-sc (LINE-1 expression for single cells), to quantify LINE-1 expression in 5’ targeted 10x genomics single cell RNA-seq datasets. Our method confirms that LINE-1 expression is high in cancer cells, but low or absent from immune cells. We also find that LINE-1 expression is elevated in epithelial compared to immune cells outside of the context of cancer and that it is also elevated in neurons compared to glia in the mouse hippocampus.

scholarly journals Mass Cytometry Enabling Absolute and Fast Quantification of Silver Nanoparticle Uptake at the Single Cell Level

2019 ◽  
Vol 91 (18) ◽  
pp. 11514-11519 ◽  
Author(s):  
Ana López-Serrano Oliver ◽  
Andrea Haase ◽  
Anette Peddinghaus ◽  
Doreen Wittke ◽  
Norbert Jakubowski ◽  
...  
Keyword(s):  
Single Cell ◽  
Silver Nanoparticle ◽  
Single Cell Level ◽  
Mass Cytometry ◽  
Nanoparticle Uptake ◽  
Cell Level

scholarly journals TMIC-06. MYELOID POPULATIONS AND THE EFFECT OF NEOADJUVANT PD-1 INHIBITION IN THE GLIOBLASTOMA MICROENVIRONMENT: A SURFACEOMIC AND TRANSCRIPTOMIC DISSECTION AT THE SINGLE-CELL LEVEL

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi248-vi248
Author(s):  
Aaron Mochizuki ◽  
Alexander Lee ◽  
Joey Orpilla ◽  
Jenny Kienzler ◽  
Mildred Galvez ◽  
...  
Keyword(s):  
Brain Tumor ◽  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cells ◽  
Single Cell Level ◽  
Mass Cytometry ◽  
Cell Level ◽  
Single Cell Rna Sequencing

Abstract INTRODUCTION Glioblastoma (GBM) is the most common malignant brain tumor in adults and is associated with a dismal prognosis. Neoadjuvant anti-PD-1 blockade has demonstrated efficacy in melanoma, non-small cell lung cancer and recurrent GBM; however, responses vary. While T cells have garnered considerable attention in the context of immunotherapy, the role of myeloid cells in the GBM microenvironment remains controversial. METHODS We isolated CD45+ immune populations from patients who underwent brain tumor resection at UCLA. We hypothesized that myeloid cells in glioblastoma contribute to T cell dysfunction; however, this immune suppression can be mitigated by neoadjuvant PD-1 inhibition. To test this, we utilized mass cytometry and single-cell RNA sequencing to characterize these immune populations. RESULTS Mass cytometry profiling of tumor infiltrating lymphocytes from patients with GBM demonstrated a preponderance of CD11b+ myeloid populations (75% versus 25% CD3+). At the transcriptomic level, myeloid cells in newly diagnosed GBMs exhibited decreased expression of CCL4 (loge fold change -1.18, Bonferroni-adjusted P = 1.62x10-254) and its ligands compared to anaplastic astrocytoma. In ranked gene set enrichment analysis, patients who received neoadjuvant pembrolizumab demonstrated enrichment in TNFα-, NFκB- and lipid metabolism-related gene sets by bootstrapped Kolmogorov-Smirnov test (Benjamini-Hochberg adjusted P = 4.74x10-3, 1.45x10-2 and 2.48x10-3, respectively) in tumor-associated myeloid populations. Additionally, single-cell trajectory analysis demonstrated increased CCL4 and decreased ISG15 with neoadjuvant checkpoint inhibition. CONCLUSIONS Here, we utilize mass cytometry and single-cell RNA sequencing to demonstrate the predominance and transcriptomic features of myeloid populations in GBM. Myeloid cells in patients who receive neoadjuvant PD-1 blockade re-express increased levels NFκB, TNFα and CCL4, a cytokine crucial for the recruitment of dendritic cells to the tumor for antigen-specific T cell activation. By delving into the GBM microenvironment at the single-cell level, we hope to better delineate the role of myeloid populations in this uniformly fatal tumor.

scholarly journals Advances in single cell technologies in immunology

BioTechniques ◽  
2020 ◽  
Vol 69 (3) ◽  
pp. 226-236
Author(s):  
Jane Ru Choi
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Immune Cell ◽  
Single Cell Level ◽  
Future Perspectives ◽  
Biological Mechanisms ◽  
Cell Level ◽  
Cell Responses ◽  
Physiological Processes ◽  
Cell Technologies

The immune system is composed of heterogeneous populations of immune cells that regulate physiological processes and protect organisms against diseases. Single cell technologies have been used to assess immune cell responses at the single cell level, which are crucial for identifying the causes of diseases and elucidating underlying biological mechanisms to facilitate medical therapy. In the present review we first discuss the most recent advances in the development of single cell technologies to investigate cell signaling, cell–cell interactions and cell migration. Each technology's advantages and limitations and its applications in immunology are subsequently reviewed. The latest progress toward commercialization, the remaining challenges and future perspectives for single cell technologies in immunology are also briefly discussed.

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