scholarly journals New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells

The Analyst ◽  
2019 ◽  
Vol 144 (3) ◽  
pp. 794-807 ◽  
Author(s):  
Sneha P. Couvillion ◽  
Ying Zhu ◽  
Gabe Nagy ◽  
Joshua N. Adkins ◽  
Charles Ansong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Cell ◽  
High Throughput ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Cell Analysis

We provide a vision for integrating pioneering mass spectrometry technologies for future applications in single cell analysis.

scholarly journals Single-cell lipidomics with high structural specificity by mass spectrometry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zishuai Li ◽  
Simin Cheng ◽  
Qiaohong Lin ◽  
Wenbo Cao ◽  
Jing Yang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Cell ◽  
Cancer Cells ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Mass Spectrometry Analysis ◽  
Human Lung Cancer ◽  
Cell Analysis ◽  
Structural Specificity ◽  
Spectrometry Analysis

AbstractSingle-cell analysis is critical to revealing cell-to-cell heterogeneity that would otherwise be lost in ensemble analysis. Detailed lipidome characterization for single cells is still far from mature, especially when considering the highly complex structural diversity of lipids and the limited sample amounts available from a single cell. We report the development of a general strategy enabling single-cell lipidomic analysis with high structural specificity. Cell fixation is applied to retain lipids in the cell during batch treatments prior to single-cell analysis. In addition to tandem mass spectrometry analysis revealing the class and fatty acyl-chain for lipids, batch photochemical derivatization and single-cell droplet treatment are performed to identify the C=C locations and sn-positions of lipids, respectively. Electro-migration combined with droplet-assisted electrospray ionization enables single-cell mass spectrometry analysis with easy operation but high efficiency in sample usage. Four subtypes of human breast cancer cells are correctly classified through quantitative analysis of lipid C=C location or sn-position isomers in ~160 cells. Most importantly, the single-cell deep lipidomics strategy successfully discriminates gefitinib-resistant cells from a population of wild-type human lung cancer cells (HCC827), highlighting its unique capability to promote precision medicine.

scholarly journals Microfluidic platform accelerates tissue processing into single cells for molecular analysis and primary culture models

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jeremy A. Lombardo ◽  
Marzieh Aliaghaei ◽  
Quy H. Nguyen ◽  
Kai Kessenbrock ◽  
Jered B. Haun
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Cell Analysis ◽  
Processing Technologies ◽  
Microfluidic Platform ◽  
Tissue Processing ◽  
Single Cell Rna Sequencing ◽  
Culture Models ◽  
Tissue Digestion

AbstractTissues are complex mixtures of different cell subtypes, and this diversity is increasingly characterized using high-throughput single cell analysis methods. However, these efforts are hindered, as tissues must first be dissociated into single cell suspensions using methods that are often inefficient, labor-intensive, highly variable, and potentially biased towards certain cell subtypes. Here, we present a microfluidic platform consisting of three tissue processing technologies that combine tissue digestion, disaggregation, and filtration. The platform is evaluated using a diverse array of tissues. For kidney and mammary tumor, microfluidic processing produces 2.5-fold more single cells. Single cell RNA sequencing further reveals that endothelial cells, fibroblasts, and basal epithelium are enriched without affecting stress response. For liver and heart, processing time is dramatically reduced. We also demonstrate that recovery of cells from the system at periodic intervals during processing increases hepatocyte and cardiomyocyte numbers, as well as increases reproducibility from batch-to-batch for all tissues.

scholarly journals High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells

2021 ◽  
Author(s):  
Ke-Yue Ma ◽  
Alexandra A. Schonnesen ◽  
Chenfeng He ◽  
Amanda Y. Xia ◽  
Eric Sun ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
High Throughput ◽  
Cd8 T Cells ◽  
Single Cell Analysis ◽  
High Dimensional ◽  
Cell Analysis

scholarly journals More than efficacy revealed by single-cell analysis of antiviral therapeutics

2019 ◽  
Author(s):  
Wu Liu ◽  
Mehmet U. Caglar ◽  
Zhangming Mao ◽  
Andrew Woodman ◽  
Jamie J. Arnold ◽  
...  
Keyword(s):  
Single Cell ◽  
Drug Targets ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Principal Component ◽  
Viral Population ◽  
Cell Analysis ◽  
Toxic Dose ◽  
Time Required

SUMMARYDevelopment of antiviral therapeutics emphasizes minimization of the effective dose and maximization of the toxic dose, first in cell culture and later in animal models. Long-term success of an antiviral therapeutic is determined not only by its efficacy but also by the duration of time required for drug-resistance to evolve. We have developed a microfluidic device comprised of ~6000 wells, with each well containing a microstructure to capture single cells. We have used this device to characterize enterovirus inhibitors with distinct mechanisms of action. In contrast to population methods, single-cell analysis reveals that each class of inhibitor interferes with the viral infection cycle in a manner that can be distinguished by principal component analysis. Single-cell analysis of antiviral candidates reveals not only efficacy but also properties of the members of the viral population most sensitive to the drug, the stage of the lifecycle most affected by the drug, and perhaps even if the drug targets an interaction of the virus with its host.

scholarly journals μCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells

2020 ◽  
Author(s):  
Tyler N. Chen ◽  
Anushka Gupta ◽  
Mansi Zalavadia ◽  
Aaron M. Streets
Keyword(s):  
High Resolution ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Protein Localization ◽  
Single Cells ◽  
Optical Measurements ◽  
Detection Sensitivity ◽  
High Resolution Imaging ◽  
Cell Analysis ◽  
Resolution Imaging

AbstractSingle-cell RNA sequencing (scRNA-seq) enables the investigation of complex biological processes in multicellular organisms with high resolution. However, many phenotypic features that are critical to understanding the functional role of cells in a heterogeneous tissue or organ are not directly encoded in the genome and therefore cannot be profiled with scRNA-seq. Quantitative optical microscopy has long been a powerful approach for characterizing diverse cellular phenotypes including cell morphology, protein localization, and chemical composition. Combining scRNA-seq with optical imaging has the potential to provide comprehensive single-cell analysis, allowing for functional integration of gene expression profiling and cell-state characterization. However, it is difficult to track single cells through both measurements; therefore, coupling current scRNA-seq protocols with optical measurements remains a challenge. Here, we report Microfluidic Cell Barcoding and Sequencing (μCB-seq), a microfluidic platform that combines high-resolution imaging and sequencing of single cells. μCB-seq is enabled by a novel fabrication method that preloads primers with known barcode sequences inside addressable reaction chambers of a microfluidic device. In addition to enabling multi-modal single-cell analysis, μCB-seq improves gene detection sensitivity, providing a scalable and accurate method for information-rich characterization of single cells.

Mass Spectrometry for Single-Cell Analysis

2020 ◽  
pp. 1-17
Author(s):  
Dinesh K. Patel ◽  
Sayan Deb Dutta ◽  
Ki-Taek Lim
Keyword(s):  
Mass Spectrometry ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Analysis

scholarly journals Methods and sensors for functional genomic studies of cell-cycle transitions in single cells

2020 ◽  
Vol 52 (10) ◽  
pp. 468-477
Author(s):  
Alexander C. Zambon ◽  
Tom Hsu ◽  
Seunghee Erin Kim ◽  
Miranda Klinck ◽  
Jennifer Stowe ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Imaging System ◽  
Single Cells ◽  
Cell Types ◽  
Cell Analysis ◽  
Mcf7 Cells ◽  
Genomic Studies ◽  
Cell Subpopulations

Much of our understanding of the regulatory mechanisms governing the cell cycle in mammals has relied heavily on methods that measure the aggregate state of a population of cells. While instrumental in shaping our current understanding of cell proliferation, these approaches mask the genetic signatures of rare subpopulations such as quiescent (G0) and very slowly dividing (SD) cells. Results described in this study and those of others using single-cell analysis reveal that even in clonally derived immortalized cancer cells, ∼1–5% of cells can exhibit G0 and SD phenotypes. Therefore to enable the study of these rare cell phenotypes we established an integrated molecular, computational, and imaging approach to track, isolate, and genetically perturb single cells as they proliferate. A genetically encoded cell-cycle reporter (K67p-FUCCI) was used to track single cells as they traversed the cell cycle. A set of R-scripts were written to quantify K67p-FUCCI over time. To enable the further study G0 and SD phenotypes, we retrofitted a live cell imaging system with a micromanipulator to enable single-cell targeting for functional validation studies. Single-cell analysis revealed HT1080 and MCF7 cells had a doubling time of ∼24 and ∼48 h, respectively, with high duration variability in G1 and G2 phases. Direct single-cell microinjection of mRNA encoding (GFP) achieves detectable GFP fluorescence within ∼5 h in both cell types. These findings coupled with the possibility of targeting several hundreds of single cells improves throughput and sensitivity over conventional methods to study rare cell subpopulations.

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