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Review
. 2017 Jan 3;89(1):2-21.
doi: 10.1021/acs.analchem.6b04255. Epub 2016 Dec 7.

Recent Advances in the Analysis of Single Cells

Lucas Armbrecht  1 , Petra S Dittrich  1
Affiliations
Review

Recent Advances in the Analysis of Single Cells

Lucas Armbrecht et al. Anal Chem. .

Erratum in

No abstract available

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Conflict of interest statement

Notes

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1. Comparison of parallel and continuous methods for single-cell positioning and analysis.
Figure 2
Figure 2. Specialized fluorescence techniques for single-cell analysis.
(A) Determination of traction forces that a cell is exerting on a substrate. Here, a technique based on Förster resonance energy transfer (FRET) is used for the determination of cell traction forces exerted on the surface. Besides localization of the force variation within a single cell, the differences between cells can be identified. Adapted with permission from Blakely, B. L.; Dumelin, C. E.; Trappmann, B.; McGregor, L. M.; Choi, C. K.; Anthony, P. C.; Duesterberg, V. K.; Baker, B. M.; Block, S. M.; Liu, D. R.; Chen, C. S. Nat. Methods 2014, 11, 1229–1232 (ref 63). Copyright 2014 Nature Publishing Group. (B) Analysis of the single cell transciptome. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) of roughly 15 00 cells allows for sequential analysis of 130 RNA targets. A small portion of these measurements is depicted in the images numbered 4–11. Adapted with permission from Moffitt, J. R.; Hao, J.; Wang, G.; Chen, K. H.; Babcock, H. P.; Zhuang, X. Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 11046–11051 (ref 64). Copyright 2016 National Academy of Sciences. (C) Multiplexed analysis of biomolecules. The combination of single-cell capture in microchambers, the use of antibody barcode arrays and three-color fluorescence microscopy facilitated the parallel detection of up to 45 parameters on the single-cell level. Adapted with permission from Lu, Y.; Xue, Q.; Eisele, M. R.; Sulistijo, E. S.; Brower, K.; Han, L.; Amir, E. D.; Pe’er, D.; Miller-Jensen, K.; Fan, R. Proc. Natl. Acad. Sci. U.S. A. 2015, 607–615 (ref 65). Copyright 2015 National Academy of Sciences. (D) Single-cell Western blotting for analysis of selected proteins of single cells. Adapted with permission from Hughes, A. J.; Spelke, D. P.; Xu, Z.; Kang, C.-C.; Schaffer, D. V; Herr, A. E. Nat. Methods 2014, 11, 749–755 (ref 66). Copyright 2014 Nature Publishing Group.
Figure 3
Figure 3. Label-free optical analysis methods for single cells.
(A) Raman spectroscopy on the single-cell level discriminates live epithelial prostate cells and lymphocytes. Adapted with permission from Casabella, S.; Scully, P.; Goddard, N.; Gardner, P. Analyst 2016, 141, 689–696 (ref 118). Published by The Royal Society of Chemistry. (B) Single-cell secretion of anti-EpCAM antibodies quantified by surface plasmon resonance. The slopes of the curves represent the differences in the production rate of the individual cells. Adapted with permission from Stojanović I.; Van Der Velden, T. J. G.; Mulder, H. W.; Schasfoort, R. B. M.; Terstappen, L. W. M. M. Anal. Biochem. 2015, 485, 112–118 (ref 121). Copyright 2015 Elsevier. (C) Evanescent light scattering microscope for detection of fluorescent and label-free particles. Adapted from Agnarsson, B.; Lundgren, A.; Gunnarsson, A.; Rabe, M.; Kunze, A.; Mapar, M.; Simonsson, L.; Bally, M.; Zhdanov, V. P.; Höök, F. ACS Nano 2015, 9, 11849–11862 (ref 124). Copyright 2015 American Chemical Society. (D) Time-lapsed 3D live-cell tomography showing the refractive index change during filopodia formation of a neuronal spine. Adapted with permission from Cotte, Y.; Toy, F.; Jourdain, P.; Pavillon, N.; Boss, D.; Magistretti, P.; Marquet, P.; Depeursinge, C. Nat. Photonics 2013, 7, 113–117 (ref 125). Copyright 2013 Nature Publishing Group.
Figure 4
Figure 4. Electrochemical single-cell analysis techniques.
(A) Nanowires (1: SEM image, scale bar 1 μm) can penetrate single cells for electrical measurements. Sixteen individual measurement arrays are placed on one chip (2 and 3, scale bars 10 and 120 μm). Images 4–6: SEM image of rat cortical cell on the vertical electrode array, confocal reconstruction, and top view on calcein AM stained cells. Adapted with permission from Robinson, J. T.; Jorgolli, M.; Shalek, A. K.; Yoon, M.-H.; Gertner, R. S.; Park, H. Nat. Nanotechnol. 2012, 7, 180–184 (ref 130). Copyright 2012 Nature Publishing Group. (B) A microfluidic chip with eight independent sensors (1) comprising of X-shaped posts (2) and on-chip electrodes are used to capture cancer cells from a given sample. Dielectrophoretic cell capture is followed by cell labeling (3) and electrochemical detection (4). Adapted from Safaei, T. S.; Mohamadi, R. M.; Sargent, E. H.; Kelley, S. O. ACS Appl. Mater. Interfaces 2015, 7, 14165–14169 (ref 136). Copyright 2015 Americal Chemical Society. (C) Impedance spectroscopy is used in this microfluidic platform to detect single CTCs after magnetic separation. If a cell is detected, external processing evokes an actuation of the microshooter to print this cell onto a microtiter plate for further analysis. Adapted from Kim, J.; Cho, H.; Han, S.-I.; Han, K.-H. Anal. Chem. 2016, 88, 4857–4863 (ref 141). Copyright 2016 American Chemical Society. (D) Scanning electrochemical microscopy images of PC12 cells. To generate the images, a microelectrode is scanned over the sample and the amperometric current and the impedance signals are measured. Analysis of the topography (1) and oxygen consumption (2) of the cell can be achieved at the same time (3). Adapted from Koch, J. A.; Baur, M. B.; Woodall, E. L.; Baur, J. E. Anal. Chem. 2012, 84, 9537–9543 (ref 142). Copyright 2012 American Chemical Society.
Figure 5
Figure 5. Mass spectrometry for single-cell analysis.
(A) Cytosol analysis by ESI-MS. A tiny microcapillary withdraws part of the cytosol and transfers it to the MS, where it is ionized and analyzed. Reprinted from Gong, X.; Zhao, Y.; Cai, S.; Fu, S.; Yang, C.; Zhang, S.; Zhang, X. Anal. Chem. 2014, 86, 3809–3816 (ref 156). Copyright 2014 American Chemical Society. (B) MALDI-MS platform for investigations of single cells that were spotted into microwells. Adapted with permission from Krismer, J.; Sobek, J.; Steinoff, R. F.; Fagerer, S. R.; Pabst, M.; Zenobi, R. Appl. Environ. Microbiol. 2015, 81, 5546–5551 (ref 159). Copyright 2015 American Society for Microbiology. (C) Label-free 3D-TOF-SIMS measurement of amiodarone-doped macrophages at different sputter depths. Many different molecules can be visualized by selecting the corresponding m/z ratio (1–3). The different slice numbers represent the sputtered z-stacks for the 3D imaging. Adapted from Passarelli, M. K.; Newman, C. F.; Marshall, P. S.; West, A.; Gilmore, I. S.; Bunch, J.; Alexander, M. R.; Dollery, C. T. Anal. Chem. 2015, 87, 6696–6702 (ref 160). Copyright 2015 American Chemical Society. (D) Mass cytometry achieves high sensitivities by employing rare earth metal tags. The isotopically pure tags allow simultaneous detection of more than 40 different targets. Besides cytometers, imaging systems based on this approach have been developed as well. Reprinted with permission from Giesen, C.; Wang, H. A. O.; Schapiro, D.; Zivanovic, N.; Jacobs, A.; Hattendorf, B.; Schuffler, P. J.; Grolimund, D.; Buhmann, J. M.; Brandt, S.; Varga, Z.; Wild, P. J.; Günther, D.; Bodenmiller, B. Nat. Methods 2014, 11, 417–422 (ref 161). Copyright 2014 Nature Publishing Group.
Figure 6
Figure 6. Special single-cell analysis platforms.
(A) The detection of intracellular microRNA is initiated by application of ultrasound. It accelerates the nanomotor-tags, and they pass the cell membrane. Upon contact with the target microRNA sequence, the fluorescent label is released from the quencher and fluorescence arises. Fluorescent signal of a MCF-7 cell before (right top) and after (right bottom) ultrasound exposure. Scale bars, 10 μm. Adapted from Esteban-Fernández de Ávila, B.; Martín, A.; Soto, F.; Lopez-Ramirez, M. A.; Campuzano, S.; Vásquez-Machado, G. M.; Gao, W.; Zhang, L.; Wang, J. ACS Nano 2015, 9, 6756−6764 (ref 200). Copyright 2015 American Chemical Society. (B) Cantilever beam resonance is affected by changes in its mass. Serial mass measurements of single cells flowing in a hollow cantilever were then employed to measure mass changes of single cells over time and detect the cells growth rates. Adapted with permission from Cermak, N.; Olcum, S.; Delgado, F. F.; Wasserman, S. C.; Payer, K. R.; Murakami, M. A.; Knudsen, S. M.; Kimmerling, R. J.; Stevens, M. M.; Kikuchi, Y.; Sandikci, A.; Ogawa, M.; Agache, V.; Baleras, F.; Weinstock, D. M.; Manalis, S. R. Nat. Biotechnol. 2016, 34, 1052–1059 (ref 201). Copyright 2016 Nature Publishing Group. (C) Single cells were thermally analyzed in an ultrasensitive and thermally well isolated microfluidic setup. The resonant frequency of a cantilever beam depending on the temperature and effects of the heat production on the single cell level can be investigated. Adapted with permission from Inomata, N.; Toda, M.; Ono, T. Lab Chip 2016, 16, 3597–3603 (ref 202). Copyright 2016 Royal Society of Chemistry. (D) A new type of microscope that visualizes magnetism has been reported. The quantum diamond microscope was used to investigate magnetically labeled cells. Scale bars, 100 μm. Reprinted with permission from Glenn, D. R.; Lee, K.; Park, H.; Weissleder, R.; Yacoby, A.; Lukin, M. D.; Lee, H.; Walsworth, R. L.; Connolly, C. B. Nat. Methods 2015, 12 (8), 736–738 (ref 203). Copyright 2015 Nature Publishing Group.
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