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Introduction: Why Analyze Single Cells?

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Book cover Single-Cell Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 853))

Abstract

Powerful methods in molecular biology are abundant; however, in many fields including hematology, stem cell biology, tissue engineering, and cancer biology, data from tools and assays that analyze the average signals from many cells may not yield the desired result because the cells of interest may be in the minority—their behavior masked by the majority—or because the dynamics of the populations of interest are offset in time. Accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. In this chapter, we discuss the rationale for performing analyses on individual cells in more depth, cover the fields of study in which single-cell behavior is yielding new insights into biological and clinical questions, and speculate on how single-cell analysis will be critical in the future.

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References

  1. Elowitz MB, Levine AJ, Siggia ED & Swain PS (2002) Stochastic Gene Expression in a Single Cell. Science 297, 1183–1186.

    Article  PubMed  CAS  Google Scholar 

  2. Miller MJ, Safrina O, Parker I & Cahalan MD (2004) Imaging the Single Cell Dynamics of CD4+ T Cell Activation by Dendritic Cells in Lymph Nodes. The Journal of Experimental Medicine 200, 847–856.

    Article  PubMed  CAS  Google Scholar 

  3. Fiering S, Northrop JP, Nolan GP, Mattila PS, Crabtree GR & Herzenberg LA (1990) Single cell assay of a transcription factor reveals a threshold in transcription activated by signals emanating from the T-cell antigen receptor. Genes & Development 4, 1823–1834.

    Article  CAS  Google Scholar 

  4. Levsky JM, Shenoy SM, Pezo RC & Singer RH (2002) Single-Cell Gene Expression Profiling. Science 297, 836–840.

    Article  PubMed  CAS  Google Scholar 

  5. Dexter DL, Kowalski HM, Blazar BA, Fligiel Z, Vogel R & Heppner GH (1978) Heterogeneity of Tumor Cells from a Single Mouse Mammary Tumor. Cancer Research 38, 3174–3181.

    PubMed  CAS  Google Scholar 

  6. Dexter DL, Spremulli EN, Fligiel Z, Barbosa JA, Vogel R, VanVoorhees A & Calabresi P (1981) Heterogeneity of cancer cells from a single human colon carcinoma. Am. J. Med 71, 949–956.

    Article  PubMed  CAS  Google Scholar 

  7. Vermeulen L, Sprick MR, Kemper K, Stassi G & Medema JP (2008) Cancer stem cells - old concepts, new insights. Cell Death Differ 15, 947–958.

    Article  PubMed  CAS  Google Scholar 

  8. Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J & Wigler M (2010) Inferring tumor progression from genomic heterogeneity. Genome Research 20, 68–80.

    Article  PubMed  CAS  Google Scholar 

  9. Orth JD, Tang Y, Shi J, Loy CT, Amendt C, Wilm C, Zenke FT & Mitchison TJ (2008) Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate. Molecular Cancer Therapeutics 7, 3480–3489.

    Article  PubMed  CAS  Google Scholar 

  10. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R, Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N & Alon U (2008) Dynamic Proteomics of Individual Cancer Cells in Response to a Drug. Science 322, 1511–1516.

    Article  PubMed  CAS  Google Scholar 

  11. Zhong JF, Chen Y, Marcus JS, Scherer A, Quake SR, Taylor CR & Weiner LP (2008) A microfluidic processor for gene expression profiling of single human embryonic stem cells. Lab Chip 8, 68.

    Article  PubMed  CAS  Google Scholar 

  12. Kim L, Vahey MD, Lee H & Voldman J (2006) Microfluidic arrays for logarithmically perfused embryonic stem cell culture. Lab Chip 6, 394–406.

    Article  PubMed  CAS  Google Scholar 

  13. Vermeulen L, Todaro M, de Sousa Mello F, Sprick MR, Kemper K, Perez Alea M, Richel DJ, Stassi G & Medema JP (2008) Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity. Proceedings of the National Academy of Sciences 105, 13427–13432.

    Article  CAS  Google Scholar 

  14. Chung BG, Flanagan LA, Rhee SW, Schwartz PH, Lee AP, Monuki ES & Jeon NL (2005) Human neural stem cell growth and differentiation in a gradient-generating microfluidic device. Lab Chip 5, 401.

    Article  PubMed  CAS  Google Scholar 

  15. Weaver WM, Dharmaraja S, Milisavljevic V & Di Carlo D (2011) The effects of shear stress on isolated receptor–ligand interactions of Staphylococcus epidermidis and human plasma fibrinogen using molecularly patterned microfluidics. Lab Chip 11, 883.

    Article  PubMed  CAS  Google Scholar 

  16. Di Carlo D, Aghdam N & Lee LP (2006) Single-Cell Enzyme Concentrations, Kinetics, and Inhibition Analysis Using High-Density Hydrodynamic Cell Isolation Arrays. Analytical Chemistry 78, 4925–4930.

    Article  PubMed  Google Scholar 

  17. Di Carlo, D & Lee LP (2006) Dynamic Single-Cell Analysis for Quantitative Biology. Analytical Chemistry 78, 7918–7925.

    Article  PubMed  Google Scholar 

  18. Gossett DR, Weaver WM, Ahmed NS & Di Carlo D (2010) Sequential Array Cytometry: Multi-Parameter Imaging with a Single Fluorescent Channel. Ann Biomed Eng 39, 1328–1334.

    Google Scholar 

  19. Wright D, Rajalingam B, Selvarasah S, Dokmeci MR & Khademhosseini A (2007) Generation of static and dynamic patterned co-cultures using microfabricated parylene-C stencils. Lab Chip 7, 1272–1279.

    Article  PubMed  CAS  Google Scholar 

  20. Chung S, Sudo R, Mack PJ, Wan C, Vickerman V & Kamm RD (2009) Cell migration into scaffolds under co-culture conditions in a microfluidic platform. Lab Chip 9, 269–275.

    Article  PubMed  CAS  Google Scholar 

  21. Ochsner M, Dusseiller MR, Grandin HM, Luna-Morris S, Textor M, Vogel V & Smith ML (2007) Micro-well arrays for 3D shape control and high resolution analysis of single cells. Lab Chip 7, 1074.

    Article  PubMed  CAS  Google Scholar 

  22. Hui EE & Bhatia SN (2007) Micromechanical control of cell–cell interactions. Proceedings of the National Academy of Sciences 104, 5722–5726.

    Article  CAS  Google Scholar 

  23. Toh Y, Ng S, Khong YM, Samper V & Yu H (2005) A configurable three-dimensional micro­environment in a microfluidic channel for primary hepatocyte culture. Assay Drug Dev Technol 3, 169–176.

    Article  PubMed  CAS  Google Scholar 

  24. Zhang MY, Lee PJ, Hung PJ, Johnson T, Lee LP & Mofrad MRK (2007) Microfluidic environment for high density hepatocyte culture. Biomed Microdevices 10, 117–121.

    Article  Google Scholar 

  25. Chung S, Sudo R, Mack PJ, Wan C, Vickerman V & Kamm RD (2009) Cell migration into scaffolds under co-culture conditions in a microfluidic platform. Lab Chip 9, 269.

    Article  PubMed  CAS  Google Scholar 

  26. Rettig JR & Folch A (2005) Large-Scale Single-Cell Trapping And Imaging Using Microwell Arrays. Analytical Chemistry 77, 5628–5634.

    Article  PubMed  CAS  Google Scholar 

  27. Di Carlo D, Edd JF, Irimia D, Tompkins RG & Toner M (2008) Equilibrium separation and filtration of particles using differential inertial focusing. Anal. Chem 80, 2204–2211.

    Article  PubMed  Google Scholar 

  28. Wang X, Yang J, Huang Y, Vykoukal J, Becker FF & Gascoyne PRC (2000) Cell Separation by Dielectrophoretic Field-flow-fractionation. Analytical Chemistry 72, 832–839.

    Article  PubMed  CAS  Google Scholar 

  29. Evander M, Johansson L, Lilliehorn T, Piskur J, Lindvall M, Johansson S, Almqvist M, Laurell T & Nilsson J (2007) Noninvasive Acoustic Cell Trapping in a Microfluidic Perfusion System for Online Bioassays. Analytical Chemistry 79, 2984–2991.

    Article  PubMed  CAS  Google Scholar 

  30. Choi J, Oh KW, Thomas JH, Heineman WR, Halsall HB, Nevin JH, Helmicki AJ, Henderson HT & Ahn CH (2002) An integrated microfluidic biochemical detection system for protein analysis with magnetic bead-based sampling capabilities. Lab Chip 2, 27.

    Article  PubMed  CAS  Google Scholar 

  31. Lu H, Koo LY, Wang WM, Lauffenburger DA, Griffith LG & Jensen KF (2004) Microfluidic Shear Devices for Quantitative Analysis of Cell Adhesion. Analytical Chemistry 76, 5257–5264.

    Article  PubMed  CAS  Google Scholar 

  32. Khandurina J, McKnight TE, Jacobson SC, Waters LC, Foote RS & Ramsey JM (2000) Integrated System for Rapid PCR-Based DNA Analysis in Microfluidic Devices. Analytical Chemistry 72, 2995–3000.

    Article  PubMed  CAS  Google Scholar 

  33. Sato K, Yamanaka M, Takahashi H, Tokeshi M, Kimura H & Kitamori T (2002) Microchip-based immunoassay system with branching multichannels for simultaneous determination of interferon-gamma. Electrophoresis 23, 734–739.

    Article  PubMed  CAS  Google Scholar 

  34. Sato K, Tokeshi M, Odake T, Kimura H, Ooi T, Nakao M & Kitamori T (2000) Integration of an immunosorbent assay system: analysis of secretory human immunoglobulin A on polystyrene beads in a microchip. Anal. Chem 72, 1144–1147.

    Article  PubMed  CAS  Google Scholar 

  35. Zare RN & Kim S (2010) Microfluidic platforms for single-cell analysis. Annu Rev Biomed Eng 12, 187–201.

    Article  PubMed  CAS  Google Scholar 

  36. Jin A, Ozawa T, Tajiri K, Obata T, Kondo S, Kinoshita K, Kadowaki S, Takahashi K, Sugiyama T, Kishi H & Muraguchi A (2009) A rapid and efficient single-cell manipulation method for screening antigen-specific antibody-secreting cells from human peripheral blood. Nat Med 15, 1088–1092.

    Article  PubMed  CAS  Google Scholar 

  37. Yamamura S, Kishi H, Tokimitsu Y, Kondo S, Honda R, Rao SR, Omori M, Tamiya E & Muraguchi A (2005) Single-Cell Microarray for Analyzing Cellular Response. Analytical Chemistry 77, 8050–8056.

    Article  PubMed  CAS  Google Scholar 

  38. Lindström S, Larsson R & Andersson Svahn H (2008) Towards high-throughput single cell/clone cultivation and analysis. Electrophoresis 29, 1219–1227.

    Article  PubMed  Google Scholar 

  39. Lindström S, Hammond M, Brismar H, Andersson-Svahn H & Ahmadian A (2009) PCR amplification and genetic analysis in a microwell cell culturing chip. Lab Chip 9, 3465.

    Article  PubMed  Google Scholar 

  40. Vanherberghen B, Manneberg O, Christakou A, Frisk T, Ohlin M, Hertz HM, Önfelt B & Wiklund M (2010) Ultrasound-controlled cell aggregation in a multi-well chip. Lab Chip 10, 2727.

    Article  PubMed  CAS  Google Scholar 

  41. Shapiro HM (2003) Practical Flow Cytometry, 4th ed. Wiley-Liss, New York.

    Book  Google Scholar 

  42. Gossett DR, Weaver WM, Mach AJ, Hur SC, Tse HTK, Lee W, Amini H & Di Carlo D (2010) Label-free cell separation and sorting in microfluidic systems. Anal Bioanal Chem 397, 3249–3267.

    Article  PubMed  CAS  Google Scholar 

  43. Vahey MD & Voldman J (2009) High-Throughput Cell and Particle Characterization Using Isodielectric Separation. Analytical Chemistry 81, 2446–2455.

    Article  PubMed  CAS  Google Scholar 

  44. Vahey MD & Voldman J (2008) An Equilibrium Method for Continuous-Flow Cell Sorting Using Dielectrophoresis. Analytical Chemistry 80, 3135–3143.

    Article  PubMed  CAS  Google Scholar 

  45. Harvey TJ, Hughes C, Ward AD, Correia Faria E, Henderson A, Clarke NW, Brown MD, Snook RD & Gardner P (2009) Classification of fixed urological cells using Raman tweezers. J Biophotonics 2, 47–69.

    Article  PubMed  CAS  Google Scholar 

  46. Snook RD, Harvey TJ, Correia Faria E & Gardner P (2009) Raman tweezers and their application to the study of singly trapped eukaryotic cells. Integr. Biol. 1, 43.

    Article  CAS  Google Scholar 

  47. Krylov SN, Arriaga E, Zhang Z, Chan NWC, Palcic MM & Dovichi NJ (2000) Single-cell analysis avoids sample processing bias. Journal of Chromatography B: Biomedical Sciences and Applications 741, 31–35.

    Article  CAS  Google Scholar 

  48. Brehm-Stecher BF & Johnson EA (2004) Single-Cell Microbiology: Tools, Technologies, and Applications. Microbiol. Mol. Biol. Rev. 68, 538–559.

    Article  PubMed  CAS  Google Scholar 

  49. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G, Geho DH, Petricoin EF & Liotta LA (2006) Laser-capture microdissection. Nat. Protocols 1, 586–603.

    Article  CAS  Google Scholar 

  50. Filliers M, De Spiegelaere W, Peelman L, Goossens K, Burvenich C, Vandaele L, Cornillie P & Van Soom A (2011) Laser capture microdissection for gene expression analysis of inner cell mass and trophectoderm from blastocysts. Analytical Biochemistry 408, 169–171.

    Article  PubMed  CAS  Google Scholar 

  51. Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, Hutchison JB, Rothberg JM, Link DR, Perrimon N & Samuels ML (2009) Droplet microfluidic technology for single-cell high-throughput screening. Proc. Natl. Acad. Sci. USA 106, 14195–14200.

    Article  PubMed  CAS  Google Scholar 

  52. Zhang Y & Yu L (2008) Microinjection as a tool of mechanical delivery. Curr. Opin. Biotechnol 19, 506–510.

    Article  PubMed  CAS  Google Scholar 

  53. Zhang Y & Yu L (2008) Single-cell microinjection technology in cell biology. Bioessays 30, 606–610.

    Article  PubMed  Google Scholar 

  54. Valero A, Post JN, van Nieuwkasteele JW, ter Braak PM, Kruijer W & van den Berg A (2008) Gene transfer and protein dynamics in stem cells using single cell electroporation in a microfluidic device. Lab Chip 8, 62.

    Article  PubMed  CAS  Google Scholar 

  55. Larsson C, Grundberg I, Soderberg O & Nilsson M (2010) In situ detection and genotyping of individual mRNA molecules. Nat Meth 7, 395–397.

    Article  CAS  Google Scholar 

  56. Heidecker B & Hare JM (2007) The use of transcriptomic biomarkers for personalized medicine. Heart Fail Rev 12, 1–11.

    Article  PubMed  CAS  Google Scholar 

  57. Liotta LA, Kohn EC & Petricoin EF (2001) Clinical Proteomics. JAMA: The Journal of the American Medical Association 286, 2211–2214.

    Article  CAS  Google Scholar 

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Correspondence to Dino Di Carlo .

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Di Carlo, D., Tse, H.T.K., Gossett, D.R. (2012). Introduction: Why Analyze Single Cells?. In: Lindström, S., Andersson-Svahn, H. (eds) Single-Cell Analysis. Methods in Molecular Biology, vol 853. Humana Press. https://doi.org/10.1007/978-1-61779-567-1_1

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  • DOI: https://doi.org/10.1007/978-1-61779-567-1_1

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  • Print ISBN: 978-1-61779-566-4

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