Abstract
Tissues and organs are composed of various kinds of cells including stem cells, progenitors, and terminally differentiated cells that have large variations of gene expression. Within a seemingly homogeneous cell population, gene expression levels may differ dramatically on a cell-to-cell level. However, differences or variations of individual cells are masked by the averaging effect of pooled samples in population analysis. Therefore, analyzing transcript levels for multiple genes across multiple individual cells could be key for understanding the unique characteristics of individual cells and for clarifying the complicated mechanisms controlling the function of individual cells. Recent advances in cDNA amplification techniques from single cell samples allow for analyzing gene expression patterns in individual cells. Amplified cDNAs are applicable to measurements of gene expression systems such as microarrays, DNA sequencing, and TaqMan assay-based high throughput nanofluidic real time PCR array analysis. Gene expression profiling at the single cell level allows us to identify specific sub-populations in heterogeneous cell populations in tissues and clarify the complex networks controlling the function of individual cells.
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Arai F, Hirao A, Ohmura M, Sato H, Matsuoka S, Takubo K, Ito K, Koh GY, Suda T (2004) Tie2/angiopoietin-1 signaling regulates hematopoietic stem cell quiescence in the bone marrow niche. Cell 118:149–161
Benveniste P, Frelin C, Janmohamed S, Barbara M, Herrington R, Hyam D, Iscove NN (2010) Intermediate-term hematopoietic stem cells with extended but time-limited reconstitution potential. Cell Stem Cell 6:48–58
Brady G, Barbara M, Iscove NN (1990) Representative in vitro cDNA amplification from individual hemopoietic cells and colonies. Method Mol Cell Biol 2:17–25
Brady G, Iscove NN (1993) Construction of cDNA libraries from single cells. Methods Enzymol 225:611–623
Calvi LM, Adams GB, Weibrecht KW, Weber JM, Olson DP, Knight MC, Martin RP, Schipani E, Divieti P, Bringhurst FR et al (2003) Osteoblastic cells regulate the haematopoietic stem cell niche. Nature 425:841–846
Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P (1992) Analysis of gene expression in single live neurons. Proc Natl Acad Sci U S A 89:3010–3014
Eilken HM, Nishikawa S, Schroeder T (2009) Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature 457:896–900
Esumi S, Wu SX, Yanagawa Y, Obata K, Sugimoto Y, Tamamaki N (2008) Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors. Neurosci Res 60:439–451
Fleming HE, Janzen V, Lo Celso C, Guo J, Leahy KM, Kronenberg HM, Scadden DT (2008) Wnt signaling in the niche enforces hematopoietic stem cell quiescence and is necessary to preserve self-renewal in vivo. Cell Stem Cell 2:274–283
Foygel K, Choi B, Jun S, Leong DE, Lee A, Wong CC, Zuo E, Eckart M, Reijo Pera RA, Wong WH et al (2008) A novel and critical role for Oct4 as a regulator of the maternal-embryonic transition. PLoS One 3:e4109
Fujisaki J, Wu J, Carlson AL, Silberstein L, Putheti P, Larocca R, Gao W, Saito TI, Lo Celso C, Tsuyuzaki H et al (2011) In vivo imaging of Treg cells providing immune privilege to the haematopoietic stem-cell niche. Nature 474:216–219
Haug JS, He XC, Grindley JC, Wunderlich JP, Gaudenz K, Ross JT, Paulson A, Wagner KP, Xie Y, Zhu R et al (2008) N-cadherin expression level distinguishes reserved versus primed states of hematopoietic stem cells. Cell Stem Cell 2:367–379
Heissig B, Hattori K, Dias S, Friedrich M, Ferris B, Hackett NR, Crystal RG, Besmer P, Lyden D, Moore MA et al (2002) Recruitment of stem and progenitor cells from the bone marrow niche requires MMP-9 mediated release of kit-ligand. Cell 109:625–637
Hosokawa K, Arai F, Yoshihara H, Iwasaki H, Hembree M, Yin T, Nakamura Y, Gomei Y, Takubo K, Shima H et al (2010) Cadherin-based adhesion is a potential target for niche manipulation to protect hematopoietic stem cells in adult bone marrow. Cell Stem Cell 6:194–198
Hosokawa K, Arai F, Yoshihara H, Nakamura Y, Gomei Y, Iwasaki H, Miyamoto K, Shima H, Ito K, Suda T (2007) Function of oxidative stress in the regulation of hematopoietic stem cell-niche interaction. Biochem Biophys Res Commun 363:578–583
Katayama Y, Battista M, Kao WM, Hidalgo A, Peired AJ, Thomas SA, Frenette PS (2006) Signals from the sympathetic nervous system regulate hematopoietic stem cell egress from bone marrow. Cell 124:407–421
Kawasaki ES (2004) Microarrays and the gene expression profile of a single cell. Ann N Y Acad Sci 1020:92–100
Kiel MJ, Morrison SJ (2008) Uncertainty in the niches that maintain haematopoietic stem cells. Nat Rev Immunol 8:290–301
Kollet O, Dar A, Shivtiel S, Kalinkovich A, Lapid K, Sztainberg Y, Tesio M, Samstein RM, Goichberg P, Spiegel A et al (2006) Osteoclasts degrade endosteal components and promote mobilization of hematopoietic progenitor cells. Nat Med 12:657–664
Kurimoto K, Saitou M (2010) Single-cell cDNA microarray profiling of complex biological processes of differentiation. Curr Opin Genet Dev 20:470–477
Kurimoto K, Yabuta Y, Ohinata Y, Saitou M (2007) Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis. Nat Protoc 2:739–752
Lapidot T, Dar A, Kollet O (2005) How do stem cells find their way home? Blood 106:1901–1910
Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma’ayan A, Boyer LA et al (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462:358–362
Mendez-Ferrer S, Lucas D, Battista M, Frenette PS (2008) Haematopoietic stem cell release is regulated by circadian oscillations. Nature 452:442–447
Mendez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, Ma’ayan A, Enikolopov GN, Frenette PS (2010) Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature 466:829–834
Moore KA, Lemischka IR (2006) Stem cells and their niches. Science 311:1880–1885
Morrison SJ, Spradling AC (2008) Stem cells and niches: mechanisms that promote stem cell maintenance throughout life. Cell 132:598–611
Nakamura Y, Arai F, Iwasaki H, Hosokawa K, Kobayashi I, Gomei Y, Matsumoto Y, Yoshihara H, Suda T (2010) Isolation and characterization of endosteal niche cell populations that regulate hematopoietic stem cells. Blood 116:1422–1432
Naveiras O, Nardi V, Wenzel PL, Hauschka PV, Fahey F, Daley GQ (2009) Bone-marrow adipocytes as negative regulators of the haematopoietic microenvironment. Nature 460:259–263
Nilsson SK, Johnston HM, Whitty GA, Williams B, Webb RJ, Denhardt DT, Bertoncello I, Bendall LJ, Simmons PJ, Haylock DN (2005) Osteopontin, a key component of the hematopoietic stem cell niche and regulator of primitive hematopoietic progenitor cells. Blood 106:1232–1239
Qian H, Buza-Vidas N, Hyland CD, Jensen CT, Antonchuk J, Månsson R, Thoren LA, Ekblom M, Alexander WS, Jacobsen SEW (2007) Critical role of thrombopoietin in maintaining adult quiescent hematopoietic stem cells. Cell Stem Cell 1:671–684
Rieger MA, Hoppe PS, Smejkal BM, Eitelhuber AC, Schroeder T (2009) Hematopoietic cytokines can instruct lineage choice. Science 325:217–218
Sacchetti B, Funari A, Michienzi S, Di Cesare S, Piersanti S, Saggio I, Tagliafico E, Ferrari S, Robey PG, Riminucci M et al (2007) Self-renewing osteoprogenitors in bone marrow sinusoids can organize a hematopoietic microenvironment. Cell 131:324–336
Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, Tamayo P, Renshaw AA, D’Amico AV, Richie JP et al (2002) Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1:203–209
Spurgeon SL, Jones RC, Ramakrishnan R (2008) High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One 3:e1662
Stahlberg A, Bengtsson M (2010) Single-cell gene expression profiling using reverse transcription quantitative real-time PCR. Methods 50:282–288
Stier S, Ko Y, Forkert R, Lutz C, Neuhaus T, Grunewald E, Cheng T, Dombkowski D, Calvi LM, Rittling SR et al (2005) Osteopontin is a hematopoietic stem cell niche component that negatively regulates stem cell pool size. J Exp Med 201:1781–1791
Sugiyama T, Kohara H, Noda M, Nagasawa T (2006) Maintenance of the hematopoietic stem cell pool by CXCL12-CXCR4 chemokine signaling in bone marrow stromal cell niches. Immunity 25:977–988
Thoren LA, Liuba K, Bryder D, Nygren JM, Jensen CT, Qian H, Antonchuk J, Jacobsen SE (2008) Kit regulates maintenance of quiescent hematopoietic stem cells. J Immunol 180:2045–2053
Thorsen T, Maerkl SJ, Quake SR (2002) Microfluidic large-scale integration. Science 298:580–584
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87:1663–1667
Warren L, Bryder D, Weissman IL, Quake SR (2006) Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc Natl Acad Sci U S A 103:17807–17812
Wilson A, Laurenti E, Oser G, van der Wath RC, Blanco-Bose W, Jaworski M, Offner S, Dunant CF, Eshkind L, Bockamp E et al (2008) Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair. Cell 135:1118–1129
Wilson A, Trumpp A (2006) Bone-marrow haematopoietic-stem-cell niches. Nat Rev Immunol 6:93–106
Yin T, Li L (2006) The stem cell niches in bone. J Clin Invest 116:1195–1201
Yoshihara H, Arai F, Hosokawa K, Hagiwara T, Takubo K, Nakamura Y, Gomei Y, Iwasaki H, Matsuoka S, Miyamoto K et al (2007) Thrombopoietin/MPL signaling regulates hematopoietic stem cell quiescence and interaction with the osteoblastic niche. Cell Stem Cell 1:685–697
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The Funding Program for Next Generation World-Leading Researchers (NEXT Program) supported this work.
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Arai, F., Hosokawa, K., Matsumoto, Y., Toyama, H., Suda, T. (2012). Gene Expression Profiling and Regulatory Networks in Single Cells. In: Ma'ayan, A., MacArthur, B. (eds) New Frontiers of Network Analysis in Systems Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4330-4_1
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DOI: https://doi.org/10.1007/978-94-007-4330-4_1
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