Abstract
Individual stem cells are functionally defined by their self-renewal and differentiation potential. Methods for clonal analysis are essential for understanding stem cells, particularly given the increasing evidence for stem-cell heterogeneity. Stem cells reside within complex microenvironments, making single-cell analysis particularly challenging. Furthermore, simultaneous molecular and functional characterization of single stem cells is not trivial. Here we explore clonal assays applied to stem cell biology and their use in understanding the cellular and molecular basis of stem-cell identity.
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References
He, S., Nakada, D. & Morrison, S.J. Mechanisms of stem cell self-renewal. Annu. Rev. Cell Dev. Biol. 25, 377–406 (2009).
O'Brien, C.A., Kreso, A. & Jamieson, C.H. Cancer stem cells and self-renewal. Clin. Cancer Res. 16, 3113–3120 (2010).
Stewart, M.H. et al. Clonal isolation of hESCs reveals heterogeneity within the pluripotent stem cell compartment. Nat. Methods 3, 807–815 (2006).
Bendall, S.C. et al. IGF and FGF cooperatively establish the regulatory stem cell niche of pluripotent human cells in vitro. Nature 448, 1015–1021 (2007).
Watanabe, K. et al. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotechnol. 25, 681–686 (2007).
Walker, A., et al. Non-muscle myosin II regulates survival threshold of pluripotent stem cells. Nat. Commun. 1, doi:10 1038/ncomms1074 (2010).
Dykstra, B. et al. Long-term propagation of distinct hematopoietic differentiation programs in vivo. Cell Stem Cell 1, 218–229 (2007).
Hope, K.J., Jin, L. & Dick, J.E. Acute myeloid leukemia originates from a hierarchy of leukemic stem cell classes that differ in self-renewal capacity. Nat. Immunol. 5, 738–743 (2004).
Notta, F. et al. Evolution of human BCR-ABL1 lymphoblastic leukaemia-initiating cells. Nature 469, 362–367 (2011).
Anderson, K. et al. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469, 356–361 (2011).
Scadden, D.T. The stem-cell niche as an entity of action. Nature 441, 1075–1079 (2006).
Bendall, S.C., Stewart, M.H. & Bhatia, M. Human embryonic stem cells: lessons from stem cell niches in vivo . Regen. Med. 3, 365–376 (2008).
Morrison, S.J., Shah, N.M. & Anderson, D.J. Regulatory mechanisms in stem cell biology. Cell 88, 287–298 (1997).
Stewart, M.H., Bendall, S.C. & Bhatia, M. Deconstructing human embryonic stem cell cultures: niche regulation of self-renewal and pluripotency. J. Mol. Med. 86, 875–886 (2008).
Adewumi, O. et al. Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat. Biotechnol. 25, 803–816 (2007).
Andrews, P.W. From teratocarcinomas to embryonic stem cells. Phil. Trans. R. Soc. Lond. B 357, 405–417 (2002).
Ellis, J. et al. Alternative induced pluripotent stem cell characterization criteria for in vitro applications. Cell Stem Cell 4, 198–199, author reply 202 (2009).
Werbowetski-Ogilvie, T. et al. Characterization of human embryonic stem cells with features of neoplastic progression. Nat. Biotechnol. 27, 91–97 (2008).
Stewart, M.H., Bendall, S.C., Levadoux-Martin, M. & Bhatia, M. Clonal tracking of hESCs reveals differential contribution to functional assays. Nat. Methods 7, 917–922 (2010).
Nagy, A., Rossant, J., Nagy, R., Abramow-Newerly, W. & Roder, J.C. Derivation of completely cell culture-derived mice from early-passage embryonic stem cells. Proc. Natl. Acad. Sci. USA 90, 8424–8428 (1993).
George, S.H. et al. Developmental and adult phenotyping directly from mutant embryonic stem cells. Proc. Natl. Acad. Sci. USA 104, 4455–4460 (2007).
Wu, A.M., Till, J.E., Siminovitch, L. & McCulloch, E.A. Cytological evidence for a relationship between normal hemotopoietic colony-forming cells and cells of the lymphoid system. J. Exp. Med. 127, 455–464 (1968).
Hong, D. et al. Initiating and cancer-propagating cells in TEL-AML1-associated childhood leukemia. Science 319, 336–339 (2008).
Bernstein, I.D. et al. Differences in the frequency of normal and clonal precursors of colony-forming cells in chronic myelogenous leukemia and acute myelogenous leukemia. Blood 79, 1811–1816 (1992).
Nienhuis, A.W., Dunbar, C.E. & Sorrentino, B.P. Genotoxicity of retroviral integration in hematopoietic cells. Mol. Ther. 13, 1031–1049 (2006).
Dick, J.E., Magli, M.C., Huszar, D., Phillips, R.A. & Bernstein, A. Introduction of a selectable gene into primitive stem cells capable of long-term reconstitution of the hemopoietic system of W/Wv mice. Cell 42, 71–79 (1985).
Keller, G., Paige, C., Gilboa, E. & Wagner, E.F. Expression of a foreign gene in myeloid and lymphoid cells derived from multipotent haematopoietic precursors. Nature 318, 149–154 (1985).
Smith, L.G., Weissman, I.L. & Heimfeld, S. Clonal analysis of hematopoietic stem-cell differentiation in vivo. Proc. Natl. Acad. Sci. USA 88, 2788–2792 (1991).
Morshead, C.M., Benveniste, P., Iscove, N.N. & van der Kooy, D. Hematopoietic competence is a rare property of neural stem cells that may depend on genetic and epigenetic alterations. Nat. Med. 8, 268–273 (2002).
Kiel, M.J., Yilmaz, O.H., Iwashita, T., Terhorst, C. & Morrison, S.J. SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121, 1109–1121 (2005).
Benveniste, P., Cantin, C., Hyam, D. & Iscove, N.N. Hematopoietic stem cells engraft in mice with absolute efficiency. Nat. Immunol. 4, 708–713 (2003).
Yilmaz, O.H., Kiel, M.J. & Morrison, S.J. SLAM family markers are conserved among hematopoietic stem cells from old and reconstituted mice and markedly increase their purity. Blood 107, 924–930 (2006).
Zhang, C.C. & Lodish, H.F. Murine hematopoietic stem cells change their surface phenotype during ex vivo expansion. Blood 105, 4314–4320 (2005).
Hacein-Bey-Abina, S. et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302, 415–419 (2003).
Schmidt, M., et al. A model for the detection of clonality in marked hematopoietic stem cells. Ann. NY Acad. Sci. 938, 146–155 (2001).
Schmidt, M. et al. Polyclonal long-term repopulating stem cell clones in a primate model. Blood 100, 2737–2743 (2002).
Gerrits, A. et al. Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood 115, 2610–2618 (2010).
Fox, D.T., Morris, L.X., Nystul, T. & Spradling, A.C. Lineage analysis of stem cells. in StemBook (The Stem Cell Research Community, 2008).
Clayton, E. et al. A single type of progenitor cell maintains normal epidermis. Nature 446, 185–189 (2007).
Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).
Dor, Y., Brown, J., Martinez, O.I. & Melton, D.A. Adult pancreatic beta-cells are formed by self-duplication rather than stem-cell differentiation. Nature 429, 41–46 (2004).
Samokhvalov, I.M., Samokhvalova, N.I. & Nishikawa, S. Cell tracing shows the contribution of the yolk sac to adult haematopoiesis. Nature 446, 1056–1061 (2007).
Smukler, S.R. et al. The adult mouse and human pancreas contain rare multipotent stem cells that express insulin. Cell Stem Cell 8, 281–293 (2011).
Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56–62 (2007).
Snippert, H.J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010).
Tang, F., Lao, K. & Surani, M.A. Development and applications of single-cell transcriptome analysis. Nat. Methods 8, S9–S14 (2011).
Itzkovitz, S. & van Oudenaarden, A. Validating transcripts with probes and imaging technology. Nat. Methods 8, S15–S22 (2011).
Rubakhin, S.S., Romanova, E.V., Nemes, P. & Sweedler, J.V. Profiling metabolites and peptides in single cells. Nat. Methods 8, S23–S32 (2011).
Billia, F., Barbara, M., McEwen, J., Trevisan, M. & Iscove, N.N. Resolution of pluripotential intermediates in murine hematopoietic differentiation by global complementary DNA amplification from single cells: confirmation of assignments by expression profiling of cytokine receptor transcripts. Blood 97, 2257–2268 (2001).
Hansson, E.M., Lindsay, M.E. & Chien, K.R. Regeneration next: toward heart stem cell therapeutics. Cell Stem Cell 5, 364–377 (2009).
Bhatia, M. Developmental biology. Microenvironment mimicry. Science 329, 1024–1025 (2010).
Lin, Y., Molter, J., Lee, Z. & Gerson, S.L. Bioluminescence imaging of hematopoietic stem cell repopulation in murine models. Methods Mol. Biol. 430, 295–306 (2008).
Lee, Z., Dennis, J.E. & Gerson, S.L. Imaging stem cell implant for cellular-based therapies. Exp. Biol. Med. (Maywood) 233, 930–940 (2008).
Eilken, H.M., Nishikawa, S. & Schroeder, T. Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature 457, 896–900 (2009).
Rieger, M.A., Hoppe, P.S., Smejkal, B.M., Eitelhuber, A.C. & Schroeder, T. Hematopoietic cytokines can instruct lineage choice. Science 325, 217–218 (2009).
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Hope, K., Bhatia, M. Clonal interrogation of stem cells. Nat Methods 8 (Suppl 4), S36–S40 (2011). https://doi.org/10.1038/nmeth.1590
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DOI: https://doi.org/10.1038/nmeth.1590
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