Chapter 5 Stem Cells: Their Potential and Their Niches

Literature Cited

Ables, J. L., J. J. Breunig, A. J. Eisch and P. Rakic. 2011. Not(ch) just development: Notch signalling in the adult brain. Nat. Rev. Neurosci. 12: 269–283.
PubMed Link

Aguirre, A., M. E. Rubio and V. Gallo. 2010. Notch and EGFR pathway interaction regulates neural stem cell number and self-renewal. Nature 467: 323–327.
PubMed Link

Akiyama, T., K. Kamimura, C. Firkus, S. Takeo, O. Shimmi and H. Nakato. 2008. Dally regulates Dpp morphogen gradient formation by stabilizing Dpp on the cell surface. Dev. Biol. 313: 408–419.
PubMed Link

Al-Drees, M. A. and 6 others. 2015. Making blood: The haematopoietic niche throughout ontogeny. Stem Cells Int. 2015: 571893.
PubMed Link

Alfonso, J., C. Le Magueresse, A. Zuccotti, K. Khodosevich and H. Monyer. 2012. Diazepam binding inhibitor promotes progenitor proliferation in the postnatal SVZ by reducing GABA signaling. Cell Stem Cell 10: 76–87.
PubMed Link

Alvarez-Dolado, M. and 8 others. 2003. Fusion of bone marrow-derived cells with Purkinje neurons, cardiomyocytes, and hepatocytes. Nature 425: 968–973
PubMed Link

Arai, F. and 8 others. 2004. Tie2/ angiopoietin-1 signaling regulates hematopoietic stem cell quiescence in the bone marrow niche. Cell 118: 149–161.
PubMed Link

Artus, J. and C. Chazaud. 2014. A close look at the mammalian blastocyst: Epiblast and primitive endoderm formation. Cell. Mol. Life Sci. 71: 3327–3338.
PubMed Link

Asumda, F. Z. 2013. Age-associated changes in the ecological niche: Implications for mesenchymal stem cell aging. Stem Cell Res. Ther. 4: 47.
PubMed Link

Bai, C.B., W. Auerbach, J. S. Lee, D. Stephen and A. L. Joyner. 2002. Gli2, but not Gli1, is required for initial Shh signaling and ectopic activation of the Shh pathway. Development 129: 4753–4761.
PubMed Link

Barker, N. and 10 others. 2007. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449: 1003–1007.
PubMed Link

Barker, N. 2014. Adult intestinal stem cells: Critical drivers of epithelial homeostasis and regeneration. Nat. Rev. Mol. Cell Biol. 15: 19–33.
PubMed Link

Basak, O., C. Giachino, E. Fiorini, H. R. Macdonald and V. Taylor. 2012. Neurogenic subventricular zone stem/progenitor cells are Notch1-dependent in their active but not quiescent state. J. Neurosci. 32: 5654–5666.
PubMed Link

Bianco, P. 2014. "Mesenchymal" stem cells. Annu. Rev. Cell Dev. Biol. 30: 677–704.
PubMed Link

Boulais, P. E. and P. S. Frenette. 2015. Making sense of hematopoietic stem cell niches. Blood 125: 2621–2629.
PubMed Link

Buczacki, S. J. and 6 others. 2013. Intestinal label-retaining cells are secretory precursors expressing Lgr5. Nature 495: 65–69.
PubMed Link

Burridge, P. W., G. Keller, J. D. Gold and J. C. Wu. 2012. Production of de novo cardiomyocytes: Human pluripotent stem cell differentiation and direct reprogramming. Cell Stem Cell 10: 16–28.
PubMed Link

Burridge, P. W. and 14 others. 2014. Chemically defined generation of human cardiomyocytes. Nat. Methods. 11: 855–860.
PubMed Link

Carulli, A. J., L. C. Samuelson and S. Schnell. 2014. Unraveling intestinal stem cell behavior with models of crypt dynamics. Integr. Biol. (Camb.) 6: 243–257.
PubMed Link

Clevers, H. 2013. Stem cells: A unifying theory for the crypt. Nature 495: 53–54.
PubMed Link

Clevers, H. 2013. The intestinal crypt, a prototype stem cell compartment. Cell 154: 274–284.
PubMed Link

Codega, P. and 6 others. 2014. Prospective identification and purification of quiescent adult neural stem cells from their in vivo niche. Neuron 82: 545–559.
PubMed Link

Colak, D. and 9 others. 2008. Adult neurogenesis requires Smad4-mediated bone morphogenic protein signaling in stem cells. J. Neurosci. 28: 434–446.
PubMed Link

Crane, A. M. and 18 others. 2015. Targeted correction and restored function of the CFTR gene in cystic fibrosis induced pluripotent stem cells. Stem Cell Reports 4: 569–577.
PubMed Link

Cullen, S. M., A. Mayle, L. Rossi and M. A. Goodell. 2014. Hematopoietic stem cell development: An epigenetic journey. Curr. Top. Dev. Biol. 107: 39–75.
PubMed Link

Curtis, M. A., V. F. Low and R. L. Faull. 2012. Neurogenesis and progenitor cells in the adult human brain: A comparison between hippocampal and subventricular progenitor proliferation. Dev. Neurobiol. 72: 990–1005.
PubMed Link

Danjo, T. and 7 others. 2011. Subregional specification of embryonic stem cell-derived ventral telencephalic tissues by timed and combinatory treatment with extrinsic signals. J. Neurosci. 31: 1919–1933.
PubMed Link

Darwich, A. S., U. Aslam, D. M. Ashcroft and A. Rostami-Hodjegan. 2014. Meta-analysis of the turnover of intestinal epithelia in preclinical animal species and humans. Drug Metab. Dispos. 42: 2016–2022.
PubMed Link

De Rubeis, S. and J. D. Buxbaum. 2015. Genetics and genomics of autism spectrum disorder: Embracing complexity. Hum. Mol. Genet. 24: R24–R31.
PubMed Link

Dimos, J. T. and 12 others. 2008. Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science 321: 1218–1221.
PubMed Link

Doetsch, F., J. M. García-Verdugo and A. Alvarez-Buylla. 1997. Cellular composition and three-dimensional organization of the subventricular germinal zone in the adult mammalian brain. J. Neurosci. 17: 5046–5061.
PubMed Link

Egawa, N. and 37 others. 2012. Drug screening for ALS using patient-specific induced pluripotent stem cells. Sci. Transl. Med. 4: 145ra104.
PubMed Link

Egerman, M. A. and 17 others. 2015. Gdf11 increases with age and inhibits skeletal muscle regeneration. Cell Metab. 22: 164–174.
PubMed Link

Eiraku, M. and Y. Sasai. 2012. Self-formation of layered neural structures in three-dimensional culture of ES cells. Curr. Opin. Neurobiol. 22: 768–777.
PubMed Link

Eiraku, M. and 9 others. 2008. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3: 519–532.
PubMed Link

Eliazer, S. and M. Buszczak. 2011. Finding a niche: Studies from the Drosophila ovary. Stem Cell Res. Ther. 2: 45.
PubMed Link

Evans, M. J. and M. H. Kaufman. 1981. Establishment in culture of pluripotential cells from mouse embryos. Nature 292: 154–156.
PubMed Link

Faigle, R. and H. Song. 2013. Signaling mechanisms regulating adult neural stem cells and neurogenesis. Biochim. Biophys. Acta. 1830: 2435–2448.
PubMed Link

Farin, H. F., J. H. Van Es and H. Clevers. 2012. Redundant sources of Wnt regulate intestinal stem cells and promote formation of Paneth cells. Gastroenterology 143: 1518–1529.
PubMed Link

Festa, E. and 6 others. 2011. Adipocyte lineage cells contribute to the skin stem cell niche to drive hair cycling. Cell 146: 761–771.
PubMed Link

Flanagan, D. J and 15 others. 2015. Frizzled7 functions as a Wnt receptor in intestinal epithelial Lgr5+ stem cells. Stem Cell Reports 4: 759–767.
PubMed Link

Fleming, T. P. 1987. A quantitative analysis of cell allocation to trophectoderm and inner cell mass in the mouse blastocyst. Dev. Biol. 119: 520–531.
PubMed Link

Formicola, L., G. Marazzi and D. A. Sassoon. 2014. The extraocular muscle stem cell niche is resistant to ageing and disease. Front. Aging Neurosci. 6: 328.
PubMed Link

Fre, S. and 9 others. 2011. Notch lineages and activity in intestinal stem cells determined by a new set of knock-in mice. PLoS One 6: e25785.
PubMed Link

Freitas, B. C., C. A. Trujillo, C. Carromeu, M. Yusupova, R. H. Herai and A. R. Muotri. 2014. Stem cells and modeling of autism spectrum disorders. Exp. Neurol. 260: 33–43.
PubMed Link

Gage, F. H. 2002. Neurogenesis in the adult brain. J. Neurosci. 22: 612–613.
PubMed Link

Gajera, C.R. and 12 others. 2010. LRP2 in ependymal cells regulates BMP signaling in the adult neurogenic niche. J. Cell Sci. 123: 1922–1930.
PubMed Link

Ganz, J., J. Kaslin, D. Freudenreich, A. Machate, M. Geffarth and M. Brand. 2012. Subdivisions of the adult zebrafish subpallium by molecular marker analysis. J. Comp. Neurol. 520: 633–655.
PubMed Link

Ganz, J., J. Kaslin, S. Hochmann, D. Freudenreich and M. Brand. 2010. Heterogeneity and Fgf dependence of adult neural progenitors in the zebrafish telencephalon. Glia 58: 1345–1363.
PubMed Link

Giachino, C. and V. Taylor. 2014. Notching up neural stem cell homogeneity in homeostasis and disease. Front. Neurosci. 8: 32.
PubMed Link

Giachino, C. and 9 others. 2014. Molecular diversity subdivides the adult forebrain neural stem cell population. Stem Cells 32: 70–84.
PubMed Link

Gilbert, S. G., A. Tyler and E. Zackin. 2005. Bioethics and the New Embryology: Springboards for Debate. Sinauer Associates, Sunderland, MA.

Goldman, S. A. and F. Nottebohm. 1983. Neuronal production, migration, and differentiation in a vocal control nucleus of the adult female canary brain. Proc. Natl. Acad. Sci. USA 80: 2390–2394.
PubMed Link

Goodrich, L.V., L. Milenkovic, K. M. Higgins and M. P. Scott. 1997. Altered neural cell fates and medulloblastoma in mouse patched mutants. Science 277: 1109–1113.
PubMed Link

Grandel, H. and M. Brand. 2013. Comparative aspects of adult neural stem cell activity in vertebrates. Dev. Genes Evol. 223: 131–147.
PubMed Link

Greenbaum, A. and 7 others. 2013. CXCL12 in early mesenchymal progenitors is required for haematopoietic stem-cell maintenance. Nature 495: 227–230.
PubMed Link

Griesi-Oliveira, K. and 24 others. 2015. Modeling non-syndromic autism and the impact of TRPC6 disruption in human neurons. Mol. Psychiatry 20: 1350–1365.
PubMed Link

Guha, P., J. W. Morgan, G. Mostoslavsky, N. P. Rodrigues and A. S. Boyd. 2013. Lack of immune response to differentiated cells derived from syngeneic induced pluripotent stem cells. Cell Stem Cell 12: 407–412.
PubMed Link

Guo, Z. and Z. Wang. 2009. The glypican Dally is required in the niche for the maintenance of germline stem cells and short-range BMP signaling in the Drosophila ovary. Development 136: 3627–3635.
PubMed Link

Handyside, A. H. 1981. Immunofluorescence techniques for determining the numbers of inner and outer blastomeres in mouse morulae. J. Reprod. Immunol. 2: 339–350.
PubMed Link

Harding, M. J., H. F. McGraw and A. Nechiporuk. 2014. The roles and regulation of multicellular rosette structures during morphogenesis. Development 141: 2549–2558.
PubMed Link

Harris, J., G. S. Tomassy and P. Arlotta. 2015. Building blocks of the cerebral cortex: from development to the dish. Wiley Interdiscip. Rev. Dev. Biol. 4: 529–544.
PubMed Link

Hayashi, K., H. Ohta, K. Kurimoto, S. Aramaki and M. Saitou. 2011. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146: 519–532.
PubMed Link

Hayashi, Y., S. Kobayashi and H. Nakato. 2009. Drosophila glypicans regulate the germline stem cell niche. J. Cell Biol. 187: 473–480.
PubMed Link

Hayashi, K., S. Ogushi, K. Kurimoto, S. Shimamoto, H. Ohta and M. Saitou. 2012. Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science 338: 971–975.
PubMed Link

He, X. C. and 11 others. 2004. BMP signaling inhibits intestinal stem cell self-renewal through suppression of Wnt-b-catenin signaling. Nat. Genet. 36: 1117–1121.
PubMed Link

Heidt, T. and 15 others. 2014. Chronic variable stress activates hematopoietic stem cells. Nat. Med. 20: 754–778.
PubMed Link

Hirate, Y. and 14 otehrs. 2013. Polarity-dependent distribution of angiomotin localizes Hippo signaling in preimplantation embryos. Curr. Biol. 23: 1181–1194.
PubMed Link

Huang, X. and 7 others. 2010. Transventricular delivery of Sonic hedgehog is essential to cerebellar ventricular zone development. Proc. Natl. Acad. Sci. USA 107: 8422–8427.
PubMed Link

Huang, X. and J. Wang. 2014. The extended pluripotency protein interactome and its links to reprogramming. Curr. Opin. Genet. Dev. 28: 16–24.
PubMed Link

Ihrie, R. A. and 7 others. 2011. Persistent sonic hedgehog signaling in adult brain determines neural stem cell positional identity. Neuron 71: 250–262.
PubMed Link

Imayoshi, I. and 8 others. 2013. Oscillatory control of factors determining multipotency and fate in mouse neural progenitors. Science 342: 1203–1208.
PubMed Link

Iossifov, I. and 46 others. 2014. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515: 216–221.
PubMed Link

Joe, A. W. and 7 others. 2010. Muscle injury activates resident fibro/adipogenic progenitors that facilitate myogenesis. Nat. Cell Biol. 12: 153–163.
PubMed Link

Kang, H. and D. Shibata. 2013. Direct measurements of human colon crypt stem cell niche genetic fidelity: the role of chance in non-Darwinian mutation selection. Front. Oncol. 3: 264.
PubMed Link

Kaslin, J., J. Ganz, M. Geffarth, H. Grandel, S. Hans and M. Brand. 2009. Stem cells in the adult zebrafish cerebellum: initiation and maintenance of a novel stem cell niche. J. Neurosci. 29: 6142–6153.
PubMed Link

Katsimpardi, L. and 9 others. 2014. Vascular and neurogenic rejuvenation of the aging mouse brain by young systemic factors. Science 344: 630–634.
PubMed Link

Kehler, J. and 10 others. 2004. Oct4 is required for primordial germ cell survival. EMBO Rep. 5: 1078–1083.
PubMed Link

Kerem, B. and 7 others. 1989. Identification of the cystic fibrosis gene: Genetic analysis. Science 245: 1073–1080.
PubMed Link

Kfoury, Y. and D. T. Scadden. 2015. Mesenchymal cell contributions to the stem cell niche. Cell Stem Cell 16: 239–53.
PubMed Link

Kiger, A. A., D. L. Jones, C. Schultz, M. B. Rogers and M. T. Fuller. 2001. Stem cell self-renewal by JAK-STAT activation in response to a support cell cue.Science 294: 2542–2545.
PubMed Link

Kim, N. G., E. Koh, X. Chen and B. M. Gumbiner. 2011. E-cadherin mediates contact inhibition of proliferation through Hippo signaling-pathway components. Proc. Natl. Acad. Sci. USA 108: 11930–11935.
PubMed Link

Klein, A. M. and B. D. Simons. 2011. Universal patterns of stem cell fate in cycling adult tissues. Development 138: 3103–3111.
PubMed Link

Kokovay, E. and 7 others. 2012. VCAM1 is essential to maintain the structure of the SVZ niche and acts as an environmental sensor to regulate SVZ lineage progression. Cell Stem Cell 11: 220–230.
PubMed Link

Kollet, O., J. Canaani, A. Kalinkovich and T. Lapidot. 2012. Regulatory cross talks of bone cells, hematopoietic stem cells and the nervous system maintain hematopoiesis. Inflamm. Allergy Drug Targets 11: 170–180.
PubMed Link

Koo, B. K. and H. Clevers. 2014. Stem cells marked by the R-spondin receptor LGR5. Gastroenterology 147: 289–302.
PubMed Link

Krausova, M. and V. Korinek. 2014. Wnt signaling in adult intestinal stem cells and cancer. Cell Signal. 26: 570–579.
PubMed Link

Kriks, S. and 15 others. 2011. Dopamine neurons derived from human ES cells efficiently engraft in animal models of Parkinson's disease. Nature 480: 547–551.
PubMed Link

Kuo, C. T. and 10 others. 2006. Postnatal deletion of Numb/Numblike reveals repair and remodeling capacity in the subventricular neurogenic niche. Cell 127: 1253–1264.
PubMed Link

Lancaster, M. A. and J. A. Knoblich. 2014. Generation of cerebral organoids from human pluripotent stem cells. Nat. Protoc. 9: 2329–2340.
PubMed Link

Lancaster, M. A. and J. A. Knoblich. 2014. Organogenesis in a dish: modeling development and disease using organoid technologies. Science 345: 124–125.
PubMed Link

Lancaster, M. A. and 9 others. 2013. Cerebral organoids model human brain development and microcephaly. Nature 501: 373–379.
PubMed Link

Le Bin, G. C. and 11 others. 2014. Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst. Development 141: 1001–1010.
PubMed Link

Licht, T. and E. Keshet. 2015. The vascular niche in adult neurogenesis. Mech. Dev. pii: S0925-4773(15)00045-3.
Link

Lim, D. A. and A. Alvarez-Buylla. 2014. Adult neural stem cells stake their ground. Trends Neurosci. 37: 563–571.
PubMed Link

Lim, D. A., A. D. Tramontin, J. M. Trevejo, D. G. Herrera, J. M. García-Verdugo and A. Alvarez-Buylla. 2000. c. Neuron 28: 713–726.
PubMed Link

Lin, H., and A. C. Spradling. 1993. Germline stem cell division and egg chamber development in transplanted Drosophila germaria. Dev. Biol. 159: 140–152.
PubMed Link

Lo Celso, C. and 9 others. 2009. Live-animal tracking of individual haematopoietic stem/progenitor cells in their niche. Nature 457: 92–96.
PubMed Link

Loffredo, F. S. and 19 others. 2013. Growth differentiation factor 11 is a circulating factor that reverses age-related cardiac hypertrophy. Cell 153: 828–839.
PubMed Link

Mariani, J. and 7 others. 2012. Modeling human cortical development in vitro using induced pluripotent stem cells. Proc. Natl. Acad. Sci. USA 109: 12770–12775.
PubMed Link

Marson, A. and 19 others. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134: 521–533.
PubMed Link

Martello, G. and A. Smith. 2014. The nature of embryonic stem cells. Annu. Rev. Cell Dev. Biol. 30: 647–675.
Link

Martin, G. R. 1981. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA 78: 7634–7638.
Link

Martin, G. R. 1980. Teratocarcinomas and mammalian embryogenesis. Science 209: 768–776.
PubMed Link

McGill, M. A. and C. J. McGlade. 2003. Mammalian numb proteins promote Notch1 receptor ubiquitination and degradation of the Notch1 intracellular domain. J. Biol. Chem. 278: 23196–23203.
PubMed Link

Méndez-Ferrer, S., D. Lucas, M. Battista and P. S. Frenette. 2008. Haematopoietic stem cell release is regulated by circadian oscillations. Nature 452: 442–447.
PubMed Link

Méndez-Ferrer, S. and 9 others. 2010. Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature 466: 829–834.
PubMed Link

Mikkola, H. K. and S. H. Orkin. 2006. The journey of developing hematopoietic stem cells. Development 133: 3733–3744.
PubMed Link

Mirzadeh, Z., Y. G. Han, M. Soriano-Navarro, J. M. García-Verdugo and A. Alvarez-Buylla. 2010. Cilia organize ependymal planar polarity. J. Neurosci. 30: 2600–2610.
PubMed Link

Mirzadeh, Z., F. T. Merkle, M. Soriano-Navarro, J. M. Garcia-Verdugo, A. Alvarez-Buylla. 2008. Neural stem cells confer unique pinwheel architecture to the ventricular surface in neurogenic regions of the adult brain. Cell Stem Cell 3: 265–278.
PubMed Link

Moad, M. and 14 others. 2013. A novel model of urinary tract differentiation, tissue regeneration, and disease: reprogramming human prostate and bladder cells into induced pluripotent stem cells. Eur. Urol. 64: 753–761.
PubMed Link

Moll, N. M. and R. M. Ransohoff. 2010. CXCL12 and CXCR4 in bone marrow physiology. Expert Rev. Hematol. 3: 315–322.
PubMed Link

Morell, M., Y. C. Tsan and K. S. O’Shea. 2015. Inducible expression of noggin selectively expands neural progenitors in the adult SVZ. Stem Cell Res. 14: 79–94.
PubMed Link

Muguruma, K. and 10 others. 2010. Ontogeny-recapitulating generation and tissue integration of ES cell-derived Purkinje cells. Nature Neurosci. 13: 1171–1180.
PubMed Link

Murry, C. E. and G. Keller. 2008. Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell 132: 661–680.
PubMed Link

Nichols, J. and 7 others. 1998. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95: 379–391.
PubMed Link

Nombela-Arrieta, C. and 9 others. 2013. Quantitative imaging of haematopoietic stem and progenitor cell localization and hypoxic status in the bone marrow microenvironment. Nat. Cell Biol. 15: 533–543.
PubMed Link

Ottone, C. and 7 others. 2014. Direct cell-cell contact with the vascular niche maintains quiescent neural stem cells. Nat. Cell Biol. 16: 1045–1056.
PubMed Link

Ottone, C. and S. Parrinello. 2015. Multifaceted control of adult SVZ neurogenesis by the vascular niche. Cell Cycle 14: 2222–2225.
PubMed Link

Pannérec, A., L. Formicola, V. Besson, G. Marazzi and D. A. Sassoon. 2013. Defining skeletal muscle resident progenitors and their cell fate potentials. Development 140: 2879–2891.
PubMed Link

Pardo, M. and 6 others. 2010. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell 6: 382–395.
PubMed Link

Park, I. H. and 9 others. 2008. Disease-specific induced pluripotent stem cells. Cell 134: 877–886.
PubMed Link

Pellegrinet, L. and 9 others. 2011. Dll1- and dll4-mediated notch signaling are required for homeostasis of intestinal stem cells. Gastroenterology 140: 1230–1240.e1–7.
PubMed Link

Pierfelice, T., L. Alberi and N. Gaiano. 2011. Notch in the vertebrate nervous system: An old dog with new tricks. Neuron 69: 840–855.
PubMed Link

Poggioli, T. and 15 others. 2015. Circulating growth differentiation factor 11/8 levels decline with age. Circ. Res. 118: 29–37.
PubMed Link

Ponti, G., K. Obernier, C. Guinto, L. Jose, L. Bonfanti and A. Alvarez-Buylla. 2013. Cell cycle and lineage progression of neural progenitors in the ventricular-subventricular zones of adult mice. Proc. Natl. Acad. Sci. USA 110: e1045–1054.
PubMed Link

Potten, C. S., W. J. Hume, P. Reid and J. Cairns. 1978. The segregation of DNA in epithelial stem cells. Cell 15: 899–906.
PubMed Link

Potten, C. S., G. Owen and D. Booth. 2002. Intestinal stem cells protect their genome by selective segregation of template DNA strands. J. Cell Sci. 115: 2381–2388.
PubMed Link

Qian, H. and 9 others. 2007. Critical role of thrombopoietin in maintaining adult quiescent hematopoietic stem cells. Cell Stem Cell 1: 671–684.
PubMed Link

Ralston, A. and 9 others. 2010. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2. Development 137: 395–403.
PubMed Link

Ralston, A. and J. Rossant. 2008. Cdx2 acts downstream of cell polarization to cell-autonomously promote trophectoderm fate in the early mouse embryo. Dev. Biol. 313: 614–629.
PubMed Link

Riordan, J. R. and 13 others. 1989. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245: 1066–1073
PubMed Link.

Ritsma, L. and 7 others. 2014. Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging. Nature 507: 362–365.
PubMed Link

Ronemus, M., I. Iossifov, D. Levy and M. Wigler. 2014. The role of de novo mutations in the genetics of autism spectrum disorders. Nat. Rev. Genet. 15: 133–141.
PubMed Link

Sanai, N. and 11 others. 2011. Corridors of migrating neurons in the human brain and their decline during infancy. Nature 478: 382–386.
PubMed Link

Shamblott, M. J. and 8 others. 1998. Derivation of pluripotent stem cells from cultured human primordial germ cells. Proc. Natl. Acad. Sci. USA 95: 13726–13731.
PubMed Link

Shi, G. and Y. Jin. 2010. Role of Oct4 in maintaining and regaining stem cell pluripotency. Stem Cell Res. Ther. 1: 39.
PubMed Link

Shook, B. A. and 9 others. 2014. Ventriculomegaly associated with ependymal gliosis and declines in barrier integrity in the aging human and mouse brain. Aging Cell 13: 340–350.
PubMed Link

Singh, V. K., M. Kalsan, N. Kumar, A. Saini and R. Chandra. 2015. Induced pluripotent stem cells: applications in regenerative medicine, disease modeling, and drug discovery. Front. Cell Dev. Biol. 3: 2.
PubMed Link

Sinha, M. and 19 others. 2014. Restoring systemic GDF11 levels reverses age-related dysfunction in mouse skeletal muscle. Science 344: 649–652.
PubMed Link

Slaidina, M. and R. Lehmann. 2014. Translational control in germline stem cell development. J. Cell Biol. 207: 13–21.
PubMed Link

Snippert, H. J. and 10 others. 2010. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143: 134–144.
PubMed Link

Song, X. and T. Xie. 2002. DE-cadherin-mediated cell adhesion is essential for maintaining somatic stem cells in the Drosophila ovary. Proc. Natl. Acad. Sci. USA 99: 14813–14818.
PubMed Link

Stephenson, R. O., J. Rossant and P. P. Tam. 2012. Intercellular interactions, position, and polarity in establishing blastocyst cell lineages and embryonic axes. Cold Spring Harb. Perspect. Biol. 4: pii: a008235.
PubMed Link

Stephenson, R. O., Y. Yamanaka and J. Rossant. 2010. Disorganized epithelial polarity and excess trophectoderm cell fate in preimplantation embryos lacking E-cadherin. Development 137: 3383–3391.
PubMed Link

Strumpf, D. and 6 others. 2005. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132: 2093–2102.
PubMed Link

Sugiyama, T., H. Kohara, M. Noda and T. Nagasawa. 2006. Maintenance of the hematopoietic stem cell pool by CXCL12-CXCR4 chemokine signaling in bone marrow stromal cell niches. Immunity 25: 977–988.
PubMed Link

Tan, K. K. and 6 others. 2015. Enhanced differentiation of neural progenitor cells into neurons of the mesencephalic dopaminergic subtype on topographical patterns. Biomaterials 43: 32–43.
PubMed Link

Tavazoie, M. and 7 others. 2008. A specialized vascular niche for adult neural stem cells. Cell Stem Cell 3: 279–288.
PubMed Link

Than-Trong, E. and L. Bally-Cuif. 2015. Radial glia and neural progenitors in the adult zebrafish central nervous system. Glia 63: 1406–1428.
PubMed Link

Theunissen, T. W. and 20 others. 2014. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Cell Stem Cell 15: 471–487.
PubMed Link

Thomson, J. and 6 others. 1998. Embryonic stem cell lines derived from human blastocysts. Science 282: 1145–1147.
PubMed Link

Tong, C. K. and 9 others. 2014. Axonal control of the adult neural stem cell niche. Cell Stem Cell 14: 500–511.
PubMed Link

Tulina, N. and E. Matunis. 2001. Control of stem cell self-renewal in Drosophila melanogaster by JAK-STAT signaling. Science 294: 2546–2549. 
PubMed Link

Tulpule, A. and 7 others. 2010. Knockdown of Fanconi anemia genes in human embryonic stem cells reveals early developmental defects in the hematopoietic lineage. Blood 115: 3453–3462.
PubMed Link

Urbán, N. and F. Guillemot. 2014. Neurogenesis in the embryonic and adult brain: same regulators, different roles. Front. Cell. Neurosci. 8: 396.
PubMed Link

Van der Jeught, M., T. O'Leary, G. Duggal, P. De Sutter, S. Chuva de Sousa Lopes and B. Heindryckx. 2015. The post-inner cell mass intermediate: implications for stem cell biology and assisted reproductive technology. Hum. Reprod. Update 21: 616–626.
PubMed Link

Via, A. G., A. Frizziero and F. Oliva. 2012. Biological properties of mesenchymal stem cells from different sources. Muscles Ligaments Tendons J. 2: 154–162.
PubMed Link

Visnjic, D., Z. Kalajzic, D. W. Rowe, V. Katavic, J. Lorenzo and H. L. Aguila. 2004. Hematopoiesis is severely altered in mice with an induced osteoblast deficiency. Blood 103: 3258–3264.
PubMed Link

Wadman, M. 2011. The Crusader. “Theresa Deisher once shunned religion for science. Now, with renewed faith, she is fighting human-embryonic-stem-cell research in court.” Nature 470: P156-159.
Link

Walther, V. and T. A. Graham. 2014. Location, location, location! The reality of life for an intestinal stem cell in the crypt. J. Pathol. 234: 1–4.
PubMed Link

Wang, X., R. E. Harris, L. J. Bayston and H. L. Ashe. 2008. Type IV collagens regulate BMP signalling in Drosophila. Nature 455: 72–77.
PubMed Link

Warmflash, A., B. Sorre, F. Etoc, E. D. Siggia and A. H. Brivanlou. 2014. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods 11: 847–854.
PubMed Link

Wilson, A. and 8 others. 2007. Dormant and self-renewing hematopoietic stem cells and their niches. Ann. NY Acad. Sci. 1106: 64–75.
PubMed Link

Wu, S. M. and K. Hochedlinger. 2011. Harnessing the potential of induced pluripotent stem cells for regenerative medicine. Nature Cell Biol. 13: 497–505.
PubMed Link

Xie, T. and A. C. Spradling. 1998. Decapentaplegic is essential for the maintenance and division of germline stem cells in the Drosophila ovary. Cell 94: 251–260.
PubMed Link

Yan, D. and 16 others. 2014. A regulatory network of Drosophila germline stem cell self-renewal. Dev. Cell. 28: 459–473.
PubMed Link

Yeom, Y. I. and 7 others. 1996. Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. Development 122: 881–894.
PubMed Link

Yoshihara, H. and 12 others. 2007. Thrombopoietin/MPL signaling regulates hematopoietic stem cell quiescence and interaction with the osteoblastic niche. Cell Stem Cell. 1: 685–697.
PubMed Link

Young, R. A. 2011. Control of embryonic stem cell state. Cell 144: 940–954.
PubMed Link

Zhang, J. and 13 others. 2003. Identification of the haematopoietic stem cell niche and control of the niche size. Nature 425: 836–841.
PubMed Link

Zhu, H., M. W. Lensch, P. Cahan and G. Q. Daley. 2011. Investigating monogenic and complex diseases with pluripotent stem cells. Nature Rev. Gen. 12: 266–275.
PubMed Link