1. KimCF, JacksonEL, WoolfendenAE, LawrenceS, BabarI, et al. (2005) Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 121: 823–835.
2. EmaH, TakanoH, SudoK, NakauchiH (2000) In vitro self-renewal division of hematopoietic stem cells. J Exp Med 192: 1281–1288.
3. ClaytonE, DoupeDP, KleinAM, WintonDJ, SimonsBD, et al. (2007) A single type of progenitor cell maintains normal epidermis. Nature 446: 185–189.
4. HeXC, YinT, GrindleyJC, TianQ, SatoT, et al. (2007) PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet 39: 189–198.
5. PottenCS, BoothC, TudorGL, BoothD, BradyG, et al. (2003) Identification of a putative intestinal stem cell and early lineage marker; musashi-1. Differentiation 71: 28–41.
6. Al-HajjM, WichaMS, Benito-HernandezA, MorrisonSJ, ClarkeMF (2003) Prospective identification of tumorigenic breast cancer cells. Proc Natl Acad Sci U S A 100: 3983–3988.
7. BonnetD, DickJE (1997) Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat Med 3: 730–737.
8. YilmazOH, ValdezR, TheisenBK, GuoW, FergusonDO, et al. (2006) Pten dependence distinguishes haematopoietic stem cells from leukaemia-initiating cells. Nature 441: 475–482.
9. GinestierC, HurMH, Charafe-JauffretE, MonvilleF, DutcherJ, et al. (2007) ALDH1 Is a Marker of Normal and Malignant Human Mammary Stem Cells and a Predictor of Poor Clinical Outcome. Cell Stem Cell 1: 555–567.
10. LiuS, GinestierC, Charafe-JauffretE, FocoH, KleerCG, et al. (2008) BRCA1 regulates human mammary stem/progenitor cell fate. Proc Natl Acad Sci U S A 105: 1680–1685.
11. BoikoAD, RazorenovaOV, van de RijnM, SwetterSM, JohnsonDL, et al. (2010) Human melanoma-initiating cells express neural crest nerve growth factor receptor CD271. Nature 466: 133–137.
12. ReyaT, MorrisonSJ, ClarkeMF, WeissmanIL (2001) Stem cells, cancer, and cancer stem cells. Nature 414: 105–111.
13. DiehnM, ChoRW, LoboNA, KaliskyT, DorieMJ, et al. (2009) Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature 458: 780–783.
14. PhillipsTM, McBrideWH, PajonkF (2006) The response of CD24(-/low)/CD44+ breast cancer-initiating cells to radiation. J Natl Cancer Inst 98: 1777–1785.
15. BaoS, WuQ, McLendonRE, HaoY, ShiQ, et al. (2006) Glioma stem cells promote radioresistance by preferential activation of the DNA damage response. Nature 444: 756–760.
16. DierksC, BeigiR, GuoGR, ZirlikK, StegertMR, et al. (2008) Expansion of Bcr-Abl-positive leukemic stem cells is dependent on Hedgehog pathway activation. Cancer Cell 14: 238–249.
17. FarnieG, ClarkeRB (2007) Mammary stem cells and breast cancer-role of notch signalling. Stem Cell Rev 3: 169–175.
18. SanchoE, BatlleE, CleversH (2004) Signaling pathways in intestinal development and cancer. Annu Rev Cell Dev Biol 20: 695–723.
19. KangJ, ShakyaA, TantinD (2009) Stem cells, stress, metabolism and cancer: a drama in two Octs. Trends Biochem Sci 34: 491–499.
20. ShakyaA, KangJ, ChumleyJ, WilliamsMA, TantinD (2011) Oct1 is a switchable, bipotential stabilizer of repressed and inducible transcriptional states. J Biol Chem 286: 450–459.
21. ShakyaA, CookseyR, CoxJE, WangV, McClainDA, et al. (2009) Oct1 loss of function induces a coordinate metabolic shift that opposes tumorigenicity. Nat Cell Biol 11: 320–327.
22. TsatmaliM, WalcottEC, CrossinKL (2005) Newborn neurons acquire high levels of reactive oxygen species and increased mitochondrial proteins upon differentiation from progenitors. Brain Res 1040: 137–150.
23. SmithJ, LadiE, Mayer-ProschelM, NobleM (2000) Redox state is a central modulator of the balance between self-renewal and differentiation in a dividing glial precursor cell. Proc Natl Acad Sci U S A 97: 10032–10037.
24. LiuJ, CaoL, ChenJ, SongS, LeeIH, et al. (2009) Bmi1 regulates mitochondrial function and the DNA damage response pathway. Nature 459: 387–392.
25. MohyeldinA, Garzon-MuvdiT, Quinones-HinojosaA (2010) Oxygen in Stem Cell Biology: A Critical Component of the Stem Cell Niche. Cell Stem Cell 7: 150–161.
26. TantinD, Schild-PoulterC, WangV, HacheRJ, SharpPA (2005) The octamer binding transcription factor Oct-1 is a stress sensor. Cancer Res 65: 10750–10758.
27. AlmeidaR, AlmeidaJ, ShoshkesM, MendesN, MesquitaP, et al. (2005) OCT-1 is over-expressed in intestinal metaplasia and intestinal gastric carcinomas and binds to, but does not transactivate, CDX2 in gastric cells. J Pathol 207: 396–401.
28. HuangEH, HynesMJ, ZhangT, GinestierC, DontuG, et al. (2009) Aldehyde dehydrogenase 1 is a marker for normal and malignant human colonic stem cells (SC) and tracks SC overpopulation during colon tumorigenesis. Cancer Res 69: 3382–3389.
29. HessDA, WirthlinL, CraftTP, HerrbrichPE, HohmSA, et al. (2006) Selection based on CD133 and high aldehyde dehydrogenase activity isolates long-term reconstituting human hematopoietic stem cells. Blood 107: 2162–2169.
30. WongVW, StangeDE, PageME, BuczackiS, WabikA, et al. (2012) Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling. Nat Cell Biol 14: 401–408.
31. PowellAE, WangY, LiY, PoulinEJ, MeansAL, et al. (2012) The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell 149: 146–158.
32. BarkerN, van EsJH, KuipersJ, KujalaP, van den BornM, et al. (2007) Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449: 1003–1007.
33. de LauW, BarkerN, LowTY, KooBK, LiVS, et al. (2011) Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature 476: 293–297.
34. CarmonKS, GongX, LinQ, ThomasA, LiuQ (2011) R-spondins function as ligands of the orphan receptors LGR4 and LGR5 to regulate Wnt/beta-catenin signaling. Proc Natl Acad Sci U S A 108: 11452–11457.
35. SangiorgiE, CapecchiMR (2008) Bmi1 is expressed in vivo in intestinal stem cells. Nat Genet 40: 915–920.
36. Charafe-JauffretE, GinestierC, IovinoF, WicinskiJ, CerveraN, et al. (2009) Breast cancer cell lines contain functional cancer stem cells with metastatic capacity and a distinct molecular signature. Cancer Res 69: 1302–1313.
37. DeRoseYS, WangG, LinYC, BernardPS, BuysSS, et al. (2011) Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes. Nat Med 17: 1514–1520.
38. YanagawaY, ChenJC, HsuLC, YoshidaA (1995) The transcriptional regulation of human aldehyde dehydrogenase I gene. The structural and functional analysis of the promoter. J Biol Chem 270: 17521–17527.
39. WuC, AlmanBA (2008) Side population cells in human cancers. Cancer Lett 268: 1–9.
40. SummerR, KottonDN, SunX, MaB, FitzsimmonsK, et al. (2003) Side population cells and Bcrp1 expression in lung. Am J Physiol Lung Cell Mol Physiol 285: L97–104.
41. GoodellMA, BroseK, ParadisG, ConnerAS, MulliganRC (1996) Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo. J Exp Med 183: 1797–1806.
42. ZhouS, SchuetzJD, BuntingKD, ColapietroAM, SampathJ, et al. (2001) The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype. Nat Med 7: 1028–1034.
43. ScharenbergCW, HarkeyMA, Torok-StorbB (2002) The ABCG2 transporter is an efficient Hoechst 33342 efflux pump and is preferentially expressed by immature human hematopoietic progenitors. Blood 99: 507–512.
44. BirneyE, StamatoyannopoulosJA, DuttaA, GuigoR, GingerasTR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816.
45. SebastianoV, DalvaiM, GentileL, SchubartK, SutterJ, et al. (2010) Oct1 regulates trophoblast development during early mouse embryogenesis. Development 137: 3551–3560.
46. WangVEH, SchmidtT, ChenJ, SharpPA, TantinD (2004) Embryonic Lethality, Decreased Erythopoiesis, and Defective Octamer-Dependent Promoter Activation in Oct-1-Deficient Mice. Mol Cell Biol 24: 1022–1032.
47. WangVE, TantinD, ChenJ, SharpPA (2004) B cell development and immunoglobulin transcription in Oct-1-deficient mice. Proc Natl Acad Sci U S A 101: 2005–2010.
48. ItoK, HiraoA, AraiF, MatsuokaS, TakuboK, et al. (2004) Regulation of oxidative stress by ATM is required for self-renewal of haematopoietic stem cells. Nature 431: 997–1002.
49. DonnerAL, EpiskopouV, MaasRL (2007) Sox2 and Pou2f1 interact to control lens and olfactory placode development. Dev Biol 303: 784–799.
50. MunozJ, StangeDE, SchepersAG, van de WeteringM, KooBK, et al. (2012) The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers. Embo J 31: 3079–3091.
51. BroadleyKW, HunnMK, FarrandKJ, PriceKM, GrassoC, et al. (2011) Side population is not necessary or sufficient for a cancer stem cell phenotype in glioblastoma multiforme. Stem Cells 29: 452–461.
52. QuintanaE, ShackletonM, SabelMS, FullenDR, JohnsonTM, et al. (2008) Efficient tumour formation by single human melanoma cells. Nature 456: 593–598.
53. LiL, LiM, SunC, FranciscoL, ChakrabortyS, et al. (2011) Altered hematopoietic cell gene expression precedes development of therapy-related myelodysplasia/acute myeloid leukemia and identifies patients at risk. Cancer Cell 20: 591–605.
54. ReymannS, BorlakJ (2008) Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: identification of the c-myc regulatory gene network. BMC Syst Biol 2: 46.
55. Ben-PorathI, ThomsonMW, CareyVJ, GeR, BellGW, et al. (2008) An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet 40: 499–507.
56. SomervailleTC, MathenyCJ, SpencerGJ, IwasakiM, RinnJL, et al. (2009) Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell 4: 129–140.
57. MattisonJ, KoolJ, UrenAG, de RidderJ, WesselsL, et al. (2010) Novel Candidate Cancer Genes Identified by a Large-Scale Cross-Species Comparative Oncogenomics Approach. Cancer Res 70: 883–895.
58. KangJ, GoodmanB, ZhengY, TantinD (2011) Dynamic Regulation of Oct1 during Mitosis by Phosphorylation and Ubiquitination. PLoS ONE 6: e23872 doi:10.1371/journal.pone.0023872
59. WangP, JinT (2010) Hydrogen peroxide stimulates nuclear import of the POU homeodomain protein Oct-1 and its repressive effect on the expression of Cdx-2. BMC Cell Biol 11: 56.
60. WangP, WangQ, SunJ, WuJ, LiH, et al. (2009) POU homeodomain protein Oct-1 functions as a sensor for cyclic AMP. J Biol Chem 284: 26456–26465.
61. KangJ, GemberlingM, NakamuraM, WhitbyFG, HandaH, et al. (2009) A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress. Genes Dev 23: 208–222.
62. ItoK, HiraoA, AraiF, TakuboK, MatsuokaS, et al. (2006) Reactive oxygen species act through p38 MAPK to limit the lifespan of hematopoietic stem cells. Nat Med 12: 446–451.
63. NemethMJ, KirbyMR, BodineDM (2006) Hmgb3 regulates the balance between hematopoietic stem cell self-renewal and differentiation. Proc Natl Acad Sci U S A 103: 13783–13788.
64. ParkIK, QianD, KielM, BeckerMW, PihaljaM, et al. (2003) Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature 423: 302–305.
65. TothovaZ, KolliparaR, HuntlyBJ, LeeBH, CastrillonDH, et al. (2007) FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell 128: 325–339.
66. TrowbridgeJJ, SnowJW, KimJ, OrkinSH (2009) DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell 5: 442–449.
67. PhelpsRA, ChidesterS, DehghanizadehS, PhelpsJ, SandovalIT, et al. (2009) A two-step model for colon adenoma initiation and progression caused by APC loss. Cell 137: 623–634.
68. PatrawalaL, CalhounT, Schneider-BroussardR, ZhouJ, ClaypoolK, et al. (2005) Side population is enriched in tumorigenic, stem-like cancer cells, whereas ABCG2+ and ABCG2− cancer cells are similarly tumorigenic. Cancer Res 65: 6207–6219.
69. ChoS, SpangrudeGS (2011) Enrichment of Functionally Distinct Mouse Hematopoietic Progenitor Cell Populations using CD62L. J Immunol 187: 5203–5210.
70. ShackletonM, VaillantF, SimpsonKJ, StinglJ, SmythGK, et al. (2006) Generation of a functional mammary gland from a single stem cell. Nature 439: 84–88.