Stem Cell Reviews

, Volume 2, Issue 1, pp 23–30

Hematopoietic stem cells

Expression profiling and beyond
  • E. Camilla Forsberg
  • Deepta Bhattacharya
  • Irving L. Weissman
Original Article


This review focuses on the genomics of mouse hematopoiesis but also draws parallels to other systems and discusses issues common to the analysis of rare populations such as stem cells. As examples from the mouse blood forming system are used to illustrate several points, the authors first give a brief introduction to mouse hematopoiesis as a model system. We review the multiple microarray analyses that have been performed on various mouse hematopoietic subpopulations and comment on both technical and biological aspects of such experiments. The concept of stemness is discussed, and the importance of biological function of gene products, protein-protein interactions and molecular pathways highlighted. Finally, the authors discuss some major unresolved issues in hematopoiesis and discuss the potential uses of future microarray analysis as well as other genomic and functional approaches that might prove useful to further our understanding of hematopoiesis and other stem cell systems.

Index Entries

Functional analysis gene expression genomics hematopoiesis hematopoietic stem cell microarray stem cell 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Spangrude GJ, Heimfeld S, Issman IL, Science 1988;241:58–62.PubMedCrossRefGoogle Scholar
  2. 2.
    Kondo M, Weissman IL, Akashi K, Cell 1997;91:661–672.PubMedCrossRefGoogle Scholar
  3. 3.
    Akashi K, Traver D, Miyamoto T, Weissman IL. Nature 2000;404: 193–197PubMedCrossRefGoogle Scholar
  4. 4.
    Morrison SJ, Wandycz AM, Hemmati HD, Wright DE, Weissman IL, Development 1997;124:1929–1939.PubMedGoogle Scholar
  5. 5.
    Christensen JL, Weissman IL, Proc Natl Acad Sci USA 2001;98: 14,541–14,546.Google Scholar
  6. 6.
    Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR. Science 2002;298:601–604.PubMedCrossRefGoogle Scholar
  7. 7.
    Zhong JF, Zhao Y, Sutton S, et al., Proc Natl Acad Sci USA 2005;102: 2448–2453.PubMedCrossRefGoogle Scholar
  8. 8.
    Akashi K, He X, Chen J, et al., Blood 2003;101:383–389.PubMedCrossRefGoogle Scholar
  9. 9.
    Forsberg EC, Prohaska SS, Katzman S, Heffner GC, Stuart JM, Weissman IL. PloS Genet, 2005;1:e28.PubMedCrossRefGoogle Scholar
  10. 10.
    Forsberg EC, Serwold TF, Kogan S, Weissman IL, Passegue E. Submitted.Google Scholar
  11. 11.
    Passegue E, Wagers AJ, Giuriato S, Anderson WC, Weissman IL. J Exp Med 2005;202:1599–1611.PubMedCrossRefGoogle Scholar
  12. 12.
    Cao YA, Wagers AJ, Beilhack A, et al., Proc. Natl Acad Sci USA 2004;101:221–226.PubMedCrossRefGoogle Scholar
  13. 13.
    Arai F, Hirao A, Ohmura M, et al., Cell 2004;118:149–161.PubMedCrossRefGoogle Scholar
  14. 14.
    Heissig B, Hattori K, Dias S, et al. Cell 2002109:625–637.PubMedCrossRefGoogle Scholar
  15. 15.
    Forsberg EC, Karsunky H, Weissman IL In preparation.Google Scholar
  16. 16.
    Bryder D, Rossi DJ, Weissman IL. Submitted.Google Scholar
  17. 17.
    Forsberg EC, Prohaska SS Weissman IL, Unpublished Observation.Google Scholar
  18. 18.
    Hosen N, Weissman IL. submitted.Google Scholar
  19. 19.
    Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA. Science 2002;298:597–600.PubMedCrossRefGoogle Scholar
  20. 20.
    Evsikov AV, Solter D Science 2003;302:393; author reply 393.PubMedCrossRefGoogle Scholar
  21. 21.
    Fortunel NO, Otu HH, Ng HH, et al. Science 2003;302:393; author reply 393.PubMedCrossRefGoogle Scholar
  22. 22.
    Jakt LM, Sakurai H, Nishikawa S-I. In preparation.Google Scholar
  23. 23.
    Fearon DT, Manders P, Wagner SD. Science 2001;293:248–250.PubMedCrossRefGoogle Scholar
  24. 24.
    McHeyzer-Williams LJ, McHeyzer-Williams MG. Annu Rev Immunol 2005;23:487–513.PubMedCrossRefGoogle Scholar
  25. 25.
    Kaech SM, Hemby S, Kersh E, Ahmed R. Cell 2002;111:837–851.PubMedCrossRefGoogle Scholar
  26. 26.
    Luckey CJ, Bhattacharya D, Goldrath AW, Weissman IL, Benoist C, Mathis D, Proc. Natl Acad. Sci USA 2005;103:3304–3309.CrossRefGoogle Scholar
  27. 27.
    Goodman JW, Hodgson GS, Blood 1962;19:702–714.PubMedGoogle Scholar
  28. 28.
    McCredie KB, Hersh EM, Freireich EJ Science 1971;171:293–294.PubMedCrossRefGoogle Scholar
  29. 29.
    Wright DE, Wagers AJ, Gulati AP, Johnson FL, Weissman IL, Science 2001;294:1933–1936.PubMedCrossRefGoogle Scholar
  30. 30.
    Passegue E, Wagner EF, Weissman IL, Cell 2004;119:431–443.PubMedCrossRefGoogle Scholar
  31. 31.
    Wright DE, Cheshier SH, Wagers AJ, Randall TD, Christensen JL, Weissman IL. Blood 2001;97:2278–2285.PubMedCrossRefGoogle Scholar
  32. 32.
    Passegue E, Prohaska SS, Wagers AJ, Forsberg EC, Weissman IL. In preparation.Google Scholar
  33. 33.
    Rossi DJ, Bryder D, Zhan JM, et al. Proc Natl Acad Sci USA 2005;102:9194–9199.PubMedCrossRefGoogle Scholar
  34. 34.
    Diehn M, Sherlock G, Binkley G, et al. Nucleic Acids Res 2003;31: 219–223.PubMedCrossRefGoogle Scholar
  35. 35.
    Smyth GK, Speed T. Methods 2003;31:265–273.PubMedCrossRefGoogle Scholar
  36. 36.
    Tusher VG, Tibshirani R, Chu G, Proc Natl Acad Sci USA 2001;98: 5116–5121.PubMedCrossRefGoogle Scholar
  37. 37.
    Bolstad BM, Irizarry RA, Astrand M, Speed TPA. Bioinformatics 2003;19:185–193.PubMedCrossRefGoogle Scholar
  38. 38.
    Paddison PJ, Silva JM, Conklin DS, et al., Nature 2004;428: 427–431.PubMedCrossRefGoogle Scholar
  39. 39.
    Silva JM, Li MZ, Chang K, et al. Nat Genet 2005;37:1281–1289.PubMedGoogle Scholar
  40. 40.
    Eckfeldt CE, Mendenhall EM, Flynn CM, et al., PLoS Biol 2005;3:e254.PubMedCrossRefGoogle Scholar
  41. 41.
    Chen CZ, Li L, Lodish HF, Bartel DP. Science 2004;303:83–86.PubMedCrossRefGoogle Scholar
  42. 42.
    Barad O, Meiri E, Avniel A, et al. Genome Res 2004;14:2486–2494.PubMedCrossRefGoogle Scholar
  43. 43.
    Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR, RNA 2004;10:1813–1819.PubMedCrossRefGoogle Scholar
  44. 44.
    Liu CG Calin GA, Meloon B, et al. Proc Natl Acad Sci USA 2004;101: 9740–9744.PubMedCrossRefGoogle Scholar
  45. 45.
    Sun Y, Koo S, White N, et al. Nucleic Acids Res 2004;32:e188.PubMedCrossRefGoogle Scholar
  46. 46.
    Fromont-Racine M, Rain JC, Legrain P. Methods Enzymol 2002;350:513–524.PubMedCrossRefGoogle Scholar
  47. 47.
    Ito T, Chiba T, Yoshida M. Trends Biotechnol 2001;19:S23-S27.PubMedCrossRefGoogle Scholar
  48. 48.
    Zhong J, Zhang H, Stanyon CA, Tromp G, Finley RL Jr, Genome Res 2003:13:2691–2699.PubMedCrossRefGoogle Scholar
  49. 49.
    Fromont-Racine M, Mayes AE, Brunet-Simon A. et al. Yeast 2000; 17:95–110.PubMedCrossRefGoogle Scholar
  50. 50.
    Fromont-Racine M, Rain JC, Legrain P. Nat Genet 1997;16:277–282.PubMedCrossRefGoogle Scholar
  51. 51.
    Migliaccio AR, Carta C, Migliaccio G. Exp Hematol 1999;27: 1655–1666.PubMedCrossRefGoogle Scholar
  52. 52.
    Bhattacharya D, Rossi DJ, Bryder D,Weissman IL. Submitted.Google Scholar
  53. 53.
    Kuo MH, Allis CD, Methods 1999;19:425–433.PubMedCrossRefGoogle Scholar
  54. 54.
    Forsberg EC, Downs KM, Bresnick EH. Blood 2000;96:334–339.PubMedGoogle Scholar
  55. 55.
    Forsberg EC, Downs KM, Christensen HM, Im H, Nuzzi PA, Bresnick EH, Proc Natl Acad Sci USA 2000;97:14,494–14,499.CrossRefGoogle Scholar
  56. 56.
    Hebbes TR, Thorne AW, Clayton AL, Crane-Robinson C. Nucleic Acids Res 1992;20:1017–1022.PubMedCrossRefGoogle Scholar
  57. 57.
    Agalioti T, Chen G, Thanos D, Cell 2002;111:381–392.PubMedCrossRefGoogle Scholar
  58. 58.
    Morshead KB, Ciccone DN, Taverna SD, Allis CD, Oettinger MA. Proc Natl Acad Sci USA 2003;100:11,577–11,582.CrossRefGoogle Scholar
  59. 59.
    Su RC, Brown KE, Saaber S, Fisher AG, Merkenschlager M, Smale ST. Nat Genet 2004;36:502–506.PubMedCrossRefGoogle Scholar
  60. 60.
    Pokholok DK, Harbison CT, Levine S, et al. Cell 2005;122:517–527.PubMedCrossRefGoogle Scholar
  61. 61.
    Liu CL, Kaplan T, Kim M, et al. PLoS Biol 2005;3:e328.PubMedCrossRefGoogle Scholar
  62. 62.
    Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. Proc Natl Acad Sci USA 2002;99:2924–2929.PubMedCrossRefGoogle Scholar
  63. 63.
    Guenther MG, Jenner RG, Chevalier B, et al. Proc Natl Acad Sci USA 2005;102:8603–8608PubMedCrossRefGoogle Scholar
  64. 64.
    Boyer LA, Lee TI, Cole MF, et al. Cell 2005;122:947–956.PubMedCrossRefGoogle Scholar
  65. 65.
    Weinmann, AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. Genes Dev 2002;16:235–244.PubMedCrossRefGoogle Scholar
  66. 66.
    Attema JL, Papathanasiou P, Forsberg EC, Weissman IL. In preparation.Google Scholar
  67. 67.
    Moore KA, Ema H, Lemischka IR, Blood 1997;89:4337–4347.PubMedGoogle Scholar
  68. 68.
    Nolta JA, Thiemann FT, Arakawa-Hoyt J, et al. Leukemia 2002;16:352–361.PubMedCrossRefGoogle Scholar
  69. 69.
    Hackney JA, Charbord P, Brunk BP, Stoeckert CJ, Lemischka IR, Moore KA. Proc Natl Acad Sci USA 2002;99:13,061–13,066.CrossRefGoogle Scholar
  70. 70.
    Kiel MJ, Yilmaz OH, Iwashita T, Terhorst C, Morrison SJ. Cell 2005;121:1109–1121.PubMedCrossRefGoogle Scholar
  71. 71.
    Venezia TA, Merchant AA, Ramos CA, et al. PLoS Biol 2004;2:e301.PubMedCrossRefGoogle Scholar
  72. 72.
    Terskikh AV, Miyamoto T, Chang C, Diatchenko L, Weissman IL. Blood 2003;102:94–101.PubMedCrossRefGoogle Scholar
  73. 73.
    Terskikh AV, Easterday MC, Li L, et al. Proc Natl Acad Sci USA 2001;98:7934–7939.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc 2006

Authors and Affiliations

  • E. Camilla Forsberg
    • 1
  • Deepta Bhattacharya
    • 1
  • Irving L. Weissman
    • 1
  1. 1.Institute of Cancer and Stem Cell Biology and Medicine, Departments of Pathology and Developmental BiologyStantord University Medical SchoolStanford

Personalised recommendations