Stem Cell Reviews

, Volume 3, Issue 1, pp 94–103

Stem Cell Chronicles: Autobiographies Within Genomes

Article

Abstract

Human stem cell studies are difficult because many of the powerful experimental approaches that mark and follow stem cells and their progeny are impractical. Moreover, humans are long-lived, and it would literally take a lifetime to follow stem cell fates prospectively. Considering these hurdles, an ideal method would not require prior experimental manipulations but still allow “observations” of human stem cells from birth to death. The purpose of this review is to outline how histories or fates are likely to be surreptitiously recorded within somatic cell genomes by replication errors (molecular clock hypothesis). It may be possible to reconstruct stem cell lifetimes by measuring the random somatic changes that accumulate within their genomes, or the genomes of their more-easy-to-identify progeny.

Keywords

Stem cell Molecular clock Genealogy 

References

  1. 1.
    Bromham, L., & Penny, D. (2003). The modern molecular clock. Nature Reviews Genetics, 4, 216–224.PubMedCrossRefGoogle Scholar
  2. 2.
    Shibata, D., & Tavaré, S. (2006). Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle, 5, 610–614.PubMedGoogle Scholar
  3. 3.
    Potten, C. S., & Loeffler, M. (1990). Stem cells: attributes, cycles, spirals, pitfalls and uncertainties. Lessons for and from the crypt. Development, 110, 1001–1020.PubMedGoogle Scholar
  4. 4.
    Kay, H. E. (1965). How many cell-generations? Lancet, 15, 418–419.CrossRefGoogle Scholar
  5. 5.
    Wang, T. L., Rago, C., Silliman, N., Ptak, J., Markowitz, S., Willson, J. K., et al. (2002). Prevalence of somatic alterations in the colorectal cancer cell genome. Proceedings of the National Academy of Sciences of the United States of America, 99, 3076–3080.Google Scholar
  6. 6.
    Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes & Development, 16, 6–21.CrossRefGoogle Scholar
  7. 7.
    Ahuja, N., Li, Q., Mohan, A. L., Baylin, S. B., & Issa, J. P. (1998). Aging and DNA methylation in colorectal mucosa and cancer. Cancer Research, 58, 5489–5494.PubMedGoogle Scholar
  8. 8.
    Issa, J. P. (2000). CpG-island methylation in aging and cancer. Current Topics in Microbiology and Immunology, 249, 101–118.PubMedGoogle Scholar
  9. 9.
    Morgan, H. D., Santos, F., Green, K., Dean, W., & Reik W. (2005). Epigenetic reprogramming in mammals. Human Molecular Genetics, 14, R47–R58.PubMedCrossRefGoogle Scholar
  10. 10.
    Jones, P. A., & Laird, P. W. (1999). Cancer epigenetics comes of age. Nature Genetics, 21, 163–167.PubMedCrossRefGoogle Scholar
  11. 11.
    Yatabe, Y., Tavaré, S., & Shibata, D. (2001). Investigating stem cells in human colon by using methylation patterns. Proceedings of the National Academy of Sciences of the United States of America, 98, 10839–10844.Google Scholar
  12. 12.
    Velicescu, M., Weisenberger, D. J., Gonzales, F. A., Tsai, Y. C., Nguyen, C. T., & Jones, P. A. (2002). Cell division is required for de novo methylation of CpG islands in bladder cancer cells. Cancer Research, 62, 2378–2384.PubMedGoogle Scholar
  13. 13.
    Kim, J. Y., Siegmund, K. D., Tavaré, S., & Shibata, D. (2005). Age-related human small intestine methylation: evidence for stem cell niches. BMC Medical, 3, 10.CrossRefGoogle Scholar
  14. 14.
    Kim, J. Y., Tavaré, S., & Shibata, D. (2005). Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proceedings of the National Academy of Sciences of the United States of America, 102, 17739–17744.Google Scholar
  15. 15.
    Kim, J. Y., Tavaré, S., & Shibata, D. (2006). Human hair genealogies and stem cell latency. BMC Biology, 4, 2.PubMedCrossRefGoogle Scholar
  16. 16.
    Fuchs, E., Tumbar, T., & Guasch, G. (2004). Socializing with the neighbors: stem cells and their niche. Cell, 116, 769–778.PubMedCrossRefGoogle Scholar
  17. 17.
    Wright, D. E., Wagers, A. J., Gulati, A. P., Johnson, F. L., & Weissman, I. L. (2001). Physiological migration of hematopoietic stem and progenitor cells. Science, 294, 1933–1936.PubMedCrossRefGoogle Scholar
  18. 18.
    Spradling, A., Drummond-Barbosa, D., & Kai, T. (2001). Stem cells find their niche. Nature, 414, 98–104.PubMedCrossRefGoogle Scholar
  19. 19.
    Nowell, P. C. (1976). The clonal evolution of tumor cell populations. Science, 194, 23–28.PubMedCrossRefGoogle Scholar
  20. 20.
    Marshman, E., Booth, C., & Potten, C. S. (2002). The intestinal epithelial stem cell. Bioessays, 24, 91–98.PubMedCrossRefGoogle Scholar
  21. 21.
    Campbell, F., Williams, G. T., Appleton, M. A., Dixon, M. F., Harris, M., & Williams, E. D. (1996). Post-irradiation somatic mutation and clonal stabilisation time in the human colon. Gut, 39, 569–573.PubMedGoogle Scholar
  22. 22.
    Calabrese, P., Tavaré, S., & Shibata, D. (2004). Pre-tumor progression: clonal evolution of human stem cell populations. American Journal of Pathology, 164, 1337–1346.PubMedGoogle Scholar
  23. 23.
    Kim, K. M., Calabrese, P., Tavaré, S., & Shibata, D. (2004). Enhanced stem cell survival in familial adenomatous polyposis. American Journal of Pathology, 164, 1369–1377.PubMedGoogle Scholar
  24. 24.
    Preston-Martin, S., Pike, M. C., Ross, R. K., Jones, P. A., & Henderson, B. E. (1990). Increased cell division as a cause of human cancer. Cancer Research, 50, 7415–7421.PubMedGoogle Scholar
  25. 25.
    Nicolas, P., Kim, K. M., Shibata, D., & Tavaré, S. (2007). The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Computational Biology, 3, e28.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  1. 1.Department of Pathology, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesUSA
  3. 3.Department of OncologyUniversity of CambridgeCambridgeUK

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