Cell fate maps describe how the sequence of cell division, migration, and apoptosis transform a zygote into an adult and are fundamental to understanding stem cell biology. Yet, it is only in the transparent worm C. elegans where tedious microscopic observation of each cell division has allowed for construction of a complete cell fate map. More complex?and opaque?animals prove less yielding. DNA replication, however, inevitably generates somatic mutations. Consequently, multicellular organisms comprise mosaics where most cells acquire unique genomes that are potentially capable of delineating their ancestry. We propose to construct mammalian cell fate maps using a phylogenetic approach to passively retrace embryonic relationships by deducing the order in which mutations have arisen during development. We have found that polyguanine repeat DNA sequences are particularly useful genetic markers, because they frequently change length during mitosis. To demonstrate feasibility, we have used phylogenetics to reconstruct the lineage of cultured mouse NIH3T3 fibroblasts based on mutations affecting the length of polyguanine markers. We have then employed whole genome amplification to genotype polyguanine markers in single cells taken from a mouse and used phylogenetics to infer the developmental relationships of the sampled tissues. Our preliminary results demonstrate the potential of this approach for retrospectively producing a complete mammalian cell fate that, in principle, could describe the developmental lineage of any cell and resolve outstanding questions relevant to stem cell biology.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
5DP1OD003278-05
Application #
8128696
Study Section
Special Emphasis Panel (ZGM1-NDPA-G (P2))
Program Officer
Wehrle, Janna P
Project Start
2007-09-30
Project End
2014-07-31
Budget Start
2011-08-01
Budget End
2014-07-31
Support Year
5
Fiscal Year
2011
Total Cost
$772,200
Indirect Cost
Name
University of Washington
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
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Carlson, Cheryl A; Kas, Arnold; Kirkwood, Robert et al. (2012) Decoding cell lineage from acquired mutations using arbitrary deep sequencing. Nat Methods 9:78-80
Salk, Jesse J; Horwitz, Marshall S (2010) Passenger mutations as a marker of clonal cell lineages in emerging neoplasia. Semin Cancer Biol 20:294-303
Salipante, Stephen J; Kas, Arnold; McMonagle, Eva et al. (2010) Phylogenetic analysis of developmental and postnatal mouse cell lineages. Evol Dev 12:84-94
Salk, Jesse J; Salipante, Stephen J; Risques, Rosa Ana et al. (2009) Clonal expansions in ulcerative colitis identify patients with neoplasia. Proc Natl Acad Sci U S A 106:20871-6