Recent, surprising, and controversial discoveries have challenged conventional concepts regarding the origins and plasticity of stem cells, and their contributions to tissue regeneration, and highlight just how little is known about mammalian development in comparison to simpler model organisms. In the case of the transparent worm, C. elegans, Sulston and colleagues used a microscope to record the birth and death of every cell during its life, and the compilation of this fate maps represents a milestone achievement of developmental biology. Determining a fate map for mammals or other higher organisms is more complicated, because they are opaque, take a long time to mature, and have a tremendous number of cells. Consequently, fate mapping experiments have relied on tagging a progenitor cell with a dye or genetic marker in order to later identify its descendants. This approach, however, extracts little information, because it only reveals that a population of cells, all inheriting the same label, share a common ancestor but tells nothing of how each cell is related to one another. To avoid that, as well as the technical limitations of current methods for mapping cell fate, we propose a new strategy for retrospectively deriving cell fate maps by using phylogenetics to infer the order in which somatic mutations have arisen in the genomes of individual cells during the development of multicellular organisms. DNA replication introduces mutations, particularly at repetitive sequences, every time a cell divides. In Preliminary Studies we demonstrate that cataloging the frequent mutations affecting the length of polyguanine tracts allows for deducing the history of mouse cells either passaged in culture or sampled from the various tissues of a single individual. Toward an ultimate goal of constructing a high resolution mammalian cell fate map, we plan three Specific Aims: 1. Compare phylogenetic fate maps to conventional fate maps derived from genetically marked mice. 2. Advance the technology of this approach. 3. Successively build a liver cell fate map in order to address controversies regarding the clonal, embryonic, and anatomic origins of hepatic stem cells during development and in disease.A goal of biology is to understand how a single cell divides and gives rise to all the different tissues and organs in the body. Fate maps describe how cells within an individual are related to one another and can be likened to a tree of life, in which the origin of a particular cell can be traced back through its progenitors to the fertilized egg. We propose a new method for exploring developmental biology by constructing fate maps based on distinctive mutations inevitably accumulating in the genome each time a cell divides. We will initially focus our studies on how the liver develops and responds to injury.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Karp, Robert W
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University of Washington
Internal Medicine/Medicine
Schools of Medicine
United States
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Zhou, Wenyu; Tan, Yunbing; Anderson, Donovan J et al. (2013) Use of somatic mutations to quantify random contributions to mouse development. BMC Genomics 14:39
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Zhou, Wenyu; Choi, Michael; Margineantu, Daciana et al. (2012) HIF1? induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition. EMBO J 31:2103-16
Salipante, Stephen J; Kas, Arnold; McMonagle, Eva et al. (2010) Phylogenetic analysis of developmental and postnatal mouse cell lineages. Evol Dev 12:84-94
Salipante, Stephen J; Thompson, James M; Horwitz, Marshall S (2008) Phylogenetic fate mapping: theoretical and experimental studies applied to the development of mouse fibroblasts. Genetics 178:967-77