Stem cells hold great promise for the fields of regenerative medicine, gene therapy and
disease modeling. Understanding the transcriptional machinery involved in their
maintenance is critical to their successful isolation and experimentation. Careful
statistical analysis of high throughput transcriptome data can provide novel insights into
the gene networks and patterns active in these cells. Public repositories are a source of
gene expression data from various studies involving stem cells. This expression data can
be overlaid on functional interactions maps of the genome to predict functional
association. Further on, comparison of stem cells of different potencies can help identify
key genes involved in the maintenance of pluripotency. The hypotheses derived from
such transcriptional profiling can be tested experimentally to confirm expression and
Transcriptome data from studies involving human and mouse pluripotent stem cells was
collected from repositories such as GEO and Arrayexpress (EBI). Non-negative matrix
factorization was used as a dimensionality reduction tool to detect biological patterns and
clusters in the data. Following the classification of data into biologically meaningful
classes, a ‘metagene’ profile characteristics of pluripotent stem cells was determined in
both species. Reverse engineering was performed for predicting gene networks and
signaling ‘hubs’. An algorithm was also developed to overlay this predicted gene
signature onto functional networks that combine a large amount of genetic and genomic iv
data from various sources, for detecting small subnetworks that are conserved in
expression in the pluripotent stem cells of both species.
Embryonic and induced pluripotent stem cells are considered as in vitro counterparts of
pluripotent cells seen in the early embryo, namely the inner cell mass (ICM) and the
epiblast. Multipotent adult progenitor cells (MAPCs), although isolated from the bone
marrow of an adult rat, bear a striking similarity with another cell types in early
embryonic development-the primitive endoderm or nascent hypoblast cells. Due to the
developmental proximity of the pluripotent cells and the primitive endoderm cells in the early embryo, MAPCs have been used as a model system for probing gene interactions in
pluripotent cells. On the basis of comparative transcriptome analysis, as well as,
experimental studies, a model of gene regulation in MAPCs has been developed. The
study of dynamics of this gene network provides novel insights into the transcriptional
regulation of key pluripotency-associated genes.
Also, using the concepts of cellular reprogramming, these multipotent stem cells
(MAPCs) have been reprogrammed to a pluripotent state. This represents a unique
reprogramming system where an Oct4 expressing extraembryonic cell has been
transformed to an embryonic stem cells (ESC) like state. While this was performed using the traditional reprogramming cocktail consisting of Oct4, Sox2, Klf4 and c-Myc, future
studies are likely to narrow down this number to one or two genes.
University of Minnesota Ph.D. April 2012. Major: Chemical Engineering. Advisor: Dr. Wei-Shou Hu. 1 computer file (PDF); xi, 178 pages, appendix p. 174-178.
Transcriptional profiling of pluripotent and multipotent stem cells to decipher pluripotency and lineage specification.
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