Pluripotency is a rare property of stem cells whereby they have the potential to make any differentiated cell types in the organism. Fortunately, planarian adult stem cells have this property. We hypothesized that because mammalian embryonic stem cells and planarian adult stem cells have the biology of pluripotency, they may also share common genetic programs. We took the following comparative genomic approach to show that this is indeed the case.
We purified planarian stem cells by FACS and deep sequenced the cells. We also deep sequenced whole, irradiated planarians that no longer have any stem cells. After comparing these tissue compartments, we found that 2,177 transcripts are specifically expressed in planarian stem cells.
After mapping planarian homologs to mammalian genes, we used mouse Gene Ontology (GO) terms to determine whether there was an enrichment of a particular cellular process in any given tissue compartment. Importantly, we found that planarian stem cells are enriched for the p53 and Retinoblastoma pathways over differentiated tissues, which supported our previous work. This gave us confidence that mouse GO terms can be used for planarian gene homologs, at least to some extent.
We compared genes that were enriched in planarian stem cells to both mouse and human embryonic stem cells. For this analysis, we only used genes that had a 1:1 match between planarians and mammals. To our surprise, we found 123 genes that are highly expressed in the pluripotent stem cells of each species.