Abstract
BackgroundThe pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expression levels of known ES cell markers. Strong correlations between these expression levels and functional assays, particularly at the early stage of cell differentiation, have usually not been observed. An effective molecular diagnostic to properly identify the differentiation state of mouse ES cells, prior to further experimentation, is needed.ResultsA novel molecular pattern recognition procedure has been developed to diagnose the differentiation state of ES cells. This is based on mRNA transcript levels of genes differentially expressed between ES cells and their differentiating progeny. Large publicly available ES cell data sets from various platforms were used to develop and test the diagnostic model. Signature patterns consisting of five gene expression levels achieved high accuracy at determining the cell state (sensitivity and specificity > 97%).ConclusionThe effective ES cell state diagnostic scheme described here can be implemented easily to assist researchers in identifying the differentiation state of their cultures. It also provides a step towards standardization of experiments relying on cells being in the stem cell or differentiating state.
Highlights
The pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expression levels of known ES cell markers
Identifying genes that correlate with maintenance or loss of pluripotency in ES cells 114 genes were found to meet the conditions to be considered differentially expressed between embryonic stem cells and their differentiating progenies after leukemia inhibitory factor (LIF) removal and so form Gstemness
These genes and their products should be necessary for the maintenance of, or need to be repressed in, cells in a proliferative, non-differentiating ES cell state
Summary
The pluripotency and self-renewal capabilities, which define the "stemness" state, of mouse embryonic stem (ES) cells, are usually investigated by functional assays or quantitative measurements of the expression levels of known ES cell markers. Strong correlations between these expression levels and functional assays, at the early stage of cell differentiation, have usually not been observed. Growth and sustenance of these cells in vitro requires the presence of mouse embryonic fibroblast (MEF) cells as feeder layers [2]. Transcription factors such as Nanog [5,6], Oct-4 [7,8],
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