Pluripotent embryonic stem cells and multipotent adult germline stem cells reveal similar transcriptomes including pluripotency-related genes

DNA microarray analysis was performed with mouse multipotent adult germline stem cells (maGSCs) and embryonic stem cells (ESCs) from different genetic backgrounds cultured under standard ESC culture conditions and under differentiation-promoting conditions by the withdrawal of Leukemia Inhibitory Factor (LIF) and treatment with Retinoic Acid (RA). The analyzed undifferentiated cell lines are very similar based on their global gene expression pattern and show 97-99% identity dependent on the analyzed background. Only 621 genes are differentially expressed in cells derived from mouse 129SV-background, and 72 genes show differences in expression in cells generated from transgenic Stra8-EGFP/Rosa26-LacZ-background. Both maGSCs and ESCs express the same genes involved in the regulation of pluripotency, and even show no differences in the expression level of these genes. When comparing maGSCs with previously published signature genes of other pluripotent cell lines we could find that maGSCs share a very similar gene expression pattern with embryonic germ cells (EGCs). Also after differentiation of maGSCs and ESCs the transcriptomes of the cell lines are nearly identical which suggests that both cell types differentiate spontaneously in a very similar way. This is the first study comparing ESCs and a pluripotent cell line derived from an adult organism (maGSCs) on transcriptome level. For the comparison of different stem cell types (6 conditions) we hybridized 3 biological replicates per condition