Proteomic comparison of human embryonic stem cells with their differentiated fibroblasts: Identification of 206 genes targeted by hES cell-specific microRNAs

Abstract Human embryonic stem (hES)-T3 (T3ES) cells were spontaneously differentiated into autogeneic fibroblast-like T3DF cells, as feeder cells with the capacity to support the growth of undifferentiated hES cells. The proteomes of undifferentiated T3ES cells and their differentiated T3DF fibroblasts were quantitatively compared. Several heterogeneous nuclear ribonucleoproteins and glycolytic enzymes, including l-lactate dehydrogenase A (M), were found to be abundantly and differentially expressed in T3ES cells and T3DF fibroblasts, respectively. Both miRNA and mRNA profiles from the undifferentiated T3ES cells and their differentiated T3DF fibroblasts had been previously determined. In this investigation, 206 genes were found to be targets of the four hES cell-specific miRNAs of miR-302d, miR-372, miR-200c, and/or miR-367 by using two-fold differential expression and inverse expression levels (highly negative correlations) of miRNAs to their target mRNAs. That YWHAZ (14-3-3 zeta) is a target of miR-302d and miR-372 was further confirmed by proteomic comparison between T3ES cells and their differentiated T3DF fibroblasts. According to GeneOntology analyses, almost 50% of these 206 target proteins are nuclear and are involved in gene transcription. Identifying the target mRNAs of hES cell-specific miRNAs will provide a better understanding of the complex regulatory networks in hES cells. Furthermore, these miRNA-targeted proteins play important roles in differentiation of hES cells and during embryo development.