Reprogramming- and pluripotency-associated membrane proteins in mouse stem cells revealed by label-free quantitative proteomics

Induced pluripotent stem cells (iPSCs), derived from somatic cells and functionally very similar to embryonic stem cells (ESCs), are at the center stage of intense research in regenerative medicine. We carried out the first membrane proteomic profiling of mouse iPSCs, in comparison with ESCs and adult mouse tail tip fibroblasts (TTFs) from which iPSCs were generated. Using a proteomic workflow combining membrane fractionation, SDS-PAGE separation and nanoUPLC-MS(E) technology, we identified 673, 679 and 682 non-redundant proteins from mouse iPSC, ESC and TTF membrane fractions, respectively. Label-free quantitation revealed 155 reprogramming-associated and 128 pluripotency-associated transmembrane proteins. Furthermore, a small group of 23 membrane proteins mainly involved in amino acid/glucose/ion transport, membrane fusion and vesicular trafficking were found potentially regulated between miPSCs and mESCs. Expression changes of selected proteins were verified by qPCR, western blot and/or immunofluorescence analyses in a wider array of cell types. Notably, epithelial cell adhesion molecules, glucose transporters 1 and 3, transferrin receptor and several nuclear membrane-associated components were highly expressed in both iPSCs and ESCs, relative to TTFs. Moreover, knock-down of glucose transporter 3 in ESCs impaired the beating function of ESC-derived cardiomyocytes, suggesting its potential role in mediating stem cell differentiation.

Biological significance: This study constitutes a membrane proteomic resource for murine iPSCs and ESCs, and offers a comparison between pluripotent stem cells and fibroblasts in the proteomic landscape. An integrated proteomics platform combining technologies of membrane fractionation, LC-MS(E) analysis and label-free quantitation was developed to identify membrane proteins with their abundances related to reprogramming of fibroblasts or maintenance of stem cell pluripotency. The high similarity in the membrane proteomic patterns between iPSCs and ESCs strengthens the usefulness of iPSCs in biomedical research and therapeutic application. Moreover, we found a small subset of membrane proteins potentially regulated between miPSCs and mESCs. This membrane proteomic resource of pluripotent stem cells would be expected to inspire further investigations leading to discovery of new regulatory factors or membrane markers for reprogramming and pluripotency.