Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs.

Owing to the clinical potential of human induced pluripotent stem cells (hiPSCs) in regenerative medicine, a thorough examination of the similarities and differences between hiPSCs and human embryonic stem cells (hESCs) has become indispensable. Moreover, as the important roles of membrane proteins in biological signalling, functional analyses of membrane proteome are therefore promising. In this study, a pathway analysis by the bioinformatics tool GSEA was first performed to identify significant pathways associated with the three comparative membrane proteomics experiments: hiPSCs versus precursor human foreskin fibroblasts (HFF), hESCs versus precursor HFF, and hiPSCs versus hESCs. A following three-way pathway comparison was conducted to identify the differentially regulated pathways that may contribute to the differences between hiPSCs and hESCs. Our results revealed that pathways related to oxidative phosphorylation and focal adhesion may undergo incomplete regulations during the reprogramming process. This hypothesis was supported by another public proteomics dataset to a certain degree. The identified pathways and their core enriched proteins could serve as the starting point to explore the possible ways to make hiPSCs closer to hESCs.

SheddomeDB: the ectodomain shedding database for membrane-bound shed markers.

BACKGROUND: A number of membrane-anchored proteins are known to be released from cell surface via ectodomain shedding. The cleavage and release of membrane proteins has been shown to modulate various cellular processes and disease pathologies. Numerous studies revealed that cell membrane molecules of diverse functional groups are subjected to proteolytic cleavage, and the released soluble form of proteins may modulate various signaling processes. Therefore, in addition to the secreted protein markers that undergo secretion through the secretory pathway, the shed membrane proteins may comprise an additional resource of noninvasive and accessible biomarkers. In this context, identifying the membrane-bound proteins that will be shed has become important in the discovery of clinically noninvasive biomarkers. Nevertheless, a data repository for biological and clinical researchers to review the shedding information, which is experimentally validated, for membrane-bound protein shed markers is still lacking. RESULTS: In this study, the database SheddomeDB was developed to integrate publicly available data of the shed membrane proteins. A comprehensive literature survey was performed to collect the membrane proteins that were verified to be cleaved or released in the supernatant by immunological-based validation experiments. From 436 studies on shedding, 401 validated shed membrane proteins were included, among which 199 shed membrane proteins have not been annotated or validated yet by existing cleavage databases. SheddomeDB attempted to provide a comprehensive shedding report, including the regulation of shedding machinery and the related function or diseases involved in the shedding events. In addition, our published tool ShedP was embedded into SheddomeDB to support researchers for predicting the shedding event on unknown or unrecorded membrane proteins. CONCLUSIONS: To the best of our knowledge, SheddomeDB is the first database for the identification of experimentally validated shed membrane proteins and currently may provide the most number of membrane proteins for reviewing the shedding information. The database included membrane-bound shed markers associated with numerous cellular processes and diseases, and some of these markers are potential novel markers because they are not annotated or validated yet in other databases. SheddomeDB may provide a useful resource for discovering membrane-bound shed markers. The interactive web of SheddomeDB is publicly available at http://bal.ym.edu.tw/SheddomeDB/ .

SecretePipe: a screening pipeline for secreted proteins with competence to identify potential membrane-bound shed markers.

The identification of secreted protein markers has been receiving great attention as part of the trend toward noninvasive biomarker discovery. In addition, certain cell membrane proteins are known to be released into the extracellular milieu via ectodomain shedding. As membrane proteins play an essential role in signaling pathways and because most of the cancer biomarkers approved by the FDA today are membrane shed proteins, a tool that can correctly predict these class shed proteins is valuable. In this study, an in-house predictor, ShedP, was developed to predict the ectodomain shedding events of membrane proteins. ShedP is the first computational method to our knowledge to allow shed membrane protein prediction. By integrating ShedP with other state-of-the-art predictors, a screening pipeline, SecretePipe, has been created that is able to identify secreted nonmembrane proteins on the basis of signal peptides and to identify released membrane proteins on the basis of ectodomain shedding. The predictive results using secretome data sets revealed that SecretePipe outperformed other state-of-the-art secreted protein predictors. When evaluated against released membrane proteins, SecretePipe performed better than other predictors in identifying membrane-bound released proteins due to the presence of ShedP. SecretePipe showed a great potential in assisting the identification of membrane-bound shed markers in biomarker discovery.

Lung defects in neonatal and adult stromal-derived factor-1 conditional knockout mice.

Stromal-derived factor (SDF)-1/CXCL12 is a cytokine that is involved in organogenesis, hematopoiesis, chemoattraction, and wound healing. An SDF-1 knockout mouse (SDF-1(-/-)) has provided important insights into the role of SDF-1 in fetal development. Because the SDF-1 knockout is lethal in the perinatal period, we have created a conditional SDF-1 knockout mouse. In the present study, we induced conditionally knocked out SDF-1 in neonatal mice and found that lung development was compromised; neonatal lungs showed increased alveolar airspace and abnormal ultrastructure. Conditional knockout of SDF-1 in adult mice resulted in an emphysemic morphology, with increased alveolar airspace and thickened alveolar septa. Fluorescence angiography showed pulmonary vessel hyperdilation. To determine whether the hyperdilation involved nitric oxide, we inhibited endothelial nitric oxide synthase (eNOS) with N (G)-nitro-L- arginine methyl ester. This resulted in the inhibition of pulmonary vessel hyperdilation. Western blot results showed increased phosphorylation of eNOS in our induced SDF-1 knockout mice, indicating that eNOS is normally repressed in the presence of SDF-1, and that activation of eNOS contributes to pulmonary pathology. Thus, a conditional knockout mouse has been successfully created for SDF-1; initial characterization indicates that SDF-1 is intimately involved in lung development and physiology.