Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry

Chronic high glucose induced INS-1β cell mitochondrial dysfunction: a comparative mitochondrial proteome with SILAC

As glucose-stimulated insulin secretion of pancreatic β cell is triggered and promoted by the metabolic messengers derived from mitochondria, mitochondria take a central stage in the normal function of β cells. β cells in diabetics were chronically exposed to hyperglycemia stimulation, which have been reported to exert deleterious effects on β-cell mitochondria. However, the mechanism of the toxic effects of hyperglycemia on β-cell mitochondria was not clear. In this study, we characterized the biological functional changes of rat INS-1β cells and their mitochondria with chronic exposure to hyperglycemia and created a research model of chronic hyperglycemia-induced dysfunctional β cells with damaged mitochondria. Then, SILAC-based quantitative proteomic approach was used to compare the mitochondrial protein expression from high glucose treated INS-1β cells and control cells. The expression of some mitochondrial proteins was found with significant changes. Functional classification revealed most of these proteins were related with oxidative phosphorylation, mitochondrial protein biosynthesis, substances metabolism, transport, and cell death. These results presented some useful information about the effect of glucotoxicity on the β-cell mitochondria.

Quantitative proteomics reveals ER-α involvement in CD146-induced epithelial-mesenchymal transition in breast cancer cells

The cell adhesion molecule CD146 is a novel inducer of epithelial-mesenchymal transition (EMT), which was associated with triple-negative breast cancer (TNBC). To gain insights into the complex networks that mediate CD146-induced EMT in breast cancers, we conducted a triple Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC), to analyze whole cell protein profiles of MCF-7 cells that had undergone gradual EMT upon CD146 expression from moderate to high levels. In this study, we identified 2293 proteins in total, of which 103 exhibited changes in protein abundance that correlated with CD146 expression levels, revealing extensive morphological and biochemical changes associated with EMT. Ingenuity Pathway Analysis (IPA) showed that estrogen receptor (ER) was the most significantly inhibited transcription regulator during CD146-induced EMT. Functional assays further revealed that ER-α expression was repressed in cells undergoing CD146-induced EMT, whereas re-expression of ER-α abolished their migratory and invasive behavior. Lastly, we found that ER-α mediated its effects on CD146-induced EMT via repression of the key EMT transcriptional factor Slug. Our study revealed the molecular details of the complex signaling networks during CD146-induced EMT, and provided important clues for future exploration of the mechanisms underlying the association between CD146 and TNBC as observed in the clinic.

BIOLOGICAL SIGNIFICANCE

This study used a proteomics screen to reveal molecular changes mediated by CD146-induced epithelial-mesenchymal transition (EMT) in breast cancer cells. Estrogen receptor (ER) was found to be the most significantly inhibited transcription regulator, which mediated its effects on CD146-induced EMT via repression of the transcriptional factor Slug. Elucidation of protein interaction networks and signal networks generated from 103 significantly changed proteins would facilitate future investigation into the mechanisms underlying CD146 induced-EMT in breast cancers.

SNO spectral counting (SNOSC), a label-free proteomic method for quantification of changes in levels of protein S-nitrosation

S-Nitrosation plays an important role in regulation of protein function and signal transduction. Discovering S-nitrosated targets is a prerequisite for further functional study. However, current proteomic methods used to quantify S-nitrosation are limited in their applicability to certain types of samples, or by the need for special reagents and complex procedures to obtain the results. Here we devised a label-free proteomic method for quantification of changes in the level of protein S-nitrosation on the basis of a spectral counting strategy, called S-nitrosothiol (SNO) spectral counting (SNOSC). With this method, samples can be from any source (cells, tissues); there is no need for labelling reagents or procedures, and the results yield quantitative information. Moreover, as it is based on the irreversible biotinylation procedure (IBP) for S-nitrosation protein enrichment, false positive targets caused by the interference of intermolecular disulphide bonds are ruled out. Using SNOSC we studied S-nitrosation in the cell line RAW264.7 induced exogenously with S-nitrosoglutathione (GSNO), or induced endogenously by lipopolysaccharides/interferon-gamma (LPS/IFN-γ). We detected a significant increase in S-nitrosation of 50 proteins after exogenous induction and 17 proteins after endogenous induction. We thus demonstrate that SNOSC is a widely applicable proteomic method for fast screening of SNO proteins.

Improved electrospray ionization efficiency compensates for diminished chromatographic resolution and enables proteomics analysis of tyrosine signaling in embryonic stem cells

Characterization of signaling pathways in embryonic stem cells is a prerequisite for future application of these cells to treat human disease and other disorders. Identification of tyrosine signaling cascades is of particular interest but is complicated by the relatively low levels of tyrosine phosphorylation in embryonic stem cells. These hurdles correlate with the primary limitations of mass spectrometry-based proteomics; namely, poor detection limit and dynamic range. To overcome these obstacles, we fabricated miniaturized LC-electrospray assemblies that provided approximately 15-fold improvement in LC-MS performance. Significantly, our characterization data demonstrate that electrospray ionization efficiency compensates for diminished chromatographic performance at effluent flow rates below Van Deemter minima. Use of these assemblies facilitated quantitative proteomics-based analysis of tyrosine signaling cascades in embryonic stem cells. Our results suggest that a renewed focus on miniaturized LC coupled to ultralow flow electrospray will provide a viable path for proteomic analysis of primary cells and rare post-translational modifications.