Porous silica enhanced proteolysis during Off-Gel separation for efficient protein identification.

An advanced approach is developed in this work for simultaneous on-line separation and digestion of proteins by combining the Off-Gel isoelectric focusing (IEF) and enzymatic nanoreactor enhanced proteolysis. The nanoreactor was prepared by preloading trypsin in amino-functionalized macroporous silica, and then directly added into Off-Gel wells. With the nanoreactor loaded Off-Gel device, effective digestion of proteins happened during IEF electrophoresis to generate directly fractionated tryptic peptides, which not only accelerated the experimental flow but also avoided sample loss, leading to a more comprehensive protein identification from complex biological samples. A successful identification of 3592 proteins was achieved from Hela cell line by using the approach followed with LC-MS/MS analysis, while only 1877 proteins were identified from the same sample when using standard in-solution proteolysis followed with Off-Gel electrophoresis and then LC-MS/MS analysis. Therefore, we have demonstrated that the approach can greatly simplify high-throughput proteomics and significantly improve protein identification.

Mitochondrial aldehyde dehydrogenase 2 plays protective roles in heart failure after myocardial infarction via suppression of the cytosolic JNK/p53 pathway in mice.

BACKGROUND: Increasing evidence suggests a critical role for mitochondrial aldehyde dehydrogenase 2 (ALDH2) in protection against cardiac injuries; however, the downstream cytosolic actions of this enzyme are largely undefined. METHODS AND RESULTS: Proteomic analysis identified a significant downregulation of mitochondrial ALDH2 in the heart of a rat heart failure model after myocardial infarction. The mechanistic insights underlying ALDH2 action were elucidated using murine models overexpressing ALDH2 or its mutant or with the ablation of the ALDH2 gene (ALDH2 knockout) and neonatal cardiomyocytes undergoing altered expression and activity of ALDH2. Left ventricle dilation and dysfunction and cardiomyocyte death after myocardial infarction were exacerbated in ALDH2-knockout or ALDH2 mutant-overexpressing mice but were significantly attenuated in ALDH2-overexpressing mice. Using an anoxia model of cardiomyocytes with deficiency in ALDH2 activities, we observed prominent cardiomyocyte apoptosis and increased accumulation of the reactive aldehyde 4-hydroxy-2-nonenal (4-HNE). We subsequently examined the impacts of mitochondrial ALDH2 and 4-HNE on the relevant cytosolic protective pathways. Our data documented 4-HNE-stimulated p53 upregulation via the phosphorylation of JNK, accompanying increased cardiomyocyte apoptosis that was attenuated by inhibition of p53. Importantly, elevation of 4-HNE also triggered a reduction of the cytosolic HSP70, further corroborating cytosolic action of the 4-HNE instigated by downregulation of mitochondrial ALDH2. CONCLUSIONS: Downregulation of ALDH2 in the mitochondria induced an elevation of 4-HNE, leading to cardiomyocyte apoptosis by subsequent inhibition of HSP70, phosphorylation of JNK, and activation of p53. This chain of molecular events took place in both the mitochondria and the cytosol, contributing to the mechanism underlying heart failure.

Reduced expression of the chromatin remodeling gene ARID1A enhances gastric cancer cell migration and invasion via downregulation of E-cadherin transcription.

The chromatin remodeling gene AT-rich interactive domain-containing protein 1A (ARID1A) encodes the protein BAF250a, a subunit of human SWI/SNF-related complexes. Recent studies have identified ARID1A as a tumor suppressor. Here, we show that ARID1A expression is reduced in gastric cancer (GC) tissues, which are significantly associated with local lymph node metastasis, tumor infiltration and poor patient prognosis. ARID1A silencing enforces the migration and invasion of GC cells, whereas ectopic expression of ARID1A inhibits migration. The adhesive protein E-cadherin is remarkably downregulated in response to ARID1A silencing, but it is upregulated by ARID1A overexpression. E-cadherin overexpression significantly inhibits GC cell migration and invasion, whereas CDH1 (coded E-cadherin) silencing promotes migration. Restored expression of CDH1 in ARID1A-silenced cell lines restores the inhibition of cell migration. Luciferase reporter assays and chromatin immunoprecipitation indicate that the ARID1A-associated SWI/SNF complex binds to the CDH1 promoter and modulates CDH1 transcription. ARID1A knockdown induces evident morphological changes of GC cells with increased expression of mesenchymal markers, indicating an epithelial-mesenchymal transition. ARID1A silencing does not alter the level of ß-catenin but induces a subcellular redistribution of ß-catenin from the plasma membrane to the cytoplasm and nucleus. Immunohistochemical studies demonstrate that reduced expression of E-cadherin is associated with local lymph node metastasis, tumor infiltration and poor clinical prognosis. ARID1A and E-cadherin expression show a strong correlation in 75.4% of the analyzed GC tissues. They are synergistically downregulated in 23.5% of analyzed GC tissues. In conclusion, ARID1A targets E-cadherin during the modulation of GC cell migration and invasion.

Microchip bioreactors based on trypsin-immobilized graphene oxide-poly(urea-formaldehyde) composite coating for efficient peptide mapping.

Trypsin was covalently immobilized to graphene oxide (GO)-poly(urea-formaldehyde) (PUF) composite coated on the channel wall of poly(methyl methacrylate) microchips to fabricate microfluidic bioreactors for highly efficient proteolysis. A mixture solution containing urea-formaldehyde prepolymer and GO nanosheets was allowed to flow through the channels. The modification layer on the channel wall could further polycondense to form GO-PUF composite coating in the presence of ammonium chloride. The primary amino groups of trypsin could react with the carboxyl groups of the GO sheets in the coating with the aid of carboxyl activating agents to realize covalent immobilization. The feasibility and performance of the novel GO-based microchip bioreactors were demonstrated by the digestion of bovine serum albumin, lysozyme, ovalbumin, and myoglobin. The digestion time was significantly reduced to less than 5s. The obtained digests were identified by MALDI-TOF MS with satisfactory sequence coverages that were comparable to those obtained by using 12-h in-solution digestion. The present proteolysis strategy is simple and efficient, offering great promise for high-throughput protein identification.

Detection and quantification of lysine acetyl-alteration using antibody microarray.

BACKGROUND: Lysine acetylation is a reversible and dynamic post-translational modification on proteins, and plays an important role in diverse biological processes. Technological limitations have so far prevented comparative quantification of lysine acetylation in different samples. RESULTS: We developed a method to efficiently study lysine acetylation on individual proteins from complex mixtures, using antibody microarrays to capture individual proteins followed by detection with lysine acetyl antibody. By profiling both protein and acetylation variations in multiple samples using this microarray, we found cancer-associated lysine acetylation alteration on VEGF in the serum of hepatocellular carcinoma patients. CONCLUSION: Microarrays of lysine acetylation are highly effective for detecting acetylation, and should be useful in identifying and validating disease-associated acetylation alterations as biomarkers under both normal and pathological circumstances.

Impact of glutathione-HbA1c on HbA1c measurement in diabetes diagnosis via array isoelectric focusing, liquid chromatography, mass spectrometry and ELISA.

Hemoglobin A1c (HbA1c) has been proven to be a key biomarker for diabetes screening, and glutathiolation of HbA1c (viz., GSS-HbA1c) has been identified. However, the impact of GSS-HbA1c on the measurement of HbA1c for diabetes screening has not been quantitatively assessed yet. To address the issue, the micropreparative capillary isoelectric focusing (cIEF) developed in our previous work was used for the high resolution separation and purification of hemoglobin (Hb) species. The main fractions of HbA0, HbA3 and HbA1c extracted from the developed cIEF were identified by validated Mono S method. The proposed GSS-HbA1c fractions in the cIEF were pooled and identified by electrospray ionization mass spectrometry (ESI-MS). The HbA1c enzyme-linked immunosorbent assay (ELISA) kit was employed for further quantitative analysis of GSS-HbA1c. A total of 34 blood samples with HbA1c levels from 4.2% to 13.4% were assessed via the above comprehensive strategy of IEF-HPLC-MS-ELISA. It was demonstrated that the HbA1c levels detected by cation exchange LC were considerably influenced by the glutathiolation of Hb and the range of detected GSS-HbA1c values was between 0.23% and 0.74%. The results and developed cIEF methods have considerable significances for investigation of diabetes and clinical diagnosis.

Novel moving reaction boundary-induced stacking and separation of human hemoglobins in slab polyacrylamide gel electrophoresis.

We developed a novel polyacrylamide gel electrophoresis (PAGE) method to stack and separate human hemoglobins (Hbs) based on the concept of moving reaction boundary (MRB). This differs from the classic isotachophoresis (ITP)-based stacking PAGE in the aspect of buffer composition, including the electrode buffer (pH 8.62 Tris-Gly), sample buffer (pH 6.78 Tris-Gly), and separation buffer (pH 8.52 Tris-Gly). In the MRB-PAGE system, a transient MRB was formed between alkaline electrode buffer and acidic sample buffer, being designed to move toward the anode. Hbs carried partial positive charges in the sample buffer due to its pH below pI values of Hbs, resulting in electromigrating to the cathode. Hbs would carry negative charges quickly when migrated into the alkaline electrode buffer and be transported to the anode until meeting the sample buffer again. Thus, Hbs were stacked within a MRB until the transient MRB reached the separation buffer and then separated by zone electrophoresis with molecular sieve effect of the gel. The experimental results demonstrated that there were three clear and sharp protein zones of Hbs (HbA1c, HbA0, and HbA2) in MRB-PAGE, in contrast to only one protein zone (HbA0) in ITP-PAGE for large-volume loading (≥15 µl), indicating high stacking efficiency, separation resolution, and good sensitivity of MRB-PAGE. In addition, MRB-PAGE was performed in a conventional slab PAGE device, requiring no special device. Thus, it could be widely used in separation and analysis of diluted protein in a standard laboratory.

Nuclear proteome profile of C57BL/6J mouse liver.

The liver proteome can serve as a reference to better understand both disease mechanisms and possible therapeutics, since the liver is an important organ in the body that performs a large number of tasks. Here we identify the organelle proteome of C57BL/6J mouse liver nuclei as a promising strategy to enrich low abundance proteins, in the sense that analysis of whole liver cells is rather complex for current techniques and may not be suitable for proteins with low abundance. Evaluation of nucleus integrity and purity was performed to demonstrate the effectiveness of the optimized isolation procedure. The extracted nuclear proteins were identified by 2-DE MS analyses, and a total of 748 proteins were identified. Bioinformatic analyses were performed to demonstrate the physicochemical properties, cellular locations and functions of the proteins.

Quantitative research of histone H3 acetylation levels of human hepatocellular carcinoma cells.

BACKGROUND: Core histone H3 is a highly conserved protein in the cell nucleus, it goes through various post-translational modifications easily, and the state of the acetylation has clinical diagnostic significance in prostate cancer, breast cancer, lung cancer and other diseases. RESULTS: In this work, the combinatorial method of chromatographic separation, methylation isotope labeling and LTQ-Orbitrap(®) MS was employed to quantify the acetylation sites of histone H3 separately within normal liver cells L02 and hepatocellular carcinoma (HCC) cells HepG2, HCC metastasis cells 97H and HCC cells HepG2, high HCC metastasis potential cells LM3 and low HCC metastasis potential cells 97L. In comparison with the quantitative results of HepG2 and L02, the amounts of five acetylated and methylated peptides were found decreased. Similarly, when comparing the 97H with HepG2, the amounts of eight acetylated and methylated peptides were found decreased, and when comparing the LM3 with 97L, the amounts of six acetylated and methylated peptides were found decreased. CONCLUSION: These results provide some fundamental reference information for the research into post-translational modifications of histones in human liver cancer and other related diseases.

Costs of jasmonic acid induced defense in aboveground and belowground parts of corn (Zea mays L.).

Costs of jasmonic acid (JA) induced plant defense have gained increasing attention. In this study, JA was applied continuously to the aboveground (AG) or belowground (BG) parts, or AG plus BG parts of corn (Zea mays L.) to investigate whether JA exposure in one part of the plant would affect defense responses in another part, and whether or not JA induced defense would incur allocation costs. The results indicated that continuous JA application to AG parts systemically affected the quantities of defense chemicals in the roots, and vice versa. Quantities of DIMBOA and total amounts of phenolic compounds in leaves or roots generally increased 2 or 4 wk after the JA treatment to different plant parts. In the first 2 wk after application, the increase of defense chemicals in leaves and roots was accompanied by a significant decrease of root length, root surface area, and root biomass. Four weeks after the JA application, however, no such costs for the increase of defense chemicals in leaves and roots were detected. Instead, shoot biomass and root biomass increased. The results suggest that JA as a defense signal can be transferred from AG parts to BG parts of corn, and vice versa. Costs for induced defense elicited by continuous JA application were found in the early 2 wk, while distinct benefits were observed later, i.e., 4 wk after JA treatment.

Immobilization of trypsin on poly(urea-formaldehyde)-coated fiberglass cores in microchip for highly efficient proteolysis.

Trypsin was covalently immobilized on poly(urea-formaldehyde)-coated fiberglass cores based on the condensation reaction between poly(urea-formaldehyde) and trypsin for efficient microfluidic proteolysis in this work. Prior to use, a piece of the trypsin-immobilized fiber was inserted into the main channel of a microchip under a magnifier to form a core-changeable bioreactor. Because trypsin was not permanently immobilized on the channel wall, the novel bioreactor was regenerable. Two standard proteins, hemoglobin (HEM) and lysozyme (LYS), were digested by the unique bioreactor to demonstrate its feasibility and performance. The interaction time between the flowing proteins and the immobilized trypsin was evaluated to be less than 10 s. The peptides in the digests were identified by MALDI-TOF MS to obtain PMF. The results indicated that digestion performance of the microfluidic bioreactor was better than that of 12-h in-solution digestion.

Quantitative proteomic analysis of a paired human liver healthy versus carcinoma cell lines with the same genetic background to identify potential hepatocellular carcinoma markers.

To comprehensively measure global changes in protein expression associated with human hepatocellular carcinoma (HCC), comparative proteomic analysis of two cell lines derived from the healthy and carcinoma tissue of a same donor respectively was conducted using quantitative amino acid-coded mass tagging /stable isotope labeling with amino acids in cell culture-based LC-MS/MS approach. Among a total of 501 proteins precisely quantified, the expressions of 128 proteins were significantly altered including 70 proteins up-regulated and 58 down-regulated in HCC cells. According to their previously characterized functions, the differentially expressed proteins were found associated with nine functional categories including glycolysis, stress response, cell communication, cell cycle, apoptosis/death, etc. For example, multiple enzymes involving glycolysis pathway were found differentially regulated in HCC cells, illustrating the critical participation of glycolysis in the HCC transformation. The accuracy of certain differentially expressed proteins identified through the amino acid-coded mass tagging-based quantification was validated in the paired cell lines, and later their pathological correlations were examined in multiple clinical pairs of normal versus tumor tissues from HCC specimen by using a variety of biological approaches including Western blotting and in situ immunoassays. These consistencies suggested that multiple proteins such as HSP27, annexin V, glyceraldehyde-3-phosphate dehydrogenase, nucleolin and elongation factor Tu could be the biomarkers candidates for diagnosis of HCC.

Comprehensive profiling of metastasis-related proteins in paired hepatocellular carcinoma cells with different metastasis potentials.

Precise and comprehensive identifications of the proteins associated with metastasis are critical for early diagnosis and therapeutic intervention of hepatocellular carcinoma (HCC). Therefore, we investigated the proteomic differences between a pair of HCC cell lines, originating from the same progenitor, with different metastasis potential using amino acid-coded mass tagging-based LC-MS/MS quantitative proteomic approach. Totally the relative abundance of 336 proteins in these cell lines were quantified, in which 121 proteins were upregulated by >30%, and 64 proteins were downregulated by >23% in the cells with high metastasis potential. Further validation studies by Western blotting in a series of HCC cell types with progressively increasing trend of metastasis showed that peroxiredoxin 4, HSP90ß and HSP27 were positively correlated with increasing metastasis while prohibitin was negatively correlated with metastasis potential. These validation results were also consistent with that obtained from comparative analysis of clinic tissues samples. Function annotations of differentially expressed HCC proteome suggested that the emergence and development of high metastasis involved the dysregulation of cell migration, cell cycle and membrane traffics. Together our results revealed a much more comprehensive profile than that from 2-DE-based method and provided more global insights into the mechanisms of HCC metastasis and potential markers for clinical diagnosis.

Comparative proteomics and molecular mechanical analysis in CDA-II induced therapy of LCI-D20 hepatocellular carcinoma model.

PURPOSE: To investigate the differential proteins and related molecular mechanism of CDA-II (cell differentiation agent-II) induced therapy on a human hepatocellular carcinoma model in nude mice with high metastatic potential (LCI-D20). METHODS: After tumors were transplanted 11 days, mice were intraperitoneally injected with CDA-II (1,800 mg/kg) for 20 days continuously. The tumor growth-inhibitory efficiency in CDA-II treated groups was calculated. Proteins extracted from tumor tissue were separated by two-dimensional gel electrophoresis (2DE) and the differential proteins were identified by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS). Western blotting (WB) was performed to verify the expression of certain candidate proteins. Reverse transcription-polymerase chain reaction (RT-PCR) was engaged to study the molecular mechanism of the therapy. RESULTS: CDA-II suppressed the growth and metastasis of tumor. The tumor growth-inhibitory efficiency was 41.8%. In total, 27 differentially expressed proteins were identified, including HSP27, UGDH, CK8, Hsp60, ENOA and AnxA5, with functions involved in oncogene expression and/or cell differentiation. In addition, apparent alternations of HSP60 and beta-actin expression levels and their different posttranslational modifications (PTMs) were investigated. RT-PCR analysis confirmed that the cancer related genes c-myc, N-ras and MMP-9 were significantly down-regulated. CONCLUSION: Our results demonstrate that CDA-II presence can change the proteome profiling and favors of the tumor suppression in LCI-D20 cell differentiation. Our results also suggest that the dynamic PTM of HSP60 expression levels could be used to predict HCC and might be a promising and useful biomarker to prognosticate CDA-II therapeutic efficacy.

Comprehensive proteome analysis of mouse liver by ampholyte-free liquid-phase isoelectric focusing.

In this study, ampholyte-free liquid-phase IEF (LIEF) was combined with narrow pH range 2-DE and SDS-PAGE RP-HPLC for comprehensive analysis of mouse liver proteome. Because LIEF prefractionation was able to reduce the complexity of the sample and enhance the loading capacity of IEF strips, the number of visible protein spots on subsequent 2-DE gels was significantly increased. A total of 6271 protein spots were detected after integrating five narrow pH range 2-DE gels following LIEF prefractionation into a single virtual 2-DE gel. Furthermore, the pH 3-5 LIEF fraction and the unfractionated sample were separated by pH 3-6 2-DE and identified by MALDI-TOF/TOF MS, respectively. In parallel, the pH 3-5 LIEF fraction was also analyzed by SDS-PAGE RP-HPLC MS/MS. LIEF-2-DE and LIEF-HPLC could obviously improve the separation efficiency and the confidence of protein identification, which identified a higher number of low-abundance proteins and proteins with extreme physicochemical characteristics or post-translational modifications compared to conventional 2-DE method. Furthermore, there were 207 proteins newly identified in mouse liver in comparison with previously reported large-scale datasets. It was observed that the combination of LIEF-2-DE and LIEF-HPLC was effective in promoting MS-based liver proteome profiling and could be applied on similar complex tissue samples.

Fabrication and performance of poly(methyl methacrylate) microfluidic chips with fiber cores.

In this work, a piece of glass fiber was inserted into the channel of a poly(methyl methacrylate) (PMMA) electrophoresis microchip to enhance the electroosmotic flow (EOF) and the separation efficiency. The EOF value of the glass fiber-containing microchannel at pH 8.2 was determined to be 4.17 x 10(-4)cm2 V(-1)s(-1). The performance of the new microchip was demonstrated by its ability to separate and detect three purines coupled with end-column amperometric detection. In addition, a piece of trypsin-immobilized glass fiber was inserted into the channel of a PMMA microchip to fabricate a core-changeable microfluidic bioreactor that can be regenerated by changing the fiber. The in-channel fiber bioreactor has been coupled with matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the digestion and peptide mapping of bovine serum albumin and myoglobin.

Fiber-packed channel bioreactor for microfluidic protein digestion.

The fabrication and performance of a fiber-packed channel bioreactor in microchip along with its application in protein analysis were reported. The feasibility and performance of the unique microfluidic bioreactor were demonstrated by the tryptic digestion of myoglobin (MYO) and BSA. The on-chip digestion was carried out at a flow rate of 2.0 microL/min and the digestion time was significantly reduced to less than 5 s. The digests were identified by MALDI-TOF MS with sequence coverages of 66% (MYO) and 40% (BSA) that were comparable to those obtained by the conventional in-solution tryptic digestion. The present fiber-based microchip bioreactor provides a promising platform for the high-throughput protein identification.

Expressed proteome analysis of human hepatocellular carcinoma in nude mice (LCI-D20) with high metastasis potential.

We report for the first time an expressed proteome for human hepatocellular carcinoma (HCC) in nude mice model. Most cases of human liver cancer are HCC with highly metastatic ability. Therefore, the early prediction or diagnosis and effective treatment are the key points of research. We have previously successfully established a human HCC nude mice model (LCI-D20) with high metastasis potential. To understand better the tumor biology of HCC it is worth to explore the relativity of all expressed protein profiles in the LCI-D20 HCC nude mice model. With advanced proteomics technologies, we have carried out a proteomic analysis with following stages: protein sample preparation of cancer tissue, including total cellular extraction and sequential fractionation, 2-DE and 2-D LC separation, ESI/MALDI-MS/MS identification, as well as data-dependent bioinformatics. The identified proteins were classified bioinformatically respective to their function, biological process and intracellular localization. Some important proteins found in HCC, e.g. metabolism enzymes, proteins regulating cell motility, signaling proteins, and heat shock proteins, are discussed in terms of their metastasis.

Enhancing TOF/TOF-based de novo sequencing capability for high throughput protein identification with amino acid-coded mass tagging.

Because of the intrinsic physical properties of single- or double-charged ions, MALDI-based CID on these peptide precursor ions tends to be incomplete, resulting in a large number of MS/MS spectra unassigned or ambiguously identified. Consequently, the TOF/TOF high throughput capability may not be fully explored and utilized. Here, we describe a novel method for de novo sequence assignment of those MALDI TOF/TOF MS/MS spectra with incomplete or weak fragment ion series. In this approach, the deuterium-labeled lysine and leucine precursors were used in parallel to mass-tag the proteome of a metastatic human hepatocellular carcinoma (HCC) cell line during in vivo cell culturing. These stable isotope precursor markers not only position at terminal but at internal MS/MS fragment ions with the characteristic isotope pattern induced by multiple mass tagging in parallel. This enhanced signal specificity evidently resolved ambiguities in those sparse poor-quality TOF/TOF spectra by providing critical sequential links among MS/MS fragment ions. Our data-dependent approach was able to reduce many false-positives in current genome sequence-based peptide sequencing. With developing new algorithms accordingly, our approach is amenable for automation that will lead to more comprehensive and reliable identification for proteomes.