The proteome: anno Domini 2002

TMT-based proteomics analysis reveals the protective effects of Xuefu Zhuyu decoction in a rat model of traumatic brain injury

ETHNOPHARMACOLOGICAL RELEVANCE

Xuefu Zhuyu decoction (XFZYD) is a traditional Chinese herbal prescription. It is effective in treating traumatic brain injury (TBI). However, the underlying molecular mechanisms remain unclear.

AIM OF THE STUDY

This study aimed to reveal the possible mechanisms of XFZYD in treating acute TBI through proteomics clues.

MATERIALS AND METHODS

Controlled Cortical Impact (CCI) rats were given gavage administration of XFZYD (9 g/kg/d) or distilled water (equal volume) for three days. The Modified Neurological Severity Score (mNSS), brain water content, HE staining, Nissl staining and immunohistochemistry were performed to assess the effects of XFZYD for TBI treatment. Additionally, tandem mass tag-based (TMT) quantitative proteomics technology was applied to detect proteins of brain cortex. Bioinformatics analysis including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Protein-protein interaction (PPI) networks were used to analyze differentially expressed proteins (DEPs). Bioinformatics Analysis Tool for Molecular mechanism of TCM (BATMAN-TCM) was conducted to anchor diseases and pathways. Besides, western blotting and immunofluorescence were exerted to verify related proteins.

RESULTS

XFZYD improved neurologic functions, reduced encephaledema and ameliorated cell morphology around the injured area in CCI rats. A total of 6099 proteins were identified with false discovery rate (FDR) < 1%. Overlapping DEPs (105 DEPs) were identified (295 DEPs and 804 DEPs in CCI/Sham or XFZYD/CCI group, respectively). Of these DEPs, 17 were regulated by XFZYD. Bioinformatics analysis showed that the 17 DEPs were predominantly related to platelet activation and PI3K-Akt signaling pathway. Next, PLG and CD34 were verified with molecular biotechnology.

CONCLUSIONS

XFZYD exerts therapeutic effects through multi-pathways regulation in the treatment of TBI. This work may provide proteomics clues for the continuation of research on TBI treatment with XFZYD.

Differential proteomics for studying action mechanisms of traditional Chinese medicines

Differential proteomics, which has been widely used in studying of traditional Chinese medicines (TCMs) during the past 10 years, is a powerful tool to visualize differentially expressed proteins and analyzes their functions. In this paper, the applications of differential proteomics in exploring the action mechanisms of TCMs on various diseases including cancers, cardiovascular diseases, diabetes, liver diseases, kidney disorders and obesity, etc. were reviewed. Furthermore, differential proteomics in studying of TCMs identification, toxicity, processing and compatibility mechanisms were also included. This review will provide information for the further applications of differential proteomics in TCMs studies.

Mass spectrometry-based proteomics in molecular diagnostics: discovery of cancer biomarkers using tissue culture

Accurate diagnosis and proper monitoring of cancer patients remain a key obstacle for successful cancer treatment and prevention. Therein comes the need for biomarker discovery, which is crucial to the current oncological and other clinical practices having the potential to impact the diagnosis and prognosis. In fact, most of the biomarkers have been discovered utilizing the proteomics-based approaches. Although high-throughput mass spectrometry-based proteomic approaches like SILAC, 2D-DIGE, and iTRAQ are filling up the pitfalls of the conventional techniques, still serum proteomics importunately poses hurdle in overcoming a wide range of protein concentrations, and also the availability of patient tissue samples is a limitation for the biomarker discovery. Thus, researchers have looked for alternatives, and profiling of candidate biomarkers through tissue culture of tumor cell lines comes up as a promising option. It is a rich source of tumor cell-derived proteins, thereby, representing a wide array of potential biomarkers. Interestingly, most of the clinical biomarkers in use today (CA 125, CA 15.3, CA 19.9, and PSA) were discovered through tissue culture-based system and tissue extracts. This paper tries to emphasize the tissue culture-based discovery of candidate biomarkers through various mass spectrometry-based proteomic approaches.

Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers

In the strictest sense, the cell secretome (conditioned media) refers to the collection of proteins that contain a signal peptide and are processed via the endoplasmic reticulum and Golgi apparatus through the classical secretion pathway. More generally, the secretome also encompasses proteins shed from the cell surface and intracellular proteins released through non-classical secretion pathway or exosomes. These secreted proteins include numerous enzymes, growth factors, cytokines and hormones or other soluble mediators. They are fundamental in the processes of cell growth, differentiation, invasion and angiogenesis by regulating cell-to-cell and cell-to-extracellular matrix interactions. The main aim of this review is to provide a synopsis of findings from the analysis of the secretome taking diabetes, cancer and neurodegenerative diseases as examples. We will also discuss the preparation of conditioned media and on the main proteomic-based methodological approaches that have been developed for the study of secreted/shed proteins.

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

The ambition of systems biology to understand complex biological systems at the molecular level implies that we need to have a concrete and correct understanding of each molecular entity and its function. However, even for the best-studied organism, Escherichia coli, a large number of proteins have never been identified and characterised from wild-type cells, and/or await unravelling of their biological role. Instead, the ORF models for these proteins have been predicted by suitable algorithms and/or through comparison with known, homologous proteins from other organisms, approaches which may be prone to error. In the present study, we used a combination of 2-DE, MALDI-TOF-MS and PMF to identify 1151 different proteins in E. coli K12 JM109. Comparison of the experimental with the theoretical Mr and pI values (4000 experimental values each) allowed the identification of numerous proteins with incorrect or incomplete ORF annotations in the current E. coli genome databases. Several inconsistencies in genome annotation were verified experimentally, and up to 55 candidates await further investigation. Our findings demonstrate how an up-to-date 2-D gel-based proteomics approach can be used for improving the annotation of prokaryotic genomes. They also highlight the need for harmonization among the different E. coli genome databases.

Novel staining-free proteomic method for simultaneous identification of proteins and determination of their pI values by using low-molecular-mass pI markers

A new proteomic staining-free method for simultaneous identification of proteins and determination of their pI values by using low-molecular-mass pI markers is described. It is based on separation of proteins in gels by IEF in combination with mass spectrometric analysis of both peptides derived by in-gel digestion and low-molecular-mass pI markers extracted form the same piece excised from the gel. In this method, the pI markers are mixed with a protein mixture (a commercial malted barley protein extract) deposited on a gel and separated in a pH gradient. Color pI markers enable supervision of progress of focusing process. Several separated bands of the pI markers (including separated proteins) were excised and the pI markers were eluted from each gel piece by water/ethanol and identified by MALDI-TOF/TOF MS. The remaining carrier ampholytes were then washed out from gel pieces and proteins were in-gel digested with trypsin or chymotrypsin. Obtained peptides were measured by MALDI-TOF/TOF MS and proteins were identified via protein database search. This procedure allows omitting time-consuming protein staining and destaining procedures, which shortens the analysis time. For comparison, other IEF gels were stained with CBB R 250 and proteins in the gel bands were identified. Similarity of the results confirmed that our approach can give information about the correct pI values of particular proteins in complex samples at significantly shorter analysis times. This method can be very useful for identification of proteins and their post-translational modifications in prefractioned samples, where post-translational modifications (e.g., glycation) are frequent.

The Biflow: An instrument for transfer-loop mediated, continuous, preparative-scale isoelectric trapping separations

The Biflow, a new isoelectric trapping instrument was designed to obtain a narrow DeltapI fraction from a complex feed in one step. The Biflow contains two identical separation units, each unit houses: an anode and cathode compartment, an anodic and cathodic membrane, an anodic and cathodic separation compartment, and a separation membrane. The separation units are connected to independent power supplies. The anodic membranes in Units 1 and 2 typically buffer at the same pH value and so do the cathodic membranes. The separation membranes in Units 1 and 2 buffer at different pH values, these determine the pI range (DeltapI) of the product. The cathodic separation compartments in Units 1 and 2 contain the feed and harvest streams. The two anodic separation compartments, connected through an electrically insulating air gap, form the transfer loop through which the transfer stream is recirculated between Units 1 and 2. Ampholytic components in the feed, with pI values lower than the pH of the buffering membrane in Unit 1, pass into the transfer stream and are shuttled into Unit 2. In Unit 2, components in the transfer stream which have pI values higher than the pH of the buffering membrane in Unit 2, pass into the harvest stream. This double transfer of the target component, oppositely directed, guarantees the complete exclusion of products outside the desired DeltapI range from the harvest stream. The utility of the Biflow unit was demonstrated by isolating carnosine from a mixture of UV-absorbing ampholytes and ovalbumin isoforms as well as 4.4 <pI <4.5 and 5.4 <pI <5.5 minor constituents from chicken egg white.

Use of a preparative-scale, recirculating isoelectric trapping device for the isolation and enrichment of acidic proteins in bovine serum

A recirculating, preparative-scale isoelectric trapping device, developed for the binary isoelectric trapping separation of proteins has been used to desalt, isolate and enrich the pI<4 protein fraction from a 150 mL sample of bovine serum. Subsequent re-separation of the 2<pI<4 fraction with pH 3.0, 3.5 and 3.9 buffering membranes resulted in distinct, narrow pI fractions whose components could be readily analyzed by reversed-phase HPLC, even though they were below the detection limit in the original bovine serum sample. The entire isoelectric trapping process (from desalting to collection of the final, narrow pI fractions) took only 7h, indicating the potential of the recirculating, preparative-scale isoelectric trapping device as a front-end component in the proteomic work-flow when sufficiently large samples are available.

Rapid isoelectric trapping in a micropreparative-scale multicompartment electrolyzer

A multicompartmental electrolyzer called membrane-separated wells for isoelectric focusing and trapping (MSWIFT) has been developed and tested for micropreparative-scale isoelectric trapping separations. In the MSWIFT, the length of the heat conduction path from the center of the compartments to the wall is less than 1 mm. The compartments are made from 99.8% nonporous alumina that has a high heat conductivity and a high specific heat capacity, leading to adequate Joule heat dissipation even at power loads as high as 5 W. The length of any compartment parallel to the electric field (the intermembrane distance) can be selected to be multiples of 1.5 mm, leading to compartment volumes that are multiples of about 60 muL. A maximum of 20 (1.5 mm long) separation compartments can be readily assembled in the current version of MSWIFT. The MSWIFT has been used to desalt samples, isolate small ampholytic components (amino acids, peptides, and dyes), prefractionate complex protein mixtures and enrich minor components; these separations were achieved in 20-60 min.

Proteomics: the next revolution in laboratory medicine?

BACKGROUND

The identification of specific genetic alterations and protein profiles associated with disease offers a unique opportunity to develop proteomics-based assays for early diagnosis. By identifying proteins in serum/plasma, a minimally invasive tool is used to assess the presence of disease and to monitor response to treatment and/or disease progression. The potential clinical applications of this tool are broad-based, including the diagnosis not only of cancer but also cardiovascular and neuromuscular diseases, organ transplantation associated conditions, and infertility.

METHODS

A number of competing chromatographic techniques have been proposed for overcoming the complexity and labor-intensive manipulations associated with the traditional technique for proteomic analysis, which is based on two-dimensional gel electrophoretic techniques. However, mass spectrometry has now assumed a central role in most proteomic workflows, and several combinations of ionization sources, analyzers and fragmentations devices have been described and developed.

RESULTS

Thanks to proteomic applications in the diagnosis of cancer, several research groups have identified proteomic patterns associated with ovarian, prostatic, colorectal and other cancers. While the sensitivity and specificity of these patterns are highly satisfactory, there are still some open questions concerning the standardization, reproducibility, and inter-laboratory agreement of these data.

CONCLUSIONS

Proteomics, and, in particular, serum mass spectroscopic proteomic pattern diagnostics, is a rapid expanding field of research. The plasma proteoma has an important position at the intersection between genes and diseases, and clinical laboratories must adapt to a new era of tests based on proteomics and genomics. In the future, mass spectrometry will become an essential tool in the clinical laboratory.

Proteome analysis in the study of lymphoma cells

This review provides an overview on recent studies in the field of proteome analysis of lymphoma cells, and highlights the potentials of such studies for a better knowledge of drug effects at the molecular level. After giving general information on the field of proteome analysis of lymphoma cells, some characteristics of the strategies used during this analysis are pointed out, such as cell extraction strategies and affinity captures. Therefore, the issue of proteome analysis of lymphoma cells content will be covered with respect to those protein extracts that can be prepared in saline solutions, such as cytoplasm proteins, or that are associated with the cell membranes. The question of which kinds of information have been retrieved from lymphoma-cell proteomics is discussed on the basis of several examples-lymphoma cell-mapping studies and constitution of protein databases, and comparative proteome analysis studies of the modifications that result from a drug treatment.

Rheumatology: a close encounter with proteomics

Proteomics is a fast-growing discipline in biomedicine that can be defined as the large-scale characterization of the entire protein complement of a cell, tissue or organism. Because protein levels and function may be critically dependent upon post-transcriptional mechanisms (e.g. post-translational modifications), there has been significant interest in directly examining protein structure and function. It is now clear that proteomics studies may unmask previously unknown functions of proteins or protein interactions. However, proteomics in the field of rheumatology is still in its infancy. This review guides the reader through the consecutive steps of a proteomics study and provides an outline of the applications in the field of rheumatology, which may range from proteome analyses of biological fluids of rheumatic diseases to identify possible new diagnostic tools, towards more pathophysiological studies on target tissues, such as synovial tissue or articular cartilage. Proteomics has great potential in the field of rheumatology and will no doubt have a great impact on our molecular understanding of these complex diseases.

Expanding the proteome two-dimensional gel electrophoresis reference map of human renal cortex by peptide mass fingerprinting

Proteomics methodologies hold great promise in basic renal research and clinical nephrology. The classical approach for proteomic analysis couples two-dimensional gel electrophoresis (2-DE) with protein identification by mass spectrometry, to produce more global information regarding normal protein expression and alterations in different physiological and pathological states. In this report we have expanded the identification of proteins in the renal cortex, improving the previously published map to facilitate the study of different diseases affecting the human kidney. About 250 spots were analyzed by peptide mass fingerprinting, 89 proteins and 74 isoforms for some of them were identified and implemented in the normal human renal cortex 2-DE reference map. This more comprehensive view of the proteome of the human renal cortex could be of invaluable help to the differential proteomic display of urological diseases.

The use of proteomics for the assessment of clinical samples in research

Proteomics, the analysis of expressed proteins, has been an important developing area of research for the past two decades [Anderson, NG, Anderson, NL. Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis 1996;17:443-453]. Advances in technology have led to a rapid increase in applications to a wide range of samples; from initial experiments using cell lines, more complex tissues and biological fluids are now being assessed to establish changes in protein expression. A primary aim of clinical proteomics is the identification of biomarkers for diagnosis and therapeutic intervention of disease, by comparing the proteomic profiles of control and disease, and differing physiological states. This expansion into clinical samples has not been without difficulties owing to the complexity and dynamic range in plasma and human tissues including tissue biopsies. The most widely used techniques for analysis of clinical samples are surface-enhanced laser desorption/ionisation mass spectrometry (SELDI-MS) and 2-dimensional gel electrophoresis (2-DE) coupled to matrix-assisted laser desorption ionisation [Person, MD, Monks, TJ, Lau, SS. An integrated approach to identifying chemically induced posttranslational modifications using comparative MALDI-MS and targeted HPLC-ESI-MS/MS. Chem. Res. Toxicol. 2003;16:598-608]-mass spectroscopy (MALDI-MS). This review aims to summarise the findings of studies that have used proteomic research methods to analyse samples from clinical studies and to assess the impact that proteomic techniques have had in assessing clinical samples.

Proteomics in pancreatic disease

Proteomics represents a novel methodological approach to investigate the expression of all proteins by a cell or organism in its entireness, similar to global strategies for DNA (genomics) and RNA (transcriptomics). This review focuses on the history of protein analysis, which made up the golden age of pancreatic physiology, the current methodology for proteomics (2D gel electrophoresis, mass spectrometry) and the few published experiences with proteomics in the field of pancreatology until now. Finally, potential applications of proteomics for the pancreas, in concert with other techniques, are cited.

Proteomic Analysis of Human Ventricular Cerebrospinal Fluid from Neurologically Normal, Elderly Subjects Using Two-Dimensional LC−MS/MS

A two-dimensional liquid chromatography separation scheme coupled to tandem mass spectrometry (2-D LC-MS/MS) was utilized to profile the proteome of human CSF. Ventricular CSF samples acquired post-mortem from 10 cognitively normal elderly subjects (mean +/- SEM Braak stage = 1.7 +/- 0.2) were analyzed to determine their protein composition. Raw CSF samples were subjected to an immunobased processing method to remove highly abundant albumin and immunoglobulin (Ig), allowing better detection of lower-abundance proteins. Samples were subjected to trypsin proteolysis followed by C18 solid-phase extraction. Tryptic CSF peptides were separated using a 2-D LC column, in which both strong cation exchange (SCX) and C18 phases were packed into a single capillary. MS/MS spectra of CSF peptides were searched against a human sub-database of the NBCI nonredundant database using the SEQUEST algorithm. Search results were further filtered using DTAselect, and individual samples were compared to one another using Contrast. Using this method, we were able to unambiguously identify 249 CSF proteins from 10 subjects. Of these proteins, 38% were unique to individual subjects, whereas only 6% were common to all 10 subjects. These results suggest considerable subject-to-subject variability in the CSF proteome.