Identification of Neuron-Specific Enolase and Nonneuronal Enolase in Human and Rat Brain on Two-Dimensional Polyacrylamide Gels

The location of the enzymes neuron-specific enolase and nonneuronal enolase on two-dimensional gels generated from tissue samples obtained from fresh human and rat cortex has been identified. This identification is based upon the following criteria: comigration on polyacrylamide gels with the appropriate purified protein and staining on nitrocellulose protein blots of human and rat cortex using antibodies specific for each protein. The results show that our preparation of neuron-specific enolase from rat and human brain is highly pure, as only one spot is obtained on two-dimensional gels. Further, the antiserum to neuron-specific enolase is highly specific, as it reacts only with neuron-specific enolase on nitrocellulose blots derived from two-dimensional gels of cortical tissue. The location of these proteins is of interest because it positively identifies two major brain proteins on two-dimensional polyacrylamide gels of fresh cortical tissue. This information will be useful in a variety of future studies aimed at both identifying specific proteins on two-dimensional gels and observing the effects of experimental manipulations on brain and other neuronal proteins.     

Local database and the search program for proteomic analysis of sperm proteins in the ascidian Ciona intestinalis

Separation of proteins by two-dimensional electrophoresis and following mass spectrometry (MS) is now a conventional technique for proteomic analysis. For proteomic analysis of a certain tissue with a limited information of primary structures of proteins, we have developed an analytical system for peptide mass fingerprinting in gene products in the testis of the ascidian Ciona intestinalis. Ciona sperm proteins were separated by two-dimensional gel electrophoresis and the tryptic fragments were subjected to MALDI-TOF/MS. The mass pattern was searched against on-line databases but resulted in less identification of these proteins. We have constructed a MS database from Ciona testis ESTs and the genome draft sequence, along with a newly devised, perl-based search program PerMS for peptide mass fingerprinting. This system could identify more than 80% of Ciona sperm proteins, suggesting that it could be widely applied for proteomic analysis for a limited tissue with less genomic information.     

Phenytoin-induced stress protein synthesis in mouse embryonic tissue

Several proteins have been shown to be synthesized in response to various environmental stimuli, including treatment with teratogens. The role of these proteins in the teratogenic process is unknown. Pregnant A/J mice were treated with either a teratogenic or a non-teratogenic dose of the anticonvulsant drug, phenytoin (PHT). Protein synthesis in embryonic craniofacial (target) tissue or forelimb buds (non-target) was determined by incorporation of radiolabeled leucine and analysis by two-dimensional polyacrylamide gel electrophoresis. Synthesis of three proteins in target tissue and one protein in non-target tissue was stimulated by drug treatment. These results suggest that synthesis of specific stress proteins may serve as biomarkers of drug-target tissue interaction.     

The determination of similarities in amino acid composition among proteins separated by two-dimensional gel electrophoresis

A simple and rapid procedure has been developed to determine similarities in amino acid composition among cellular proteins separated by two-dimensional gel electrophoresis. Cells in tissue culture are simultaneously labeled with two different amino acids each tagged with a different radioisotope. The proteins are then separated on two-dimensional gels and their location on the gels determined by Coomassie-blue staining or autoradiography. Elution of the protein from the appropriate region of the gel followed by liquid scintillation counting yields an isotope ratio which reflects the ratio of the two amino acids in the protein. Examples of the use of this technique in analyzing mutant proteins, proteins altered by carbamylation, and cell proteins with similar amino acid composition (e.g., actin and tubulin) are given.     

Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry

Laser capture microdissection (LCM) is a powerful tool that enables the isolation of specific cell types from tissue sections, overcoming the problem of tissue heterogeneity and contamination. This study combined the LCM with isotope-coded affinity tag (ICAT) technology and two-dimensional liquid chromatography to investigate the qualitative and quantitative proteomes of hepatocellular carcinoma (HCC). The effects of three different histochemical stains on tissue sections have been compared, and toluidine blue stain was proved as the most suitable stain for LCM followed by proteomic analysis. The solubilized proteins from microdissected HCC and non-HCC hepatocytes were qualitatively and quantitatively analyzed with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) alone or coupled with cleavable ICAT labeling technology. A total of 644 proteins were qualitative identified, and 261 proteins were unambiguously quantitated. These results show that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.     

Comparison of synexin isotypes in secretory and non-secretory tissues

Three synexin isotypes were identified in bovine liver or adrenal medullary tissues by immune blotting of one- or two-dimensional SDS gels and by two-dimensional tryptic peptide mapping of gel bands or spots. These isotypes were: alpha-synexin, mass 47 kDa, pI 6.9; beta-synexin, mass 47 kDa, pI 6.5; and mu-synexin, mass 51 kDa, pI 6.1. A non-secretory tissue, bovine skeletal muscle, was found to contain only mu-synexin. The absence of alpha- and beta-synexins in a non-secretory tissue suggests these proteins may perform specific roles in the process of exocytosis.     

Topography of the total protein population from cultured cells upon fractionation by chemical extractions

Chemical extractions are proposed as a major tool for a fractionation of cellular proteins. As a model system, proteins from cultured hamster lens cells have been divided by independent extractions into seven subcellular fractions, corresponding to water-soluble proteins and the proteins from membranes, microfilaments (and other deoxycholate-soluble proteins), intermediate filaments, microtubules, polysomes and nuclei respectively. The latter two fractions have been subfractionated yielding ribosomal proteins, the elongation and initiation factors of the protein-synthesis machinery, chromatin proteins and non-chromatin proteins. The protein compositions of the fractions have been analyzed by one-dimensional and two-dimensional gel electrophoresis. This resulted in an almost complete topography of the proteins detected on two-dimensional gels of total-cell lysates. Comparison of two-dimensional patterns of proteins from the total-cell lysate and proteins from hamster erythrocytes or from liver, muscle or brain tissue showed that the different cell types have only few proteins in common. Two proteins are common to all of these cell types, namely actin and a 68-kDa protein. The latter protein was, like actin, vimentin and the tubulin subunits, also present in most cell fractions. Evidence is presented that this protein is identical to a 68-kDa heat-shock protein.     

Studies on middle silkgland proteins of cocoon colour sex-limited silkworm (<Emphasis Type="Italic">Bombyx mori</Emphasis> L.) using two-dimensional polyacrylamide gel electrophoresis

Qualitative and quantitative differences in proteins expressed in the middle silkglands of male and female silkworm larvae that differ in silk colour were investigated by high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by computer assisted image analysis. About 1000 protein spots were resolved in both the sexes and most proteins were shown to be distributed in the area from 15 kDa to 70 kDa and pH 4–8. It was found that some proteins displayed higher expression in yellow cocoon, while two proteins were only expressed in female silkworm silkgland tissue through the comparison and analysis by two-D software. These proteins especially existed in female silkworm middle silkgland tissue of yellow cocoon. Furthermore, these proteins might be involved in the expression of cocoon colour phenotype     

Proteomic analysis of livers of patients with primary hepatolithiasis

Primary hepatolithiasis or intrahepatic calculi (IHC), which is characterized by the formation of gallstones in the intrahepatic bile duct, is an intractable liver disease and suspected to be one of the causes of cholangiocellular carcinoma. To obtain an insight into the disease, we performed proteomic analysis of liver tissue specimens of paired affected and unaffected hepatic segments from patients with primary hepatolithiasis by two-dimensional gel electrophoresis followed by identification of proteins. For the specimens from the unaffected segments, 125 spots out of 613 spots were identified, defining 83 unique protein names. For the specimens from the affected segments, 102 spots out of 671 spots were identified, defining 74 unique protein names. To further precisely compare, we used two-dimensional fluorescence difference gel electrophoresis. Consequently we identified 12 up-regulated proteins and 21 down-regulated proteins. The up-regulated proteins contained the proteins related to liver fibrosis and to cellular oxidoreduction. The down-regulated proteins contained RAF kinase inhibitor protein, chaperonin and proteins related to principal liver function.     

Characterization of deciduoma marker proteins in hamster uterus: detection in decidual cell cultures

The objective of this study was first, to identify the proteins associated with decidualization of the hamster uterus by comparing the protein maps of decidualized and nondecidualized endometrium in vivo, and second, to determine whether decidual cell cultures produced these characteristic proteins. Decidualization was induced in one uterine horn, and the contralateral horn was not stimulated (control tissue). Animals were ovariectomized and a subcutaneous progesterone implant was used to maintain decidualization. Uterine proteins from nuclear and cytosol fractions were analyzed by two-dimensional electrophoresis using a highly sensitive protein staining technique. Analysis of nuclear extract and cytosol from decidualized and nondecidualized endometrium from Days 6, 7, and 8 of pseudopregnancy demonstrated the presence of 11 nuclear and five cytosolic deciduoma-associated proteins. Serum and erythrocyte proteins were identified by two-dimensional electrophoresis, and none of the 16 deciduoma-associated proteins was a serum or erythrocyte contaminant. Forty-eight-hour cultures of decidual cells harvested from Day 5 of pseudopregnancy produced all 16 of the deciduoma-associated proteins found in whole tissue in situ. Culture conditions minimized serum and erthrocyte contamination, enhancing the detection of deciduomal cell proteins. Four nuclear and two cytosolic proteins were considered deciduoma specific, i.e., they were not associated with cellular proliferation, as evidenced by their absence from cultures of rapidly dividing fetal hamster fibroblasts. Thus, these studies show that the detection of deciduomal proteins may be a useful criterion for the assessment of decidualization in vitro and in vivo.     

Comparative proteome analysis of breast cancer and normal breast

Breast cancer is a leading cause of death for women. The underlying molecular mechanism is still not well understood. In this study, two-dimensional gel electrophoresis combined with mass spectrometry was used to analyze changes in the proteome of infiltrating ductal carcinoma compared to normal breast tissue. Ten sets of two-dimensional gels per experimental condition were analyzed and more than 500 spots each were detected. This revealed 39 spots for which expression in breast cancer cells were reproducibly altered more than twofold compared to normal controls (p<0.01). These spots represented 25 different proteins after identification using the database search after mass spectrometry, comprising cell defense proteins, enzymes involved in glycolytic energy metabolism and homeostasis, protein folding and structural proteins, proteins involved in cytoskeleton and cell motility, and proteins involved in other functions. In addition, 28 nondifferentially expressed proteins with different functions were also mapped and identified, which might help to establish a two-dimensional gel electrophoresis reference map of human breast cancer. Our study shows that proteomics offers a powerful methodology to detect the proteins that show different expression patterns in breast cancer tissue and may provide an accurate molecular classification. The differentially expressed proteins may be used as potential candidate markers for diagnostic purposes or for determination of tumor sensitivity to therapy. The functional implications of the identified proteins are discussed.     

Two-Dimensional Characterization of Paired Helical Filament-Tau from Alzheimer's Disease: Demonstration of an Additional 74-kDa Component and Age-Related Biochemical Modifications

Abstract: PHF-tau proteins are the major components of the paired helical filament (PHF) from Alzheimer's disease (AD) neurofibrillary lesions. They differ both qualitatively and quantitatively in their degree of phosphorylation when compared with native tau proteins. However, little is known about the extent and heterogeneity of phosphorylated sites or the isoform composition and the isoelectric variants of PHF-tau. Therefore, we have characterized PHF-tau proteins from cortical brain tissue homogenates of 13 AD patients using two-dimensional gel electrophoresis. Whatever the topographical origin of brain tissue homogenates, PHF-tau proteins shared the same two-dimensional gel electrophoresis profile made of a tau triplet of 55, 64, and 69 kDa. A 74-kDa hyperphosphorylated tau component was detected particularly in the youngest and most severely affected AD patients. This additional component of hyperphosphorylated tau was shown to correspond to the longest brain tau isoform. Furthermore, the isoelectric points of PHF-tau from older AD patients were significantly more basic, indicating a lower degree of phosphorylation. These results show that the severity of neurofibrillary degeneration of AD is modulated by age.     

High performance two-dimensional gel electrophoresis using a wetting agent Tergitol NP7

Two-dimensional electrophoresis is an efficient method for the analysis of a broad range of complex protein samples. Current two-dimensional gel techniques are not suited for analysis of the small amount of proteins from tissue samples in the presence of high concentration of salts. Here we describe an improved two-dimensional gel electrophoresis procedure based on the use of a nonionic wetting agent, Tergitol NP7, in rehydration solution combined with the application of a linear potential sweep during isoelectrofocusing. This experimental approach yields a dramatic increase in the resolution and focusing of proteins visualized on two-dimensional gels. This technique is less time-consuming and laborious than the current techniques and can be used for a variety of two-dimensional electrophoresis applications, including proteome analysis.     

Skeletal muscle acetylcholine receptor. Purification, characterization, and turnover in muscle cell cultures

Acetylcholine receptor has been purified from embryonic skeletal muscle cells grown and allowed to differentiate in tissue culture. The polypeptide composition of purified receptor has been determined by two-dimensional electrophoresis. The purest preparations are composed of a single Mr = 41,000 class of polypeptide which exhibits some charge heterogeneity. By high resolution two-dimensional electrophoresis a spot corresponding to acetylcholine receptor was localized among total proteins of muscle membrane extracts. Synthesis of this component is shown to be developmentally regulated. Quantitative analysis of receptor synthesis and degradation has led to the conclusion that receptor is one of a class of proteins whose synthesis is tightly regulated during terminal steps of myogenesis.     

Effect of Phencyclidine on the Metabolism of Individual Brain Proteins

The effect of phencyclidine on the metabolism of a selected number of rat brain proteins was determined using two-dimensional gel electrophoresis and quantitative fluorography. When rats were injected with phencyclidine, modulation of individual protein metabolism occurred in the pituitary and cortex. That is, a few proteins showed increased and others decreased incorporation of [35S]methionine, whereas total protein metabolism was unaltered. In contrast, in vitro treatment of brain tissue with phencyclidine inhibited incorporation of radiolabel into all proteins by approximately 50%, as shown by quantitative fluorography of individual proteins.     

Proteomic analysis of articular cartilage shows increased type II collagen synthesis in osteoarthritis and expression of inhibin betaA (activin A), a regulatory molecule for chondrocytes

We show that proteomic analysis can be applied to study cartilage pathophysiology. Proteins secreted by articular cartilage were analyzed by two-dimensional SDS-PAGE and mass spectrometry. Cartilage explants were cultured in medium containing [35S]methionine/cysteine to radiolabel newly synthesized proteins. To resolve the cartilage proteins by two-dimensional electrophoresis, it was necessary to remove the proteoglycan aggrecan by precipitation with cetylpyridinium chloride. 50-100 radiolabeled protein spots were detected on two-dimensional gels of human cartilage cultures. Of 170 silver-stained proteins identified, 19 were radiolabeled, representing newly synthesized gene products. Most of these were known cartilage constituents. Several nonradiolabeled cartilage proteins were also detected. The secreted protein pattern of explants from 12 osteoarthritic joints (knee, hip, and shoulder) and 14 nonosteoarthritic adult joints were compared. The synthesis of type II collagen was strongly up-regulated in osteoarthritic cartilage. Normal adult cartilage synthesized little or no type II collagen in contrast to infant and juvenile cartilage. Potential regulatory molecules novel to cartilage were identified; pro-inhibin betaA and processed inhibin betaA (which dimerizes to activin A) were produced by all the osteoarthritic samples and half of the normals. Connective tissue growth factor and cytokine-like protein C17 (previously only identified as an mRNA) were also found. Activin induced the tissue inhibitor for metalloproteinases-1 in human chondrocytes. Its expression was induced in isolated chondrocytes by growth factors or interleukin-1. We conclude that type II collagen synthesis in articular cartilage is down-regulated at skeletal maturity and reactivated in osteoarthritis in attempted repair and that activin A may be an anabolic factor in cartilage.     

Characterization of Postmortem Human Brain Proteins by Two-Dimensional Gel Electrophoresis

Abstract: The proteins of membrane and cytosol fractions from frozen human postmortem brain were analyzed by two-dimensional gel electrophoresis (isoelectric range: 5.1–6.0) and both Coomassie-blue and ammoniacal silver staining. Cytosol preparations were analyzed from six different postmortem brains from patients with various neurologic diagnoses and immediate causes of death. Intervals between death and brain freezing (−70^oC) ranged from 2 to 20 h. The vast majority of proteins detected in these cytosol fractions had identical molecular weights and isoelectric points in each of six human brains examined. However, in some tissue samples tubulin was either quantitatively decreased or undetectable. The possibility that this partial or complete depletion of tubulin was related to postmortem interval and/or brain freezing was studied using rat forebrain tissue. Rat brain incubated at room temperature for up to 24 h did not reproduce the changes seen in the region of human cytosol tubulin. However, other changes seen in the two-dimensional electrophoretic pattern of rat cytosol proteins did relate to postmortem interval, brain freezing, or both. Rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum were prepared from three human brains, with highly reproducible two-dimensional patterns. Protein analysis of these membrane fractions revealed that human RER contained significant amounts of tubulin, in contrast to rat RER which contained no detectable tubulin. This discrepancy was elucidated by allowing rat brains to remain at room temperature for 24 h before freezing; gels of rat RER prepared from this tissue showed that tubulin subunits were present.     

Nonchromatin nuclear proteins of mammalian lens epithelial cells

The nuclear matrix (NM) proteins of six tissue cultured lens epithelial cell lines and one embryonic rabbit epidermal cell line were analyzed to determine possible tissue and species specificity of these proteins. The NM proteins were isolated by the modified Penman technique. The tissue cultured cells were pulsed with [³⁵S] methionine and nuclear matrix proteins were fractionated by two-dimensional (2-D) gel electrophoresis. The 2-D gels were dried and autoradiographed. The relative abundance of spot patterns of nuclear matrix proteins of different cells were compared. The data from these experiments revealed that all the examined cell lines have distinct spot patterns, however, all of NM profile showed a spot pattern in the 45 kDa region with acidic pH. Some of these spots cross-reacted with anti-vimentin antibodies, whereas a prominent protein spot in this region did not cross react with either vimentin or actin antibodies. The observed variations in the NM protein patterns of lens epithelial cells may reflect tissue and species specificity and also a role in the regulatory properties of these nuclear proteins in the eye tissue development. J. Cell. Biochem. 64:644–650. © 1997 Wiley-Liss, Inc.     

宫颈腺癌发生相关蛋白的蛋白质组学初步研究

目的：为了研究宫颈腺癌和正常宫颈组织的差异表达蛋白,为宫颈腺癌的发生和早期诊断提供有意义的生物标志物。方法：以正常宫颈组织和宫颈腺癌组织为研究对象,提取组织总蛋白,依次进行二维凝胶电泳,凝胶图象分析,基质辅助激光解吸附／离子化飞行时间质谱及生物信息学分析。Western Blot方法验证部分蛋白表达情况。结果：建立了宫颈腺癌和正常宫颈组织的二维电泳图谱,进行质谱和生物信息学分析比较鉴定宫颈腺癌和正常宫颈组织差异表达蛋白7个,与正常宫颈组织比较,宫颈腺癌表达降低的蛋白有3个,包括抑制素（inhibin-beta）,PTEN,乳铁蛋白（lactoferrin）;宫颈腺癌表达升高的蛋白有4个,包括谷胱甘肽S-转移酶（GSTT1＊0）,Homeodomain—interacting protein kinase2（HIPK2）,CD44v5,galectin-7。Western Blot方法检测结果显示inhibin-beta和PTEN在宫颈腺癌中表达变化情况与蛋白质组学结果一致。结论：宫颈腺癌和正常宫颈组织存在差异表达蛋白,这些差异表达蛋白可能是宫颈腺癌发生相关蛋白,可能作为宫颈腺癌早期诊断的标志物。     

Two-dimensional gel analysis of proteins from human trisomy 21 fetal liver tissue after DEAE-Sepharose chromatography

Summary Isoelectrofocusing two-dimensional polyacrylamide gel electrophoresis (IEF-2D-PAGE) offers the opportunity to detect typical alterations in the protein pattern from directly prepared liver tissue of fetuses with trisomy 21 and normal controls. The fractionation of the cell lysate by differential centrifugation into various subcellular components (nuclei, membranes, polyribosomes, cytoplasmic proteins) and fractionation of the proteins through DEAE-Sepharose chromatography allows detection of protein differences. In the 19th week of pregnancy it is possible to establish only three differences in the protein patterns between liver tissue from trisomy 21-fetuses and normal controls. All three proteins are synthesized in euploid controls at a higher level than in trisomy 21-liver tissue and are supposed to be consequences of primary gene dosage effects. The molecular mass of the individual proteins ranges from 14 kdaltons to 31 kdaltons. The data reported here raise the question whether some of the differences found by others represent different gene expression of cells under tissue culture conditions and/or of cells derived from different tissues, or developmental stages.