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PubMed2006

Double-hexahistidine tag with high-affinity binding for protein immobilization, purification, and detection on ni-nitrilotriacetic acid surfaces.

There is a particular need in protein analysis and purification for specific, functional, and generic methods of protein immobilization on solid supports. Here we describe a double-hexahistidine (His6) tag sequence, comprising two hexahistidines separated by an 11-amino acid spacer, which shows at least 1 order of magnitude stronger binding to Ni-NTA-modified surfaces than a conventional single-His6 tag or two single-His6 tags at N- and C-termini. Using, as a model, tagged versions of green fluorescent protein (GFP), stable and tight binding of the double-His6 tag/Ni-NTA interaction was demonstrated by competitive elution from Ni-NTA agarose beads, surface plasmon resonance on a Ni-NTA chip, and ELISA in Ni-NTA microwell plates. Protein purification by Ni-NTA chromatography was improved by a 6-8-fold increase in imidazole concentration required for elution, while the dissociation rate of double-His6 GFP from Ni-NTA chips in SPR (BIAcore) was 10 times slower than for single-His6-tagged proteins. ELISA assays and protein microarrays constructed with double-His6 GFP demonstrated greater detection sensitivity with anti-His antibodies and Ni-NTA conjugates. Moreover, the double-His6 tag could serve simultaneously both for protein immobilization and for detection on surfaces. The double-His6 peptide has the potential to be a universal tag for protein immobilization and detection on arrays and single-step purification of proteins from crude mixtures.

Binding Sites↗

PubMed2006

Biomarker discovery by imaging mass spectrometry: transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat.

Adverse drug effects are often associated with pathological changes in tissue. An accurate depiction of the undesired affected area, possibly supported by mechanistic data, is important to classify the effects with regard to relevance for human patients. MALDI imaging MS represents a new analytical tool to directly provide the spatial distribution and the relative abundance of proteins in tissue. Here we evaluate this technique to investigate potential toxicity biomarkers in kidneys of rats that were administered gentamicin, a well known nephrotoxicant. Differential analysis of the mass spectrum profiles revealed a spectral feature at 12,959 Da that strongly correlates with histopathology alterations of the kidney. We unambiguously identified this spectral feature as transthyretin (Ser(28)-Gln(146)) using an innovative combination of tissue microextraction and fractionation by reverse-phase liquid chromatography followed by a top-down tandem mass spectrometric approach. Our findings clearly demonstrate the emerging role of imaging MS in the discovery of toxicity biomarkers and in obtaining mechanistic insights concerning toxicity mechanisms.

Amino Acid Sequence↗

PubMed2004

A serum proteomics approach to the diagnosis of ectopic pregnancy.

An ectopic pregnancy (EP) occurs when implantation of the embryo occurs outside of the uterus. If left untreated, the developing fetus will continue to grow, leading to life-threatening consequences for the mother. A major difficulty with the diagnosis of ectopic pregnancy is that methods of detection are limited, and some, such as ultrasound, are not very reliable in the earliest days of gestation. Currently, no effective serum test exists to distinguish an ectopic pregnancy from a normal intrauterine pregnancy. The incidence of ectopic pregnancy is increasing and has doubled in the last 20 years. It is now the second most common cause of maternal death in the first trimester of pregnancy. To address this issue, we initiated a project to identify serum markers of ectopic pregnancy. The subjects for these studies presented at the Hospital of the University of Pennsylvania. We obtained over 140 serum samples from women with suspected ectopic pregnancy: women presenting with pain and/or bleeding in the first trimester of pregnancy. The approximate racial breakdown of the subjects is as follows: African American, 36%; Caucasian, 3%; Asian, 2%; Hispanic, 1%; unknown, 58%. Serum samples from 139 women (62 with ectopic pregnancy and 77 with a normal intrauterine pregnancy) were applied to WCX2 (weak ion exchange) protein chip surfaces and analyzed for serum markers using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Several proteins in the 7500-18,000 Da mass range were identified that may discriminate an ectopic pregnancy from an intrauterine pregnancy. The most promising markers were analyzed using classification and regression tree analysis (CART) with and without clinical variables (serum hCG value, length of amenorrhea). Two different algorithms were developed that classify the patients on the basis of sensitivity (number of EPs who screen positive/# of EPs) or specificity (# of healthy patients who screen negative/# of healthy). Our current approach is to refine these two "rule sets" to segregate patients into three groups: those who need immediate intervention for a probable ectopic pregnancy, those who appear to have a normal pregnancy, and those who need further monitoring for diagnosis.

Biomarkers↗

PubMedDate not supplied

Proteomic strategies and their application in cancer research.

The understanding of carcinogenesis and tumor progression on a molecular basis needs a detailed study of proteins as effector molecules and as critical components of the multiple interconnected signaling pathways that drive the neoplastic phenotype. Thus, the proteomic approach represents a powerful tool for the challenge of the post-genomic era. The term "cancer proteome" refers to the collection of proteins expressed by a given cancer cell and should be considered as a highly dynamic entity within the cell, which affects a variety of cellular activities. The emerging proteomic analysis platforms including 2D-PAGE, mass spectrometry technologies, and protein microarrays represent powerful tools to study and understand cancer. These systems aim to not only identify, catalogue, and characterize cancer proteins, but also to unveil how they interact to affect overall tumor progression. Moreover, recent studies on various cancers have reported promising results concerning the detection of novel molecular biomarkers useful in the early diagnosis of cancer and in drug discovery. Thus, a new subdiscipline named clinical proteomics, concomitant with new molecular technologies that are developed, demonstrates promise to discover new cancer biomarkers. The early diagnosis of cancer, even in a premalignant state, is crucial for the successful treatment of this disease. For these reasons, it is clear that the identification of biomarkers for the early diagnosis of cancer should represent one of the main goals of this emerging field of study.

Animals↗

PubMed2005

A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.

BACKGROUND: This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear. RESULTS: In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 muM MPP+ treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+ treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+ treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures. CONCLUSION: Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.

1-Methyl-4-phenylpyridinium↗

PubMed2004

Abscisic acid promoted changes in the protein profiles of rice seedling by proteome analysis.

This study investigates the influence of exogenously applied abscisic acid (ABA) on the leaves and leaf sheaths of two-week-old rice seedling at the level of the proteome. Significant differences were observed in the two-dimensional polyacrylamide gel electrophoresis protein profiles between control and ABA treated samples. Amino-acid sequence analysis of affected proteins revealed that ABA caused drastic changes in the major photosynthetic protein, ribulose 1,5-bisphosphate carboxylase/oxygenase and accumulation of certain defense/stress-related proteins. Moreover, cutting or treating leaf sheaths with jasmonic acid (JA) rapidly increased the endogenous level of ABA, suggesting a role for ABA during the defense/stress-response. Comparative study indicated a potential overlap between ABA and JA as detected at the level of the proteome. Furthermore, in vitro protein phosphorylation experiments and in-gel kinase assays also revealed considerable changes in the phosphorylation status of some proteins, and differential effects on myelin basic protein and calcium-dependent protein kinase activities by ABA treatment, which suggests involvement of kinase in the downstream signaling cascade. These results provide evidence at proteome level for the involvement of ABA in stress-response in rice seedling.

Abscisic Acid↗

PubMed2005

The molecular make-up of a tumour: proteomics in cancer research.

The enormous progress in proteomics, enabled by recent advances in MS (mass spectrometry), has brought protein analysis back into the limelight of cancer research, reviving old areas as well as opening new fields of study. In this review, we discuss the basic features of proteomic technologies, including the basics of MS, and we consider the main current applications and challenges of proteomics in cancer research, including (i) protein expression profiling of tumours, tumour fluids and tumour cells; (ii) protein microarrays; (iii) mapping of cancer signalling pathways; (iv) pharmacoproteomics; (v) biomarkers for diagnosis, staging and monitoring of the disease and therapeutic response; and (vi) the immune response to cancer. All these applications continue to benefit from further technological advances, such as the development of quantitative proteomics methods, high-resolution, high-speed and high-sensitivity MS, functional protein assays, and advanced bioinformatics for data handling and interpretation. A major challenge will be the integration of proteomics with genomics and metabolomics data and their functional interpretation in conjunction with clinical results and epidemiology.

Biomarkers, Tumor↗

PubMed2006

Global protein expression profiling underlines reciprocal regulation of caveolin 1 and endothelial nitric oxide synthase expression in ovariectomized sheep uterine artery by estrogen/progesterone replacement therapy.

Ovariectomized (OVX) ewes were assigned to receive vehicle, progesterone (P4, 0.9-g controlled internal drug release vaginal implants), estradiol-17beta (E2, 5 microg/kg bolus + 6 microg kg(-1) day(-1)), or P4 + E2 for 10 days (n = 3/group). Uterine artery endothelial proteins were mechanically isolated on Day 10. The samples were used for protein expression profiling by the Ciphergen Proteinchip system and immunoblotting analysis of endothelial nitric oxide synthase (NOS3, also termed eNOS) and caveolin 1. Uterine artery rings were cut and analyzed by immunohistochemistry to localize NOS3 and caveolin 1 expression. With the use of the IMAC3 protein chip with loading as little as 2 microg protein/sample, many protein peaks could be detected. Compared to vehicle controls, a approximately 133.1-kDa protein was identified to be upregulated by 2- to 4-fold in OVX ewes receiving E2, P4, and their combination, whereas a approximately 22.6-kDa protein was downregulated by 2- to 4-fold in OVX ewes receiving E2 and E2/P4, but not P4 treatments. Western blot analysis revealed that E2, P4, and their combination all increased NOS3 protein, whereas E2 and its combination with P4, but not P4 alone, downregulated caveolin 1 expression. Immunohistochemical analysis revealed that NOS3 was mainly localized in the endothelium and upregulated by E2, whereas caveolin 1 was localized in both endothelium and smooth muscle and downregulated by E2. Thus, our data demonstrate that uterine artery endothelial NOS3 and caveolin 1 are regulated reciprocally by estrogen replacement therapy. In keeping with the facts that E2, but not P4, causes uterine vasodilatation and that E2 and P4 increase NOS3 expression, but only E2 decrease caveolin 1 expression, our current study suggests that both increased NOS3 expression and decreased caveolin 1 expression are needed to facilitate estrogen-induced uterine vasodilatation.

Animals↗

PubMed2003

Proteomic analyses in Waldenstrom's macroglobulinemia and other plasma cell dyscrasias.

The proteomic analysis of tumor cells emerges as a key complement to gene expression profiling, primarily because regulation of protein expression (at the translational and post-translational levels) can buffer the magnitude of changes occurring at the gene transcription level, in order to fine tune cellular functions. Herein we describe the concept of proteomic analysis of the signaling state of tumor cells, as well as its application in the study of signaling pathways in plasma cell dyscrasias, such as Waldenstrom's macroglobulinemia (WM) and multiple myeloma (MM). Comparative studies of WM versus MM cells at baseline and in the setting of drug treatment reveals proteomic profiles of the signaling state with significant overlap (that could reflect a putative B-cell lineage-related proteomic signature), but also distinct differences, possibly associated with differential features in the biologic behavior and drug sensitivity of these diseases. These proteomic studies pave the way for a more comprehensive insight into the molecular basis of WM versus other B-cell malignancies.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2005

Oral cancer plasma tumor marker identified with bead-based affinity-fractionated proteomic technology.

BACKGROUND: There is no plasma marker for detecting oral cancer, one of the most frequent cancers worldwide. We developed a bead-based affinity-fractionated proteomic method to discover a novel plasma marker for oral cancer. METHODS: Affinity purification of heparinized plasma with magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were used to screen potential oral cancer markers. We compiled MS protein profiles for 57 patients with oral cancer and compared them with profiles from 29 healthy controls. The spectra were analyzed statistically using flexAnalysis and ClinProt bioinformatic software. In each MS analysis, the peak intensities of interest were normalized with an internal standard (adrenocorticotropic hormone 18-39). For identification, affinity bead-purified plasma protein was subjected to MALDI TOF/TOF analysis followed by Mascot identification of the peptide sequences and a search of the National Center for Biotechnology Information protein database. RESULTS: To optimize MALDI-TOF analysis based on the best discriminator of the cancer and control spectra, copper-chelated beads were used for plasma protein profiling. The within- and between-run CVs for assays were <4% and 7%, respectively. Six markers that differentiated between cancer and control spectra were found, with mean (SD) molecular masses of 2664 (1), 2850 (1), 3250 (1), 7735 (2), 7927 (2), and 9240 (2) Da. The 2664-Da marker, identified as a fragment of the fibrinogen alpha-chain, had the highest sensitivity (100%) and specificity (97%) for cancer. CONCLUSION: The high specificity and sensitivity of the fibrinogen alpha-chain fragment suggest that it may be a clinical useful tumor marker.

Adult↗

PubMed2005

Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites.

A versatile integrated system has been developed for the automated enrichment and analysis of phosphopeptides by immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry (IMAC/nano-LC/ESI-MS). This system utilizes two independently controlled high-performance liquid chromatography (HPLC) pumps, an autosampler and microvalves to prepare and elute samples into an ion trap mass spectrometer. The use of robust reversed-phase HPLC columns with integrated ESI emitter tips enables the reproducible detection and identification of low-femtomole quantities of phosphopeptides. The entire system is coordinated through a simple user interface by customized software. The ruggedness of the system is demonstrated by highly reproducible analyses of single and multi-protein digests, while its utility is demonstrated by the thorough evaluation of the relative immunoprecipitation efficiencies of several commercially available anti-phosphotyrosine antibodies.

Amino Acid Sequence↗

PubMed2005

SELDI-MS-based expression profiling of ductal invasive and lobular invasive human breast carcinomas.

Expression profiling using proteomic techniques has a great potential to identify new biomarkers that might help to better diagnose and treat diseases such as breast cancer, which is one of the leading causes of cancer death in women. Surface-enhanced laser desorption ionization mass spectrometry (SELDI-MS) combines chromatographic separation of peptides and proteins with mass spectrometry and is a fast, user-friendly tool to analyze protein and peptide profiles. SELDI-MS was employed for a comparative analysis of lobular invasive versus ductal invasive breast tumors to find differentially expressed proteins and peptides, and to validate this technique for biomarker identification using complex samples such as tissue. After optimization of sample preparation using HMEC and MCF-7 cell lines, 20 breast tumors were analyzed, and about 550 mass signals corresponding to an estimated 140 native peptides and proteins were detected in each tumor. Only 14% of the mass signals were present in more than six tumors of one subgroup or in more than 12 tumors of both groups showing a great overall heterogeneity of the peptide and protein profiles obtained. Peptide mass signals specific for each of the analyzed groups were identified. In addition, we detected peptides from laser-microdissected ductal invasive and intraductal tumor parts corresponding to peptides present in whole tumors. The low amount of identified peptides and proteins and the observed heterogeneity suggest that SELDI-MS is not well suited for biomarker identification of and profiling experiments on complex samples such as tumor tissue.

Breast Neoplasms↗

PubMed2003

Amplification of a 280-kilobase core region at the ERBB2 locus leads to activation of two hypothetical proteins in breast cancer.

Amplification of the ERBB2 oncogene at 17q12 is clinically the most relevant genetic aberration in breast cancer and several studies have linked ERBB2 activation to poor clinical outcome. The development of targeted antibody-based therapy for ERBB2-overexpressing tumors and the possible role of ERBB2 as a predictor of chemotherapy treatment response have further emphasized the essential role of ERBB2 in breast cancer. Here, we performed a detailed characterization of the molecular events occurring at the ERBB2 amplicon in primary breast tumors. Analysis of the amplicon structure in 330 breast tumors by fluorescence in situ hybridization to a tissue microarray revealed a 280-kb common region of amplification that contains 10 transcribed sequences, including eight known genes. The expression levels of these 10 transcripts were determined in 36 frozen samples of grade-matched ERBB2-amplified and -nonamplified (as determined by fluorescence in situ hybridization) primary breast tumors by using quantitativereal-time reverse transcriptase-polymerase chain reaction. A highly significant association between amplification and expression levels was observed for six of these genes, including ERBB2 and two uncharacterized hypothetical proteins, MGC9753 and MGC14832. These results support the recent findings on the influence of copy number on gene expression levels and highlight novel genes that might contribute to the clinical behavior of ERBB2-amplified breast tumors.

Breast Neoplasms↗

PubMed2006

Application of serum protein fingerprint in diagnosis of papillary thyroid carcinoma.

To find new biomarkers and establish serum protein fingerprint models for early diagnosis and preoperative staging of papillary thyroid carcinoma, we employed SELDI-TOF-MS and bioinformatics tools. A total of 116 samples were analyzed in this study. The first 80 samples were analyzed by SELDI-TOF-MS and two biomarker patterns were identified. Pattern 1 distinguishes patients with papillary thyroid carcinoma from healthy individuals. Pattern 2 distinguishes papillary thyroid carcinoma from benign thyroid nodes. The remaining 29 samples were analyzed on the second day and served as an independent test set. The analysis of this independent test set yielded a specificity of 80.0% and a sensitivity of 88.9% for pattern 1 and a specificity of 80.0% and a sensitivity of 80.0% for pattern 2. Two additional biomarker patterns were identified to distinguish different stages of the papillary thyroid carcinoma (pattern 3) with an accuracy of 77.1% and different pathological types of thyroid carcinoma (pattern 4) with an accuracy of 88.1%. Taken together, the SELDI-TOF-MS technique combined with bioinformatics approaches can not only facilitate the discovery of better biomarkers for papillary thyroid carcinoma but also provide a useful tool for molecular diagnosis in the future.

Adenocarcinoma, Follicular↗

PubMed2006

Proteomic analysis of individual human embryos to identify novel biomarkers of development and viability.

OBJECTIVE: To develop a method to analyze the proteome of individual human blastocysts and identify differentially expressed proteins prior to implantation. DESIGN: Experimental study. SETTING: Research environment. PATIENT(S): Couples undergoing infertility treatment donated with consent cryopreserved human cleavage-stage embryos for research. INTERVENTION(S): Individual embryos were extracted and analyzed by time-of-flight mass spectrometry. MAIN OUTCOME MEASURE(S): The protein expression profiles of individual embryos. RESULT(S): Differential protein expression profiles were observed between early and expanded blastocysts, as well as between developing blastocysts and degenerate embryos. Significantly, several up-regulated and down-regulated proteins were detected in degenerating embryos. A search in the protein databases highlighted several candidates, including an inhibitor of Tcf-4 (transcription factor mediating Wnt signaling) and an apoptotic protease-activating factor. CONCLUSION(S): This is the first study to successfully analyze the proteome of individual human embryos. This study has shown that protein expression profiles relate to morphology, with degenerating embryos exhibiting significant up-regulation of several potential biomarkers that might be involved in apoptotic and growth-inhibiting pathways.

Biomarkers↗

PubMed2004

Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer.

BACKGROUND: Although prostate-specific antigen (PSA) is a prototypic biomarker for prostate cancer, it has poor specificity. Expression of alpha-methylacyl-CoA racemase (AMACR), which is involved in the conversion of R-stereoisomers of branched-chain fatty acids to S-stereoisomers, has been shown to be specifically increased in prostate cancer epithelia. However, attempts to detect AMACR in circulation have not been successful. Hence, we determined whether an immune response to AMACR could be used as a serum biomarker for prostate cancer. METHODS: Sera from patients with biopsy-proven prostate cancer and from control subjects were screened for a humoral immune response to selected tumor antigens, including AMACR, by using protein microarrays (46 patients, 28 control subjects). Humoral immune response to AMACR was then validated using high-throughput immunoblot analysis (151 patients, 259 control subjects) and enzyme-linked immunosorbent assay (ELISA) (54 patients, 55 control subjects). Receiver operating characteristic curves were used to determine the sensitivity and specificity of the immune response to AMACR to detect prostate cancer. RESULTS: Immunoreactivity against AMACR was statistically significantly higher in sera from patients with prostate cancer than in control subjects by all three techniques (P(protein microarray) =.009, P(immunoblot)<.001, P(ELISA) =.011). High-throughput immunoblot analysis revealed that, in subjects with intermediate PSA levels (4-10 ng/mL), the immune response against AMACR was more sensitive and specific than was PSA in distinguishing sera from prostate cancer patients relative to control subjects (sensitivity and specificity of 77.8% and 80.6% versus 45.6% and 50%, respectively; area under the curve of 0.789 versus 0.492; P<.001). CONCLUSION: Assays to detect a humoral immune response against AMACR may have the potential to supplement PSA screening in identifying patients with clinically significant prostate cancer, especially those with intermediate PSA levels.

Adult↗

PubMed2006

Identification of biomarkers from mass spectrometry data using a "common" peak approach.

BACKGROUND: Proteomic data obtained from mass spectrometry have attracted great interest for the detection of early-stage cancer. However, as mass spectrometry data are high-dimensional, identification of biomarkers is a key problem. RESULTS: This paper proposes the use of "common" peaks in data as biomarkers. Analysis is conducted as follows: data preprocessing, identification of biomarkers, and application of AdaBoost to construct a classification function. Informative "common" peaks are selected by AdaBoost. AsymBoost is also examined to balance false negatives and false positives. The effectiveness of the approach is demonstrated using an ovarian cancer dataset. CONCLUSION: Continuous covariates and discrete covariates can be used in the present approach. The difference between the result for the continuous covariates and that for the discrete covariates was investigated in detail. In the example considered here, both covariates provide a good prediction, but it seems that they provide different kinds of information. We can obtain more information on the structure of the data by integrating both results.

Algorithms↗

PubMed2005

Proteomic analysis of formalin-fixed prostate cancer tissue.

Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue would enable retrospective biomarker investigations of this vast archive of pathologically characterized clinical samples that exist worldwide. These FFPE tissues are, however, refractory to proteomic investigations utilizing many state of the art methodologies largely due to the high level of covalently cross-linked proteins arising from formalin fixation. A novel tissue microdissection technique has been developed and combined with a method to extract soluble peptides directly from FFPE tissue for mass spectral analysis of prostate cancer (PCa) and benign prostate hyperplasia (BPH). Hundreds of proteins from PCa and BPH tissue were identified, including several known PCa markers such as prostate-specific antigen, prostatic acid phosphatase, and macrophage inhibitory cytokine-1. Quantitative proteomic profiling utilizing stable isotope labeling confirmed similar expression levels of prostate-specific antigen and prostatic acid phosphatase in BPH and PCa cells, whereas the expression of macrophage inhibitory cytokine-1 was found to be greater in PCa as compared with BPH cells.

Amino Acid Sequence↗