Searching for serum tumor markers for colorectal cancer using a 2‐D DIGE approach

Identification of specific protein markers for colorectal cancer (CRC) could provide a basis for its early diagnosis and detection, as well as clues to the molecular mechanisms governing cancer progression. In the present study, 2‐D DIGE coupled with MS was used to screen for biomarker candidates in the serum proteome of ten human CRC samples and ten healthy control samples. After pooling identical amounts of serum proteins (based on total protein concentration), albumin/IgG was depleted under partially denaturing conditions. Subsequently, the serum samples were labeled with three different CyDyes, and separated by 2‐D DIGE. After analysis with the biological variation analysis module of the DeCyder software, only three spots were found to be significantly elevated in all patient groups (with ratios from 1.52 to 9.08), whereas five spots were significantly down‐regulated in patients (with ratios from ?1.23 to ?10.21) (t‐test; p<0.05). Finally, two potential biomarkers, Transaldolase 1 and thyroid receptor interactor, were chosen for validation and analysis by ELISA with the serum of 30 CRC patients and 30 healthy controls. The serum levels of the two proteins correlated well with the 2‐D DIGE results. Thus, 2‐D DIGE approaches show great promise for biomarker discovery in CRC.     

Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples

Proteomic platforms that enable researchers to profile a high number of proteins across large sets of complex samples hold a great potential for biomarker discovery. LC-MS/MS-based methods can be used to analyse many samples without the need for protein labelling. As the analysis is a sequential process, the performance of the system has to be consistent throughout the entire experiment. In this study we used a set of spiked serum samples as well as a set of 55 clinical serum samples from schizophrenia patients and healthy volunteers to show that the label-free proteomic approach yields reproducible results across a large number of samples and can be used to accurately measure the relative protein abundance. Using this approach, we identified 1709 serum proteins covering a dynamic range of over three orders of magnitude. We believe that label-free quantitative proteomics is especially suited for biomarker discovery in large sample sets.     

Peptide correlation: a means to identify high quality quantitative information in large-scale proteomic studies

A major challenge of proteomic studies is the accurate quantitation of proteins. LC-MS/MS-based methods are especially suited for profiling proteins in large sample sets. In this setup, the measurement of relative protein abundance relies on the correct quantitation of tryptic peptides. However, peptide intensities often do not unequivocally reflect the abundance of the native proteins in the sample. In this study, we show that peptides that accurately reflect relative protein abundances in large-scale sample sets can be selected based on the correlation to each other. This strategy was tested in a well-controlled experiment using a set of spiked serum samples as well as 55 clinical serum samples from schizophrenia patients and healthy volunteers. The peptide correlation analysis we present here provides an intuitive and simple procedure to obtain a high quality quantitative information from proteomics data.     

Simultaneous determination of amino acids and neurotransmitters in plasma samples from schizophrenic patients by hydrophilic interaction liquid chromatography with tandem mass spectrometry

A sensitive, reproducible, and rapid method was developed for the simultaneous determination of underivatized amino acids (aspartate, serine, glycine, alanine, methionine, leucine, tyrosine, and tryptophan) and neurotransmitters (glutamate and γ‐aminobutyric acid) in plasma samples using hydrophilic interaction liquid chromatography coupled to triple quadrupole tandem mass spectrometry. The plasma concentrations of amino acids and neurotransmitters obtained from 35 schizophrenic patients in treatment with clozapine (27 patients) and olanzapine (eight patients) were compared with those obtained from 38 healthy volunteers to monitor the effectiveness of treatment. The chromatographic conditions separated ten target compounds within 3 min. This method presented linear ranges that varied from (lower limit of quantification: 9.7–13.3 nmol/mL) to (upper limit of quantification: 19.4–800 nmol/mL), intra‐ and interassay precision with coefficients of variation lower than 10%, and relative standard error values of the accuracy ranged from –2.1 to 9.9%. The proposed method appropriately determines amino acids and neurotransmitters in plasma from schizophrenic patients. Compared with the control group (healthy volunteers), the plasma levels of methionine in schizophrenic patients treated with olanzapine are statistically significantly higher. Moreover, schizophrenic patients treated with clozapine tend to have increased plasma levels of glutamate.     

Proteomics-driven progress in neurodegeneration research

Proteomics technologies have been widely used in the investigation of neurodegenerative and psychiatric disorders, and in particular in the detection of differences between healthy individuals and patients suffering from such diseases. Thus, brain and cerebrospinal fluid (CSF) samples from patients with Alzheimer's disease, Down syndrome, Pick's disease, Parkinson's disease, schizophrenia, and other disorders as well as brain and CSF from animals serving as models of neurological disorders have been analyzed by proteomics. 2-DE followed by MALDI-TOF-MS has been mainly applied as this proteomics approach provides the possibility of convenient quantification of protein levels and detection of post-translational modifications. About 330 unique proteins with deranged levels and modifications have been detected by proteomics approaches to be related to neurodegeneration and psychiatric disorders. They are mainly involved in metabolism pathways, cytoskeleton formation, signal transduction, guidance, detoxification, transport, and conformational changes. In this article, we provide a summary of the major contributions of proteomics technologies in the study of neurodegenerative and psychiatric diseases, in particular, in the detection of changes in protein levels and modifications related to these disorders.     

Glutamate Concentration in the Serum of Patients with Schizophrenia

Glutamate is the major neurotransmitter with multiple functions in the central nervous system. Glutamate-mediated excitotoxicity is involved in the pathophysiological processes in schizophrenia. The purpose of this study was to determine the concentration of glutamate in the serum of patients with paranoid schizophrenia compared with healthy individuals, and depending on the duration of the schizophrenic process and leading clinical symptoms. We investigated the level of glutamate in the serum of 158 patients with paranoid schizophrenia and 94 healthy persons. Higher concentrations of glutamate in schizophrenic patients compared with healthy persons have been found. The maximum concentrations of glutamate were detected in patients with disease duration of more than ten years. Glutamate level in the serum does not depend on the prevailing negative or positive clinical symptoms. The increased concentration of glutamate can hypothetically contribute to dopaminergic and glutamatergic imbalance, leading to the development of psychotic symptoms and cognitive dysfunction.     

Characterization of Potential Protein Biomarkers for Major Depressive Disorder Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry

Matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry is a sensitive analytical tool for characterizing various biomolecules in biofluids. In this study, MALDI-TOF was used to characterize potential plasma biomarkers for distinguishing patients with major depressive disorder (MDD) from patients with schizophrenia and healthy controls. To avoid interference from albumin—the predominant protein in plasma—the plasma samples were pretreated using acid hydrolysis. The results obtained by MALDI-TOF were also validated by electrospray ionization-quadrupole time-of-flight (ESI-QTOF) mass spectrometry. The analytical results were further treated with principal component analysis (PCA), hierarchical clustering analysis (HCA), and receiver operating characteristic (ROC) curve analysis. The statistical analyses showed that MDD patients could be distinguished from schizophrenia patients and healthy controls by the lack of apolipoprotein C1 (Apo C1), which, in fact, was detected in healthy controls and schizophrenia patients. This protein is suggested to be a potential plasma biomarker for distinguishing MDD patients from healthy controls and schizophrenia patients. Since sample preparation for MALDI-TOF is very simple, high-throughput plasma apolipoprotein analysis for clinical purposes is feasible.     

Prostaglandin D2 synthase and its post-translational modifications in neurological disorders

Prostaglandin D2 synthase (PGDS) (beta-trace protein) is a highly abundant cerebrospinal fluid (CSF) glycoprotein. A number of studies have been performed to determine the potential value of this protein for the diagnosis of various neurological disorders. The measurement of total PGDS levels in CSF has proved marginally useful for this purpose, but promising results were obtained while investigating changes in the posttranslational modifications (PTM) pattern. Using 2-DE analysis, we previously showed that PGDS is differentially expressed in ante- and post mortem CSF samples. In the present study, we examined whether the PGDS isoforms may help to distinguish stroke and neurodegenerative disease patients from healthy subjects. The pattern of PGDS PTM was analyzed in CSF from patients with various neurological disorders (n = 44) using IEF/immunoblotting techniques. Strong alterations of this pattern were detected in patients with different forms of degenerative dementia. These findings are consistent with PGDS being altered in some neurological diseases and provide new opportunities for clinical applications.     

Analysis of breath samples for lung cancer survival

Analyses of exhaled air by means of electronic noses offer a large diagnostic potential. Such analyses are non-invasive; samples can also be easily obtained from severely ill patients and repeated within short intervals. Lung cancer is the most deadly malignant tumor worldwide, and monitoring of lung cancer progression is of great importance and may help to decide best therapy. In this report, twenty-two patients with diagnosed lung cancer and ten healthy volunteers were studied using breath samples collected several times at certain intervals and analysed by an electronic nose. The samples were divided into three sub-groups; group d for survivor less than one year, group s for survivor more than a year and group h for the healthy volunteers. Prediction models based on partial least square and artificial neural nets could not classify the collected groups d, s and h, but separated well group d from group h. Using artificial neural net, group d could be separated from group s. Excellent predictions and stable models of survival day for group d were obtained, both based on partial least square and artificial neural nets, with correlation coefficients 0.981 and 0.985, respectively. Finally, the importance of consecutive measurements was shown.     

甲亢患者血清和尿液的核磁共振代谢组学研究

应用基于核磁共振(NMR)的代谢组学方法, 研究甲状腺功能亢进(简称甲亢)患者和健康人群的血清和尿液, 分析甲亢疾病的特征代谢物. 实验收集33个甲亢患者和17个健康志愿者的血清样品以及53个甲亢患者和58个健康志愿者的尿液样品, 采用多元统计分析方法研究甲亢组和对照组血清和尿液中的内源性代谢差异. 结果表明, 甲亢组血清中的胆碱、葡萄糖和三甲胺等物质的含量升高, 而VLDL, LDL和胆固醇等脂质以及乳酸、糖蛋白和丙氨酸等代谢物的含量下降; 甲亢组尿液中的葡萄糖、柠檬酸、牛磺酸以及肌氨酸等代谢物的含量升高, 而马尿酸、TMAO、甲酸和琥珀酸等代谢物的含量下降. 结果表明, 甲亢病不仅影响了糖类、脂类和蛋白质三大物质的代谢, 还对能量代谢、肝肠循环和肠道微生物等多个生理系统产生显著影响, 并且可能造成肝脏及肾脏等器官的损伤.     

肝细胞癌、肝硬化患者血清中代谢物组研究

采用核磁共振方法检测肝硬化、肝细胞癌(简称肝癌)患者和健康人血清中代谢物,研究3组血清代谢物组的差异.利用偏最小二乘法-判别式分析(partial least square-discriminant analysis, PLS-DA)对NMR谱数据进行模式识别分析,探讨利用基于1H NMR代谢组学技术诊断肝癌的可行性.结果表明,与健康人相比,肝硬化、肝癌患者血清中脂质(低密度脂蛋白和极低密度脂蛋白)、胆碱、乙酰乙酸等含量减少,谷氨酰胺、丙酮酸、苯丙氨酸、酪氨酸等含量增加.PLS-DA分析结果显示肝癌患者可与健康人、肝硬化患者鉴别开来,肝癌诊断灵敏度达921%,假阳性率为5.7%,优于血清甲胎蛋白(alpha-fetoprotein, AFP)检测.研究结果表明,基于1H NMR代谢组学技术结合PLS-DA的方法具有灵敏、准确、重复性好等优点,有助于肝癌早期诊断.     

Analysis of chiral amino acids in cerebrospinal fluid samples linked to different stages of Alzheimer disease

Chiral micellar electrokinetic chromatography with laser-induced fluorescence detection (chiral-MEKC-LIF) was used to investigate D- and L-amino acid contents in cerebrospinal fluid (CSF) samples related to different Alzheimer disease (AD) stages. CSF samples were taken from (i) control subjects (S1 pool), (ii) subjects showing a mild cognitive impairment who remained stable (S2 pool), (iii) subjects showing an mild cognitive impairment that progressed to AD (S3 pool) and (iv) subjects diagnosed with AD (S4 pool). The optimized procedure only needed 10 μL of CSF and it included sample cleaning, derivatization with FITC and chiral-MEKC-LIF separation. Eighteen standard amino acids were baseline separated with efficiencies up to 703,000 plates/m, high sensitivity (LODs in the nM range) and good resolution (values ranging from 2.6 to 9.5). Using this method, L-Arg, L-Leu, L-Gln, γ-aminobutyric acid, L-Ser, D-Ser, L-Ala, Gly, L-Lys, L-Glu and L-Asp were detected in all the CSF samples. S3 and S4 samples (i.e. AD subjects) showed significant lower amounts of L-Arg L-Lys, L-Glu and L-Asp compared to the non-AD S1 and S2 samples, showing in the S4 group the lowest amounts of L-Arg L-Lys, L-Glu and L-Asp. Moreover, γ-aminobutyric acid was significantly higher in AD subjects with the highest amount also found for S4. No significant differences were observed for the rest of amino acids including D-Ser. Based on the obtained chiral-MEKC-LIF data, it was possible to correctly classify all the samples into the four groups. These results demonstrate that the use of enantioselective procedures as the one developed in this work can provide some new light on the investigations of AD, including the discovery of new biomarkers related to different stages of AD.     

Associations between DRDs and schizophrenia in a Korean population: multi-stage association analyses

The dysregulation of the dopaminergic system has been implicated in the pathophysiology of major psychosis, including schizophrenia, with dopamine receptor genes (DRDs) presently targeted as the most promising candidate genes. We investigated DRD1-5 for association with schizophrenia using a multi-stage approach in a Korean sample. One hundred forty-two SNPs in DRD1-5 were selected from the dbSNP, and the associations of each SNP were then screened and typed by MALDI-TOF mass spectrometry using pooled DNA samples from 150 patients with major psychosis and 150 controls. Each of the suggested SNPs was then genotyped and tested for an association within the individual samples comprising each pool. Finally, the positively associated SNPs were genotyped in an extended sample of 270 patients with schizophrenia and 350 controls. Among the 142 SNPs, 88 (62%) SNPs in our Korean population were polymorphic. At the pooling stage, 10 SNPs (DRD1: 2, DRD2: 3, and DRD4: 5) were identified (P<0.05). SNPs rs1799914 of DRD1 (P=0.046) and rs752306 of DRD4 (P=0.017) had significantly different allele frequencies in the individually genotyped samples comprising the pool. In the final stage, with the extended sample, the suggestive association of DRD4 with rs752306 was lost, but the association of DRD1 with rs1799914 gained greater significance (P=0.017). In these large-scale multi-stage analyses, we were able to find a possible association between DRD1 and schizophrenia. These findings suggested the potential contribution of a multi-step strategy for finding genes related to schizophrenia.     

Prerequisites for peptidomic analysis of blood samples: II. Analysis of human plasma after oral glucose challenge -- a proof of concept

Mass spectrometric plasma analysis for biomarker discovery has become an exploratory focus in proteomic research: the challenges of analyzing plasma samples by mass spectrometry have become apparent not only since the human proteome organization (HUPO) has put much emphasis on the human plasma proteome. This work demonstrates fundamental proteomic research to reveal sensitivity and quantification capabilities of our Peptidomics technologies by detecting distinct changes in plasma peptide composition in samples after challenging healthy volunteers with orally administered glucose. Differential Peptide Display (DPD) is a technique for peptidomics studies to compare peptides from distinct biological samples. Mass spectrometry (MS) is used as a qualitative and quantitative analysis tool without previous trypsin digestion or labeling of the samples. Circulating peptides (< 15 kDa) were extracted from 1.3 mL plasma samples and the extracts separated by liquid chromatography into 96 fractions. Each fraction was subjected to MALDI MS, and mass spectra of all fractions were combined resulting in a 2D-display of > 2,000 peptides from each sample. Endogenous peptides that responded to oral glucose challenge were detected by DPD of pre-and post-challenge plasma samples from 16 healthy volunteers and subsequently identified by nESI-qTOF MS. Two of the 15 MS peaks that were significantly modulated by glucose challenge were subsequently identified as insulin and C-peptide. These results were validated by using immunoassays for insulin and C-peptide. This paper serves as a proof of principle for proteomic biomarker discovery down to the pM concentration range by using small amounts of human plasma.     

Simultaneous determination of catecholamines and their metabolites related to Alzheimer's disease in human urine

A simple and specific high-performance liquid chromatography method coupled with fluorescence detection (HPLC-FL) has been developed for the simultaneous determination of L-3,4-dihydroxyphenylalanine, norepinephrine, dopamine, epinephrine and 3,4-dihydroxyphenylacetic acid in human urine. The samples were derivatized by 1,2-diphenylethylenediamine with isoprenaline as internal standard. The factors affecting the fluorescence yield were investigated, including the reaction and separation conditions. The catecholamine derivatives were separated on a Kromasil C(18) column with methanol and sodium acetate buffer as mobile phase. The limits of detection for all catecholamines ranged from 0.2 to 1.1 ng/mL. The linear ranges were from 2.5 to 200 ng/mL except 3,4-dihydroxyphenylacetic acid from 5 to 200 ng/mL. The intra- and interday RSDs for all catecholamines were 1.0-8.0 and 2.1-14%, respectively. The method was successfully applied to determine the catecholamines in human urine from 14 Alzheimer's disease patients and 14 healthy volunteers. It was concluded that the mean levels of catecholamines in urine of Alzheimer's disease patients were all lower than those in healthy volunteers. The cluster analysis and independent samples T-test were used to distinguish the Alzheimer's disease patients and healthy volunteers.     

Identification of metabolic markers in patients with type 2 Diabetes by Ultrafast gas chromatography coupled to electronic nose. A pilot study

Metabolomics is a potential tool for the discovery of new biomarkers in the early diagnosis of diseases. An ultra-fast gas chromatography system equipped to an electronic nose detector (FGC eNose) was used to identify the metabolomic profile of Volatile Organic Compounds (VOCs) in type 2 diabetes (T2D) urine from Mexican population. A cross-sectional, comparative, and clinical study with translational approach was performed. We recruited twenty T2D patients and twenty-one healthy subjects. Urine samples were taken and analyzed by FGC eNose. Eighty-eight compounds were identified through Kovats's indexes. A natural variation of 30% between the metabolites, expressed by study groups, was observed in Principal Component 1 and 2 with a significant difference (p < 0.001). The model, performed through a Canonical Analysis of Principal coordinated (CAP), allowed a correct classification of 84.6% between healthy and T2D patients, with a 15.4% error. The metabolites 2-propenal, 2-propanol, butane- 2,3-dione and 2-methylpropanal, were increased in patients with T2D, and they were strongly correlated with discrimination between clinically healthy people and T2D patients. This study identified metabolites in urine through FGC eNose that can be used as biomarkers in the identification of T2D patients. However, more studies are needed for its implementation in clinical practice.     

Neutron activation analysis for determination of metal ions in biological fluids of patients after CoCrMo arthroplasty

Determination of metals and trace elements in patients with total knee or hip arthroplasty with CoCrMo alloy was performed. Blood, urine and cerebrospinal fluid (CSF) samples were analyzed and compared with samples from healthy people. Levels of Co, Cr as well as Na, Ca, Fe, Zn, Se, Rb, Sb and Br were determined by means of neutron activation analysis. The values of Cr and Co of the blood and urine measurements were elevated in patients with replacement, and according to the statistical analysis, significant differences of the elements Zn, Br, Co and Sb were found in the CSF (p?<?0.05).

     

Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry

The discovery of biomarkers is currently attracting much interest as it harbors great potential for the diagnosis and monitoring of human diseases. Here we have used two advanced mass spectroscopy based technologies, surface enhanced laser desorption ionization (SELDI-MS) and capillary electrophoresis/mass spectrometry (CE/MS), to obtain proteomic patterns of urine samples from patients suffering from membranous glomerulonephritis (MGN) and healthy volunteers. The results indicate that CE/MS analysis is able to display a rich and complex pattern of polypeptides with high resolution and high mass accuracy. In order to analyze these patterns, the MosaiqueVisu software was developed for peak identification, deconvolution and the display of refined maps in a three-dimensional format. The polypeptide profiles obtained with SELDI-MS from the same samples are much sparser and show lower resolution and mass accuracy. The SELDI-MS profiles are further heavily dependent on analyte concentration. SELDI-MS analysis identified three differentially expressed polypeptides, which are potential biomarkers that can distinguish healthy donors from patients with MGN. In contrast, approximately 200 potential biomarkers could be identified by CE/MS. Thus, while SELDI-MS is easy to use and requires very little sample, CE/MS generates much richer data sets that enable an in-depth analysis.     

The determination of selenium concentration in blood and tumour tissues of breast cancer patients in Syria using instrumental neutron activation analysis

The aim of this study was to investigate the relationship of selenium concentration in blood components and tumour tissues of breast cancer patients and healthy volunteers (control), in Syria, using instrumental neutron activation analysis (INAA). Red blood cells and serum selenium concentrations were determined in 50 healthy volunteers aged 25-70 years and 70 breast cancer patients aged 25-84 years. Selenium levels were also measured in malignant and adjacent normal tissues from breast cancer patients. The accuracy of the analysis was evaluated by co-analyses of international reference materials. The results showed that selenium concentration in serum and RBC was significantly lower among breast cancer patients compared to healthy volunteers (P<0.001). The results also showed that the selenium concentration was significantly higher in the cancer tissues compared to adjacent normal tissues (P<0.001). We conclude that there is a good indication for selenium deviation in blood and malignant tissue of breast cancer patients compared to that of healthy volunteers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Studies on the application of dynamic surface tensiometry of serum and cerebrospinal liquid for diagnostics and monitoring of treatment in patients who have rheumatic, neurological or oncological diseases

Human biological liquids comprise various surfactants, which adsorb at liquid interfaces and lead to a variation in surface tension. The adsorption processes involving low molecular weight surfactants, proteins and phospholipids play a vital role in the physiological functions of the human organism, especially if large surfaces are involved (e.g., gas exchange in lungs, metabolism of kidneys, liver and brain). Dynamic surface tensiometric studies of biological liquids like serum and cerebrospinal fluid provide surrogate parameters that reflect surface tension phenomena. We provide dynamic surface tension data of serum and cerebrospinal fluid that were collected from healthy volunteers and patients with rheumatic, neurological or oncological diseases. Our studies indicate that dynamic surface tension data are helpful for diagnostic purposes and for monitoring of therapeutic interventions.