Three disease phenotypes, Barrett's esophagus (BE), highgrade dysplasia (HGD), esophageal adenoca... more Three disease phenotypes, Barrett's esophagus (BE), highgrade dysplasia (HGD), esophageal adenocarcinoma (EAC), and a set of normal control (NC) serum samples are examined using a combination of ion mobility spectrometry (IMS), mass spectrometry (MS), and principal component analysis (PCA) techniques. Samples from a total of 136 individuals were examined, including 7 characterized as BE, 12 as HGD, 56 as EAC, and 61 as NC. In typical data sets, it was possible to assign ∼20 to 30 glycan ions based on MS measurements. Ion mobility distributions for these ions show multiple features. In some cases, such as the [S 1 H 5 N 4 + 3Na] 3+ and [S 1 F 1 H 5 N 4 + 3Na] 3+ glycan ions, the ratio of intensities of high-mobility features to lowmobility features vary significantly for different groups. The degree to which such variations in mobility profiles can be used to distinguish phenotypes is evaluated for 11 N-linked glycan ions. An outlier analysis on each sample class followed by an unsupervised PCA using a genetic algorithm for pattern recognition reveals that EAC samples are separated from NC samples based on 46 features originating from the 11-glycan composite IMS distribution.
Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recogni... more Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recognition analysis of MALDI-TOF mass spectra of serum N-linked glycans, Mi
Carbohydrate Analysis by Modern Liquid Phase Separation Techniques
Abstract Glycomic and glycoproteomic analyses include the characterization of oligosaccharides (g... more Abstract Glycomic and glycoproteomic analyses include the characterization of oligosaccharides (glycans) conjugated to proteins. Glycan characterization is critical to obtain a comprehensive vision of the regulation and functions of glycoproteins of interest. Glycans are created through a complicated nontemplate-driven process by a set of competing enzymes that lengthen the embryonic chain. The complex nature of these structures, stemming from variable compositions and linkages, and the poor ionization efficiency make it challenging to characterize the oligosaccharides. However, there have been significant developments and progressive separation, in which mass spectrometry (MS) approaches have been at the center and have been the main reason for this development. The primary purpose of this chapter is to discuss and evaluate the current LC separation techniques conjugated with MS, with an emphasis on the isomeric resolution of glycans and glycopeptides.
Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median su... more Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median survival rate does not exceed two years, indicating an imminent need to develop novel therapies. The atypical adamantyl retinoid ST1926 induces apoptosis and growth inhibition in different cancer types. We have shown that ST1926 is an inhibitor of the catalytic subunit of DNA polymerase alpha (POLA1), which is involved in initiating DNA synthesis in eukaryotic cells. POLA1 levels are elevated in GBM versus normal brain tissues. Therefore, we studied the antitumor effects of ST1926 in several human GBM cell lines. We further explored the global protein expression profiles in GBM cell lines using liquid chromatography coupled with tandem mass spectrometry to identify new targets of ST1926. Low sub-micromolar concentrations of ST1926 potently decreased cell viability, induced cell damage and apoptosis, and reduced POLA1 protein levels in GBM cells. The proteomics profiles revealed 197 protein...
The retention time provides critical information for glycan annotation and quantification from th... more The retention time provides critical information for glycan annotation and quantification from the Liquid Chromatography Mass Spectrometry (LC-MS) data. However, the variation of the precise retention time of glycans is highly dependent on the experimental conditions such as the specific separating columns, MS instruments and/or the buffer used. This variation hampers the exploitation of retention time for the glycan annotation from LC-MS data, especially when inter-laboratory data are compared. To incorporate the retention time of glycan across experiments, Glucose Unit Index (GUI) can be computed using the dextrin ladder as internal standard. The retention time of glycans are then calibrated with respect to glucose units derived from dextrin ladders. Despite the successful application of the GUI approach, the manual calibration process is quite tedious and often error prone. In this work, we present a standalone software tool GlycanGUI, with a graphic user interface to automatical...
The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid... more The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatograph/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA resulting in a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds.
Traumatic brain injury (TBI) is a major cause of disability and death. Mild TBI (mTBI) constitute... more Traumatic brain injury (TBI) is a major cause of disability and death. Mild TBI (mTBI) constitutes ~75% of all TBI cases. Repeated exposure to mTBI (rmTBI), leads to the exacerbation of the symptoms compared to single mTBI. To date, there is no FDA-approved drug for TBI or rmTBI. This research aims to investigate possible rmTBI neurotherapy by targeting TBI pathology-related mechanisms. Oxidative stress is partly responsible for TBI/rmTBI neuropathologic outcomes. Thus, targeting oxidative stress may ameliorate TBI/rmTBI consequences. In this study, we hypothesized that mitoquinone (MitoQ), a mitochondria-targeted antioxidant, would ameliorate TBI/rmTBI associated pathologic features by mitigating rmTBI-induced oxidative stress. To model rmTBI, C57BL/6 mice were subjected to three concussive head injuries. MitoQ (5 mg/kg) was administered intraperitoneally to rmTBI+MitoQ mice twice per week over one month. Behavioral and cognitive outcomes were assessed, 30 days following the first head injury, using a battery of behavioral tests. Immunofluorescence was used to assess neuroinflammation and neuronal integrity. Also, qRT-PCR was used to evaluate the expression levels of antioxidant enzymes. Our findings indicated that MitoQ alleviated fine motor function and learning impairments caused by rmTBI. Mechanistically, MitoQ reduced astrocytosis, microgliosis, dendritic and axonal shearing, and increased the expression of antioxidant enzymes. MitoQ administration following rmTBI may represent an efficient approach to ameliorate rmTBI neurological and cellular outcomes with no observable side effects.
In the version of this article initially published, extraneous references 29, 44-47, 19-22 were l... more In the version of this article initially published, extraneous references 29, 44-47, 19-22 were listed in Extended Data Fig. 4 caption and ref. 48 was listed in Extended Data Fig. 7 caption. The references have been removed from the HTML and PDF versions of the article.
other sleep disorders allows us to exclude a significant recruitment bias and probably indicates ... more other sleep disorders allows us to exclude a significant recruitment bias and probably indicates the validity of these results also for non-clinical populations. Support (If Any): .
Cancer Epidemiology and Prevention Biomarkers, 2007
A68 Increasing incidence of hepatocellular carcinoma (HCC) was associated with hepatitis C (HCV) ... more A68 Increasing incidence of hepatocellular carcinoma (HCC) was associated with hepatitis C (HCV) viral infection. Our study of HCC in Egypt, a country with an epidemic of HCV, identified a set of glycans as candidate markers for early detection of HCC. Glycans enzymatically released from serum proteins were analyzed by MALDI-TOF/TOF following solid phase permethylation. Analysis of less than 0.05 ml of serum allowed relative quantification of 80 glycans. Approximately half of the glycans changed significantly at p
Three disease phenotypes, Barrett's esophagus (BE), highgrade dysplasia (HGD), esophageal adenoca... more Three disease phenotypes, Barrett's esophagus (BE), highgrade dysplasia (HGD), esophageal adenocarcinoma (EAC), and a set of normal control (NC) serum samples are examined using a combination of ion mobility spectrometry (IMS), mass spectrometry (MS), and principal component analysis (PCA) techniques. Samples from a total of 136 individuals were examined, including 7 characterized as BE, 12 as HGD, 56 as EAC, and 61 as NC. In typical data sets, it was possible to assign ∼20 to 30 glycan ions based on MS measurements. Ion mobility distributions for these ions show multiple features. In some cases, such as the [S 1 H 5 N 4 + 3Na] 3+ and [S 1 F 1 H 5 N 4 + 3Na] 3+ glycan ions, the ratio of intensities of high-mobility features to lowmobility features vary significantly for different groups. The degree to which such variations in mobility profiles can be used to distinguish phenotypes is evaluated for 11 N-linked glycan ions. An outlier analysis on each sample class followed by an unsupervised PCA using a genetic algorithm for pattern recognition reveals that EAC samples are separated from NC samples based on 46 features originating from the 11-glycan composite IMS distribution.
Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recogni... more Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recognition analysis of MALDI-TOF mass spectra of serum N-linked glycans, Mi
Carbohydrate Analysis by Modern Liquid Phase Separation Techniques
Abstract Glycomic and glycoproteomic analyses include the characterization of oligosaccharides (g... more Abstract Glycomic and glycoproteomic analyses include the characterization of oligosaccharides (glycans) conjugated to proteins. Glycan characterization is critical to obtain a comprehensive vision of the regulation and functions of glycoproteins of interest. Glycans are created through a complicated nontemplate-driven process by a set of competing enzymes that lengthen the embryonic chain. The complex nature of these structures, stemming from variable compositions and linkages, and the poor ionization efficiency make it challenging to characterize the oligosaccharides. However, there have been significant developments and progressive separation, in which mass spectrometry (MS) approaches have been at the center and have been the main reason for this development. The primary purpose of this chapter is to discuss and evaluate the current LC separation techniques conjugated with MS, with an emphasis on the isomeric resolution of glycans and glycopeptides.
Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median su... more Glioblastoma Multiforme (GBM) is the most aggressive form of malignant brain tumor. The median survival rate does not exceed two years, indicating an imminent need to develop novel therapies. The atypical adamantyl retinoid ST1926 induces apoptosis and growth inhibition in different cancer types. We have shown that ST1926 is an inhibitor of the catalytic subunit of DNA polymerase alpha (POLA1), which is involved in initiating DNA synthesis in eukaryotic cells. POLA1 levels are elevated in GBM versus normal brain tissues. Therefore, we studied the antitumor effects of ST1926 in several human GBM cell lines. We further explored the global protein expression profiles in GBM cell lines using liquid chromatography coupled with tandem mass spectrometry to identify new targets of ST1926. Low sub-micromolar concentrations of ST1926 potently decreased cell viability, induced cell damage and apoptosis, and reduced POLA1 protein levels in GBM cells. The proteomics profiles revealed 197 protein...
The retention time provides critical information for glycan annotation and quantification from th... more The retention time provides critical information for glycan annotation and quantification from the Liquid Chromatography Mass Spectrometry (LC-MS) data. However, the variation of the precise retention time of glycans is highly dependent on the experimental conditions such as the specific separating columns, MS instruments and/or the buffer used. This variation hampers the exploitation of retention time for the glycan annotation from LC-MS data, especially when inter-laboratory data are compared. To incorporate the retention time of glycan across experiments, Glucose Unit Index (GUI) can be computed using the dextrin ladder as internal standard. The retention time of glycans are then calibrated with respect to glucose units derived from dextrin ladders. Despite the successful application of the GUI approach, the manual calibration process is quite tedious and often error prone. In this work, we present a standalone software tool GlycanGUI, with a graphic user interface to automatical...
The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid... more The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatograph/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA resulting in a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds.
Traumatic brain injury (TBI) is a major cause of disability and death. Mild TBI (mTBI) constitute... more Traumatic brain injury (TBI) is a major cause of disability and death. Mild TBI (mTBI) constitutes ~75% of all TBI cases. Repeated exposure to mTBI (rmTBI), leads to the exacerbation of the symptoms compared to single mTBI. To date, there is no FDA-approved drug for TBI or rmTBI. This research aims to investigate possible rmTBI neurotherapy by targeting TBI pathology-related mechanisms. Oxidative stress is partly responsible for TBI/rmTBI neuropathologic outcomes. Thus, targeting oxidative stress may ameliorate TBI/rmTBI consequences. In this study, we hypothesized that mitoquinone (MitoQ), a mitochondria-targeted antioxidant, would ameliorate TBI/rmTBI associated pathologic features by mitigating rmTBI-induced oxidative stress. To model rmTBI, C57BL/6 mice were subjected to three concussive head injuries. MitoQ (5 mg/kg) was administered intraperitoneally to rmTBI+MitoQ mice twice per week over one month. Behavioral and cognitive outcomes were assessed, 30 days following the first head injury, using a battery of behavioral tests. Immunofluorescence was used to assess neuroinflammation and neuronal integrity. Also, qRT-PCR was used to evaluate the expression levels of antioxidant enzymes. Our findings indicated that MitoQ alleviated fine motor function and learning impairments caused by rmTBI. Mechanistically, MitoQ reduced astrocytosis, microgliosis, dendritic and axonal shearing, and increased the expression of antioxidant enzymes. MitoQ administration following rmTBI may represent an efficient approach to ameliorate rmTBI neurological and cellular outcomes with no observable side effects.
In the version of this article initially published, extraneous references 29, 44-47, 19-22 were l... more In the version of this article initially published, extraneous references 29, 44-47, 19-22 were listed in Extended Data Fig. 4 caption and ref. 48 was listed in Extended Data Fig. 7 caption. The references have been removed from the HTML and PDF versions of the article.
other sleep disorders allows us to exclude a significant recruitment bias and probably indicates ... more other sleep disorders allows us to exclude a significant recruitment bias and probably indicates the validity of these results also for non-clinical populations. Support (If Any): .
Cancer Epidemiology and Prevention Biomarkers, 2007
A68 Increasing incidence of hepatocellular carcinoma (HCC) was associated with hepatitis C (HCV) ... more A68 Increasing incidence of hepatocellular carcinoma (HCC) was associated with hepatitis C (HCV) viral infection. Our study of HCC in Egypt, a country with an epidemic of HCV, identified a set of glycans as candidate markers for early detection of HCC. Glycans enzymatically released from serum proteins were analyzed by MALDI-TOF/TOF following solid phase permethylation. Analysis of less than 0.05 ml of serum allowed relative quantification of 80 glycans. Approximately half of the glycans changed significantly at p
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