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1.  Prediction of Glycan Motifs Using Quantitative Analysis of Multi-lectin Binding: Motifs on MUC1 Produced by Cultured Pancreatic Cancer Cells 
Proteomics. Clinical applications  2013;10.1002/prca.201300069.
Lectins are valuable tools for detecting specific glycans in biological samples, but the interpretation of the measurements can be ambiguous due to the complexities of lectin specificities. Here we present an approach to improve the accuracy of interpretation by converting lectin measurements into quantitative predictions of the presence of various glycan motifs. The conversion relies on a database of analyzed glycan array data that provides information on the specificities of the lectins for each of the motifs. We tested the method using measurements of lectin binding to glycans on glycan arrays and found that the combined measurements from several lectins are more accurate than individual measurements for predicting the presence or absence of motifs. We then applied the method to predicting motifs on the protein MUC1 expressed in eight different pancreatic cancer cell lines. Each cell line expressed a unique pattern of MUC1 glycoforms, and the glycoforms significantly differed between MUC1 collected from conditioned media and MUC1 collected from cell lysates. This new method could provide more accurate analyses of glycans in biological sample and make the use of lectins more practical and effective for a broad range of researchers.
PMCID: PMC3929537  PMID: 23956151
2.  Targeted glycoprotein enrichment and identification in stromal cell secretomes using azido sugar metabolic labeling 
Effectively identifying the proteins present in the cellular secretome is complicated due to the presence of cellular protein leakage and serum protein supplements in culture media. A metabolic labeling and click chemistry capture method is described that facilitates the detection of lower abundance glycoproteins in the secretome, even in the presence of serum.
Experimental design
Two stromal cell lines were incubated with tetraacetylated sugar-azide analogs for 48 h in serum-free and low-serum conditions. Sugar-azide labeled glycoproteins were covalently linked to alkyne-beads, followed by on-bead trypsin digestion and MS/MS. The resulting glycoproteins were compared between media conditions, cell lines, and azide-sugar labels.
Alkyne-bead capture of sugar-azide modified glycoproteins in stromal cell culture media significantly improved the detection of lower abundance secreted glycoproteins compared to standard serum-free secretome preparations. Over 100 secreted glycoproteins were detected in each stromal cell line and significantly enriched relative to a standard secretome preparation.
Conclusion and clinical relevance
Sugar-azide metabolic labeling is an effective way to enrich for secreted glycoproteins present in cell line secretomes, even in culture media supplemented with serum. The method has utility for identifying secreted stromal proteins associated with cancer progression and the epithelial-to-mesenchymal transition.
PMCID: PMC4331031  PMID: 23687070
Glycoproteins; Metabolic labeling; Prostate cancer; Secretome; Stroma
3.  [No title available] 
PMCID: PMC3965623  PMID: 24259517
4.  N-Glycoprotein Surfaceomes of Four Developmentally Distinct Mouse Cell Types 
Detailed knowledge of cell surface proteins present during early embryonic development remains limited for most cell lineages. Due to the relevance of cell surface proteins in their functional roles controlling cell signaling and their utility as accessible, non-genetic markers for cell identification and sorting, the goal of this study was to provide new information regarding the cell surface proteins present during early mouse embryonic development.
Experimental Design
Using the Cell Surface Capture Technology, the cell surface N-glycoproteomes of three cell lines and one in vitro differentiated cell type representing distinct cell fates and stages in mouse embryogenesis were assessed.
Altogether, more than 600 cell surface N-glycoproteins were identified represented by >5500 N-glycopeptides.
Conclusions and Clinical Relevance
The development of new, informative cell surface markers for the reliable identification and isolation of functionally defined subsets of cells from early developmental stages will advance the use of stem cell technologies for mechanistic developmental studies, including disease modeling and drug discovery.
PMCID: PMC4151168  PMID: 24920426
Biomarkers; Cardiovascular; Glycoproteins; Plasma membrane; Glycoproteomics
5.  Increased Bisecting N-Acetylglucosamine and Decreased Branched Chain Glycans of N-linked Glycoproteins in Expressed Prostatic Secretions Associated with Prostate Cancer Progression 
Proteomics. Clinical applications  2013;10.1002/prca.201200134.
Using prostatic fluids rich in glycoproteins like prostate specific antigen (PSA) and prostatic acid phosphatase (PAP) , the goal of this study was to identify the structural types and relative abundance of glycans associated with prostate cancer status for subsequent use in emerging mass spectrometry-based glycopeptide analysis platforms.
Experimental Design
A series of pooled samples of expressed prostatic secretions (EPS) and exosomes reflecting different stages of prostate cancer disease were used for N-linked glycan profiling by three complementary methods, MALDI-TOF profiling, normal-phase HPLC separation, and triple quadropole MS analysis of PAP glycopeptides.
Glycan profiling of N-linked glycans from different EPS fluids indicated a global decrease in larger branched tri- and tetra-antennary glycans. Differential exoglycosidase treatments indicated a substantial increase in bisecting N-acetylglucosamines correlated with disease severity. A triple quadrupole MS analysis of the N-linked glycopeptides sites from PAP in aggressive prostate cancer pools was done to cross-reference with the glycan profiling data.
Conclusion and clinical relevance
Changes in glycosylation as detected in EPS fluids reflect the clinical status of prostate cancer. Defining these molecular signatures at the glycopeptide level in individual samples could improve current approaches of diagnosis and prognosis.
PMCID: PMC3969874  PMID: 23775902
Glycomics; N-linked glycosylation; Prostatic acid phosphatase; Urine Exosome; Prostate Cancer; Expressed Prostatic Secretion
6.  Imaging Mass Spectrometry: A New Tool for Pathology in a Molecular Age 
Mass spectrometry provides unique advantages for the analysis of clinical specimens, and these capabilities have been critical to the advancement of diagnostic medicine. To date, liquid chromatography mass spectrometry (LC-MS) is the platform most commonly used for diagnostics; however, LC-MS based proteomics is very labor intensive and costly to implement for high volume assays. Furthermore, when analyzing tissue samples, additional laborious sample preparation steps must be employed (e.g., extraction methods or laser microdissection). The direct analysis of cells and tissues by matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) has developed significant momentum for applications that have diagnostic potential. MALDI IMS provides molecular information from specific cell types within tissue sections; however, this laser-based approach significantly reduces the analysis time for each location sampled. This Viewpoint discusses the technologies for direct analysis of tissues, the potential for diagnostic applications using MALDI IMS, and the challenges faced in the transfer of the technology to the clinical laboratory.
PMCID: PMC3919023  PMID: 24178781
7.  O-GlcNAcomics – Revealing Roles of O-GlcNAcylation in Disease Mechanisms and Development of Potential Diagnostics 
Proteomics. Clinical applications  2013;10.1002/prca.201300001.
O-linked-β-N-acetylglucosamine (O-GlcNAc) is a dynamic post-translational modification of the 3′-hydroxyl groups of serine or threonine residues of nuclear, cytoplasmic, and mitochondrial proteins. The cycling of this modification is regulated in response to nutrients, stress, and other extracellular stimuli by the catalytic activities of O-GlcNAc transferase and O-GlcNAcase. O-GlcNAc is functionally similar to phosphorylation and has been demonstrated to play critical roles in numerous biological processes, including cell signaling, transcription, and disease etiology. Since its discovery nearly thirty years ago, studies have demonstrated that the O-GlcNAc is highly abundant and widespread, like phosphorylation however, the development of methodologies to study O-GlcNAc at the site level has been challenging. Recently, a number of studies have overcome these challenges and describe new tagging, enrichment, and mass spectrometric-based approaches to study O-GlcNAc in terms of its site identification, stoichiometry, and dynamics on proteins. The development of these methods are key for elucidation of O-GlcNAc’s functional crosstalk with phosphorylation and other PTMs, and will serve to provide the necessary information for the development of site-specific antibodies, which will aid in the determination of a particular protein’s site specific function. In this review, we describe these methods and summarize results obtained from them demonstrating the roles of O-GlcNAc in diabetes, cancer, Alzheimer’s, and in learning and memory, while also describing how these new strategies have implicated O-GlcNAc as a potential diagnostic for the screening of patients for prediabetes.
PMCID: PMC3883918  PMID: 23640805
Alzheimer’s; Cancer; Diabetes; Glycomics; O-GlcNAc
8.  Enrichment strategies in glycomics based lung cancer biomarker development 
Proteomics. Clinical applications  2013;10.1002/prca.201200131.
There is a need to identify better glycan biomarkers for diagnosis, early detection and treatment monitoring in lung cancer using biofluids such as blood. Biofluids are complex mixtures of proteins dominated by a few high abundance proteins that may not have specificity for lung cancer. Therefore two methods for protein enrichment were evaluated; affinity capturing of IgG and enrichment of medium abundance proteins, thus allowing us to determine which method yields the best candidate glycan biomarkers for lung cancer.
Experimental design
N-glycans isolated from plasma samples from 20 cases of lung adenocarcinoma and 20 matched controls were analyzed using nLC-PGC-chip-TOF-MS. N-glycan profiles were obtained for five different fractions: total plasma, isolated IgG, IgG depleted plasma, and the bound and flow-through fractions of protein enrichment.
Four glycans differed significantly (FDR<0.05) between cases and controls in whole unfractionated plasma, while four other glycans differed significantly by cancer status in the IgG fraction. No significant glycan differences were observed in the other fractions.
Conclusions and clinical relevance
These results confirm that the N-glycan profile in plasma of lung cancer patients is different from healthy controls and appears to be dominated by alterations in relatively abundant proteins.
PMCID: PMC3884000  PMID: 23640812
N-glycan; mass spectrometry; non-small cell lung cancer; biomarker; protein enrichment
9.  Comparison of two phenotypically distinct lattice corneal dystrophies caused by mutations in the transforming growth factor beta induced (TGFBI) gene 
In this study, we investigated whether the phenotypic difference observed between two lattice corneal dystrophy type 1 (LCD type 1) cases caused by either a single A546D substitution or a A546D/P551Q double substitution in TGFBIp, can be ascribed to (I) a difference in the proteomes of corneal amyloid deposits, (II) altered proteolysis of TGFBIp or (III) structural changes of TGFBIp introduced by the P551Q amino acid substitution.
Experimental design
Amyloid deposits were isolated from the corneas of two siblings with LCD type 1 resulting from A546D/P551Q mutations in TGFBI using laser capture microdissection and a subsequently analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Proteolytic processing of TGFBIp was addressed by counting peptide spectra. Lastly, to study the possible effect of the P551Q substitution, recombinant FAS1-4 domain variants were subjected to in vitro stability assays.
The amyloid proteomes and TGFBIp processing of the two A546D/P551Q LCD type 1 cases were similar to each other as well as to the A546D amyloid proteome previously reported by us. The stability assays revealed a minor destabilization of the FAS1-4 domain upon the addition of the P551Q mutation, moreover, it resulted in different accessibility to tryptic cleavage sites between the A546D and A546D/P551Q mutant FAS1-4 domain variants.
The difference in A546D and A546D/P551Q LCD type 1 phenotypes cannot be ascribed to altered corneal amyloid composition or altered in vivo proteolytic processing of TGFBIp. Instead, a small difference in thermodynamic stability introduced by the P551Q mutation most likely causes structural changes of TGFBIp.
PMCID: PMC4163973  PMID: 24302499
Amyloid deposits; cornea; laser capture microdissection; lattice corneal dystrophy; paraffin embedded tissue
10.  A versatile protein microarray platform enabling antibody profiling against denatured proteins 
We aim to develop a protein microarray platform capable of presenting both natural and denatured forms of proteins for antibody biomarker discovery. We will further optimize plasma screening protocols to improve detection.
Experimental design
We developed a new covalent capture protein microarray chemistry using HaloTag fusion proteins and ligand. To enhance protein yield, we used HeLa cell lysate as an in vitro transcription translation system (IVTT). E. coli lysates were added to the plasma blocking buffer to reduce non-specific background. These protein microarrays were probed with plasma samples and autoantibody responses were quantified and compared with or without denaturing buffer treatment.
We demonstrated that protein microarrays using the covalent attachment chemistry endured denaturing conditions. Blocking with E. coli lysates greatly reduced the background signals and expression with IVTT based on HeLa cell lysates significantly improved the antibody signals on protein microarrays probed with plasma samples. Plasma samples probed on denatured protein arrays produced autoantibody profiles distinct from those probed on natively displayed proteins.
Conclusions and clinical relevance
This versatile protein microarray platform allows the display of both natural and denatured proteins, offers a new dimension to search for disease-specific antibodies, broadens the repertoire of potential biomarkers, and will potentially yield clinical diagnostics with greater performance.
PMCID: PMC4127978  PMID: 23027520
Antibody; Autoantibody; Biomarker; Protein microarray; Denaturation
11.  Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling 
Proteomics. Clinical applications  2013;7(0):10.1002/prca.201200109.
Polymorphonuclear neutrophils (PMNs) play an important role in mediating the innate immune response after severe traumatic injury; however, the cellular proteome response to traumatic condition is still largely unknown.
We applied 2D-LC-MS/MS based shotgun proteomics to perform comparative proteome profiling of human PMNs from severe trauma patients and healthy controls.
A total of 197 out of ~2500 proteins (being identified with at least two peptides) were observed with significant abundance changes following the injury. The proteomics data were further compared with transcriptomics data for the same genes obtained from an independent patient cohort. The comparison showed that the protein abundance changes for the majority of proteins were consistent with the mRNA abundance changes in terms of directions of changes. Moreover, increased protein secretion was suggested as one of the mechanisms contributing to the observed discrepancy between protein and mRNA abundance changes. Functional analyses of the altered proteins showed that many of these proteins were involved in immune response, protein biosynthesis, protein transport, NRF2-mediated oxidative stress response, the ubiquitin-proteasome system, and apoptosis pathways.
Our data suggest increased neutrophil activation and inhibited neutrophil apoptosis in response to trauma. The study not only reveals an overall picture of functional neutrophil response to trauma at the proteome level, but also provides a rich proteomics data resource of trauma-associated changes in the neutrophil that will be valuable for further studies of the functions of individual proteins in PMNs.
PMCID: PMC3737403  PMID: 23589343
human neutrophil; LC-MS/MS; Proteomics; Trauma; Genomics
12.  Proteomic Patterns of Colonic Mucosal Tissues Delineate Crohn’s Colitis and Ulcerative Colitis 
Proteomics. Clinical applications  2013;7(0):10.1002/prca.201200107.
Although Crohn’s colitis (CC) and ulcerative colitis (UC) share several clinical features, they have different causes, mechanisms of tissue damage, and treatment options. Therefore, the accurate diagnosis is of paramount importance in terms of medical care. The distinction between UC/CC is made on the basis of clinical, radiologic, endoscopic, and pathologic interpretations but cannot be differentiated in up to 15% of IBD patients. Correct management of this “indeterminate colitis” (IC) depends on the accuracy of future, and yet not known, destination diagnosis (CC/UC).
Experimental design
We have developed a proteomic methodology that has the potential to discriminate between UC/CC. The histologic layers of 62 confirmed UC/CC tissues were analyzed using MALDI-MS for proteomic profiling.
A Support Vector Machine algorithm consisting of 25 peaks was able to differentiate spectra from CC and UC with 76.9% spectral accuracy when using a leave-20%-out cross validation. Application of the model to the entire data set resulted in accurate classification of 19/26 CC patients and 36/36 UC patients when using a 2/3 correct cutoff. A total 114 peaks were found to have Wilcoxin p-values of less than 0.05.
Conclusion/Clinical relevance
This information may provide new avenues for the development of novel personalized therapeutic targets.
PMCID: PMC3737405  PMID: 23382084
Crohn’s colitis; Ulcerative colitis; Colon tissue profiling; Proteomics; Mass Spectrometry
13.  Mass Spectrometric Immunoassay and Multiple Reaction Monitoring as Targeted MS-based Quantitative Approaches in Biomarker Development: Potential Applications to Cardiovascular Disease and Diabetes 
Type 2 diabetes (T2DM) is an important risk factor for cardiovascular disease (CVD)—the leading cause of death in the US. Yet not all subjects with T2DM are at equal risk for CVD complications; the challenge lies in identifying those at greatest risk. Therapies directed towards treating conventional risk factors have failed to significantly reduce this residual risk in T2DM patients. Thus newer targets and markers are needed for the development and testing of novel therapies. Herein we review two complementary mass spectrometry-based approaches—Mass Spectrometric Immunoassay (MSIA) and tandem mass spectrometry as multiple reaction monitoring (MRM)—for the analysis of plasma proteins and post translational modifications (PTMs) of relevance to T2DM and CVD. Together, these complementary approaches allow for high-throughput monitoring of many PTMs and the absolute quantification of proteins near the low picomolar range. In this review article, we discuss the clinical relevance of the HDL proteome and Apolipoprotein A-I PTMs to T2DM and CVD as well as provide illustrative MSIA and MRM data on high density lipoprotein (HDL) proteins from T2DM patients to provide examples of how these mass spectrometry approaches can be applied to gain new insight regarding cardiovascular risk factors. Also discussed are the reproducibility, interpretation and limitations of each technique with an emphasis on their capacities to facilitate the translation of new biomarkers into clinical practice.
PMCID: PMC4029342  PMID: 23696124
Proteomics; HDL; Apolipoprotein A-I; Diabetes; Cardiovascular Disease
14.  Using Proteomics to Uncover Extracellular Matrix Interactions During Cardiac Remodeling 
Proteomics. Clinical applications  2013;7(0):10.1002/prca.201200100.
The left ventricle (LV) responds to a myocardial infarction (MI) with an orchestrated sequence of events that results in fundamental changes to both the structure and function of the myocardium. This collection of responses is termed LV remodeling. Myocardial ischemia resulting in necrosis is the initiating event that culminates in the formation of an extracellular matrix (ECM)-rich infarct scar that replaces necrotic myocytes. While the cardiomyocyte is the major cell type that responds to ischemia, infiltrating leukocytes and cardiac fibroblasts coordinate the subsequent wound healing response. The matrix metalloproteinase (MMP) family of enzymes regulates the inflammatory and ECM responses that modulate scar formation. Matridomics is the proteomic evaluation focused on ECM, while degradomics is the proteomic evaluation of proteases as well as their inhibitors and substrates. This review will summarize the use of proteomics to better understand MMP roles in post-MI LV remodeling.
PMCID: PMC3815558  PMID: 23532927
matridomics; degradomics; matrix metalloproteinases; myocardial infarction; proteomics
15.  SILAC-based quantitative proteomic analysis of gastric cancer secretome 
Gastric cancer is a commonly occurring cancer in Asia and one of the leading causes of cancer deaths. However, there is no reliable blood-based screening test for this cancer. Identifying proteins secreted from tumor cells could lead to the discovery of clinically useful biomarkers for early detection of gastric cancer.
Experimental design
A SILAC-based quantitative proteomic approach was employed to identify secreted proteins that were differentially expressed between neoplastic and non-neoplastic gastric epithelial cells. Proteins from the secretome were subjected to SDS-PAGE and SCX-based fractionation, followed by mass spectrometric analysis on an LTQ-Orbitrap Velos mass spectrometer. Immunohistochemical labeling was employed to validate a subset of candidates using tissue microarrays.
We identified 2,205 proteins in the gastric cancer secretome of which 263 proteins were overexpressed >4-fold in gastric cancer-derived cell lines as compared to non-neoplastic gastric epithelial cells. Three candidate proteins, proprotein convertase subtilisin/kexin type 9 (PCSK9), lectin mannose binding 2 (LMAN2) and PDGFA associated protein 1 (PDAP1), were validated by immunohistochemical labeling.
Conclusions and clinical relevance
We report here the largest cancer secretome described to date. The novel biomarkers identified in the current study are excellent candidates for further testing as early detection biomarkers for gastric adenocarcinoma.
PMCID: PMC3804263  PMID: 23161554
Secreted proteins; cell supernatants; in vivo labeling; gastric carcinoma; biomarkers; early diagnosis
16.  Reconstructing the Pipeline by Introducing Multiplexed Multiple Reaction Monitoring Mass Spectrometry for Cancer Biomarker Verification: An NCI-CPTC Initiative Perspective 
Proteomics. Clinical applications  2010;4(12):904-914.
PMCID: PMC4035121  PMID: 21137031
Biomarkers; clinical proteomics; quantification; biomarker verification (analytical validation); biomarker qualification (clinical validation); MRM-MS
17.  Aptamers and the Next Generation of Diagnostic Reagents 
Antibodies have been extensively used as capture and detection reagents in diagnostic applications of proteomics-based technologies. Proteomic assays need high sensitivity and specificity, a wide dynamic range for detection, and accurate, reproducible quantification with small confidence values. However, several inherent limitations of monoclonal antibodies in meeting the emerging challenges of proteomics led to the development of a new class of oligonucleotide-based reagents. Natural and derivatized nucleic acid aptamers are emerging as promising alternatives to monoclonal antibodies. Aptamers can be effectively used to simultaneously detect thousands of proteins in multiplex discovery platforms, where antibodies often fail due to cross-reactivity problems. Through chemical modification, vast range of additional functional groups can be added at any desired position in the oligonucleotide sequence, therefore the best features of small molecule drugs, proteins and antibodies can be brought together into aptamers, making aptamers the most versatile reagent in proteomics. In this review we discuss the recent developments in aptamer technology, including new selection methods and the aptamers’ application in proteomics.
PMCID: PMC4021847  PMID: 23090891
aptamer-chips; bead-based selection; cancer biomarkers; X-aptamers; thioaptamers
18.  Complete Solubilization of Formalin-Fixed, Paraffin-Embedded Tissue May Improve Proteomic Studies 
Tissue-based proteomic approaches (tissue proteomics) are essential for discovering and evaluating biomarkers for personalized medicine. In any proteomics study, the most critical issue is sample extraction and preparation. This problem is especially difficult when recovering proteins from formalin-fixed, paraffin-embedded (FFPE) tissue sections. However, improving and standardizing protein extraction from FFPE tissue is a critical need because of the millions of archival FFPE tissues available in tissue banks worldwide. Recent progress in the application of heat-induced antigen retrieval (AR) principles for protein extraction from FFPE tissue has resulted in a number of published FFPE tissue proteomics studies. However, there is currently no consensus on the optimal protocol for protein extraction from FFPE tissue or accepted standards for quantitative evaluation of the extracts. Standardization is critical to ensure the accurate evaluation of FFPE protein extracts by proteomic methods such as reverse phase protein arrays (RPPA), which is now in clinical use. In our view, complete solubilization of FFPE tissue samples is the best way to achieve the goal of standardizing the recovery of proteins from FFPE tissues. However, further studies are recommended to develop standardized protein extraction methods to ensure quantitative and qualitative reproducibility in the recovery of proteins from FFPE tissues.
PMCID: PMC3779364  PMID: 23339100
antigen retrieval; FFPE; Formalin-fixed; paraffin-embedded; proteomics; tissue proteomics; protein extraction; elevated pressure
19.  Discrimination of ischemic and hemorrhagic strokes using a multiplexed, mass spectrometry-based assay for serum apolipoproteins coupled to multi-marker ROC algorithm 
Typically, apolipoproteins are individually measured in blood by immunoassay. In this report, we describe the development of a multiplexed selected reaction monitoring (SRM) based assay for a panel of apolipoproteins and its application to a clinical cohort of samples derived from acute stroke patients.
Experimental Design
An SRM assay for a panel of nine apolipoproteins was developed on a triple quadrupole mass spectrometer. Quantitative data for each apolipoprotein were analyzed to determine expression ratio and receiver operating characteristic (ROC) values for ischemic versus hemorrhagic stroke.
The optimized SRM assay was used to interrogate a small cohort of well-characterized plasma samples obtained from patients with acute ischemic and hemorrhagic strokes. The ROC analyses demonstrated good classification power for several single apolipoproteins, most notably apoC-III and apoC-I. When a novel multi-marker ROC algorithm was applied, the ischemic versus hemorrhagic groups were best differentiated by a combination of apoC-III and apoA-I with an area under the curve (AUC) value of 0.92.
Conclusions and clinical relevance
This proof-of-concept study provides interesting and provocative data for distinguishing ischemic versus hemorrhage within first week of symptom onset. However, the observations are based on one cohort of patient samples and further confirmation will be required.
PMCID: PMC3910141  PMID: 22532455
Biomarker; Cerebrovascular; Hemorrhagic; Ischemic; Mass spectrometry
20.  Protein profiling of formalin fixed paraffin embedded tissue: Identification of potential biomarkers for pediatric brainstem glioma 
Little is known about the molecular characteristics of pediatric brainstem gliomas (BSG), which continue to have a dismal prognosis. Targeted molecular strategies are limited due to rarity of biopsy BSG specimen coupled with obstacles associated with the analyses of formalin-fixed paraffin- embedded (FFPE) autopsies. The objective of this study was to develop methodologies to successfully identify the proteome profile from these archived FFPE specimens. Peptides were extracted from both tumor and adjacent normal FFPE brainstem specimen and quantified using 18O proteolytic labeling strategy and LC-MS/MS analysis. The ingenuity pathway analysis software was used to elucidate interactions amongst differentially expressed proteins. We identified 188 proteins of which 54 (29%) were found up-regulated (≥1.5-fold) in BSG compared to normal sections. Of these, 15 (28%) proteins have previously been reported as potential biomarkers for supratentorial malignant gliomas, while the rest appear to be exclusive to pediatric BSG. Because the majority of differentially expressed proteins are unique to BSG, we conclude that pediatric BSG is distinct from supratentorial gliomas. To the best of our knowledge, this is the first proteome profile of pediatric BSG, which may facilitate discovery of novel therapeutic targets for early diagnostics and improving prognostics.
PMCID: PMC3907167  PMID: 21136889
Formalin fixed paraffin embedded; Ingenuity pathway analysis; Pediatric brainstem
21.  Apolipoprotein A-I: Insights from Redox Proteomics for its Role in Neurodegeneration 
Proteomics has a wide range of applications, including determination of differences in the proteome in terms of expression and post-translational protein modifications. Redox proteomics allows the identification of specific targets of protein oxidation in a biological sample. Using proteomic techniques, apolipoprotein A-I (ApoA-I) has been found at decreased levels in subjects with a variety of neurodegenerative disorders including in the serum and cerebrospinal fluid (CSF) of Alzheimer disease (AD), Parkinson disease (PD) and Down syndrome (DS) with gout subjects. ApoA-I plays roles in cholesterol transport and regulation of inflammation. Redox proteomics further showed ApoA-I to be highly oxidatively modified and particularly susceptible to modification by 4-hydroxy-2-trans-nonenal (HNE), a lipid peroxidation product. In the current review, we discuss the consequences of oxidation of ApoA-I in terms of neurodegeneration. ROS-associated chemotherapy related ApoA-I oxidation leads to elevation of peripheral levels of tumor necrosis factor-α (TNF-α) that can cross the blood-brain barrier (BBB) causing a signaling cascade that can contribute to neuronal death, likely a contributer to what patients refer to as “chemobrain.” Current evidence suggests ApoA-I to be a promising diagnostic marker as well as a potential target for therapeutic strategies in these neurodegenerative disorders.
PMCID: PMC3760000  PMID: 23027708
Alzheimer disease; Apolipoprotein A-I; neurodegeneration; proteomics; Tumor necrosis factor-α
23.  Solid-phase glycan isolation for glycomics analysis 
Glycosylation is one of the most significant protein PTMs. The biological activities of proteins are dramatically changed by the glycans associated with them. Thus, structural analysis of the glycans of glycoproteins in complex biological or clinical samples is critical in correlation with the functions of glycans with diseases. Profiling of glycans by HPLC-MS is a commonly used technique in analyzing glycan structures and quantifying their relative abundance in different biological systems. Methods relied on MS require isolation of glycans from negligible salts and other contaminant ions since salts and ions may interfere with the glycans, resulting in poor glycan ionization. To accomplish those objectives, glycan isolation and clean-up methods including SPE, liquid-phase extraction, chromatography, and electrophoresis have been developed. Traditionally, glycans are isolated from proteins or peptides using a combination of hydrophobic and hydrophilic columns: proteins and peptides remain on hydrophobic absorbent while glycans, salts, and other hydrophilic reagents are collected as flowthrough. The glycans in the flowthrough are then purified through graphite-activated carbon column by hydrophilic interaction LC. Yet, the drawback in these affinity-based approaches is nonspecific binding. As a result, chemical methods by hydrazide or oxime have been developed for solid-phase isolation of glycans with high specificity and yield. Combined with high-resolution MS, specific glycan isolation techniques provide tremendous potentials as useful tools for glycomics analysis.
PMCID: PMC3674833  PMID: 23090885
Dynamic covalent chemistry; Hydrazide; Immobilization; MALDI-TOF MS; Solid-phase extraction
24.  Autoimmunoreactive IgGs from patients with postural orthostatic tachycardia syndrome 
Autoantibodies are implicated in the pathogenesis of cardiovascular diseases and cardiac arrhythmias. In this pilot study, we tested the hypothesis that autoantibodies are present in patients with postural orthostatic tachycardia syndrome (POTS).
Experimental design
Seven control subjects (6 F:1 M, average age 36.1 years) and 10 patients with the diagnosis of POTS (7 F: 3 M, average age 35.1 years) provided informed consent and 30 ml of venous blood. Human heart membrane proteins were resolved by 2DE and immunoblotted against purified IgGs from controls and patients.
Eighteen protein spots immunoreactive specifically against patient IgGs were detected and they were excised from gels, trypsin-digested, and analyzed by nanoLC-electrospray tandem MS. Forty unique proteins were identified and these include proteins that are associated with cardiac hypertrophy (mimecan, myozenin), cardiac remodeling (periostin), cardiomyopathy (desmin, desmoplakin), cell survival (laminin), structural integrity (filamin), chaperone proteins (crystalline, HSP70), mitochondrial enzymes and channel proteins. Ingenuity Pathway Analysis showed multiple pathways were involved including those that regulate energy metabolism, redox, fibrosis, cardiac hypertrophy and degeneration.
Conclusions and clinical relevance
Autoantibodies are present in patients with POTS. These autoantibodies cross-react with a wide range of cardiac proteins and may induce alterations in cardiac function. Autoimmune pathogenetic mechanisms should be further explored in these patients.
PMCID: PMC3786406  PMID: 23002038
Autoantibodies; cell membrane; proteomics; postural orthostatic tachycardia syndrome (POTS)
25.  Characterizations and validations of novel antibodies toward translational research 
Proteomics. Clinical applications  2010;4(0):10.1002/prca.200900186.
One of the most challenging issues in the post-genome era is to explore and understand the function of all proteins encoded by the genome of an organism. Advances in tissue-based proteomic profiling have led to the discovery of many candidate molecular biomarkers and therapeutic targets. For this reason, we have focused on the development and validation of antibodies to proteins associated with cancer. We developed a new antibody validation and characterization method that is systematic and high-throughput. This novel strategy is based on a novel protein array coupled with immunohistochemistry. In the first phase, we screened NCI60 panel of cell lines by means of protein array. Subsequently, we validated selected antibodies with the NCI60 cell microarray. In the final stage, we created a tissue-based protein expression map using multi-tumor tissue microarray. The success rate of this systematic antibody-screening tool, based on our antibody cohort to date, was 92.7% as measured by the results from the protein array. The present strategy of antibody validation and characterization provides a new tool for exploration of the human proteome.
PMCID: PMC3839105  PMID: 21137080
Antibody specificity; Immunohistochemistry; Protein array; Proteomics; Tissue microarray

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