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1.  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.
Purpose
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.
Results
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.
doi:10.1002/prca.201200134
PMCID: PMC3969874  PMID: 23775902
Glycomics; N-linked glycosylation; Prostatic acid phosphatase; Urine Exosome; Prostate Cancer; Expressed Prostatic Secretion
2.  Single center TAVR experience with a focus on the prevention and management of catastrophic complications 
Background
Transcatheter aortic valve replacement (TAVR) is an important treatment option for patients with severe symptomatic aortic stenosis (AS) who are inoperable or at high risk for complications with surgical aortic valve replacement. We report here our single-center data on consecutive patients undergoing transfemoral (TF) TAVR since the inception of our program, with a special focus on minimizing and managing complications.
Methods
The patient population consists of all consecutive patients who underwent an attempted TF-TAVR at our institution, beginning with the first proctored case in May 2006, through December 2012. Clinical, procedural, and echocardiographic data were collected by chart review and echo database query. All events are reported according to Valve Academic Research Consortium-2.
Results
During the study period, 255 patients with AS had attempted TF-TAVR. The procedure was successful in 244 (95.7%) patients. Serious complications including aortic annular rupture (n = 2), coronary occlusion (n = 2), iliac artery rupture (n = 1), and ventricular embolization (n = 1) were successfully managed. Death and stroke rate at 30 days was 0.4% and 1.6%, respectively. One-year follow-up was complete in 171 (76%) patients. One-year mortality was 17.5% with a 3.5% stroke rate. Descending aortic rupture, while advancing the valve, was the only fatal procedural event. There were 24.4% patients with ≥2+ aortic regurgitation.
Conclusions
TAVR can be accomplished with excellent safety in a tertiary center with a well-developed infrastructure for the management of serious complications. The data presented here provide support for TAVR as an important treatment option, and results from randomized trials of patients with lower surgical risk are eagerly awaited.
doi:10.1002/ccd.25356
PMCID: PMC4231228  PMID: 24407775
aortic stenosis; percutaneous intervention; TAVR; complications; vascular access; comparative effectiveness/patient centered outcomes research
3.  A MALDI Imaging Mass Spectrometry Workflow for Spatial Profiling Analysis of N-linked Glycan Expression in Tissues 
Analytical chemistry  2013;85(20):9799-9806.
A new Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in tissues is described. Application of an endoglycosidase, peptide N-glycosidase F (PNGaseF), directly on tissues followed by incubation releases N-linked glycan species amenable to detection by MALDI-IMS. The method has been designed to simultaneously profile the multiple glycan species released from intracellular organelle and cell surface glycoproteins, while maintaining histopathology compatible preparation workflows. A recombinant PNGaseF enzyme was sprayed uniformly across mouse brain tissue slides, incubated for two hours, then sprayed with 2,5-dihydroxybenzoic acid matrix for MALDI-IMS analysis. Using this basic approach, global snapshots of major cellular N-linked glycoforms were detected, including their tissue localization and distribution, structure and relative abundance. Off-tissue extraction and modification of glycans from similarly processed tissues and further mass spectrometry or HPLC analysis was done to assign structural designations. MALDI-IMS has primarily been utilized to spatially profile proteins, lipids, drug and small molecule metabolites in tissues, but it has not been previously applied to N-linked glycan analysis. The translatable MALDI-IMS glycan profiling workflow described herein can readily be applied to any tissue type of interest. From a clinical diagnostics perspective, the ability to differentially profile N glycans and correlate their molecular expression to histopathological changes can offer new approaches to identifying novel disease related targets for biomarker and therapeutic applications.
doi:10.1021/ac402108x
PMCID: PMC3969840  PMID: 24050758
4.  MALDI Imaging Mass Spectrometry Profiling of N-Glycans in Formalin-Fixed Paraffin Embedded Clinical Tissue Blocks and Tissue Microarrays 
PLoS ONE  2014;9(9):e106255.
A recently developed matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) method to spatially profile the location and distribution of multiple N-linked glycan species in frozen tissues has been extended and improved for the direct analysis of glycans in clinically derived formalin-fixed paraffin-embedded (FFPE) tissues. Formalin-fixed tissues from normal mouse kidney, human pancreatic and prostate cancers, and a human hepatocellular carcinoma tissue microarray were processed by antigen retrieval followed by on-tissue digestion with peptide N-glycosidase F. The released N-glycans were detected by MALDI-IMS analysis, and the structural composition of a subset of glycans could be verified directly by on-tissue collision-induced fragmentation. Other structural assignments were confirmed by off-tissue permethylation analysis combined with multiple database comparisons. Imaging of mouse kidney tissue sections demonstrates specific tissue distributions of major cellular N-linked glycoforms in the cortex and medulla. Differential tissue distribution of N-linked glycoforms was also observed in the other tissue types. The efficacy of using MALDI-IMS glycan profiling to distinguish tumor from non-tumor tissues in a tumor microarray format is also demonstrated. This MALDI-IMS workflow has the potential to be applied to any FFPE tissue block or tissue microarray to enable higher throughput analysis of the global changes in N-glycosylation associated with cancers.
doi:10.1371/journal.pone.0106255
PMCID: PMC4153616  PMID: 25184632
5.  Lectin-reactive Anti-α-Gal in Patients with Crohn’s Disease: Correlation with Clinical Phenotypes 
Inflammatory bowel diseases  2013;19(13):2796-2800.
Background
Patients with inflammatory bowel disease have higher proportions of immunoglobulin G (IgG) antibodies lacking N-galactose, also called agalactosyl IgG, in their serum. Such agalactosyl IgGs have been associated with disease activity and the immunogenicity of biologics. The aim was to describe the relationship between circulating levels of a subset of agalactosyl IgGs (anti-α-Gal) and Crohn’s disease (CD) phenotypes.
Methods
Prospectively collected serum samples of a well-characterized cohort of patients with inflammatory bowel disease and controls were used. Serum anti-α-Gal levels were measured by a high-affinity enzyme-linked immunosorbent assay and referenced to a standard control.
Results
Serum samples from 167 subjects were tested; 62 with CD, 76 with ulcerative colitis, and 29 controls. Agalactosyl anti-α-Gal levels were significantly higher in active CD than in active ulcerative colitis (P = 0.0043) or healthy controls (P < 0.0001). Among patients with CD, agalactosyl anti-α-Gal levels were significantly higher in those with a history of arthritis, than those without (P = 0.0002), but lower in those taking immunomodulators (P = 0.03). There was no correlation between agalactosyl anti-α-Gal levels and indices of Crohn’s severity, including C-reactive protein levels or Harvey– Bradshaw index. Patients who were primary or secondary nonresponders to infliximab had similar agalactosyl anti-α-Gal levels to clinical responders.
Conclusions
Patients with CD have greater amounts of agalactosylated anti-α-Gal antibodies in their serum, particularly in those with associated joint disease. This increase seems to be independent of indices of disease activity, but is influenced by immunomodulator use.
doi:10.1097/01.MIB.0000435437.76741.cb
PMCID: PMC4112456  PMID: 24185312
glycosylated antibodies; Crohn’s disease; arthropathy
6.  Small molecule inhibitors of ER α-glucosidases are active against multiple hemorrhagic fever viruses 
Antiviral research  2013;98(3):432-440.
Host cellular endoplasmic reticulum α-glucosidases I and II are essential for the maturation of viral glycosylated envelope proteins that use the calnexin mediated folding pathway. Inhibition of these glycan processing enzymes leads to the misfolding and degradation of these viral glycoproteins and subsequent reduction in virion secretion. We previously reported that, CM-10-18, an imino sugar α-glucosidase inhibitor, efficiently protected the lethality of dengue virus infection of mice. In the current study, through an extensive structure-activity relationship study, we have identified three CM-10-18 derivatives that demonstrated superior in vitro antiviral activity against representative viruses from four viral families causing hemorrhagic fever. Moreover, the three novel imino sugars significantly reduced the mortality of two of the most pathogenic hemorrhagic fever viruses, Marburg virus and Ebola virus, in mice. Our study thus proves the concept that imino sugars are promising drug candidates for the management of viral hemorrhagic fever caused by variety of viruses.
doi:10.1016/j.antiviral.2013.03.023
PMCID: PMC3663898  PMID: 23578725
7.  Chronic hepatitis B: What should be the goal for new therapies? 
Antiviral research  2013;98(1):27-34.
Chronic hepatitis B can currently be medically managed with either pegylated interferon-alpha (pegIFN-α) or one of the five nucleos(t)ide analogue Direct Acting Antivirals (DAAs) that inhibit the hepatitis B virus (HBV) DNA polymerase. While pegIFN-α is effective in approximately one-third of the treated patients, the polymerase inhibitors significantly reduce viral load in the vast majority of those treated. However, neither pegIFN-α nor nucleosid(t)e analogues are capable of reliably eliminating the virus and achieving a cure. Moreover, the interferons and polymerase inhibitors are recommended by US, European and Asian professional society practice guidelines for use in only a subset of those infected with HBV. This subset is the population with the greatest levels of circulating viral DNA and abnormal liver function. Although this is the population at the highest risk for cirrhosis and liver cancer, those who fall outside the treatment guidelines, with low levels of viral replication and normal serum ALTs, may also benefit from antiviral therapy. The questions are thus: are new classes of drugs needed to manage chronic hepatitis B? Is a cure possible? Is a cure even necessary? It is therefore important to define the meaning of a cure and determine what the goals of new therapies should be. In this article, we address those questions and propose two operational definitions of medically attainable cures. The first is a “functional cure” based on the clinical outcome, in which the patient’s life expectancy becomes the same as that of an individual who has resolved his HBV infection without therapy. Because such an outcome cannot be measured over the short term, we also define an “apparent virological cure,” based on the stable off-drug suppression of HBV viremia and antigenemia and the normalization of ALTs and other laboratory tests. We suggest that such a virological cure should be the goal of future therapeutics in all patients with chronic hepatitis B. The extent to which a virological cure predicts a functional cure will only be determined by long-term follow-up.
doi:10.1016/j.antiviral.2013.01.006
PMCID: PMC3627746  PMID: 23391846
8.  Characterization of HIV-HBV co-infection in a multi-national HIV-infected cohort 
AIDS (London, England)  2013;27(2):191-201.
Objective
To understand the HIV-hepatitis B virus (HBV) epidemic from a global perspective by clinically and virologically characterizing these viruses at the time of antiretroviral therapy (ART) initiation in a multi-national cohort.
Methods and design
HIV-infected subjects enrolled in two international studies were classified as HIV-HBV co-infected or HIV monoinfected prior to ART. HIV-HBV co-infected subjects were tested for HBV characteristics, hepatitis D virus (HDV), a novel non-invasive marker of liver disease, and drug-resistant HBV. Comparisons between discrete covariates used chi-square or Fisher’s exact tests (and Jonchkheere-Terpstra for trend tests) while continuous covariates were compared using Wilcoxon Rank-Sum Test.
Results
Of the 2105 HIV-infected subjects from 11 countries, the median age was 34 years and 63% were Black. The 115 HIV-HBV co-infected subjects had significantly higher ALT and AST values, lower body mass index, and lower CD4+ T-cell counts than HIV monoinfected subjects (median 159 cells/mL and 137 cells/mL, respectively, P=0.04). In the co-infected subjects, 49.6% had HBeAg-negative HBV, 60.2% had genotype A HBV, and 13% were HDV positive. Of the HBeAg-negative subjects, 66% had HBV DNA ≤2000 IU/ml compared to 5.2% of the HBeAg-positive subjects. Drug-resistant HBV was not detected.
Conclusions
Screening for HBV in HIV-infected patients in resource-limited settings is important since it is associated with lower CD4+ T-cell counts. In settings where HBV DNA is not available, HBeAg may be useful to assess the need for HBV treatment. Screening for drug-resistant HBV is not needed prior to starting ART in settings where this study was conducted.
doi:10.1097/QAD.0b013e32835a9984
PMCID: PMC3763734  PMID: 23032418
HIV; HBV; coinfection; global
10.  Improved biomarker performance for the detection of hepatocellular carcinoma by inclusion of clinical parameters 
We have previously identified several biomarkers of hepatocellular carcinoma (HCC). The levels of three of these biomarkers were analyzed individually and in combination with the currently used marker, alpha fetoprotein (AFP), for the ability to distinguish between a diagnosis of cirrhosis (n=113) and HCC (n=164). We have utilized several novel biostatistical tools, along with the inclusion of clinical factors such as age and gender, to determine if improved algorithms could be used to increase the probability of cancer detection. Using several of these methods, we are able to detect HCC in the background of cirrhosis with an AUC of at least 0.95. The use of clinical factors in combination with biomarker values to detect HCC is discussed.
doi:10.1109/BIBM.2012.6392612
PMCID: PMC3845221  PMID: 24307972
Hepatocellular Carcinoma; biomarkers; Hepatitis B virus; logistic regression; penalized logistic regression; classification and regression trees
11.  A comparison of statistical methods for the detection of hepatocellular carcinoma based on serum biomarkers and clinical variables 
BMC Medical Genomics  2013;6(Suppl 3):S9.
Background
Currently, a surgical approach is the best curative treatment for those with hepatocellular carcinoma (HCC). However, this requires HCC detection and removal of the lesion at an early stage. Unfortunately, most cases of HCC are detected at an advanced stage because of the lack of accurate biomarkers that can be used in the surveillance of those at risk. It is believed that biomarkers that could detect HCC early will play an important role in the successful treatment of HCC.
Methods
In this study, we analyzed serum levels of alpha fetoprotein, Golgi protein, fucosylated alpha-1-anti-trypsin, and fucosylated kininogen from 113 patients with cirrhosis and 164 serum samples from patients with cirrhosis plus HCC. We utilized two different methods, namely, stepwise penalized logistic regression (stepPLR) and model-based classification and regression trees (mob), along with the inclusion of clinical and demographic factors such as age and gender, to determine if these improved algorithms could be used to increase the detection of cancer.
Results and discussion
The performance of multiple biomarkers was found to be better than that of individual biomarkers. Using several statistical methods, we were able to detect HCC in the background of cirrhosis with an area under the receiver operating characteristic curve of at least 0.95. stepPLR and mob demonstrated better predictive performance relative to logistic regression (LR), penalized LR and classification and regression trees (CART) used in our prior study based on three-fold cross-validation and leave one out cross-validation. In addition, mob provided unparalleled intuitive interpretation of results and potential cut-points for biomarker levels. The inclusion of age and gender improved the overall performance of both methods among all models considered, while the stratified male-only subset provided the best overall performance among all methods and models considered.
Conclusions
In addition to multiple biomarkers, the incorporation of age and gender into statistical models significantly improved their predictive performance in the detection of HCC.
doi:10.1186/1755-8794-6-S3-S9
PMCID: PMC3980825  PMID: 24564861
12.  Substance abuse, HIV-1 and hepatitis 
Current HIV research  2012;10(7):557-571.
During the course of human immunodeficiency virus type 1 (HIV-1) disease, the virus has been shown to effectively escape the immune response with the subsequent establishment of latent viral reservoirs in specific cell populations within the peripheral blood (PB) and associated lymphoid tissues, bone marrow (BM), brain, and potentially other end organs. HIV-1, along with hepatitis B and C viruses (HBV and HCV), are known to share similar routes of transmission, including intravenous drug use, blood transfusions, sexual intercourse, and perinatal exposure. Substance abuse, including the use of opioids and cocaine, is a significant risk factor for exposure to HIV-1 and the development of acquired immune deficiency syndrome, as well as HBV and HCV exposure, infection, and disease. Thus, coinfection with HIV-1 and HBV or HCV is common and may be impacted by chronic substance abuse during the course of disease. HIV-1 impacts the natural course of HBV and HCV infection by accelerating the progression of HBV/HCV-associated liver disease toward end-stage cirrhosis and quantitative depletion of the CD4+ T-cell compartment. HBV or HCV coinfection with HIV-1 is also associated with increased mortality when compared to either infection alone. This review focuses on the impact of substance abuse and coinfection with HBV and HCV in the PB, BM, and brain on the HIV-1 pathogenic process as it relates to viral pathogenesis, disease progression, and the associated immune response during the course of this complex interplay. The impact of HIV-1 and substance abuse on hepatitis virus-induced disease is also a focal point.
PMCID: PMC3708479  PMID: 22973853
bone marrow; brain; cocaine; HBV; HCV; HIV-1; opioids
13.  Altered Functionality of Anti-Bacterial Antibodies in Patients with Chronic Hepatitis C Virus Infection 
PLoS ONE  2013;8(6):e64992.
Background
Using comparative glycoproteomics, we have previously identified a glycoprotein that is altered in both amount and glycosylation as a function of liver cirrhosis. The altered glycoprotein is an agalactosylated (G0) immunoglobulin G molecule (IgG) that recognizes the heterophilic alpha-gal epitope. Since the alpha gal epitope is found on gut enterobacteria, it has been hypothesized that anti-gal antibodies are generated as a result of increased bacterial exposure in patients with liver disease.
Methods
The N-linked glycosylation of anti-gal IgG molecules from patients with fibrosis and cirrhosis was determined and the effector function of anti-bacterial antibodies from over 100 patients examined. In addition, markers of microbial exposure were determined.
Results
Surprisingly, the subset of agalactosylated anti-gal antibodies described here, was impaired in their ability to mediate complement mediated lysis and inhibited the complement-mediated destruction of common gut bacteria. In an analysis of serum from more than 100 patients with liver disease, we have shown that those with increased levels of this modified anti-gal antibody had increased levels of markers of bacterial exposure.
Conclusions
Anti-gal antibodies in patients with liver cirrhosis were reduced in their ability to mediate complement mediated lysis of target cells. As bacterial infection is a major complication in patients with cirrhosis and bacterial products such as LPS are thought to play a major role in the development and progression of liver fibrosis, this finding has many clinical implications in the etiology, prognosis and treatment of liver disease.
doi:10.1371/journal.pone.0064992
PMCID: PMC3672197  PMID: 23750224
14.  Increased levels of tetra-antennary N-linked glycan but not core fucosylation are associated with hepatocellular carcinoma tissue 
Background
Alterations in glycosylation have long been associated with the development of cancer. In the case of primary hepatocellular carcinoma (HCC), one alteration that has often been associated is increased amounts of fucose attached to the N-glycans of serum proteins secreted by the liver.
Methods
In an effort to determine the origin of this increased fucosylation, we have performed N-linked glycan analysis of HCC tissue, the surrounding non tumor tissue, and compared this to tissue from a non diseased adult liver.
Results
Surprisingly, no difference in the level of fucosylation was observed from the three donor groups, suggesting that the increased levels of fucosylation observed in serum of those with HCC is not the result of increased synthesis of fucosylated proteins in the cancer tissue. On the other hand, increased levels of a tetra-antennary glycan were observed in the HCC tissue as compared to the surrounding tissue or to the non diseased livers.
Conclusions
This represents, to our knowledge, one of the first reports associating increased levels of branching with the development of HCC.
Impact
The identification of increased levels of tetra-antennary glycan on liver tumor tissue, as opposed to adjacent or non diseased tissue may lead to improved detection of HCC.
doi:10.1158/1055-9965.EPI-11-1183
PMCID: PMC3380809  PMID: 22490318
15.  Interleukin-6 and Oncostatin M are elevated in liver disease in conjunction with candidate hepatocellular carcinoma biomarker GP73 
The Golgi phosphoprotein GP73 is elevated in the circulation of individuals with a diagnosis of hepatocellular carcinoma. Its usefulness as a biomarker of HCC is questioned, since it has also been reported to be elevated in the circulation of people with liver cirrhosis. Regulation of GP73 by inflammatory cytokines is therefore of interest. The interleukin-6 (IL-6) family cytokines were tested for effects on GP73 mRNA and/or protein levels in human hepatoblastoma HepG2 cells. Levels of GP73 mRNA and protein were up-regulated in HepG2 cells following treatment with either proinflammatory cytokine IL-6 or the related cytokine oncostatin M (OSM). Induction required the shared receptor subunit gp130, and correlated with increased tyrosine phosphorylation of STAT3. Maximal cytokine-mediated induction was not observed in the presence of protein synthesis inhibitor cycloheximide, suggesting additional regulatory factors play an important role. ELISA measurement of GP73 and IL-6 levels in the sera of patients with pre-malignant liver disease revealed a significant correlation between circulating levels of the two proteins. Similarly, a sensitive ELISA assay was developed to measure circulating OSM. OSM levels were elevated 6–7 fold in sera from patients with either cirrhosis or HCC relative to controls without liver disease. Although there was an association between levels of GP73 and OSM in serum from people with liver cirrhosis, there was not a statistically significant correlation in HCC, suggesting that the role of the cytokines in determining circulating levels may be complex. To our knowledge, this is the first report of OSM elevation being associated with liver disease.
doi:10.3233/CBM-2012-00276
PMCID: PMC3496283  PMID: 23144154
Golgi phosphoprotein; GOLPH2; GOLM1; cirrhosis
16.  Development of recombinant Aleuria aurantia lectins with altered binding specificities to fucosylated glycans 
Changes in glycosylation have long been associated with disease. While there are many methods to detect changes in glycosylation, plant derived lectins are often used to determine changes on specific proteins or molecules of interest. One change in glycosylation that has been observed by us and by others is a disease or antigen associated increase in fucosylation on N-linked glycans. To measure this change, the fucose binding Aleuria aurantia lectin (AAL) is often utilized in plate and solution based assays. AAL is a mushroom derived lectin that contains five fucose binding sites that preferentially bind fucose linked (α-1,3, α-1,2, α-,4, and α-1,6) to N-acetyllactosamine related structures. Recently, several reports by us and by others have indicated that specific fucose linkages found on certain serum biomarker glycoprotein's are more associated with disease than others. Taking a site-directed mutagenesis approach, we have created a set of recombinant AAL proteins that display altered binding affinities to different analytes containing various fucose linkages.
doi:10.1016/j.bbrc.2011.09.027
PMCID: PMC3202172  PMID: 21945439
Lectin; Cancer; Glycobiology; Fucosylation; Hepatitis
17.  Investigation of Plasma Biomarkers in HIV-1/HCV Mono- and Coinfected Individuals by Multiplex iTRAQ Quantitative Proteomics 
Abstract
The analysis of plasma samples from HIV-1/HCV mono- and coinfected individuals by quantitative proteomics is an efficient strategy to investigate changes in protein abundances and to characterize the proteins that are the effectors of cellular functions involved in viral pathogenesis. In this study, the infected and healthy plasma samples (in triplicate) were treated with ProteoMiner beads to equalize protein concentrations and subjected to 4-plex iTRAQ labeling and liquid chromatography/mass spectrometry (LC-MS/MS) analysis. A total of 70 proteins were identified with high confidence in the triplicate analysis of plasma proteins and 65% of the proteins were found to be common among the three replicates. Apolipoproteins and complement proteins are the two major classes of proteins that exhibited differential regulation. The results of quantitative analysis revealed that APOA2, APOC2, APOE, C3, HRG proteins were upregulated in the plasma of all the three HIV-1 mono-, HCV mono-, and coinfected patient samples compared to healthy control samples. Ingenuity pathway analysis (IPA) of the upregulated proteins revealed that they are implicated in the hepatic lipid metabolism, inflammation, and acute-phase response signaling pathways. Thus, we identified several differentially regulated proteins in HIV-1/HCV mono and coinfected plasma samples that may be potential biomarkers for liver disease.
doi:10.1089/omi.2011.0004
PMCID: PMC3243494  PMID: 21978398
18.  The Immune Response to a Vesicular Stomatitis Virus Vaccine Vector Is Independent of Particulate Antigen Secretion and Protein Turnover Rate 
Journal of Virology  2012;86(8):4253-4261.
Vesicular stomatitis virus (VSV) is a highly cytopathic virus being developed as a vaccine vector due to its ability to induce strong protective T cell and antibody responses after a single dose. However, little is known regarding the mechanisms underlying the potent immune responses elicited by VSV. We previously generated a VSV vector expressing the hepatitis B virus middle envelope surface glycoprotein (MS) that induces strong MS-specific T cell and antibody responses in mice. After synthesis in the cytoplasm, the MS protein translocates to the endoplasmic reticulum, where it forms subviral particles that are secreted from the cell. To better understand the contributions of secreted and intracellular protein to the VSV-induced immune response, we produced a vector expressing a secretion-deficient MS mutant (MSC69A) and compared the immunogenicity of this vector to that of the wild-type VSV-MS vector in mice. As expected, the MSC69A protein was not secreted from VSV-infected cells and displayed enhanced proteasome-mediated degradation. Surprisingly, despite these differences in intracellular protein processing, the T cell and antibody responses generated to MSC69A were comparable to those elicited by virus expressing wild-type MS protein. Therefore, when it is expressed from VSV, the immune responses to MS are independent of particulate antigen secretion and the turnover rate of cytoplasmic protein. These results are consistent with a model in which the immune responses to VSV are strongly influenced by the replication cycle of the vector and demonstrate that characteristics of the vector have the capacity to affect vaccine efficacy more than do the properties of the antigen itself.
doi:10.1128/JVI.05991-11
PMCID: PMC3318607  PMID: 22345454
20.  Aleuria Aurantia Lectin (AAL)-Reactive Immunoglobulin G Rapidly Appears in Sera of Animals following Antigen Exposure 
PLoS ONE  2012;7(9):e44422.
We have discovered an Aleuria Aurantia Lectin (AAL)-reactive immunoglobulin G (IgG) that naturally occurs in the circulation of rabbits and mice, following immune responses induced by various foreign antigens. AAL can specifically bind to fucose moieties on glycoproteins. However, most serum IgGs are poorly bound by AAL unless they are denatured or treated with glycosidase. In this study, using an immunogen-independent AAL-antibody microarray assay that we developed, we detected AAL-reactive IgG in the sera of all animals that had been immunized 1–2 weeks previously with various immunogens with and without adjuvants and developed immunogen-specific responses. All of these animals subsequently developed immunogen-specific immune responses. The kinetics of the production of AAL-reactive IgG in mice and rabbits were distinct from those of the immunogen-specific IgGs elicited in the same animals: they rose and fell within one to two weeks, and peaked between four to seven days after exposure, while immunogen-specific IgGs continued to rise during the same period. Mass spectrometric profiling of the Fc glycoforms of purified AAL-reactive IgGs indicates that these are mainly comprised of IgGs with core-fucosylated and either mono-or non-galactosylated Fc N-glycan structures. Our results suggest that AAL-reactive IgG could be a previously unrecognized IgG subset that is selectively produced at the onset of a humoral response.
doi:10.1371/journal.pone.0044422
PMCID: PMC3443102  PMID: 23024749
21.  Novel Changes in Glycosylation of Serum Apo-J in Patients with Hepatocellular Carcinoma 
Background
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and the occurrence of HCC has more than doubled in the United States (USA) in the last decade. Early detection is considered key to reducing the mortality of HCC.
Methods
Using two-dimensional gel electrophoresis and high performance liquid chromatography (HPLC) we have analyzed the glycosylation of Apo-J from healthy controls, patients with liver cirrhosis or with hepatocellular carcinoma.
Results
Apo-J in the serum from patients with HCC had decreased levels of (β-1,4) triantennary N-linked glycan compared with the healthy controls or patients with liver cirrhosis. We analyzed this change in an independent cohort of 76 patients with HCC, 32 with cirrhosis, and 43 infected with hepatitis C virus using the Datura stramonium lectin (DSL), which binds to (β-1,4) triantennary N-linked glycan. The level of DSL-reactive Apo-J allowed us to differentiate HCC from cirrhosis with an area under the receiver operating characteristic curve (AUROC) of 0.852. When Apo-J was combined with other serum biomarkers such as alpha-fetoprotein or fucosylated kininogen using a multivariate logistic regression model, the AUROC increased to 0.944, a value much greater than that observed with AFP alone (AUROC of 0.765).
Conclusions
The glycosylation of Apo-J is a useful marker when used alone or in combination with outer makers for the early detection of HCC.
Impact
The potential use of a combination of alpha-fetoprotein, DLS-reactive Apo-J, and fucosylated kininogen as a biomarker of HCC would have great value in the management of patients with liver disease.
doi:10.1158/1055-9965.EPI-10-1047
PMCID: PMC3111882  PMID: 21467232
22.  Glucosidase inhibition enhances presentation of de-N-glycosylated hepatitis B virus epitopes by MHC class I in vitro and in woodchucks 
Hepatology (Baltimore, Md.)  2010;52(4):1242-1250.
In this report, the possibility of pharmacologically altering the hepatitis B virus (HBV) epitopes presented by major histocompatibility complex (MHC) class I on infected cells is demonstrated. The HBV middle envelope glycoprotein MHBs maturation appears to require calnexin mediated folding. This interaction is dependent upon glucosidases in the endoplasmic reticulum. Prevention of HBV envelope protein maturation in cultured cells with glucosidase inhibitors, such as 6-O-butanoyl castanospermine and N-nonyl deoxynorjirmycin, resulted in MHBs degradation by proteasomes. The de-N-glycosylation associated with polypeptide degradation was predicted to result in conversion of asparagine residues into aspartic acid residues. This prediction was confirmed by showing that peptides corresponding to the N-glycosylation sequons of MHBs, but with aspartic acid replacing asparagine, (a) can prime human CTLs that recognize HBV producing cells and (b) that the presentation of these envelope motifs by MHC class I is enhanced by incubation with glucosidase inhibitors. Moreover, although peripheral blood mononuclear cells isolated from woodchucks chronically infected with woodchuck hepatitis virus (WHV) and vaccinated with WHV surface antigen could be induced to recognize the natural MHBs asparagine-containing peptides, only cells isolated from glucosidase inhibitor treated animals recognized the aspartic containing peptides. Conclusion: These data suggest that pharmacological intervention with glucosidase inhibitors can alter the MHBs epitopes presented. This editing of the amino acid sequence of the polypeptide results in a new epitope, or “editope”, with possible medical significance.
doi:10.1002/hep.23806
PMCID: PMC2947625  PMID: 20658465
envelope glycoprotein; imino sugars; 6-O-butanoyl castanospermine; HBV
23.  A Ubiquitin Independent Degradation Pathway Utilized by a Hepatitis B Virus Envelope Protein to Limit Antigen Presentation 
PLoS ONE  2011;6(9):e24477.
Hepatitis B virus envelope glycoproteins Large (L), Middle (M) and Small (S) are targets of the host cellular immune system. The extent to which the host recognizes viral antigens presented by infected cells is believed to play a decisive role in determining if an infection will be resolved or become chronic. As with other antigens, HBV envelope polypeptides must be degraded, presumably by cellular proteasomes, to be presented by the MHC I pathway. We have used M as a model to study this process and determine how ER quality control monitors these foreign polymeric proteins and disposes of them through the ER-associated degradation (ERAD) pathway. Using both wild type and mutant HBV M protein, we found that unlike most ERAD substrates, which require ubiquitination for retrotranslocation and degradation, the HBV M protein, which only contains two lysine residues, can undergo rapid and complete, ubiquitin independent, proteasome dependent degradation. The utilization of this pathway had a functional consequence, since proteins degraded through it, were poorly presented via MHC I. To test the hypothesis that the level of ubiquitination, independent of protein degradation, controls the level of antigen presentation, we inserted two additional lysines into both the wild type and mutant M protein. Amazingly, while the addition of the lysine residues dramatically increased the level of ubiquitination, it did not alter the rate of degradation. However and remarkably, the increased ubiquitination was associated with a dramatic increase in the level of antigen presentation. In conclusion, using the HBV surface protein as a model, we have identified a novel ubiquitin independent degradation pathway and determined that this pathway can have implications for antigen presentation and potentially viral pathogenesis.
doi:10.1371/journal.pone.0024477
PMCID: PMC3182176  PMID: 21969857
24.  Analysis of GP73 in patients with HCC as a function of anti-cancer treatment 
In this study, we examined the level of Golgi protein 73 (GP73) in the serum of 9 patients as a function of anti-liver cancer treatment. Although the numbers are small, a clear trend was observed. Patients who remained tumor free (up to 6 years post-treatment) showed reductions in GP73 at the first time point available post-treatment. In contrast, patients who had high levels GP73 post treatment all had re-occurrence within a 5 year period. These data are preliminary but dramatically imply that this marker may have value in the monitoring of HCC patients and may be elevated even when small, undetectable tumors are present.
doi:10.3233/CBM-2010-0190
PMCID: PMC3152975  PMID: 21694465
25.  Emphysematous cystitis with clinical subcutaneous emphysema 
Emphysematous cystitis (EC) is the presence of intramural gas, with or without luminal gas, within the bladder as a result of a primary infection of the lower urinary tract with a gas-producing organism. It is a well-recognised complication of urinary tract infections involving Escherichia coli in diabetic patients. Clinical subcutaneous emphysema is a rare complication of EC that appears to have poor prognosis. Only careful clinical judgement, and a high degree of suspicion, will lead to its early diagnosis and treatment. Here, we report a case of subcutaneous emphysema due to EC based on a clinical diagnosis confirmed using computed tomography (CT).
doi:10.1186/1865-1380-4-26
PMCID: PMC3123544  PMID: 21668949

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