Decoding the glycoproteome: a new frontier for biomarker discovery in cancer

Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.

Milk: A Scientific Model for Diet and Health Research in the 21st Century

The origin of lactation and the composition, structures and functions of milk's biopolymers highlight the Darwinian pressure on lactation as a complete, nourishing and protective diet. Lactation, under the driving pressure to be a sustainable bioreactor, was under selection pressure of its biopolymers with diverse functions acting from the mammary gland through the digestive system of the infant. For example, milk is extensively glycosylated and the glycan structures and their functions are now emerging. Milk contains free oligosaccharides; complex polymers of sugars whose stereospecific linkages are not matched by glycosidic enzymes within the mammalian infant gut. These glycan polymers reach the lower intestine undigested. In this microbe-rich environment, bacteria compete to release and ferment the sugars via different hydrolytic strategies. One specific type of bacteria, Bifidobacterium longum subsp. infantis, (B. infantis) is uniquely equipped with a repertoire of genes encoding enzymes capable of taking up, hydrolyzing and metabolizing the complex glycans of human milk. This combination of a distinct food supply and unique genetic capability shapes the composition and metabolic products of the entire microbial community within the lower intestine of breast fed infants. The intestinal microbiome dominated by B. infantis, shields the infant from the growth of gram negative enteropathogens and their endotoxins as a clear health benefit. The world is facing unprecedented challenges to produce a food supply that is both nourishing, safe and sustainable. Scientists need to guide the future of agriculture and food in response to these 21st century challenges. Lactation provides an inspiring model of what that future research strategy could be.

Diversity of Monosaccharide Composition of Diets Consumed by Healthy U.S. Adults Is Highly Variable and Positively Associated With the Healthy Eating Index

Objectives

Advances in analytical chemistry now make it possible to analyze the monosaccharide composition of foods thereby expanding dietary assessment of carbohydrates. We sought to characterize the monosaccharide composition of diets consumed in a healthy U.S. adult cohort (ClinicalTrials.gov Identifier: NCT02367287).

Methods

Dietary records consisting of two to three Automated Self-Administered 24-hour Dietary Recalls (ASA24) were obtained from 341 participants in the USDA Nutritional Phenotyping Study which assessed healthy U.S. adults balanced for age, sex, and BMI. Dietary recalls were merged with the Food and Nutrient Database for Dietary Studies (FNDDS) 2017–2018 to retrieve ingredient level data. From this dataset, recall items were mapped to the food glycan database (Glycopedia) to retrieve monosaccharide quantities for matching food items. Participants with at least 75% of calories consumed from carbohydrates mappable to the Glycopedia were included in the final analysis (n = 180).

Results

On average, glucose comprised the majority of dietary monosaccharides consumed by the cohort (83.4% ± 5.3%, mean, SD) followed by fructose (5.9% ± 2.9%, mean, SD), galactose (4.7% ± 2.7%, mean, SD), arabinose (2.1% ± 0.9%, mean, SD) xylose (1.3% ± 0.4%, mean, SD), GalA (1.2% ± 0.8%, mean, SD) and mannose (0.8% ± 0.6%, mean, SD). Seven additional monosaccharides were present at < 0.5% on average. Monosaccharide diversity in the diet was positively correlated with the Healthy Eating Index score after adjusting for age, sex, and BMI (Pearson's r, r = 0.475, p < 1e-11).

Conclusions

This is the first study to investigate population-based dietary intake at this resolution of food glycan composition. Greater diversity of monosaccharides in the diet corresponds to a healthier eating pattern which may be attributed to reduced intake of simple sugars.

Funding Sources

This project was supported by United States Department of Agriculture (USDA) Agricultural Research Service grant 2032–51,530-026–00D, National Institutes of Health (NIH) award R01DK124193, and the USDA/NSF AI Institute for Next Generation Food Systems (AIFS), USDA award number 2020-67,021-32,855.

Prolonged Fasting Alters the Size, Function, and Glycoproteomic Profile of HDL Particles

Objectives

To investigate the effects of a single 36-hour fast on HDL glycoproteomic composition on isolated HDL particles.

Methods

We obtained plasma from a previous study where 20 healthy subjects, age 20–40, fasted for 36 hours. HDL was isolated using density-based ultracentrifugation steps, followed by size-exclusion chromatography. Glycoproteomic was analyzed using a targeted LC-MS/MS method, and lipoprotein particle size distribution analysis using nuclear magnetic resonance (NMR) spectroscopy.

Results

HDL-associated apolipoprotein A-IV (ApoA-IV) content was significantly reduced (8918.39 +/− 3823.39 normalized ion counts vs 3690.82 +/− 2147.29 normalized ion count, p adjusted < 0.0001), suggesting a reduction in intestinally-derived HDL after a 36-hour fast. HDL associated apolipoprotein C-III (ApoC-III) di-sialylated glycopeptides decreased in HDL following a 36-hour fast compared to an overnight 12-hour fast (0.1680 +/− 0.0342 normalized ion counts vs 0.1315 +/− 0.0373 normalized ion counts, p adjusted = 0.041). Additionally, particle size distribution analysis showed an increase in abundance of calibrated large HDL of size 9.6–13nm (3.42 +/− 2.218 μmol/L vs 3.885 +/− 2.134 μmol/L, p adjusted = 0.011) and a decrease in abundance of medium HDL of size 8.1–9.5nm (6.88 +/− 1.86 μmol/L vs 5.82 +/− 2.048 μmol/L, p adjusted = 0.019) after a 36-hour fast. There were no significant changes in LDL particle size (21.115 +/− nm s 21.205 +/− 0.458 nm, p adjusted = 0.655) but there was a significant increase in overall calibrated LDL particle concentration (1138.05 +/− 357.94 μmol/L vs 1262.3 +/− 313.33 μmol/L, p adjusted = 0.011) and calibrated small LDL particle concentration (454.85 +/− 187.76 μmol/L vs 598.8 +/− 190.84 μmol/L, p adjusted = 0.025).

Conclusions

Our findings indicate that prolonged fasting alters lipoprotein profiles by affecting the proportions of large and small HDL and LDL particles, as well as altering the protein composition of HDL particles, specifically by reducing the abundance of ApoA-IV, which suggests a reduction in the contribution of intestinally-derived HDL particles to the circulating HDL pool. Future studies are needed to determine the long-term effects of multiple bouts of prolonged fasting.

Funding Sources

University of California Davis, National Institute on Aging.

The glycoproteomics of hawk and caiman tears

BACKGROUND

Glycoproteins are important tear components that participate in the stability of the ocular surface. However, the glycopeptides that are present in the tears of wild animals have not yet been described. This work aimed to describe the glycoproteomic profile of roadside hawk (Rupornis magnirostris) and caiman (Caiman latirostris) tears.

METHODS

Tears collected from 10 hawks and 70 caimans using Schirmer tear test strips were used in this study. The samples were submitted to trypsin digestion and separated using a reverse-phase column coupled to a mass spectrometer associated to a nanospray ionization source. The glycoproteins were categorized as: cellular components, biological processes and molecular function, according to the UniProt Knowledgebase.

RESULTS

As shown by the liquid chromatography-mass spectrometry, all glycopeptides found were classified as N-type. Of the 51 glycoproteins that were identified in the hawk tear film, the most abundant were ovotransferrin, globulins and complement system proteins. In the caiman tear film, 29 glycoproteins were identified. The most abundant caiman glycoproteins were uncharacterized proteins, ATPases, globulins and proteasome components. Ontological characterization revealed that the glycoproteins were extracellular, and the most identified molecular function was endopeptidase activity for both species.

CONCLUSION

Glycoproteins are abundant in the tear film of the bird and reptile species studied herein, and all these molecules were shown to have N-type modifications. Location at the extracellular space and an endopeptidase inhibitor activity were the main cell component and molecular function for both species, respectively. These profiles showed differences when compared to human tears, are possibly linked to adaptive processes and can be the basis for further studies on the search of disease biomarkers.

Normal-phase chromatographic separation of pigmented wine tannin by nano-HPLC quadrupole time-of-flight tandem mass spectrometry and identification of candidate molecular features

BACKGROUND

As a wine ages, altered sensory properties lead to changes in perceived quality and value. Concurrent modifications of anthocyanin and tannin occur forming pigmented tannin, softening astringency and retaining persistent color. Wine tannin extracts of 1990 and 2010 vintages of Oakville Station Cabernet Sauvignon have been analyzed using normal-phase chromatography with tandem quadrupole time-of-flight mass spectrometry (QToF) to investigate the compositional differences in their pigmented tannin fractions.

RESULTS

The older wine demonstrates much greater structural diversity and a range of more polar compounds, while the younger wine contains fewer observed ion peaks. Several hundred molecular features are observable, and, as expected, there is progression to higher molecular weights after long aging. Between 7% and 16% of molecular features could be matched to a database of anticipated pigmented tannin compounds. Many signals had multiple possible isomeric identities, but fragmentation to resolve their identity was stymied by low sensitivity of the tandem mass spectrometric capability provided by QToF, so isomeric disambiguation is incomplete.

CONCLUSIONS

The chromatography displayed a high degree of resolution in aged wines, separating many of the known pigment types, including aldehyde bridged compounds, pyranoanthocyanins and direct condensation products among others, as well as resolving a great number of unknown compounds. Expanding our understanding of red wine pigments will lead to better wines as winemakers will be able to associate quality with particular wine pigment profiles once we can distinguish the relevant patterns in those pigments. © 2021 Society of Chemical Industry.

Maternal and Child Supplementation With Small-Quantity Lipid-Based Nutrient Supplements Increases Child HDL Cholesterol Efflux Capacity

Objectives

The purpose of this secondary outcome analysis is to investigate whether small-quantity lipid-based nutrient supplements (SQ-LNS) alters lipid, protein or glycan composition, or the cholesterol efflux capacity (CEC), of high-density lipoprotein (HDL) particles in children in the International Lipid-Based Nutrient Supplements (iLiNS) DYAD trial in Ghana.

Methods

Plasma samples were obtained from a subcohort of 80 children at 18 months of age from the iLiNS-DYAD-Ghana trial. Mothers were randomized to either iron and folic acid (IFA) in pregnancy and 200 mg/d calcium for 6 months postpartum or SQ-LNS (pregnancy and 6 months postpartum). Children in the SQ-LNS group received SQ-LNS from 6 to 18 months while children in the IFA group did not receive supplements. HDL was isolated from plasma by sequential ultracentrifugation followed by size-exclusion chromatography. Assay of cholesterol efflux was performed in vitro, and glycoproteomic and lipidomic composition were analyzed by mass spectrometry. The primary analysis was a comparison of the effects of intervention groups on HDL lipidome, proteome, and CEC. In the exploratory analysis, we compared the enrichment of glycopeptides in measured HDL-associated proteins between groups.

Results

Mean (±SD) HDL CEC was higher among children in the SQ-LNS vs. IFA group (20.9 ± 4.1% vs. 19.4 ± 3.3%; one-tailed p = 0.038). We found no differences in HDL lipidomic or proteomic composition between groups.

Conclusions

Prenatal and postnatal SQ-LNS may improve the CEC of child HDL particles. These improvements may have a potential impact on child health outcomes.

Funding Sources

Supported by Bill & Melinda Gates Foundation grant to the University of California, Davis.

The N-glycome regulates the endothelial-to-hematopoietic transition

Definitive hematopoietic stem and progenitor cells (HSPCs) arise from the transdifferentiation of hemogenic endothelial cells (hemECs). The mechanisms of this endothelial-to-hematopoietic transition (EHT) are poorly understood. We show that microRNA-223 (miR-223)-mediated regulation of N-glycan biosynthesis in endothelial cells (ECs) regulates EHT. miR-223 is enriched in hemECs and in oligopotent nascent HSPCs. miR-223 restricts the EHT of lymphoid-myeloid lineages by suppressing the mannosyltransferase alg2 and sialyltransferase st3gal2, two enzymes involved in protein N-glycosylation. ECs that lack miR-223 showed a decrease of high mannose versus sialylated sugars on N-glycoproteins such as the metalloprotease Adam10. EC-specific expression of an N-glycan Adam10 mutant or of the N-glycoenzymes phenocopied miR-223 mutant defects. Thus, the N-glycome is an intrinsic regulator of EHT, serving as a key determinant of the hematopoietic fate.

Glycobiology of Serum Proteins Following Exposure to a DGA 2010 Based Dietary Pattern in Women

Objectives

Post translational glycosylation (PTG) creates glycoproteins. Glycosylation adds glycan sugars such as sialic acid and fucose to peptides. The type, number and location of these glycans affect the peptides' function and efficacy. Sialic acid is becoming a target biomarker of interest in cardiovascular disease, while fucose has been shown to be elevated in inflammation. The objective of this study was to determine if these glycans (on specific glycoproteins) were different following an 8-wk exposure in women at-risk for cardiometabolic disease to two different dietary patterns – one based on the DGA 2010 (DGA), another based on typical American diet (TAD).

Methods

Forty-four women were screened and enrolled in to an 8-wk controlled feeding trial, 22 each in DGA and TAD groups. Women were enrolled based on either having elevated fasting glucose, triglycerides, LDL-c, or total cholesterol, 2 h glucose following a glucose challenge, or low HDL-c. Fasting serum samples at baseline (Wk0), following 2-wks of exposure (Wk2) and following 8 weeks of exposure (Wk8) were digested (tryptic) and characterized using a UHPLC MS protocol to evaluate 17 different circulating proteins that were associated with cardiometabolic disease. Primary characterizations involved evaluating overall protein concentrations, as well as glycovariant estimations. Change between Wk8 and Wk0 were calculated to evaluate the effect of the diet, and used in non-parametric van der Waerdan's tests comparing DGA vs TAD.

Results

Sialylated glycopeptides were higher following the 8-wk diet in DGA compared to TAD for all proteins (P &lt; 0.005), in particular for alpha-1-acid glycoprotein (P = 0.008) and alpha-2-macroglobulin(P = 0.013), while fucosylation was lower in DGA compared to TAD (alpha-1-acid glycoprotein (P = 0.013).

Conclusions

Diet patterns affect protein post-translational glycosylation, which in turn affects the protein function likely affecting health and disease. Further investigation will help elucidate potential causal links.

Funding Sources

USDA CRIS 2032–51,530-022 and 2032–51,530-025, A grant from the National Dairy Council in cooperation with the Campbell Soup Co.; Innovative Development Awards UC Davis Academic Federation.

Serum glycoproteomic-based liquid biopsy for the detection of pancreatic ductal adenocarcinoma

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Background: Non-invasive biomarkers with high sensitivity and specificity would be of great value for patients with Pancreatic Ductal Adenocarcinoma (PDAC). This would aid in early detection and serve other purposes that 'liquid biopsies' are being explored in. Besides circulating tumor DNA (ctDNA) and methylation markers, glycosylation markers hold great potential promise. We developed a novel workflow using high-resolution quantification of site-specific protein glycosylation by liquid chromatography and tandem mass spectrometry to evaluate the clinical utility of glycoprotemics signature for patients with PDAC. Methods: Serum samples from newly diagnosed PDAC patients and controls were obtained from a commercial biobank (Indivumed, Hamburg, Germany), and a panel of 504 glycan motifs, representing 73 previously reported proteomic markers, was determined. Age-adjusted generalized linear regression models were used to evaluate the differential abundance of each marker, and stepwise variable selection was used for model construction. Results: We analyzed 45 PDAC and 136 control samples. PDAC patients (60% male) had a mean age of 67 (±11) years. with 4.4%, 71.1%, 4.4%, and 20% at stage 1, 2, 3,4, respectively. Controls were women with benign histology after pelvic mass surgery; with a mean age of 61 (±11) years. Twenty-six glycoproteomic markers showed statistically highly significant differential abundance among cases and controls (p<1e-4 each) and were highly reproducible(Pearson’s r > 0.85), which were glycoforms in proteins that have previously been found to be associated with PDAC. Fourteen of these markers displayed >0.8 area under the curve of the receiver operating characteristic (AUC). Multivariate logistic regression modeling with backward selection yielded a classification model with an AUC of 0.94 (95% CI: 0.89-0.99), sensitivity of 91% (95% CI: 75-97%) and specificity of 86% (95% CI: 81-92%). Conclusions: Circulating glycoproteomic biomarkers may be useful in the early detection and clinical management of PDAC patients; offering a new platform to explore and validate.

Omics Forecasting: Predictive Calculations Permit the Rapid Interpretation of High-Resolution Mass Spectral Data from Complex Mixtures

For some complex mixtures, chromatographic techniques are insufficient to separate the large numbers of compounds present. In addition, these mixtures often contain compounds with similar or identical molecular masses and shared fragmentation transitions. Advancements in mass spectrometry have provided more and more detailed molecular profiles with significant increases in resolution. This has led to a capacity to distinguish a very large number of compounds in complex mixtures, providing overwhelming data sets. The approach of calculating molecular formulas from a mass list has become more and more problematic as the number of signals has increased exponentially, to the point that it has become impossible to manually interpret the thousands of mass signals. The current approach is to calculate a list of possible formulas that fall within a specific mass error of the observed signal. Then, one must look for possible structures that can be derived from each entry on the list of formulas. However, an alternative approach is to anticipate the possible structures of a particular set of compounds, such as red wine pigments, and then compare the ion signals against a predicted list. To that end, starting with known wine pigment types, we have generated a set of expected wine pigment variants based on known derivatives of condensed tannin oligomers, anthocyanins, and fermentation products. After the ability to distinguish compounds by mass spectrometry was accounted for, over 1 million results were generated consisting of known and anticipated wine pigments. A comparison with a small sample of wine phenolic fractions show a large number of matches, suggesting that this approach may be helpful.

Nod-like receptors are critical for gut-brain axis signalling in mice

KEY POINTS

•Nucleotide binding oligomerization domain (Nod)-like receptors regulate cognition, anxiety and hypothalamic-pituitary-adrenal axis activation. •Nod-like receptors regulate central and peripheral serotonergic biology. •Nod-like receptors are important for maintenance of gastrointestinal physiology. •Intestinal epithelial cell expression of Nod1 receptors regulate behaviour.

ABSTRACT

Gut-brain axis signalling is critical for maintaining health and homeostasis. Stressful life events can impact gut-brain signalling, leading to altered mood, cognition and intestinal dysfunction. In the present study, we identified nucleotide binding oligomerization domain (Nod)-like receptors (NLR), Nod1 and Nod2, as novel regulators for gut-brain signalling. NLR are innate immune pattern recognition receptors expressed in the gut and brain, and are important in the regulation of gastrointestinal physiology. We found that mice deficient in both Nod1 and Nod2 (NodDKO) demonstrate signs of stress-induced anxiety, cognitive impairment and depression in the context of a hyperactive hypothalamic-pituitary-adrenal axis. These deficits were coupled with impairments in the serotonergic pathway in the brain, decreased hippocampal cell proliferation and immature neurons, as well as reduced neural activation. In addition, NodDKO mice had increased gastrointestinal permeability and altered serotonin signalling in the gut following exposure to acute stress. Administration of the selective serotonin reuptake inhibitor, fluoxetine, abrogated behavioural impairments and restored serotonin signalling. We also identified that intestinal epithelial cell-specific deletion of Nod1 (VilCre⁺ Nod1^f/f ), but not Nod2, increased susceptibility to stress-induced anxiety-like behaviour and cognitive impairment following exposure to stress. Together, these data suggest that intestinal epithelial NLR are novel modulators of gut-brain communication and may serve as potential novel therapeutic targets for the treatment of gut-brain disorders.

The Glycosylation and Glycoprotein Signature of Immunoglobulins in Patients with Autoimmune Liver Diseases

Glycosylation of antibodies, particularly in the Fc domain, critically modulate the ability of antibodies to bind to FcRs, maintaining immune quiescence and marshaling appropriate immune response to achieve a finely orchestrated immune response. Alterations in the glycosylation profile of immunoglobulin (Ig) have been implicated in various autoimmune conditions, which may arise prior to symptoms and have been considered diagnostic for autoimmune disease. We applied QqQ mass spectroscopy with subsequent multiple reaction monitoring (MRM) to elucidate the overall profile, composition and linkage of the sugar residues of plasma IgG, IgM and IgA glycans in 225 serum samples from healthy donors (HD; n=50), PBC (n=100) and PSC (n=75) with or without IBD, using an Agilent 6490 triple quadruple (QqQ) mass spectrometer. Our data demonstrate that most of IgA 1 and 2 glycopeptides significantly distinguish PBC from PSC, which are associated with lower level of Bi anterary glycoforms and elevated HexNac containing glycoforms in PBC samples as compared to both controls and PSC. HexNac terminated IgG1 glycoforms are enriched in both PBC and PSC. The levels of IgM glycopeptide, IgM_439_5200, IgM_439_6200 and J chain distinguish among three categories of samples. Most importantly, a distinct pattern of glycoforms exists in PSC patients with IBD. Neu5Ac terminated IgA and IgM are enriched, while the galactosylated forms are lower in PSC with IBD. Ig glycosylation pattern can be a novel serological marker to distinguish between PBC and PSC. This novel technology highlights the importance of glycan biology in the immune response and as a potential mechanism in the loss of tolerance and/or a disease specific chronic signal of inflammation.

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage

Analytic advances are enabling more precise definitions of the molecular composition of key food staples incorporated into contemporary diets and how the nutrient landscapes of these staples vary as a function of cultivar and food processing methods. This knowledge, combined with insights about the interrelationship between consumer microbiota configurations and biotransformation of food ingredients, should have a number of effects on agriculture, food production, and strategies for improving the nutritional value of foods and health status. These effects include decision-making about which cultivars of current or future food staples to incorporate into existing and future food systems, and which components of waste streams from current or future food manufacturing processes have nutritional value that is worth capturing. They can also guide which technologies should be applied, or need to be developed, to produce foods that support efficient microbial biotransformation of their ingredients into metabolic products that sustain health.

Human milk secretory immunoglobulin a and lactoferrin N-glycans are altered in women with gestational diabetes mellitus

Very little is known about the effects of gestational diabetes mellitus (GDM) on lactation and milk components. Recent reports suggested that hyperglycemia during pregnancy was associated with altered breast milk immune factors. Human milk oligosaccharides (HMOs) and N-glycans of milk immune-modulatory proteins are implicated in modulation of infant immunity. The objective of the current study was to evaluate the effect of GDM on HMO and protein-conjugated glycan profiles in breast milk. Milk was collected at 2 wk postpartum from women diagnosed with (n = 8) or without (n = 16) GDM at week 24-28 in pregnancy. Milk was analyzed for HMO abundances, protein concentrations, and N-glycan abundances of lactoferrin and secretory immunoglobulin A (sIgA). HMOs and N-glycans were analyzed by mass spectrometry and milk lactoferrin and sIgA concentrations were analyzed by the Bradford assay. The data were analyzed using multivariate modeling confirmed with univariate statistics to determine differences between milk of women with compared with women without GDM. There were no differences in HMOs between milk from women with vs. without GDM. Milk from women with GDM compared with those without GDM was 63.6% lower in sIgA protein (P < 0.05), 45% higher in lactoferrin total N-glycans (P < 0.0001), 36-72% higher in lactoferrin fucose and sialic acid N-glycans (P < 0.01), and 32-43% lower in sIgA total, mannose, fucose, and sialic acid N-glycans (P < 0.05). GDM did not alter breast milk free oligosaccharide abundances but decreased total protein and glycosylation of sIgA and increased glycosylation of lactoferrin in transitional milk. The results suggest that maternal glucose dysregulation during pregnancy has lasting consequences that may influence the innate immune protective functions of breast milk.

Aberrant glycosylation of plasma proteins in HIV-infected patients (P6361)

Background: Glycosylation is one of the most abundant post-translational modifications, and is involved in protein structure formation and protein-protein interactions. Aberrant glycosylation profiles are often observed on plasma proteins from patients with inflammatory diseases. Increased levels of non-galactosylated glycans have been reported on serum IgGs of HIV-infected patients. We investigated the effects of HIV infection on protein glycosylation by N-glycomic profiling of plasma and plasma IgG. Methods: We obtained plasma samples of 22 HIV infected patients (11 therapy-naïve, 11 receiving anti-retroviral therapy) and 11 HIV-negative controls. First, a nano-LC-TOF-MS strategy was employed for the evaluation of plasma N-glycan profiles in each of the samples. Then, a UPLC-QQQ-MS method was used to evaluate the IgG specific glycosylation patterns. N-glycan peak integrals were used for biostatistical analysis. Results and conclusion: Several neutral, fucosylated and sialylated glycan compositions as well as high mannose type glycans in plasma samples were significantly altered in therapy-naïve HIV infected patients compared to controls. Moreover, galactose-deficient glycans were increased on the IgG in these patients, independent of IgG subclass. Interestingly, these effects were largely reduced in HIV infected patients receiving therapy. These results suggest an important role for protein glycosylation in immune dysfunction that is driven by active HIV infection.

Comparison of the T cell surface glycome of activated and naïve T cells (P1210)

Protein glycosylation plays an important role in a variety of cellular activities including migration, activation, and adhesion. Although the majority of cellular proteins are glycosylated, little is known about the cell surface glycome of the T cell. Here we characterize the glycans expressed on the surface of naïve, activated and malignant T cells. Using a variety of techniques including density centrifugation, PNGase F enzyme glycan release, lectin column affinity chromatography, nanospray HPLC-chip/time-of-flight mass spectrometry, and flow cytometry we were able to characterize the entire surface glycome of naïve T cells and the associated changes following T cell activation with anti-CD3/CD28. The cell surface proteins expressing these glycans were also identified. Using specific-exoglycosidases to remove the glycans of interest, while leaving their associated proteins intact, the effects of these glycans on T cell proliferation, TCR signal transduction, and TCR down-regulation was determined.

Enhancing peptide ligand binding to vascular endothelial growth factor by covalent bond formation

Formation of a stable covalent bond between a synthetic probe molecule and a specific site on a target protein has many potential applications in biomedical science. For example, the properties of probes used as receptor-imaging ligands may be improved by increasing their residence time on the targeted receptor. Among the more interesting cases are peptide ligands, the strongest of which typically bind to receptors with micromolar dissociation constants, and which may depend on processes other than simple binding to provide images. The side chains of cysteine, histidine, or lysine are attractive for chemical attachment to improve binding to a receptor protein, and a system based on acryloyl probes attaching to engineered cysteine provides excellent positron emission tomographic images in animal models (Wei et al. (2008) J. Nucl. Med. 49, 1828-1835). In nature, lysine is a more common but less reactive residue than cysteine, making it an interesting challenge to modify. To seek practically useful cross-linking yields with naturally occurring lysine side chains, we have explored not only acryloyl but also other reactive linkers with different chemical properties. We employed a peptide-VEGF model system to discover that a 19mer peptide ligand, which carried a lysine-tagged dinitrofluorobenzene group, became attached stably and with good yield to a unique lysine residue on human vascular endothelial growth factor (VEGF), even in the presence of 70% fetal bovine serum. The same peptide carrying acryloyl and related Michael acceptors gave low yields of attachment to VEGF, as did the chloroacetyl peptide.

Protein-Linked Glycan Degradation in Infants Fed Human Milk

Many human milk proteins are glycosylated. Glycosylation is important in protecting bioactive proteins and peptide fragments from digestion. Protein-linked glycans have a variety of functions; however, there is a paucity of information on protein-linked glycan degradation in either the infant or the adult digestive system. Human digestive enzymes can break down dietary disaccharides and starches, but most of the digestive enzymes required for complex protein-linked glycan degradation are absent from both human digestive secretions and the external brush border membrane of the intestinal lining. Indeed, complex carbohydrates remain intact throughout their transit through the stomach and small intestine, and are undegraded by in vitro incubation with either adult pancreatic secretions or intact intestinal brush border membranes. Human gastrointestinal bacteria, however, produce a wide variety of glycosidases with regio- and anomeric specificities matching those of protein-linked glycan structures. These bacteria degrade a wide array of complex carbohydrates including various protein-linked glycans. That bacteria possess glycan degradation capabilities, whereas the human digestive system, perse, does not, suggests that most dietary protein-linked glycan breakdown will be of bacterial origin. In addition to providing a food source for specific bacteria in the colon, protein-linked glycans from human milk may act as decoys for pathogenic bacteria to prevent invasion and infection of the host. The composition of the intestinal microbiome may be particularly important in the most vulnerable humans-the elderly, the immunocompromised, and infants (particularly premature infants).

Use of real-time, label-free analysis in revealing low-affinity binding to blood group antigens by Helicobacter pylori

Infectious diseases are often initiated by microbial adherence that is mediated by the binding of attachment molecules, termed adhesins, to cell surface receptors on host cells. We present an experimental system, oblique-incidence reflectivity difference (OI-RD) microscopy, which allows the detection of novel, low-affinity microbial attachment mechanisms that may be essential for infectious processes. OI-RD microscopy was used to analyze direct binding of the oncopathogen, Helicobacter pylori ( H. pylori ) to immobilized glycoconjugates in real time with no need for labeling tags. The results suggest the presence of additional Lewis b blood group antigen (Le(b)) binding adhesins that have not been detected previously. OI-RD microscopy also confirmed the high-affinity binding of H. pylori outer-membrane protein BabA to Le(b). The OI-RD microscopy method is broadly applicable to real-time characterization of intact microbial binding to host receptors and offers new strategies to elucidate the molecular interactions of infectious agents with human host cells.

Comparison of methods for profiling O-glycosylation: Human Proteome Organisation Human Disease Glycomics/Proteome Initiative multi-institutional study of IgA1

The Human Proteome Organisation Human Disease Glycomics/Proteome Initiative recently coordinated a multi-institutional study that evaluated methodologies that are widely used for defining the N-glycan content in glycoproteins. The study convincingly endorsed mass spectrometry as the technique of choice for glycomic profiling in the discovery phase of diagnostic research. The present study reports the extension of the Human Disease Glycomics/Proteome Initiative's activities to an assessment of the methodologies currently used for O-glycan analysis. Three samples of IgA1 isolated from the serum of patients with multiple myeloma were distributed to 15 laboratories worldwide for O-glycomics analysis. A variety of mass spectrometric and chromatographic procedures representative of current methodologies were used. Similar to the previous N-glycan study, the results convincingly confirmed the pre-eminent performance of MS for O-glycan profiling. Two general strategies were found to give the most reliable data, namely direct MS analysis of mixtures of permethylated reduced glycans in the positive ion mode and analysis of native reduced glycans in the negative ion mode using LC-MS approaches. In addition, mass spectrometric methodologies to analyze O-glycopeptides were also successful.

Glycomics analysis of serum: a potential new biomarker for ovarian cancer?

We recently reported the use of matrix-assisted laser desorption ionization (MALDI) Fourier transformation mass spectrometry (FTMS) techniques to identify unique glycan markers in ovarian cancer cell lines which may be biomarkers for diagnosis of ovarian cancer. Glycan markers and CA125 levels are compared in a series of ovarian cancer patients and normal control subjects. Oligosaccharides (OS) were cleaved from the serum glycoproteins and isolated using solid phase extraction. MALDI-FTMS was then used to identify unique mass spectrometry (MS) peaks. Sensitivity, specificity, and the area under the receiver operating characteristic (ROC) curve were calculated to measure the test performance of glycan markers. Sixteen unique OS MS signals were identified in ovarian cancer patient sera. Their additive mass/charge intensities were used to determine their presence or absence. The ovarian cancer patients varied in their disease status, with initial cancer stages ranging from IC to IV. Forty-four of 48 patients had detectable OS signals, with CA125 values between 2 and 17,044. Four patients had undetectable signals and their CA125 ranged between 7 and 10. Twenty-three of 24 control subjects had no detectable glycan markers, with CA125 levels between 10 and 64. Sensitivity and specificity values were determined to be 91.6% and 95.8%, respectively. The area under the ROC curve for all 72 samples was 0.954 (95% CI: 0.896, 1.0) using the glycomics assay, which was superior to CA125 in discriminating between cases and controls. This preliminary study suggests that glycomics profiling may be useful for the detection of ovarian cancer.

Serum glycan analysis in metastatic breast cancer

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Background: There is a need for a reliable breast cancer biomarker that can predict a patient’s response to therapy. Serum glycans, or oligosaccharides, are of particular interest as over half of all proteins are glycosylated and alterations in glycosylation influence growth, adhesion, metastasis and immune surveillance of tumor, among other important functions. Serum glycans can be analyzed by high resolution mass spectrometry. Methods: Sera from patients with known metastatic breast cancer and age-matched healthy controls without medical problems were prospectively analyzed by mass spectroscopy. Women over the age of 18, who were not pregnant or breastfeeding, and who were without other active cancers were eligible. Samples were de-identified for laboratory personnel who analyzed sera by matrix-assisted laser desoprtion/ionization (MALDI) and Fourier transform ion-cyclotron resonance mass sepctrometry (FT ICR MS). Glycans were also profiled by chromatographic separation using a microchip nanoLC (Agilent) with a time-of-flight (TOF) mass analyzers. Results: Sera from 25 patients with metastatic breast cancer and 25 controls were evaluated. The mass profiles were obtained corresponding to both N-linked oligosaccharides (N-glycans) and O-linked oligosaccharides (O-glycans). Distinct variations in glycosylation were observed among sera analyzed from patients with metastatic breast cancer compared to controls. Specific glycan masses were analyzed and found to correspond to N-glycans. The chromatographic glycan profile showed individual glycans that were distinct for the cancer patients. Conclusions: Analysis of serum gylcans by mass spectrometry represents a new paradigm of cancer biomarker studies, focusing on post-translational modifications of proteins, rather than protein expression. Further refinement of this technology may be clinically useful in monitoring response to therapy in metastatic breast cancer.

No significant financial relationships to disclose.

Achieving high detection sensitivity (14 zmol) of biomolecular ions in bioaerosol mass spectrometry

Bioaerosol mass spectrometry (BAMS) performs single-cell analysis in real time. However, the specificity of BAMS mass signatures has been limited by low sensitivity at high masses. To increase the mass range and sensitivity of BAMS, a novel design was developed that utilizes a linear flight tube with delayed extraction and an electrostatic ion guide. This study quantifies the sensitivity limits of the novel BAMS design and evaluates the feasibility of BAMS to detect higher mass biomarkers from single cells. All experiments were carried out using MALDI aerosol particles that were nebulized from solution. Sensitivity was assessed by generating particles with decreasing amounts of analyte via serial dilutions. The amount of analyte contained within each particle was calculated based on particle size, density, and molarity of the analyte within solution. A variety of biomolecular ions were studied and signals obtained from particles containing 300 zmol of maltopentaose, 132 zmol of alpha-cyclodextrin, and 14 zmol (approximately 8400 molecules) of gramicidin S are reported. The detection of 14 zmol of gramicidin S is to the best of our knowledge a record in sensitivity for MALDI TOF-MS.

Characterization of human aspartoacylase: the brain enzyme responsible for Canavan disease

Aspartoacylase catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate and is the only brain enzyme that has been shown to effectively metabolize NAA. Although the exact role of this enzymatic reaction has not yet been completely elucidated, the metabolism of NAA appears to be necessary in the formation of myelin lipids, and defects in this enzyme lead to Canavan disease, a fatal neurological disorder. The low catalytic activity and inherent instability observed with the Escherichia coli-expressed form of aspartoacylase suggested the need for a suitable eukaryotic expression system that would be capable of producing a fully functional, mature enzyme. Human aspartoacylase has now been successfully expressed in Pichia pastoris. While the expression yields are lower than in E. coli, the purified enzyme is significantly more stable. This enzyme form has the same substrate specificity but is 150-fold more active than the E. coli-expressed enzyme. The molecular weight of the purified enzyme, measured by mass spectrometry, is higher than predicted, suggesting the presence of some post-translational modifications. Deglycosylation of aspartoacylase or mutation at the glycosylation site causes decreased enzyme stability and diminished catalytic activity. A carbohydrate component has been removed and characterized by mass spectrometry. In addition to this carbohydrate moiety, the enzyme has also been shown to contain one zinc atom per subunit. Chelation studies to remove the zinc result in a reversible loss of catalytic activity, thus establishing aspartoacylase as a zinc metalloenzyme.

Nanoliquid chromatography-mass spectrometry of oligosaccharides employing graphitized carbon chromatography on microchip with a high-accuracy mass analyzer

The nanoLC separations of oligosaccharides using microchip-based columns are described. Mixtures of alditols from mucins and human milk are separated on graphitized carbon. The nanoLC-MS device showed high mass accuracy for the oligosaccharides ranging between 1 and 6 ppm on routine analyses. The high mass accuracy readily allowed identification of oligosaccharide peaks and the determination of their compositions. High retention time reproducibility was exhibited by the microchip LC. Little variation was observed for standard sample either alone or in a complex heterogeneous mixture. The nanoLC-MS exhibits excellent capabilities in profiling mixtures of oligosaccharides.

Toward understanding the ionization of biomarkers from micrometer particles by bio-aerosol mass spectrometry

The appearance of informative signals in the mass spectra of laser-ablated bio-aerosol particles depends on the effective ionization probabilities (EIP) of individual components during the laser ionization process. This study investigates how bio-aerosol chemical composition governs the EIP values of specific components and the overall features of the spectra from the bio-aerosol mass spectrometry (BAMS). EIP values were determined for a series of amino acid, dipicolinic acid, and peptide aerosol particles to determine what chemical features aid in ionization. The spectra of individual amino acids and dipicolinic acid, as well as mixtures, were examined for extent of fragmentation and the presence of molecular ion dimers, which are indicative of ionization conditions. Standard mixtures yielded information with respect to the significance of secondary ion plume reactions on observed spectra. A greater understanding of how these parameters affect EIP and spectra characteristics of bio-aerosols will aid in the intelligent selection of viable future biomarkers for the identification of bio-terrorism agents.