Nutritional and Clinical Glycomics Research

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Glycans and Glycoproteins in Mass Spectrometry

TWO-DAY COURSE, Saturday and Sunday
Glycans and Glycoproteins for Mass Spectrometry

Instructors

Jon Amster
University of Georgia
Carlito Lebrilla
University of California, Davis
Ron Orlando
University of Georgia
Joe Zaia
Boston University

This course is designed for scientists who want to learn specific techniques for the MS and MS/MS characterization of glycans and glycoproteins. The course will address fundamental aspects of glycobiology, sample preparation and handling, mass spectrometry (hardware and software), and bioinformatic tools for interpretation of results.

Real-world examples of the application of these techniques will include characterization of intact glycoproteins, characterization of released glycans, analysis of complex mixtures of glycoproteins and glycans. The role of MS-based methods in interdisciplinary efforts to solve these complex problems will also be addressed.

Day 1
 Introduction to glycosylation
 Chemical manipulation/derivatization of oligosaccharides, GC-MS for linkage and composition analyses
 MALDI MS and ESI of oligosaccharides
 Tandem MS of oligosaccharides
 Glycoproteins — release and analyze, and glycomic approaches
 Glycopeptides, methods for site specific glycosylation analysis, glycoproteomic approaches

Day 2
 Glycoprotein applications and case studies
 Glycosaminoglycans: Background, fundamentals, Tandem MS
 Glycolipids
 Glycan Quantitation
 Bioinformatics

Pre-requisites: A basic knowledge of mass spectrometry and some rudimentary knowledge of biology
and chemistry is desirable.

New Publications!

Dallas, D.C., A. Guerrero, N. Khaldi, R. Borghese, A. Bhandari, M.A. Underwood, C.B. Lebrilla, J.B. German, and D. Barile, A Peptidomic Analysis of Human Milk Digestion in the Infant Stomach Reveals Protein-Specific Degradation Patterns. J Nutr, 2014.

In vitro digestion of isolated milk proteins results in milk peptides with a variety of actions. However, it remains unclear to what degree protein degradation occurs in vivo in the infant stomach and whether peptides previously annotated for bioactivity are released. This study combined nanospray liquid chromatography separation with time-of-flight mass spectrometry, comprehensive structural libraries, and informatics to analyze milk from 3 human mothers and the gastric aspirates from their 4- to 12-d-old postpartum infants. Milk from the mothers contained almost 200 distinct peptides, demonstrating enzymatic degradation of milk proteins beginning either during lactation or between milk collection and feeding. In the gastric samples, 649 milk peptides were identified, demonstrating that digestion continues in the infant stomach. Most peptides in both the intact milk and gastric samples were derived from beta-casein. The numbers of peptides from beta-casein, lactoferrin, alpha-lactalbumin, lactadherin, kappa-casein, serum albumin, bile salt-associated lipase, and xanthine dehydrogenase/oxidase were significantly higher in the gastric samples than in the milk samples (P < 0.05). A total of 603 peptides differed significantly in abundance between milk and gastric samples (P < 0.05). Most of the identified peptides have previously identified biologic activity. Gastric proteolysis occurs in the term infant in the first 2 wk of life, releasing biologically active milk peptides with immunomodulatory and antibacterial properties of clinical relevance to the proximal intestinal tract. Data are available via ProteomeXchange (identifier PXD000688).

 

New Publications! 2/2014

Hong, Q., et al. (2014). “Label Free Absolute Quantitation of Oligosaccharides using Multiple Reaction Monitoring.Anal Chem.

An absolute quantitation method for measuring free human milk oligosaccharides (HMOs) in milk samples was developed using multiple reaction monitoring (MRM). To obtain the best sensitivity, the instrument conditions were optimized to reduce the source and post source fragmentation prior to the quadrupole transmission. Fragmentation spectra of HMOs using collision-induced dissociation were studied to obtain the best characteristic fragments. At least two MRM transitions were used to quantify and identify each structure in the same run. The fragment ions corresponded to the production of singly charged mono, di, and tri-saccharide fragments. The sensitivity and accuracy of the quantitation using MRM were determined, with the detection limit in the femtomole level and the calibration range spanning over five orders of magnitude. Seven commercial HMO standards were used to create calibration curves and were used to determine a universal response for all HMOs. The universal response factor was used to estimate absolute amounts of other structures and the total oligosaccharide content in milk. The quantitation method was applied to 20 human milk samples to determine the variations in HMO concentrations from women classified as secretors and nonsecretors, a phenotype that can be identified by the concentration of 2′-fucosylation in their milk.

 

Ozcan, S., et al. (2014). “Serum glycan signatures of gastric cancer.” Cancer Prev Res (Phila) 7(2): 226-235.

Glycomics, a comprehensive study of glycans expressed in biologic systems, is emerging as a simple yet highly sensitive diagnostic tool for disease onset and progression. This study aimed to use glycomics to investigate glycan markers that would differentiate patients with gastric cancer from those with nonatrophic gastritis. Patients with duodenal ulcer were also included because they are thought to represent a biologically different response to infection with Helicobacter pylori, a bacterial infection that can cause either gastric cancer or duodenal ulcer. We collected 72 serum samples from patients in Mexico City that presented with nonatrophic gastritis, duodenal ulcer, or gastric cancer. N-glycans were released from serum samples using the generic method with PNGase F and were analyzed by matrix-assisted laser desorption/ionization Fourier transform-ion cyclotron resonance mass spectrometry. The corresponding glycan compositions were calculated based on accurate mass. ANOVA-based statistical analysis was performed to identify potential markers for each subgroup. Nineteen glycans were significantly different among the diagnostic groups. Generally, decreased levels of high-mannose-type glycans, glycans with one complex type antenna, bigalactosylated biantennary glycans, and increased levels of nongalactosylated biantennary glycans were observed in gastric cancer cases. Altered levels of serum glycans were also observed in duodenal ulcer, but differences were generally in the same direction as gastric cancer. Serum glycan profiles may provide biomarkers to differentiate gastric cancer cases from controls with nonatrophic gastritis. Further studies will be needed to validate these findings as biomarkers and identify the role of protein glycosylation in gastric cancer pathology. Cancer Prev Res; 7(2); 226-35. (c)2013 AACR.

 

New Publications!

Hua, S., et al. (2014). “Differentiation of Cancer Cell Origin and Molecular Subtype by Plasma Membrane N-Glycan Profiling..” J Proteome Res.
In clinical settings, biopsies are routinely used to determine cancer type and grade based on tumor cell morphology, as determined via histochemical or immunohistochemical staining. Unfortunately, in a significant number of cases, traditional biopsy results are either inconclusive or do not provide full subtype differentiation, possibly leading to inefficient or ineffective treatment. Glycomic profiling of the cell membrane offers an alternate route toward cancer diagnosis. In this study, isomer-sensitive nano-LC/MS was used to directly obtain detailed profiles of the different N-glycan structures present on cancer cell membranes. Membrane N-glycans were extracted from cells representing various subtypes of breast, lung, cervical, ovarian, and lymphatic cancer. Chip-based porous graphitized carbon nano-LC/MS was used to separate, identify, and quantify the native N-glycans. Structure-sensitive N-glycan profiling identified hundreds of glycan peaks per cell line, including multiple isomers for most compositions. Hierarchical clusterings based on Pearson correlation coefficients were used to quickly compare and separate each cell line according to originating organ and disease subtype. Based simply on the relative abundances of broad glycan classes (e.g., high mannose, complex/hybrid fucosylated, complex/hybrid sialylated, etc.), most cell lines were readily differentiated. More closely related cell lines were differentiated based on several-fold differences in the abundances of individual glycans. Based on characteristic N-glycan profiles, primary cancer origins and molecular subtypes could be distinguished. These results demonstrate that stark differences in cancer cell membrane glycosylation can be exploited to create an MS-based biopsy, with potential applications toward cancer diagnosis and direction of treatment.

Huang, J., et al. (2014). “Glycomic Analysis of High Density Lipoprotein Shows a Highly Sialylated Particle.” J Proteome Res.
Many of the functional proteins and lipids in HDL particles are potentially glycosylated yet very little is known about the glycoconjugates of HDL. In this study, HDL was isolated from plasma by sequential micro-ultracentrifugation, followed by glycoprotein and glycolipid analysis. N-glycans, glycopeptides, and gangliosides were extracted and purified followed by analysis with nano-HPLC-Chip Q-TOF MS and MS/MS. HDL particles were found to be highly sialylated. Most of the N-glycans (~90%) from HDL glycoproteins were sialylated with one or two neuraminic acids (Neu5Ac). The most abundant N-glycan was a biantennary complex type glycan with two sialic acids (Hexose5HexNAc4Neu5Ac2), and was found in multiple glycoproteins using site-specific glycosylation analysis. The observed O-glycans were all sialylated and most contained a core 1 structure with two Neu5Acs, including those that were associated with apolipoprotein CIII (ApoC-III) and fetuin A. GM3 (monosialoganglioside, NeuAc2-3Gal1-4Glc-Cer) and GD3 (disialoganglioside, NeuAc2-8NeuAc2-3Gal1-4Glc-Cer) were the major gangliosides in HDL. A 60% GM3 and 40% GD3 distribution was observed. Both GM3 and GD3 were composed of heterogeneous ceramide lipid tails, including d18:1/16:0 and d18:1/23:0. This report describes for the first time a glycomic approach for analyzing HDL, highlighting that HDL are highly sialylated particles.

Kailemia, M. J., et al. (2014). “Oligosaccharide Analysis by Mass Spectrometry- A Review of Recent Developments.” Anal Chem 86(1): 196-212.

New Publications!

Bondoc, K. G., et al. (2013). “Chemical fingerprinting and phylogenetic mapping of saponin congeners from three tropical holothurian sea cucumbers.” Comp Biochem Physiol B Biochem Mol Biol 166(3-4): 182-193.
Holothurians are sedentary marine organisms known to produce saponins (triterpene glycosides), secondary metabolites exhibiting a wide range of biological activities. In this paper, we investigated the saponin contents of semi-purified and membranolytic HPLC fractionated extracts from the body wall of three species of Holothuriidae as an attempt to examine its chemical diversity in relation to phylogenetic data. MALDI-FTICR MS and nano-HPLC-chip Q-TOF MS were used for mass profiling and isomer separation, respectively giving a unique chemical saponin fingerprint. Moreover, the methods used yield the highest number of congeners. However, saponin concentration, bioactivity and chemical diversity had no apparent relationship. MS fingerprint showed the presence of holothurinosides, which was observed for the first time in other Holothuria genera besides the basally positioned Holothuria forskali. This congener is proposed to be a primitive character that could be used for taxonomic purposes. The phylogenetic mapping also showed that the glycone part of the compound evolved from non-sulfated hexaosides to sulfated tetraosides, which have higher membranolytic activity and hydrophilicity, the two factors affecting the total ecological activity (i.e. chemical defense) of these compounds. This might be an adaptation to increase the fitness of the organism.

Guerrero, A. and C. B. Lebrilla (2013). “New strategies for resolving oligosaccharide isomers by exploiting mechanistic and thermochemical aspects of fragment ion formation.” Int J Mass Spectrom 354-355.
Three complementary experimental approaches for elucidating human milk oligosaccharide (HMOs) isomers by Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR) are described: tandem-MS disruption by double resonance to distinguish different fragmentation pathways, examination of fragment intensity ratios arising from differential alkali metal ion affinities and monitoring competitive fragmentation rates. The interpretation of the fragmentation pattern from a mechanistic and thermochemical point of view permits the assignment of not only pure isomers but, in some cases, mixtures of them. Methodologically the procedures are simple, reliable and rapid making unnecessary both the use of previous separation techniques and tedious chemical modifications of the HMOs. In principle, the rationale can be expanded to resolve other isomeric mixtures of biological nature.

Hong, Q., et al. (2013). “Absolute quantitation of immunoglobulin G and its glycoforms using multiple reaction monitoring.” Anal Chem 85(18): 8585-8593.
Studies aimed toward glycan biomarker discovery have focused on glycan characterization by the global profiling of released glycans. Site-specific glycosylation analysis is less developed but may provide new types of biomarkers with higher sensitivity and specificity. Quantitation of peptide-conjugated glycans directly facilitates the differential analysis of distinct glycoforms associated with specific proteins at distinct sites. We have developed a method using MRM to monitor protein glycosylation normalized to absolute protein concentrations to examine quantitative changes in glycosylation at a site-specific level. This new approach provides information regarding both the absolute amount of protein and the site-specific glycosylation profile and will thus be useful to determine if altered glycosylation profiles in serum/plasma are due to a change in protein glycosylation or a change in protein concentration. The remarkable sensitivity and selectivity of MRM enable the detection of low abundance IgG glycopeptides, even when IgG was digested directly in serum with no cleanup prior to the liquid chromatography. Our results show a low limit of detection of 60 amol and a wide dynamic range of 3 orders magnitude for IgG protein quantitation. The results show that IgG glycopeptides can be analyzed directly from serum (without enrichment) and yield more accurate abundances when normalized to the protein content. This report represents the most comprehensive study so far of the use of multiple reaction monitoring for the quantitation of glycoproteins and their glycosylation patterns in biofluids.

Hua, S., et al. (2013). “Glyco-analytical multispecific proteolysis (Glyco-AMP): a simple method for detailed and quantitative Glycoproteomic characterization.” J Proteome Res 12(10): 4414-4423.
Despite recent advances, site-specific profiling of protein glycosylation remains a significant analytical challenge for conventional proteomic methodology. To alleviate the issue, we propose glyco-analytical multispecific proteolysis (Glyco-AMP) as a strategy for glycoproteomic characterization. Glyco-AMP consists of rapid, in-solution digestion of an analyte glycoprotein (or glycoprotein mixture) by a multispecific protease (or protease cocktail). Resulting glycopeptides are chromatographically separated by isomer-specific porous graphitized carbon nano-LC, quantified by high-resolution MS, and structurally elucidated by MS/MS. To demonstrate the consistency and customizability of Glyco-AMP methodology, the glyco-analytical performances of multispecific proteases subtilisin, pronase, and proteinase K were characterized in terms of quantitative accuracy, sensitivity, and digestion kinetics. Glyco-AMP was shown be effective on glycoprotein mixtures as well as glycoproteins with multiple glycosylation sites, providing detailed, quantitative, site- and structure-specific information about protein glycosylation.

Hua, S., et al. (2013). “Differentiation of Cancer Cell Origin and Molecular Subtype by Plasma Membrane N-Glycan Profiling.” J Proteome Res.
In clinical settings, biopsies are routinely used to determine cancer type and grade based on tumor cell morphology, as determined via histochemical or immunohistochemical staining. Unfortunately, in a significant number of cases, traditional biopsy results are either inconclusive or do not provide full subtype differentiation, possibly leading to inefficient or ineffective treatment. Glycomic profiling of the cell membrane offers an alternate route towards cancer diagnosis. In this study, isomer-sensitive nano-LC/MS was used to directly obtain detailed profiles of the different N-glycan structures present on cancer cell membranes. Membrane N-glycans were extracted from cells representing various subtypes of breast, lung, cervical, ovarian, and lymphatic cancer. Chip-based porous graphitized carbon nano-LC/MS was used to separate, identify, and quantify the native N-glycans. Structure-sensitive N-glycan profiling identified hundreds of glycan peaks per cell line, including multiple isomers for most compositions. Hierarchical clusterings based on Pearson correlation coefficients were used to quickly compare and separate each cell line according to originating organ and disease subtype. Based simply on the relative abundances of broad glycan classes (e.g. high mannose, complex/hybrid fucosylated, complex/hybrid sialylated, etc.) most cell lines were readily differentiated. More closely-related cell lines were differentiated based on several-fold differences in the abundances of individual glycans. Based on characteristic N-glycan profiles, primary cancer origins and molecular subtypes could be distinguished. These results demonstrate that stark differences in cancer cell membrane glycosylation can be exploited to create an MS-based biopsy, with potential applications towards cancer diagnosis and direction of treatment.

Kailemia, M. K., et al. (2013). “Oligosaccharide Analysis By Mass Spectrometry: A Review Of Recent Developments.” Anal Chem.
This review covers developments in the application of mass spectrometry to the analysis of carbohydrates, focusing on work published between January 2011 through October 2013. These developments include approaches for improved ionization, new and improved methods of ion activation, advances in chromatographic separations of carbohydrates, the hybridization of ion mobility and mass spectrometry, and better software for data collection and interpretation. The impact of the developments are considered in terms of their ability to solve new problems or provide new capabilities for carbohydrate analysis, particularly for structure characterization by mass spectrometry and tandem mass spectrometry.

Lee, H., et al. (2013). “Quantitative analysis of gangliosides in bovine milk and colostrum-based dairy products by ultrahigh performance liquid chromatography-tandem mass spectrometry.” J Agric Food Chem 61(40): 9689-9696.
Milk gangliosides have gained considerable attention because they participate in diverse biological processes, including neural development, pathogen binding, and activation of the immune system. Herein, we present a quantitative measurement of the gangliosides present in bovine milk and other dairy products and byproducts. Ultrahigh performance liquid chromatography separation was used for high-throughput analysis and achieved a short running time without sacrificing chromatographic resolution. Dynamic multiple reaction monitoring was conducted for 12 transitions for GM3 and 12 transitions for GD3. Transitions to sialic acid fragments (m/z 290.1) were chosen for the quantitation. There was a considerable amount of gangliosides in day 2 milk (GM3, 0.98 mg/L; GD3, 15.2 mg/L) which dramatically decreased at day 15 and day 90. GM3 and GD3 were also analyzed in pooled colostrum, colostrum cream, colostrum butter, and colostrum buttermilk. The separation and analytical approaches here proposed could be integrated into the dairy industry processing adding value to side-streams.

Ozcan, S., et al. (2013). “Serum glycan signatures of gastric cancer.” Cancer Prev Res (Phila).
Glycomics, a comprehensive study of glycans expressed in biological systems, is emerging as a simple yet highly sensitive diagnostic tool for disease onset and progression. This study aimed to use glycomics to investigate glycan markers that would differentiate patients with gastric cancer (GC) from those with non-atrophic gastritis (NAG). Patients with duodenal ulcer (DU) were also included because they are thought to represent a biologically different response to infection with Helicobacter pylori, a bacterial infection that can cause either GC or DU. We collected 72 serum samples from patients in Mexico City that presented with NAG, DU, or GC. N-glycans were released from serum samples using the generic method with PNGase F and were analyzed by MALDI FT-ICR MS. The corresponding glycan compositions were calculated based on accurate mass. ANOVA based statistical analysis was performed to identify potential markers for each sub-group. Nineteen glycans were significantly different among the diagnostic groups. Generally, decreased levels of high-mannose type glycans, glycans with one complex type antenna, bigalactosylated biantennary glycans, and increased levels of non-galactosylated biantennary glycans were observed in gastric cancer cases. Altered levels of serum glycans were also observed in DU, but differences were generally in the same direction as GC. Serum glycan profiles may provide biomarkers to differentiate GC cases from controls with NAG. Further studies will be needed to validate these findings as biomarkers and identify the role of protein glycosylation in GC pathology.

Peacock, K. S., et al. (2013). “Isomer-Specific Consumption of Galactooligosaccharides by Bifidobacterial Species.” J Agric Food Chem.
Prebiotics are nondigestible substrates that stimulate the growth of beneficial microbes in the human intestine. Galactooligosaccharides (GOS) are food ingredients that possess prebiotic properties, in particular, promoting the growth of bifidobacteria in situ. However, precise mechanistic details of GOS consumption by bifidobacteria remain poorly understood. Because GOS are mixtures of polymers of different lengths and linkages, there is interest in determining which specific structures provide prebiotic effects to potentially create better supplements. This paper presents a method comprising porous graphitic carbon separation, isotopic labeling, and mass spectrometry analysis for the structure-specific analysis of GOS isomers and their bacterial consumption rate. Using this strategy, the differential bacterial consumption of GOS by the bifidobacteria species Bifidobacterium longum subsp. infantis, Bifidobacterium animalis subsp. lactis, and Bifidobacterium adolescentis was determined, indicating that the use of specific GOS isomers in infant formula may provide enrichment of distinct species.

Smilowitz, J. T., et al. (2013). “Human milk secretory immunoglobulin a and lactoferrin N-glycans are altered in women with gestational diabetes mellitus.” J Nutr 143(12): 1906-1912.
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.

Underwood, M. A., et al. (2013). “Prebiotic Oligosaccharides In Premature Infants.” J Pediatr Gastroenterol Nutr.
OBJECTIVE:: To determine the impact of increasing doses of two prebiotic oligosaccharides and the impact of an “all-human diet” on the intestinal microbiota of premature infants. METHODS:: Twelve premature infants receiving formula feedings were randomly assigned to receive either galacto-oligosaccharide (F+GOS) or a pooled concentrated donor human milk product containing human milk oligosaccharides (F+HMO) in increasing doses over a five week period. A second group of fifteen premature infants received their mother’s own milk fortified with either a concentrated donor human milk product (H+H) or a bovine powdered fortifier (H+B). Serial stool specimens from each infant were analyzed by terminal restriction fragment length polymorphism and quantitative polymerase chain reaction for bacterial composition. RESULTS:: All infants studied had relatively low levels of bifidobacteria and no measurable Lactobacilli. Infants in the F+GOS and F+HMO groups demonstrated an increase in relative numbers of Clostridia with increasing doses. Compared to the H+B group, the infants in the F+HMO and the H+H groups showed an unexpected trend towards an increase in gamma-Proteobacteria over time/dose. Principal Coordinate Analyses and Shannon diversity scores were not significantly different among the four groups. Infants in the H+H group received more antibiotics during the study period than those in the other groups. Two of the infants receiving GOS developed feeding intolerance. CONCLUSIONS:: None of the prebiotic interventions resulted in significant increases in bifidobacteria compared to baseline specimens or to the H+B group, however many of the infants did not receive the highest doses of GOS and HMO and antibiotic use in the H+H group was high.

 

New Publications!

G. Leiserowitz, K. Kim, S. Miyamoto, R. Ruhaak, S. Hua, L. Dimapasoc, C. Williams, C. Lebrilla, “Glycomics analysis as a potential diagnostic test for ovarian cancer“, Gynecologic Oncology, Volume 130, Issue 1, July 2013, Page e21

Ruiz-Moyano, S., S. M. Totten, D. Garrido, J. T. Smilowitz, J. B. German, C. B. Lebrilla and D. A. Mills (2013). “Variation in consumption of human milk oligosaccharides by infant-gut associated strains of Bifidobacterium breve.” Appl Environ Microbiol.
Human milk contains a high concentration of complex oligosaccharides that influence the composition of the intestinal microbiota in breast-fed infants. Previous studies have indicated that select species such as Bifidobacterium longum subsp. infantis and B. bifidum can utilize human milk oligosaccharides (HMO) in vitro as the sole carbon source, while the relatively few B. longum subsp. longum and B. breve isolates tested appear less adapted to these substrates. Considering the high frequency at which B. breve is isolated from breast-fed infant feces, we postulated that some B. breve strains can more vigorously consume HMOs and thus are enriched in the breast-fed infant gastrointestinal tract. To examine this a number of B. breve isolates from breast-fed infant feces were characterized for the presence of different glycosyl hydrolases that participate in HMO utilization, as well as by their ability to grow on HMO or specific HMO species such as lacto-N-tetraose (LNT) and fucosyllactose. All B. breve strains showed a high growth on lacto-N-tetraose and lacto-N-neotetraose (LNnT), and, in general, growth on total HMO was moderate for most of the strains, with several strain differences. Growth and consumption of fucosylated HMO was strain-dependent, mostly in isolates possessing a Glycosyl Hydrolase family 29 alpha-fucosidase. Glycoprofiling of the spent supernatant after HMO fermentation by select strains revealed that all B. breve can utilize sialylated HMO to a certain extent, especially sialyl-lacto-N-tetraose. Interestingly, this specific oligosaccharide was depleted before neutral LNT by strain SC95. In aggregate, this work indicates that the HMO consumption phenotype in B. breve is variable, however specific strains display specific adaptations to these substrates enabling more vigorous consumption of fucosylated and sialylated HMO. These results provide a rationale for the predominance of this species in breast-fed infant feces, and contribute to a more accurate picture of the ecology of the developing infant intestinal microbiota.

De Leoz, M. L., C. B. Lebrilla and M. A. Underwood (2013). “Response to Letter to the Editor regarding “A quantitative and comprehensive method to analyze human milk oligosaccharide structures in the urine and feces of infants“.” Anal Bioanal Chem.

New Publications

Strum, J. S., C. C. Nwosu, S. Hua, S. R. Kronewitter, R. R. Seipert, R. J. Bachelor, H. J. An and C. B. Lebrilla (2013). “Automated Assignments of N- and O-Site Specific Glycosylation with Extensive Glycan Heterogeneity of Glycoprotein Mixtures.” Anal Chem.
Site-specific glycosylation (SSG) of glycoproteins remains a considerable challenge and limits further progress in the areas of proteomics and glycomics. Effective methods require new approaches in sample preparation, detection, and data analysis. While the field has advanced in sample preparation and detection, automated data analysis remains an important goal. A new bioinformatics approach implemented in software called GP Finder automatically distinguishes correct assignments from random matches and complements experimental techniques that are optimal for glycopeptides, including nonspecific proteolysis and high mass resolution liquid chromatography/tandem mass spectrometry (LC/MS/MS). SSG for multiple N- and O-glycosylation sites, including extensive glycan heterogeneity, was annotated for single proteins and protein mixtures with a 5% false-discovery rate, generating hundreds of nonrandom glycopeptide matches and demonstrating the proof-of-concept for a self-consistency scoring algorithm shown to be compliant with the target-decoy approach (TDA). The approach was further applied to a mixture of N-glycoproteins from unprocessed human milk and O-glycoproteins from very-low-density-lipoprotein (vLDL) particles.

 

Ruhaak, L. R., U. T. Nguyen, C. Stroble, S. L. Taylor, A. Taguchi, S. M. Hanash, C. B. Lebrilla, K. Kim and S. Miyamoto (2013). “Enrichment strategies in glycomics based lung cancer biomarker development.” Proteomics Clin Appl.
PURPOSE: 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. RESULTS: 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. This article is protected by copyright. All rights reserved.

Dallas, D. C., A. Guerrero, N. Khaldi, P. A. Castillo, W. F. Martin, J. T. Smilowitz, C. L. Bevins, D. Barile, J. B. German and C. B. Lebrilla (2013). “Extensive in vivo Human Milk Peptidomics Reveals Specific Proteolysis Yielding Protective Antimicrobial Peptides.” J Proteome Res 12(5): 2295-2304.
Milk is traditionally considered an ideal source of the basic elemental nutrients required by infants. More detailed examination is revealing that milk represents a more functional ensemble of components with benefits to both infants and mothers. A comprehensive peptidomics method was developed and used to analyze human milk yielding an extensive array of protein products present in the fluid. Over 300 milk peptides were identified originating from major and many minor protein components of milk. As expected, the majority of peptides derived from beta-casein, however no peptide fragments from the major milk proteins lactoferrin, alpha-lactalbumin, and secretory immunoglobulin A were identified. Proteolysis in the mammary gland is selective-released peptides were drawn only from specific proteins and typically from only select parts of the parent sequence. A large number of the peptides showed significant sequence overlap with peptides with known antimicrobial or immunomodulatory functions. Antibacterial assays showed the milk peptide mixtures inhibited the growth of Escherichia coli and Staphylococcus aureus . The predigestion of milk proteins and the consequent release of antibacterial peptides may provide a selective advantage through evolution by protecting both the mother’s mammary gland and her nursing offspring from infection.

 

New Publications

Latest Publications from the Lebrilla Team!

Hua, S., et al. (2013). “Isomer-Specific LC/MS and LC/MS/MS Profiling of the Mouse Serum N-Glycome Reveals a Number of Novel Sialylated N-Glycans.” Anal Chem.
Mice are the premier mammalian models for studies of human physiology and disease, bearing extensive biological similarity to humans with far fewer ethical, economic, or logistic complications. To facilitate glycomic studies based on the mouse model, we comprehensively profiled the mouse serum N-glycome using isomer-specific nano-LC/MS and -LC/MS/MS. N-glycans were identified by accurate mass MS and structurally elucidated by MS/MS. Porous graphitized carbon nano-LC was able to separate out nearly 300 N-linked glycan compounds (including isomers) from just over 100 distinct N-linked glycan compositions. Additional MS/MS structural analysis was performed on a number of novel N-glycans, revealing the structural characteristics of modifications such as dehydration, O-acetylation, and lactylation. Experimental findings were combined with known glycobiology to generate a theoretical library of all biologically-possible mouse serum N-glycan compositions. The library may be used for automated identification of complex mixtures of mouse N-glycans, with possible applications to a wide range of mouse-related research endeavors, including pharmaceutical drug development and biomarker discovery.

Ruhaak, L. R., et al. (2013). “Chip-based nLC-TOF-MS is a highly stable technology for large-scale high-throughput analyses.” Anal Bioanal Chem.
Many studies focused on the discovery of novel biomarkers for the diagnosis and treatment of disease states are facilitated by mass spectrometry-based technology. HPLC coupled to mass spectrometry is widely used; miniaturization of this technique using nano-liquid chromatography (LC)-mass spectrometry (MS) usually results in better sensitivity, but is associated with limited repeatability. The recent introduction of chip-based technology has significantly improved the stability of nano-LC-MS, but no substantial studies to verify this have been performed. To evaluate the temporal repeatability of chip-based nano-LC-MS analyses, N-glycans released from a serum sample were repeatedly analyzed using nLC-PGC-chip-TOF-MS on three non-consecutive days. With an average inter-day coefficient of variation of 4 %, determined on log10-transformed integrals, the repeatability of the system is very high. Overall, chip-based nano-LC-MS appears to be a highly stable technology, which is suitable for the profiling of large numbers of clinical samples for biomarker discovery.

 

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