Analysis Of Glycopeptides Research Articles

A Phase 1 Study of CD38-Bispecific Antibody (XmAb18968) for Patients with Relapsed/Refractory T-Cell Acute Lymphoblastic Leukemia

Background: Outcomes of adults with relapsed/refractory T-cell acute lymphoblastic leukemia (T-ALL) has remained poor. CD38 is a transmembrane glycoprotein that is highly expressed in T-ALL and is potentially targetable with CD38 blocking agents [Naik J et al. Haematologica 2019, Bride KL et al. Blood 2018, Tembhare et al. J Immunother Cancer 2020]. XmAb18968 is a novel CD38-CD3 bi-specific T-cell engager with Fc domain modified to minimize Fcγ receptor binding and non-selective T-cell activation resulting in reduced cytokine release without compromising target cell killing. We designed a phase I clinical trial to assess the safety and tolerability of XmAb18968 in patients with T-ALL. Methods: We conducted a multicenter, open label, phase I dose escalation study of XmAb18968 (NCT05038644). Patients aged ≥18 years with relapsed/refractory T-ALL or T-lymphoblastic lymphoma (T-LBL), ECOG PS 0-2 and adequate organ function were eligible. Major exclusion criteria are hematopoietic cell transplantation within 6 months of enrollment, prior therapy with daratumumab in the last 6 months and active acute graft-versus-host disease. Dose escalation was conducted using 3+3 design, and 4 separate dose levels were studied [0.8mg, 1mg, 1.3mg, 1.5mg]. XmAb18968 was administered intravenously on days 1, 8, 15, 22 on a 28-day cycle. During cycle 1 alone, day 1 dose was fractionated and administered over 2 days to minimize the risk of significant cytokine release syndrome (CRS). Treatment was continued until progression or unacceptable toxicity. The primary objective was to determine the safety and dose limiting toxicity (DLT) and secondary objective was to determine the preliminary efficacy. Correlative studies included pharmacokinetics, characterizing changes in serum cytokines and phenotypic expression of activated T-cells and leukemic cells, correlation of the phenotypic expression with changes in transcriptome at the single-cell level, proteomics evaluation of cytokine secretion at the single-cell level and correlation of response with N-glycan profiling, quantitative site-occupancy, and direct glycopeptide analysis. Results: Four patients with relapsed/refractory T-ALL have been enrolled so far at dose level 1 (0.8mg) with 3 of them being evaluable for response (one patient came off study before DLT period). Median age was 62 years (34-74), all response evaluable patients had early T-precursor ALL (ETP-ALL), and one patient (25%) was previously treated with allogeneic HCT, CD7 CAR-T therapy and daratumumab. Grade 3 or higher adverse events are summarized in Table 1. CRS grades 1 was noted in 25% of patients, no grade ≥3 CRS or neurotoxicity (any grade) was seen. Of the 3 evaluable total patients, 2 patients had achieved complete response (CR) after 1 cycle of therapy (one patient had prior allogeneic HCT, CD7 CAR-T therapy and daratumumab) (Table 2). The two responders remain on treatment. Conclusions: XmAb18968, a novel CD-38 bispecific antibody appears safe and is showing response at the starting dose level in T-ALL. The study is currently enrolling additional patients with T-ALL. Updated analysis with additional patients and details on correlative studies examining mechanisms of therapeutic efficacy will be reported at the main meeting.

Glycan Complexity and Heterogeneity of Glycoproteins in Somatic Extracts and Secretome of the Infective Stage of the Helminth Fasciola hepatica

Fasciola hepatica is a global helminth parasite of humans and their livestock. The invasive stage of the parasite, the newly excysted juvenile (NEJs), relies on glycosylated excreted-secreted (ES) products and surface/somatic molecules to interact with host cells and tissues and to evade the host's immune responses, such as disarming complement and shedding bound antibody. While -omics technologies have generated extensive databases of NEJs’ proteins and their expression, detailed knowledge of the glycosylation of proteins is still lacking. Here, we employed glycan, glycopeptide, and proteomic analyses to determine the glycan profile of proteins within the NEJs’ somatic (Som) and ES extracts. These analyses characterized 123 NEJ glycoproteins, 71 of which are secreted proteins, and allowed us to map 356 glycopeptides and their associated 1690 N-glycan and 37 O-glycan forms to their respective proteins. We discovered abundant micro-heterogeneity in the glycosylation of individual glycosites and between different sites of multi-glycosylated proteins. The global heterogeneity across NEJs’ glycoproteome was refined to 53 N-glycan and 16 O-glycan structures, ranging from highly truncated paucimannosidic structures to complex glycans carrying multiple phosphorylcholine (PC) residues, and included various unassigned structures due to unique linkages, particularly in pentosylated O-glycans. Such exclusive glycans decorate some well-known secreted molecules involved in host invasion, including cathepsin B and L peptidases, and a variety of membrane-bound glycoproteins, suggesting that they participate in host interactions. Our findings show that F. hepatica NEJs generate exceptional protein variability via glycosylation, suggesting that their molecular portfolio that communicates with the host is far more complex than previously anticipated by transcriptomic and proteomic analyses. This study opens many avenues to understand the glycan biology of F. hepatica throughout its life-stages, as well as other helminth parasites, and allows us to probe the glycosylation of individual NEJs proteins in the search for innovative diagnostics and vaccines against fascioliasis.

Glycosylation as regulator of human B-cell leukaemias in bone marrow

Leukemic B-cells are lodged in the bone marrow [BM], a complex organ composed of many cell types and extracellular matrix. Determining how the reciprocal interactions between these components are regulated is critical to our understanding of the factors that allow leukemia cells to survive, multiply and withstand treatment. All cells in the bone marrow are surrounded by a glycocalyx, a glycan-rich layer of high complexity, which regulates such cell-cell and cell-matrix interactions. However, the structure and function of the glycan components of the biomolecules that constitute this layer have not been explored in much detail. Gaps are difficult to fill due to technical limitations as well as the fact that the composition of the BM in health, disease and aging is not static. This also applies to B-lineage malignancies that develop or persist in BM such as B-cell precursor acute lymphoblastic leukemia and Multiple Myeloma, and the effects of their treatment. In contrast, the proteomes and transcriptomes of different human bone marrow cells have been studied more extensively. A combination of technologies now increasingly allows correlations to be made between the expression of glycosyltransferases and glycan structures in cell lines, which could be extrapolated to RNAseq data from primary cells. Glycopeptide analysis will also be invaluable in providing details of specific glycan occupancy on glycoproteins, even if only as a snapshot in time. Functional studies on CD19, CD138/SDC1 and BCMA/TNFRSF17 have already demonstrated the importance of their glycosylation. Additional studies using such approaches are likely to find many more other instances in which malignant B-cell homeostasis is regulated by glycosylation, and lead to the identification of new targets to treat B-cell malignancies.

Identification of animal species of origin in meat based on glycopeptide analysis by UPLC-QTOF-MS.

Adulteration of meat and meat products causes a concerning threat for consumers. It is necessary to develop novel robust and sensitive methods which can authenticate the origin of meat species to compensate forthe drawbacks of existing methods. In the present study, the sarcoplasmic proteins of six meat species, namely, pork, beef, mutton, chicken, duck and turkey, were analyzed by one-dimensional gel electrophoresis. It was found that enolase could be used as a potential biomarker protein to distinguish between livestock and poultry meats. The glycosylation sites and glycans of enolase were analyzed by UPLC-QTOF-MS and a total of 41 glycopeptides were identified, indicating that the enolase N-glycopeptide profiles of different meats were species-specific. The identification models of livestock meat, poultry and mixed animal were established based on the glycopeptide contents, and the explanation degree of the three models was higher than 90%. The model prediction performance and feasibility results showed that the average prediction accuracy of the three models was 75.43%, with the animal-derivedmeat identification model showing superiority in identifying more closely related species. The obtained results indicated that the developed strategy was promising for application in animal-derivedmeat species monitoring and the quality supervision of animal-derived food.

Site-Specific Profiling of N-Glycans in Drosophila melanogaster.

Drosophila melanogaster is a well-studied and highly tractable genetic model system for deciphering the molecular mechanisms underlying various biological processes. Although being one of the most critical post-translational modifications of proteins, the understanding of glycosylation in Drosophila is still lagging behind compared with that of other model organisms. In this study, we systematically investigated the site-specific N-glycan profile of Drosophila melanogaster using intact glycopeptide analysis technique. This approach identified the glycans, proteins, and their glycosites in Drosophila, as well as information on site-specific glycosylation, which allowed us to know which glycans are attached to which glycosylation sites. The results showed that the majority of N-glycans in Drosophila were high-mannose type (69.3%), consistent with reports in other insects. Meanwhile, fucosylated N-glycans were also highly abundant (22.7%), and the majority of them were mono-fucosylated. In addition, 24 different sialylated glycans attached with 16 glycoproteins were identified, and these proteins were mainly associated with developmental processes. Gene ontology analysis showed that N-glycosylated proteins in Drosophila were involved in multiple biological processes, such as axon guidance, N-linked glycosylation, cell migration, cell spreading, and tissue development. Interestingly, we found that seven glycosyltransferases and four glycosidases were N-glycosylated, which suggested that N-glycans may play a regulatory role in the synthesis and degradation of N-glycans and glycoproteins. To our knowledge, this work represents the first comprehensive analysis of site-specific N-glycosylation in Drosophila, thereby providing new perspectives for the understanding of biological functions of glycosylation in insects.

A Phase 1 Study of CD38-Bispecific Antibody (XmAb18968) for Patients with CD38 Expressing Relapsed/Refractory Acute Myeloid Leukemia

Background: Outcomes of adults with relapsed/refractory acute myeloid leukemia (RR-AML) have remained poor. CD38 is a transmembrane glycoprotein that is highly expressed in AML and is potentially targetable with CD38 blocking agents [Naik J et al. Haematologica 2019, Tembhare et al. J Immunother Cancer 2020]. XmAb18968 is a novel CD38-CD3 bi-specific T-cell engager with Fc domain modified to minimize Fcγ receptor binding and non-selective T-cell activation resulting in reduced cytokine release without compromising target cell killing. We designed a phase I clinical trial to assess the safety and tolerability of XmAb18968 in patients with RR-AML. Methods: We conducted a multicenter, open label, phase I dose escalation study of XmAb18968 (NCT05038644). Patients aged ≥18 years with relapsed/refractory AML, ECOG PS 0-2 and adequate organ function were eligible. Major exclusion criteria are hematopoietic cell transplantation within 6 months of enrollment, active acute graft-versus-host disease, and acute promyelocytic leukemia. Dose escalation was conducted using 3+3 design and 4 separate dose levels were studied [0.8mg, 1mg, 1.3mg, 1.5mg]. XmAb18968 was administered intravenously on days 1, 8, 15, 22 on a 28-day cycle. During cycle 1 alone, day 1 dose was fractionated and administered over 2 days to minimize the risk of significant cytokine release syndrome (CRS). Treatment was continued until progression or unacceptable toxicity. The primary objective was to determine the safety and dose limiting toxicity (DLT) and secondary objective was to determine the preliminary efficacy. Measurable residual disease (MRD) status was assessed using multicolor flow cytometry with 0.01% sensitivity. Correlative studies included pharmacokinetics, characterizing changes in serum cytokines and phenotypic expression of activated T-cells and leukemic cells, correlation of the phenotypic expression with changes in transcriptome at the single-cell level, proteomics evaluation of cytokine secretion at the single-cell level and correlation of response with N-glycan profiling, quantitative site-occupancy, and direct glycopeptide analysis. Results: Thirteen patients with RR-AML were enrolled, 12 of whom were evaluable (1 patient came off study before DLT period). Median age was 63 years (45-77), 77% with adverse risk disease, 38% with secondary AML, and received median two (range 2-7) prior lines of therapy. Twelve of 13 patients (92%) were previously treated with venetoclax based regimen and 31% had prior allogeneic HCT. Adverse risk mutations included TP53 (31%), RUNX1 (23%), and ASXL1 (15%). Grade 3 or higher adverse events included anemia (8%), neutropenia (15%), and thrombocytopenia (23%) (Table 1). CRS grades 1-2 were noted in 62% of patients, no grade ≥3 CRS or neurotoxicity (any grade) was seen. There was no dose limiting toxicity (DLT). Of the 12 evaluable total patients, clinically meaningful response was noted in two patients who were MRD positive by flow cytometry prior to study entry and achieved MRD negative CR (Table 2). These two patients who achieved MRD negative CR subsequently proceeded to allogeneic HCT. Median time to response was 1 cycle. Median OS of the cohort was 6.2 months (1.8-NR). Conclusions: XmAb18968 is safe and well tolerated in patients with RR-AML. Dose escalation yielded MRD negative CR in RR-AML patients who were MRD positive at study entry. Details on correlative studies examining mechanisms of therapeutic efficacy and resistance will be reported in the main meeting.

Oriented assembly of hydrophilic nanochains modified by porous zirconium-based coordination polymers for glycopeptides analysis

Mass spectrometry (MS)-based glycoproteomics research requires additional sample pretreatment to improve the effective identification of low-abundance glycopeptides without interference from non-glycoproteins. Herein, an attractive strategy using resorcinol-formaldehyde (RF) resin and zirconium-based coordination polymer (Zr-BCP) was established to prepare one-dimensional porous coordination polymer composites for glycopeptide enrichment before MS analysis. The obtained Fe3O4@RF@Zr-BCP nanochains feature excellent magnetic response (42.26 emu/g), high hydrophilicity (16.0°), and large specific surface area (140.84 m2/g), which provides abundant affinity sites for specific capture of glycopeptides. The materials exhibit outstanding performance in the enrichment of glycopeptides in terms of sensitivity (15 fmol/μL IgG), selectivity (1:200, molar ratio of IgG/BSA), loading capacity (200 mg/g) and recovery (106.4 ± 3.5%). In addition, the developed method based on Fe3O4@RF@Zr-BCP has been successfully applied to capture glycopeptides in tryptic digest of mouse teratoma cell extracts. It is worth emphasizing that compared with dispersed nanoparticles, the one-dimensional chain structure brings extraordinary reusability to Fe3O4@RF@Zr-BCP nanochains, which is conducive to the rapid cyclic enrichment of glycopeptides. This present work provides a potential enrichment platform for comprehensive glycoprotein analysis, and opens a new avenue for the application of oriented-assembly nanochains.

Dual-ligand hydrogen-bonded organic framework: Tailored for mono-phosphopeptides and glycopeptides analysis

Hydrogen-bonded organic frameworks (HOFs) have emerged as a promising class of materials for applications of separation and enrichment. Utilizing multiple-ligands to construct HOFs is a promising avenue towards the development of structurally stable and functionally diverse frameworks, offering opportunities to create customized binding sites for selective recognition of biomolecules. In recent years, due to the crucial role that protein post-translational modifications (PTMs) play in maintaining protein function and regulating signaling pathways, and the growing recognition of the extensive cross-talk that can occur between PTMs, simultaneous analysis of different types of PTMs represents a requirement of a new generation of enrichment materials. Here, for the first attempt, we report a dual-ligand HOF constructed from borate anion and guanidinium cation for the simultaneous identification of glycopeptides and phosphopeptides, especially mono-phosphopeptides. According to theoretical calculations, the HOF functional sites display a synergistic “matching” effect with mono-phosphopeptides, resulting in a stronger enrichment effect for mono-phosphopeptides as compared to multi-phosphopeptides. Also, due to its high hydrophilicity and boronate affinity, this material can efficiently capture glycoproteins. HOF is set to become an active research direction in the development of highly efficient simultaneous protein enrichment materials, and offers a new approach for comprehensive PTMs analysis.

Improved analysis ZIC-HILIC-HCD-Orbitrap method for mapping the glycopeptide by mass spectrometry

Glycosylation is one of the most common post-translational modifications (PTMs). Protein glycosylation analysis is the bottleneck to deeply understand their functions. At present, the LC-MS analysis of glycosylated post-translational modification is mainly focused on the analysis of glycopeptides. However, the factors affecting the identification of glycopeptides were not fully elucidated. In the paper, we have carefully studied the factors, e.g., HILIC materials, search engines, protein amount, gradient duration, extraction solution, etc. According to the results, HILIC materials were the most important factors affecting the glycopeptides identification, and the amphoteric sulfoalkyl betaine stationary phase enriched glycopeptides 6-fold more compared to the amphiphilic ion-bonded fully porous spherical silica stationary phase. We explored the influence of the extraction solutions on glycan identification. Comparing sodium dodecyl sulfate (SDS) and urea (UA), the results showed that N-glycolylneuraminic acid (NeuGc) type of glycan content was found to be increased 1.4-fold in the SDS compared to UA. Besides, we explored the influence of the search engine on glycopeptide identification. Comparing pGlyco3.0 and MSFragger-Glyco, it was observed that pGlyco3.0 outperformed MSFragger-Glyco in identifying glycopeptides. Then, using our optimized method we found that there was a significant difference in the distribution of monosaccharide types in plasma and brain tissue, e.g., the content of NeuAc in brain was 5-fold higher than that in plasma. To importantly, two glycoproteins (Neurexin-2 and SUN domain-containing protein 2) were also found for the first time by our method. In summary, we have comprehensively studied the factors influencing glycopeptide identification than any previous research, and the optimized method could be widely used for identifying the glycoproteins or glycolpeptides biomarkers for disease detection and therapeutic targets.

Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics

Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based and glycan-based search strategies to address the challenge of complex fragmentation of glycopeptides. A deep learning model is designed to capture glycan tree structures and their fragment ions for de novo sequencing of glycans that do not exist in the database. We performed extensive analyses to validate the false discovery rates (FDRs) at both peptide and glycan levels and to evaluate GlycanFinder based on comprehensive benchmarks from previous community-based studies. Our results show that GlycanFinder achieved comparable performance to other leading glycoproteomics softwares in terms of both FDR control and the number of identifications. Moreover, GlycanFinder was also able to identify glycopeptides not found in existing databases. Finally, we conducted a mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses, which had been a challenging problem to previous studies.

#4547 IDENTIFICATION OF GLYCOSYLATED IGF2 IN HUMAN URINARY PEPTIDOME AND ITS ASSOCIATION WITH CKD

Abstract Background and Aims Chronic kidney disease (CKD) is prevalent in 10% of world's adult population, with estimated glomerular filtration rate (eGFR) and albuminuria employed in its diagnosis. Role of protein glycosylation in causal mechanisms of CKD progression is largely unknown. Aim of this study was to identify urinary O-linked glycopeptides in association to CKD for better characterization of CKD molecular manifestations. Method Urine samples from eight CKD and two healthy subjects were analyzed by Capillary Electrophoresis-Tandem Mass Spectroscopy (CE-MS/MS) and glycopeptide analysis using Proteome Discoverer 1.4 was performed. Distribution of identified glycopeptides and correlation with Age, eGFR and Albuminuria were evaluated in 3810 datasets from the Human Urinary Proteome database using Spearman's rank correlation test and multiple linear regression analysis by statistical software R. The quantification of Insulin-like growth factor-II (IGF2) protein (7.5 kDa) was performed by enzyme-linked immunosorbent assay (ELISA) in two matched (for age, sex, no diabetes and no cardiovascular history) groups of 12 plasma samples each (eGFR < 30 ml/min/1.73m2 and eGFR > 90 ml/min/1.73m2). An open-source tool “Proteasix” was used to predict proteases involved in cleavage of the identified glycopeptides. The transcriptomics database and analysis tool “Nephroseq v4” were utilized to investigate the expression of predicted proteases in existing human transcriptomics CKD datasets. Results In total, 17 O-linked glycopeptides from 7 different proteins were identified, derived primarily from Insulin-like growth factor-II (IGF2) (n = 6). Glycosylation occurred at the surface exposed IGF2 Threonine 96 position. Further Investigation of the human proteome database containing 3810 datasets, showed that only three unglycosylated urinary peptides of IGF2 were identified, at significantly lower abundance and frequency (0-2.5% in the database) in comparison to the glycosylated forms (frequency of 23-90%). Interestingly, all identified IGF2 peptides belonged to E-domain of IGF2, i.e., 92 – 180 aa; which cleaves after undergoing O-linked glycosylation during the post-translational process yielding the “mature IGF2” (25-91 aa) protein. Results of multiple linear regression analysisa indicated that three IGF2 glycopeptides, DVStPPTVLPDNFPRYPVGKF [β(1024) = 0.08, p = 1.42*10−4], DVStPPTVLPDNFPRYPVG [β(560) = 0.01, p = 5.22*10−5] and DVStPPTVLPDNFPRYP [β(290) = 0.02, p = 1.07*10−4], exhibited positive correlation with Age and the glycopeptide tPPTVLPDNFPRYP showed strong negative association with eGFR [β(177) = -0.01, p = 4.21*10−9]. Along the same lines, the latter urinary IGF2 glycopeptide tPPTVLPDNFPRYP was found at increased [p < 2.2*10−16] abundance in CKD (n = 686) in comparison to healthy control (n = 229) datasets. In addition, IGF2 increased [p = 0.042] plasma levels were observed in CKD patients (eGFR < 30 ml/min/1.73m2 group) as supported by ELISA measurements. Protease predictions, considering also available transcriptomics data, suggest activation of cathepsin S with CKD potentially involved in the cleavage of the CKD-associated glycopeptide of IGF2. Conclusion Collectively, this study indicates that with aging and deteriorating kidney function, alterations in IGF2 proteoforms take place; which may be reflective of respective changes in the mature IGF2 protein abundance and function; as well as associated protease activity. Further, correlation analyses of the levels of the CKD-associated urinary IGF2 glycopeptide with the plasma IGF2 levels with CKD progression is planned. a Results of multiple linear regression where regression Co-efficient is β; degree of freedom is stated in (brackets); and p-value <0.05 was considered statistically significant

Characterization of aberrant glycosylation associated with osteoarthritis based on integrated glycomics methods

BackgroundOsteoarthritis (OA) is the most common form of arthritis, affecting millions of aging people. Investigation of abnormal glycosylation is essential for the understanding of pathological mechanisms of OA.MethodsThe total protein was isolated from OA (n = 13) and control (n = 11) cartilages. Subsequently, glycosylation alterations of glycoproteins in OA cartilage were investigated by lectin microarrays and intact glycopeptides analysis. Finally, the expression of glycosyltransferases involved in the synthesis of altered glycosylation was assessed by qPCR and GEO database.ResultsOur findings revealed that several glycopatterns, such as α-1,3/6 fucosylation and high-mannose type of N-glycans were altered in OA cartilages. Notably, over 27% of identified glycopeptides (109 glycopeptides derived from 47 glycoproteins mainly located in the extracellular region) disappeared or decreased in OA cartilages, which is related to the cartilage matrix degradation. Interestingly, the microheterogeneity of N-glycans on fibronectin and aggrecan core protein was observed in OA cartilage. Our results combined with GEO data indicated that the pro-inflammatory cytokines altered the expression of glycosyltransferases (ALG3, ALG5, MGAT4C, and MGAT5) which may contribute to the alterations in glycosylation.ConclusionOur study revealed the abnormal glycopatterns and heterogeneities of site-specific glycosylation associated with OA. To our knowledge, it is the first time that the heterogeneity of site-specific N-glycans was reported in OA cartilage. The results of gene expression analysis suggested that the expression of glycosyltransferases was impacted by pro-inflammatory cytokines, which may facilitate the degradation of protein and accelerate the process of OA. Our findings provide valuable information for the understanding of molecular mechanisms in the pathogenesis of OA.

Unraveling the glycosylated immunopeptidome with HLA-Glyco

Recent interest in targeted therapies has been sparked by the study of MHC-associated peptides (MAPs) that undergo post-translational modifications (PTMs), particularly glycosylation. In this study, we introduce a fast computational workflow that merges the MSFragger-Glyco search algorithm with a false discovery rate control for glycopeptide analysis from mass spectrometry-based immunopeptidome data. By analyzing eight large-scale publicly available studies, we find that glycosylated MAPs are predominantly presented by MHC class II. Here, we present HLA-Glyco, a comprehensive resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights, including high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between HLA allele groups. We integrate the workflow within the FragPipe computational platform and provide HLA-Glyco as a free web resource. Overall, our work provides a valuable tool and resource to aid the nascent field of glyco-immunopeptidomics.

The 2022 Nobel Prize in Chemistry-sweet!

On 2022 October 5, The Royal Swedish Academy of Sciences announced its decision to award the Nobel Prize in Chemistry 2022 to Carolyn R. Bertozzi (Stanford University), Morten Meldal (University of Copenhagen), and K. Barry Sharpless (Scripps Research) “for the development of click chemistry and bioorthogonal chemistry.” The glycobiology community was exultant! To understand why, one must appreciate how challenges in glycoscience research motivated the development of these transformative chemical tools. Glycoscience has a storied history contributing significant discoveries to hematology, metabolism, microbiology, and other fields of biomedical research throughout much of the 20th century. But when the 1970s and 80s ushered in new molecular biology methods that accelerated studies of nucleic acid and protein function, studies of glycans began to lag behind (National Research Council 2012; Agre et al. 2016). Fortunately, since then, vast improvements have been made in areas such as carbohydrate synthesis and glycan arrays (Rillahan and Paulson 2011; Li and Bennett 2022), availability of glyco-enzymes and small molecule inhibitors (Moremen et al. 2018; Almahayni et al. 2022), mass spectrometry analysis of glycans and glycopeptides (Ruhaak et al. 2018; Suttapitugsakul et al. 2020; Bagdonaite et al. 2022), as well understanding of biological systems (Varki 2017), all of which have facilitated studies of glycan function. Notwithstanding these and other important advances, glycan detection has presented a recurrent challenge. Indeed, much of the modern practice of biological research hinges on the ability to specifically address a biomolecule of interest so that it can be isolated, visualized, or quantified. For nucleic acids, this can often be achieved via hybridization, whereas specific proteins can be detected and tracked using antibodies or protein tagging methods. But genetically encoded tags cannot be used to track glycans, which are not primary gene products. For the glycobiologist, lectins and antibodies have been essential tools but can suffer from limitations relating to specificity and affinity (Cummings et al. 2022).

Recent trends in glycoproteomics by characterization of intact glycopeptides

This trends article provides an overview of the state of the art in the analysis of intact glycopeptides by proteomics technologies based on LC–MS analysis. A brief description of the main techniques used at the different steps of the analytical workflow is provided, giving special attention to the most recent developments. The topics discussed include the need for dedicated sample preparation for intact glycopeptide purification from complex biological matrices. This section covers the common approaches with a special description of new materials and innovative reversible chemical derivatization strategies, specifically devised for intact glycopeptide analysis or dual enrichment of glycosylation and other post-translational modifications. The approaches are described for the characterization of intact glycopeptide structures by LC–MS and data analysis by bioinformatics for spectra annotation. The last section covers the open challenges in the field of intact glycopeptide analysis. These challenges include the need of a detailed description of the glycopeptide isomerism, the issues with quantitative analysis, and the lack of analytical methods for the large-scale characterization of glycosylation types that remain poorly characterized, such as C-mannosylation and tyrosine O-glycosylation. This bird’s-eye view article provides both a state of the art in the field of intact glycopeptide analysis and open challenges to prompt future research on the topic.Graphical

Sensitive Analysis of Recombinant Human Erythropoietin Glycopeptides by On-Line Phenylboronic Acid Solid-Phase Extraction Capillary Electrophoresis Mass Spectrometry.

In this study, several chromatographic sorbents: porous graphitic carbon (PGC), aminopropyl hydrophilic interaction (aminopropyl-HILIC), and phenylboronic acid (PBA) were assessed for the analysis of glycopeptides by on-line solid-phase extraction capillary electrophoresis mass spectrometry (SPE-CE-MS). As the PBA sorbent provided the most promising results, a PBA-SPE-CE-MS method was developed for the selective and sensitive preconcentration of glycopeptides from enzymatic digests of glycoproteins. Recombinant human erythropoietin (rhEPO) was selected as the model glycoprotein and subjected to enzymatic digestion with several proteases. The tryptic O126 and N83 glycopeptides from rhEPO were targeted to optimize the methodology. Under the optimized conditions, intraday precision, linearity, limits of detection (LODs), and microcartridge lifetime were evaluated, obtaining improved results compared to that from a previously reported TiO2-SPE-CE-MS method, especially for LODs of N-glycopeptides (up to 500 times lower than by CE-MS and up to 200 times lower than by TiO2-SPE-CE-MS). Moreover, rhEPO Glu-C digests were also analyzed by PBA-SPE-CE-MS to better characterize N24 and N38 glycopeptides. Finally, the established method was used to analyze two rhEPO products (EPOCIM and NeuroEPO plus), demonstrating its applicability in biopharmaceutical analysis. The sensitivity of the proposed PBA-SPE-CE-MS method improves the existing CE-MS methodologies for glycopeptide analysis and shows a great potential in glycoprotein analysis to deeply characterize protein glycosites even at low concentrations of the protein digest.

Comprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation

BackgroundPlatelet glycoprotein (GP) Ibα is the major ligand-binding subunit of the GPIb-IX-V complex that binds von Willebrand factor. GPIbα is heavily glycosylated, and its glycans have been proposed to play key roles in platelet clearance, von Willebrand factor binding, and as target antigens in immune thrombocytopenia syndromes. Despite its importance in platelet biology, the glycosylation profile of GPIbα is not well characterized. ObjectivesThe aim of this study was to comprehensively analyze GPIbα amino acid sites of glycosylation (glycosites) and glycan structures. MethodsGPIbα ectodomain that was recombinantly expressed or that was purified from human platelets was analyzed by Western blot, mass spectrometry glycomics, and mass spectrometry glycopeptide analysis to define glycosites and the structures of the attached glycans. ResultsWe identified a diverse repertoire of N- and O-glycans, including sialoglycans, Tn antigen, T antigen, and ABO(H) blood group antigens. In the analysis of the recombinant protein, we identified 62 unique O-glycosites. In the analysis of the endogenous protein purified from platelets, we identified 48 unique O-glycosites and 1 N-glycosite. The GPIbα mucin domain is densely O-glycosylated. Glycosites are also located within the macroglycopeptide domain and mechanosensory domain. ConclusionsThis comprehensive analysis of GPIbα glycosylation lays the foundation for further studies to determine the functional and structural roles of GPIbα glycans.

Systems-Wide Site-Specific Analysis of Glycoproteins.

Glycosylation is one of the most common and complex post-translation modifications that influence the structural and functional properties of proteins. Glycoproteins are highly heterogeneous and exhibit site- and protein-specific expression differences. Mass spectrometry in combination with liquid chromatography has emerged as the most powerful tool for the comprehensive characterization of glycosylation. The analysis of intact glycopeptides has emerged as a promising strategy to analyze glycoproteins for their glycan heterogeneity at both protein- and site-specific levels. Nevertheless, intact glycopeptide characterization is challenging as elucidation of the glycan and peptide moieties requires specific sample preparation workflows that, combined with the tandem mass spectrometry approach, enable the identification of single glycopeptide species. In this chapter, we provide a detailed description of the methods that include procedures for (i) proteolytic digestion using specific proteases, (ii) optional glycopeptide enrichment using hydrophilic interaction liquid chromatography, (iii) nano-LC-MS/MS analysis of glycopeptides, and (iv) data analysis for identification of glycopeptides. Together, our workflow provides a framework for the system-wide site-specific analysis of N- and O-glycopeptides derived from complex biological or clinical samples.

Simultaneous enrichment optimization of glycopeptides and phosphopeptides with the highly hydrophilic DZMOF-FDP.

Protein glycosylation and phosphorylation play essential roles in biological systems. The crosstalk of both glycosylation and phosphorylation on one protein represents an unveiled biological function. To realize the analyses of both glycopeptides and phosphopeptides, a simultaneous enrichment method of N-glycopeptides, mono-phosphopeptides and multi-phosphopeptides was developed based on a multi-functional dual-metal centered zirconium metal-organic framework that provided multiple interactions for HILIC, IMAC, and MOAC for glycopeptides and phosphopeptides. Based on a careful optimization of sample loading and elution conditions for the simultaneous enrichment of glycopeptides and phosphopeptides with the zirconium metal-organic framework, a total of 1011 N-glycopeptides derived from 410 glycoproteins and 1996 phosphopeptides including 741 multi-phosphopeptides derived from 1189 phosphoproteins could be identified from a HeLa cell digest. The simultaneous enrichment approach for glycopeptides and mono-/multi-phosphopeptides demonstrates the great potential of the combined interactions for HILIC, IMAC, and MOAC in integrated post-translational modification proteomics research.

Recognition of Core-Fucosylated Glycopeptides Based on the Y1+Fuc/Y1 Ratio in Low-Energy HCD Spectra.

Accurate identification of core fucosylation on N-glycopeptides remains challenging due to fucose migration during mass spectrometry analysis. Here, we introduce a simple and straightforward method for core-fucosylated glycopeptide recognition based on the relative intensities of Y1+Fuc ions compared with their corresponding Y1 ions (labeled as Y1+Fuc/Y1 or simply Y1F/Y1 ratio > 0.1) in low-energy HCD-based spectra. The method was first developed by systematically evaluating the influence of fucose migration on the Y1F ion from antenna fucoses based on the distribution of the Y1F/Y1 ratios in the MS/MS spectra of antenna-fucosylated glycopeptides from Fut8-/- mouse brain. The feasibility of the method was then confirmed by using two standard glycoproteins, comparison with glycopeptides in Fut8+/+ mouse brain with/without in silico core-fucosylation removal, and Y1F/Y1 ratio alterations under a lower HCD energy. This method will be applicable to the manual interpretation and software-based high-throughput analysis of core-fucosylated glycopeptides.