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Thaysen-Andersen, M.

Publications and source records attributed to Thaysen-Andersen, M..

16 recordsLinked to original sources

Real-time mass defect-driven prediction of glycopeptide precursors enables enrichment-free serum glycoproteomics

Glycopeptide enrichment remains a cornerstone in glycoproteomics, but bias and reproducibility issues continue to hinder biological insight and clinical translation. Employing curated glycoproteomics datasets and machine learning, we trained a glycopeptide classifier to recognize N-glycopeptide precursors through mass defect signatures. Integration of the classifier into a data-dependent acquisition framework facilitated real-time prediction of N-glycopeptides from human serum and revealed sex differences in murine plasma fucosylation opening avenues for enrichment-free glycoproteomics.

bioinformatics↗

Multi-omics definition of the sex-specific glycoproteome of murine tissues

Sex-specific differences in the glycoproteome remain poorly defined despite growing evidence that protein glycosylation is a key determinant of sex biology. Here we present a tissue-resolved glycoproteome atlas of adult male and female C57BL/6J mice, integrating transcriptomics, proteomics and glycoproteomics with sialic acid speciation and lectin microarray profiling across 19 tissues. Quantitative analysis of >26,800 protein- and site-specific N-glycoforms from 1,512 glycoproteins revealed highly distinct tissue glycoproteomes shaped by coordinated regulation of protein abundance and glyco-enzyme expression. Multi-omics integration identified strong glycophenotype-enzyme relationships, including control of tissue sialylation by Cmas and Cmah, suggesting rate-limiting roles in glycosylation. Pronounced sex-linked glycophenotypes were observed in salivary gland, liver and kidney, driven by differences in fucosylation, sialylation and protein abundance, whereas the brain glycome was largely conserved between sexes. An interactive online database (https://igcore.cloud/mta/atlas-viewer/) provides a resource for exploring sex-biased glycosylation across mouse tissues.

cell biology↗

Serum Lewis fucosylation reports on survivorship of patients with septic shock upon admission to intensive care unit

Septic shock, the excessive immune response to pathogen infection, poses a major health concern accounting globally for [~]20% of all deaths. Current methods to establish disease severity are unacceptably slow, unspecific and insensitive, hindering timely and effective treatment. Aiming to identify easy-to-assay glyco-signatures that may identify and guide the clinical management of the most critically unwell patients, we applied quantitative glycomics and glycoproteomics to sera longitudinally collected from septic shock survivors (n=29) and non-survivors (n=8). Glycomics of all 134 serum samples (sampled daily until recovery/death) revealed significant N-glycome dynamics across both patient groups. Unsupervised clustering of the serum N-glycome upon ICU admission (day 1) indicated survivorship-specific glyco- signatures. We therefore employed machine learning to train a random forest model using the serum N-glycome data. The model accurately classified survivorship outcomes of 35 of 37 patients (specificity 94.6%) and correctly predicted 6 of 8 non-survivors (sensitivity 75%) based on ICU day 1 data. Further interrogation of the serum N-glycome data revealed elevated Lewis fucosylation in non-survivors relative to survivors at ICU admission, a finding recapitulated by glycoproteomics. Amongst 58 other serum proteins strongly linked to acute phase response and stress pathways, alpha-1-acid-glycoprotein was identified as a principal carrier of Lewis fucosylation with a potential to stratify septic shock survivors from non- survivors (AUC 0.935). This study lays a foundation for risk stratification of septic shock patients by uncovering easy-to-assay glyco-signatures that identify individuals with poor survival outcomes upon ICU admission, with the potential to translate to early individualised clinical care at the bedside.

biochemistry↗

ST6GAL1-mediated sialyl linkage switching in tumor-associated macrophages drives cancer-promoting nanotubes carrying α2,6-sialylation in anti-inflammatory cells

Tumor-associated macrophages (TAMs) form functionally diverse populations of innate immune cells in the tumor microenvironment (TME). Pro- and anti-inflammatory TAMs are central to cancer progression by shaping inflammation and immune (im)balance, but it remains unknown if polarization-induced remodeling of the TAM glycocalyx critical for cellular communication occurs within the TME. Taking a systems glycobiology approach, we here firstly used cell surface-focused glycomics and lectin flow cytometry of ex vivo polarized monocyte-derived macrophages to demonstrate profound sialyl linkage switching of the surface N-glycome in pro-inflammatory (2,3-sialo-favored) and anti-inflammatory (2,6-sialo-dominant) macrophages. In contrast, no polarization-induced alterations in sialylation were observed in the surface O-glycome. ST6GAL1 that modifies N-glycans with 2,6-sialylation was elevated in anti-inflammatory compared to levels in pro-inflammatory macrophages providing a mechanistic basis for the sialyl linkage switching, which was supported by ST6GAL1 silencing. Interestingly, SNA-focused lectin cytochemistry of anti-inflammatory macrophages revealed dense networks of dynamic 2,6-sialylated protein-based nanotubules forming inter-connecting cellular structures that were absent in pro-inflammatory macrophages. Temporal ST6GAL1 silencing in anti-inflammatory macrophages caused nanotubule disintegration as evidenced by SNA and biotin fluorescence microscopy. Moreover, live cell recordings of anti-inflammatory macrophages cultured with and without colorectal cancer (CRC) cells showed reduced macrophage motility, attenuated inter-macrophage and macrophage-CRC cell interactions and diminished CRC cell proliferation upon ST6GAL1 disruption indicating functional roles of the 2,6-sialylated nanotubules. Finally, sialyl linkage switching was recapitulated in pro- and anti-inflammatory TAMs from tumor tissues of patients with advanced CRC. We report on the mechanistic basis for and functional consequences of glycocalyx remodeling accompanying TAM polarization.

immunology↗

Tumor- and immune-derived N-acetyl-β-D-hexosaminidase drive colorectal cancer and stratify patient risk

Non-invasive prognostic markers are needed to improve survival of colorectal cancer (CRC) patients. Towards this goal, we applied integrative systems glycobiology approaches to tumor tissues and PBMCs from CRC patients and matching controls as well as to a CRC patient-derived cell line. Firstly, quantitative glycomics and glycoproteomics revealed that non-canonical paucimannosidic proteins from monocytic and cancer cell origins are prominent signatures in CRC tumor tissues, and that their expression associates with CRC progression. Guided by these associations, we then showed that N-acetyl-{beta}-D-hexosaminidase (Hex) facilitates paucimannosidic protein biosynthesis in CRC cells and is intimately involved in processes underpinning CRC metastasis (adhesion, migration, invasion, proliferation). Finally, Hex activity was found to be elevated in PBMCs and plasma from patients with advanced CRC relative to matching controls while plasma Hex activity correlated strongly with CRC patient survival. Our study opens avenues for better prognostication, disease risk stratification and therapeutic interventions in CRC. HighlightsO_LI* Non-canonical truncated glycans of immune and cancer origins dominate in CRC tumors C_LIO_LI* N-acetyl-{beta}-D-hexosaminidase, a truncating glycoenzyme, drives tumorigenesis in CRC C_LIO_LI* Activity of plasma N-acetyl-{beta}-D-hexosaminidase stratifies risk in CRC patients C_LI

cancer biology↗

Ratios in Disguise, Truths Arise: Glycomics Meets Compositional Data Analysis

Comparative glycomics data are an instance of compositional data defined by the Aitchison simplex, where measured glycans are parts of a whole, indicated by relative abundances, which are then compared between conditions. Applying traditional statistical analyses to this type of data often results in misleading conclusions, such as spurious "decreases" of glycans between conditions when other structures sharply increase in abundance, or routine false-positive rates of >25% for differential abundance. Our work introduces a compositional data analysis framework, specifically tailored to comparative glycomics, to account for these data dependencies. We employ center log-ratio (CLR) and additive log-ratio (ALR) transformations, augmented with a model incorporating scale uncertainty/information, to introduce the most robust and sensitive glycomics data analysis pipeline. Applied to many publicly available comparative glycomics datasets, we show that this model controls false-positive rates and results in new biological findings. Additionally, we present new modalities to analyze comparative glycomics data with this framework. Alpha- and beta-diversity enable exploration of glycan distributions within and between biological samples, while cross-class glycan correlations shed light on complex and previously undetected interdependencies. These new approaches have revealed deeper insights into glycome variations that are critical to understanding the roles of glycans in health and disease.

bioinformatics↗

Glycoproteome remodelling and granule-specific N-glycosylation accompany neutrophil granulopoiesis

Neutrophils store microbicidal glycoproteins in cytosolic granules to fight intruding pathogens, but their granule distribution and formation mechanism(s) during granulopoiesis remain unmapped. Herein, we perform comprehensive spatiotemporal N-glycoproteome profiling of isolated granule populations from blood-derived neutrophils and during their maturation from bone marrow-derived progenitors using glycomics-assisted glycoproteomics. Interestingly, the granules of resting neutrophils exhibited distinctive glycophenotypes including, most strikingly, peculiar highly truncated N-glycosylation in the azurophilic granules. Excitingly, proteomics and transcriptomics data from discrete myeloid progenitor stages revealed that profound glycoproteome remodelling underpins the promyelocytic-to-metamyelocyte transition and that remodelling is driven primarily by changes in protein expression and less by the glycosylation machinery. Notable exceptions were the oligosaccharyltransferase subunits responsible for initiation of N-glycoprotein biosynthesis that were strongly expressed in early myeloid progenitors correlating with high glycosylation efficiencies of the azurophilic granule proteins. Our study provides spatiotemporal insights into the complex neutrophil N-glycoproteome featuring an intriguing granule-specific N-glycosylation formed by dynamic remodelling during myeloid progenitor-to-neutrophil maturation. Key pointsO_LISystems glycobiology reveals that profound N-glycoproteome remodelling accompanies early neutrophil granulopoiesis C_LIO_LIPrecision glycoproteomics produces detailed cartography of neutrophils that exhibit site-, protein- and granule-specific N-glycosylation C_LI

systems biology↗

Comprehensive glycoprofiling of oral tumours associates N-glycosylation with lymph node metastasis and patient survival

While altered protein glycosylation is regarded a trait of oral squamous cell carcinoma (OSCC), its heterogeneous glycoproteome and dynamics with disease progression remain unmapped. To this end, we here employ an integrated multi-omics approach comprising unbiased and quantitative glycomics and glycoproteomics applied to a valuable cohort of resected tumour tissues from OSCC patients with (n = 19) and without (n = 12) lymph node metastasis. While all tumour tissues displayed uniform N-glycome profiles suggesting relatively stable global N-glycosylation during lymph node metastasis, glycoproteomics and advanced correlation analysis notably uncovered altered site-specific N-glycosylation and previously unknown associations with several key clinicopathological features. Importantly, focused analyses of the multi-omics data unveiled two N-glycans and three N-glycopeptides that were closely associated with patient survival. This study provides novel insight into the complex OSCC tissue N-glycoproteome forming an important resource to further explore the underpinning disease mechanisms and uncover new prognostic glyco-markers for OSCC. TeaserDeep survey of the dynamic landscape of complex sugars in oral tumours paves a way for new prognostic disease markers.

cancer biology↗

Ultra-sensitive platelet proteome maps the O-glycosylation landscape and charts the response to thrombin dosage

Platelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets tendency to pre-activate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1,300 proteins. Unbiased scanning for post-translational modifications within releasate proteins highlighted O-glycosylation as being a major component. For the first time, we detected O-fucosylation on previously uncharacterised sites including multimerin-1 (MMRN1), a major alpha granule protein that supports platelet adhesion to collagen and is a carrier for platelet factor V. The N-terminal EMI domain of MMRN1, a key site for protein-protein interaction, was O-fucosylated at a conserved threonine within a new consensus sequence. Our data suggest that Protein O-fucosyltransferase 1 (POFUT1) is responsible for this modification. Secretion of MMRN1 was reduced in cells lacking POFUT1, supporting a key role of O-fucosylation in MMRN1 function. By comparing releasates from resting and thrombin-treated platelets, 202 proteins were found to be significantly released after high-dose thrombin stimulation. Complementary quantification of the platelet lysates identified >3,800 proteins, which confirmed the platelet origin of releasate proteins by anti-correlation analysis. Low-dose thrombin treatment yielded a smaller subset of significantly regulated proteins with fewer secretory pathway enzymes. The comprehensive platelet proteome resource provided here (larancelab.com/platelet-proteome) allows identification of novel regulatory mechanisms for drug targeting to address platelet dysfunction and thrombosis. Key PointsO_LIHigh-sensitivity proteome mapping of human platelets identifies O-glycosylation of platelet proteins at key functional sites C_LIO_LIPlatelet O-fucosyltransferase POFUT1 regulates the secretion of adhesive protein multimerin-1 (MMRN1) C_LI

biochemistry↗

Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay

A new method to probe the conformational changes of glycoproteins on a systems-wide scale, termed limited deglycosylation assay (LDA), is described. The method measures the differential rate of deglycosylation of N-glycans on natively folded proteins by the common peptide:N-glycosidase F (PNGase F) enzyme which in turn informs on their spatial presentation and solvent exposure on the protein surface hence ultimately the glycoprotein conformation. LDA involves 1) protein-level N-deglycosylation under native conditions, 2) trypsin digestion under denaturing conditions, 3) glycopeptide enrichment, 4) peptide-level N-deglycosylation and 5) quantitative MS-based analysis of the formerly N-glycosylated peptides. LDA was initially developed and the experimental conditions optimized using bovine RNase B and fetuin. The method was then applied to glycoprotein extracts from LLC-MK2 epithelial cells upon treatment with dithiothreitol to induce endoplasmic reticulum stress and promote protein misfolding. Data from the LDA and 3D structure analysis showed that glycoproteins predominantly undergo structural changes in loops/turns upon ER stress as exemplified with detailed analysis of ephrin-A5, GALNT10, PVR and BCAM. These results show that LDA accurately reports on systems-wide conformational changes of glycoproteins induced under controlled treatment regimes. Thus, LDA opens avenues to study glycoprotein structural changes in a range of other physiological and pathophysiological conditions relevant to acute and chronic diseases.

biochemistry↗

Oligomannosylation and MAN1A1 expression associate strongly with a subset of human cancer types

Aberrant protein glycosylation is a prominent cancer feature. While many tumour-associated glycoepitopes have been reported, advances in glycoanalytics continue to uncover new associations between glycoproteins and cancer. Guided by a comprehensive literature survey suggesting that oligomannosylation (Man5-9GlcNAc2, M5-M9) is a widespread albeit poorly studied glyco-signature in human cancers, we here re-visit a valuable compilation of nearly 500 LC-MS/MS N-glycomics datasets acquired across 11 human cancer types to systematically test for oligomannose-cancer associations. Firstly, our quantitative glycomics data obtained across 34 cancerous cell lines demonstrated that oligomannosylation, particularly the under-processed M7-M9, is a strong pan-cancer feature. We then showed cell surface expression of oligomannosidic epitopes in the promyelocytic leukemic HL-60 cell line using concanavalin A-based flow cytometry. In keeping with literature, our quantitative glycomics data of tumour and matching control tissues and new MALDI-MS imaging data of tissue microarrays showed a strong cancer-associated elevation of oligomannosylation in both basal cell (p = 1.78 x 10-12) and squamous cell (p = 1.23 x 10-11) skin cancer and colorectal cancer (p = 8.0 x 10-4). The glycomics data also indicated that few cancer types including gastric and liver cancer exhibit unchanged or reduced oligomannose levels, observations also supported by literature and MALDI-MSI. Finally, data from cancer repositories indicated that three 1,2-mannosidases dictate oligomannose expression in cancer cells, and further suggested that deleterious mutations and reduced expression of MAN1A1 are key contributors to the cancer-associated oligomannose elevation. Collectively, these findings open hitherto unexplored avenues for the development of new cancer biomarkers and therapeutic targets.

biochemistry↗

An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms

Withdrawal statement"The authors have withdrawn their manuscript because the authors need to re-organize the data and writing, meanwhile more experimental evidence from human cellular N-glycome will be added to support their viewpoints. In this preprint, only one human cell line, Acute Promyelocytic Leukemia (APL) cells, was deeply investigated to show the N-glycome landscape. To provide the shared features of human N-glycome, more human cells should be investigated. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author."

biochemistry↗

Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells

Understanding and eliciting protective immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent priority. To facilitate these objectives, we have profiled the repertoire of human leukocyte antigen class II (HLA-II)-bound peptides presented by HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein. We identify 209 unique HLA-II-bound peptide sequences, many forming nested sets, which map to sites throughout S including glycosylated regions. Comparison of the glycosylation profile of the S protein to that of the HLA-II-bound S peptides revealed substantial trimming of glycan residues on the latter, likely introduced during antigen processing. Our data also highlight the receptor-binding motif in S1 as a HLA-DR-binding peptide-rich region. Results from this study have application in vaccine design, and will aid analysis of CD4+ T cell responses in infected individuals and vaccine recipients.

immunology↗

Hyper-Truncated N-Acetyl-β-D-Glucosamine Decorations Augment the Activity and Inhibition Potential of Neutrophil Granule Myeloperoxidase

Myeloperoxidase (MPO) plays essential roles in neutrophil-mediated immunity via the generation of reactive oxidation products. Complex carbohydrates decorate MPO at discrete sites, but their functional relevance remain elusive. To this end, we have characterised the structure-biosynthesis-activity relationship of neutrophil MPO (nMPO). Mass spectrometry demonstrated that nMPO carries both characteristic under-processed and hyper-truncated glycans. Occlusion of the Asn355/Asn391-glycosylation sites and the Asn323-/Asn483-glycans, located in the MPO dimerisation zone, was found to affect the local glycan processing, thereby providing a molecular basis of the site-specific nMPO glycosylation. Native mass spectrometry, mass photometry, and glycopeptide profiling revealed significant molecular complexity of diprotomeric nMPO arising from heterogeneous glycosylation, oxidation, chlorination and polypeptide truncation variants, and a previously unreported low-abundance monomer. Longitudinal profiling of maturing, mature, granule-separated, and pathogen-stimulated neutrophils demonstrated that nMPO is dynamically expressed during granulopoiesis, unevenly distributed across granules and degranulated upon activation. We also show that proMPO-to-MPO maturation occurs during early/mid-stage granulopoiesis. While similar global MPO glycosylation was observed across conditions, the conserved Asn355-/Asn391-sites displayed elevated glycan hyper-truncation, which correlated with higher enzyme activities of MPO in distinct granule populations. Enzymatic trimming of the Asn355-/Asn391-glycans recapitulated the activity gain and showed that nMPO carrying hyper-truncated glycans at these positions exhibits increased thermal stability, polypeptide accessibility, and ceruloplasmin-mediated inhibition potential relative to native nMPO. Finally, structural modelling revealed that hyper-truncated Asn355-glycans positioned in the MPO-ceruloplasmin interface are critical for uninterrupted inhibition. Here, through an innovative and comprehensive approach, we report novel functional roles of MPO glycans, providing new insight into neutrophil-mediated immunity. SignificanceMyeloperoxidase (MPO) is an important microbicidal glycoprotein critical for fighting pathogens. We report, for the first time, the intriguingly complex relationship between glycobiology and MPO immune function by demonstrating that uncommon and strategically positioned hyper-truncated glycans both elevate the activity and the inhibition potential of this pathogen-combating enzyme. We have used a multifaceted approach employing integrated biomolecular analytics to generate new insights into the sugar code of MPO. The findings described in this study improve our understanding of key innate immune processes and may guide future glycoengineering efforts aiming to generate therapeutically relevant recombinant MPO products with tuneable activity and inhibition potential tailored to biomedical applications involving persisting and severe pathogen infections.

biochemistry↗

Integrated glycoproteomics identifies a role of N-glycosylation and galectin-1 on myogenesis and muscle development

ABSTRACTMany cell surface and secreted proteins are modified by the covalent addition of glycans that play an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signaling. Aberrant protein glycosylation has been associated with the development of several muscular diseases suggesting essential glycan- and lectin-mediated functions in myogenesis and muscle development but our molecular understanding of the precise glycans, catalytic enzymes and lectins involved remain only partially understood. Here, we quantified dynamic remodeling of the membrane-associated proteome during a time-course of myogenesis in cell culture. We observed wide-spread changes in the abundance of several important lectins and enzymes facilitating glycan biosynthesis. Glycomics-based quantification of released N-linked glycans confirmed remodeling of the glycome consistent with the regulation of glycosyltransferases and glycosidases responsible for their formation including a previously unknown di-galactose-to-sialic acid switch supporting a functional role of these glycoepitopes in myogenesis. Furthermore, dynamic quantitative glycoproteomic analysis with multiplexed stable isotope labelling and analysis of enriched glycopeptides with multiple fragmentation approaches identified glycoproteins modified by these regulated glycans including several integrins and growth factor receptors. Myogenesis was also associated with the regulation of several lectins most notably the up-regulation of galectin-1 (LGALS1). CRISPR/Cas9-mediated deletion of Lgals1 inhibited differentiation and myotube formation suggesting an early functional role of galectin-1 in the myogenic program. Importantly, similar changes in N-glycosylation and the up-regulation of galectin-1 during postnatal skeletal muscle development were observed in mice. Treatment of new-born mice with recombinant adeno-associated viruses to overexpress galectin-1 in the musculature resulted in enhanced muscle mass. Our data form a valuable resource to further understand the glycobiology of myogenesis and will aid the development of intervention strategies to promote healthy muscle development or regeneration.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsAAV adeno-associated virusANOVAanalysis of variationCBDscarbohydrate binding domainsCDGscongenital disorders of glycosylationCRISPRclustered regularly interspaced short palindromic repeatsCIDcollisional induced dissociationDTTdithiothreitolECMextracellular matrixEThcDelectron transfer dissociation with higher collisional dissociation supplemental activationFBSfetal bovine serumFDRfalse discovery rateFAformic acidGBPsglycan-binding proteinsHCDhigher collisional dissociationHILIChydrophilic interaction liquid chromatographyMCSmultiple cloning siteMeCNacetonitrileNMJneuromuscular junctionsPCAprincipal component analysisPGCporous graphitized carbonPSMpeptide spectral matchTEABtriethylammonium bicarbonateTFAtrifluoroacetic acidTMTtandem mass tagsView Full Text

biochemistry↗

Glycan analysis of human neutrophil granules implicates a maturation-dependent glycosylation machinery

Protein glycosylation is essential to trafficking and immune functions of human neutrophils. During granulopoeisis in the bone marrow, distinct neutrophil granules are successively formed. Distinct receptors and effector proteins, many of which are glycosylated, are targeted to each type of granule according to their time of expression, a process called targeting-by-timing. Therefore, these granules are time capsules reflecting different times of maturation that can be used to understand how glycosylation evolves during granulopoiesis. Herein, neutrophil subcellular granules were fractionated by Percoll density gradient centrifugation and N- and O-glycans present in each compartment were analyzed by liquid chromatography and tandem mass spectrometry. We found abundant paucimannosidic N-glycans and lack of O-glycans in early-formed azurophil granules (AG), whereas later-formed specific and gelatinase granules (SG and GG) contained complex N- and O-glycans with remarkably elongated N-acetyllactosamine repeats with Lewis-x and sialyl-Lewis-x epitopes. Many glycans identified are unique to neutrophils and their complexity increased progressively from AG to SG and then to GG, suggesting temporal changes in the glycosylation machinery indicative of glycosylation-by-timing during granulopoiesis. In summary, this comprehensive neutrophil granule glycome map, the first of its kind, highlights novel granule-specific glycosylation features and is a crucial first step towards a better understanding of the mechanisms regulating protein glycosylation during neutrophil granulopoiesis and a more detailed understanding of neutrophil biology and function.

biochemistry↗