379 results on '"Daniel Kolarich"'
Search Results
2. Genome-Wide Methylation Profiling in 229 Patients With Crohn’s Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn’s Disease (TOPPIC)Summary
- Author
-
Nicholas T. Ventham, Nicholas A. Kennedy, Rahul Kalla, Alex T. Adams, Alexandra Noble, Holly Ennis, Craig Mowat, Malcolm G. Dunlop, Jack Satsangi, Ian Arnott, Aiden Cahill, Malcolm Smith, Tariq Ahmad, Sreedhar Subramanian, Simon Travis, John Morris, John Hamlin, Anjan Dhar, Chuka Nwokolo, Cathryn Edwards, Tom Creed, Stuart Bloom, Mohamed Yousif, Linzi Thomas, Simon Campbell, Stephen J. Lewis, Shaji Sebastian, Sandip Sen, Simon Lal, Chris Hawkey, Charles Murray, Fraser Cummings, Jason Goh, James O. Lindsay, Naila Arebi, Lindsay Potts, Aileen J. McKinley, John M. Thomson, John A. Todd, Mhairi Collie, Ashley Mowat, Daniel R. Gaya, Jack Winter, Graham D. Naismith, Catriona Keerie, Steff Lewis, Robin J. Prescott, Gordan Lauc, Harry Campbell, Dermot P.B. McGovern, Vito Annese, Vlatka Zoldoš, Iain K. Permberton, Manfred Wuhrer, Daniel Kolarich, Daryl L. Fernandes, Evropi Theorodorou, Victoria Merrick Daniel I. Spencer, Richard A. Gardner, Ray Doran, Archana Shubhakar, Ray Boyapati, Igor Rudan, Paolo Lionetti, Irena Trbojević Akmačić, Jasminka Krištić, Frano Vuč ković, Jerko Štambuk, Mislav Novokmet, Maja Pučić-Baković, Olga Gornik, Angelo Andriulli, Laura Cantoro, Giancarlo Sturniolo, Gionata Fiorino, Natalia Manetti, Anna Latiano, Anna Kohn, Renata D’Inca`, Silvio Danese, Ian D. Arnott, Colin L. Noble, Charlie W. Lees, Alan G. Shand, Gwo-Tzer Ho, Lee Murphy, Jude Gibson, Louise Evenden, Nicola Wrobel, Tamara Gilchrist, Angie Fawkes, Guinevere S.M. Kammeijer, Florent Clerc, Noortje de Haan, Aleksandar Vojta, Ivana Samaržija, Dora Markulin, Marija Klasić, Paula Dobrinić, Yurii Aulchenko, Tim van den Heuve, Daisy Jonkers, and Marieke Pierik
- Subjects
Crohn's disease ,Surgery ,DNA methylation ,Epigenetics ,Inflammatory bowel disease ,Aging ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background & Aims: DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn’s disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. Methods: TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). Results: CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10-9, Holm P = .002) and EFNA3 (P = 4.9 × 10-8, Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2–2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19, SBNO2 = 1.2 × 10-11) and regions (TXK [false discovery rate, P = 3.6 × 10-14], WRAP73 [false discovery rate, P = 1.9 × 10-9], VMP1 [false discovery rate, P = 1.7 × 10-7], and ITGB2 [false discovery rate, P = 1.4 × 10-7]). Conclusions: We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.
- Published
- 2023
- Full Text
- View/download PDF
3. GlycoBioinformatics
- Author
-
Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, Niclas Karlsson, Daniel Kolarich, and Nicolle H. Packer
- Subjects
bioinformatics ,glycobioinformatics ,glycoinformatics ,Science ,Organic chemistry ,QD241-441 - Published
- 2021
- Full Text
- View/download PDF
4. Multi-Faceted Effects of ST6Gal1 Expression on Precursor B-Lineage Acute Lymphoblastic Leukemia
- Author
-
Mingfeng Zhang, Tong Qi, Lu Yang, Daniel Kolarich, and Nora Heisterkamp
- Subjects
sialyltransferase ,BCP-ALL ,drug resistance ,vincristine ,microenvironment ,N-linked glycan ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Normal early human B-cell development from lymphoid progenitors in the bone marrow depends on instructions from elements in that microenvironment that include stromal cells and factors secreted by these cells including the extracellular matrix. Glycosylation is thought to play a key role in such interactions. The sialyltransferase ST6Gal1, with high expression in specific hematopoietic cell types, is the only enzyme thought to catalyze the terminal addition of sialic acids in an α2-6-linkage to galactose on N-glycans in such cells. Expression of ST6Gal1 increases as B cells undergo normal B-lineage differentiation. B-cell precursor acute lymphoblastic leukemias (BCP-ALLs) with differentiation arrest at various stages of early B-cell development have widely different expression levels of ST6GAL1 at diagnosis, with high ST6Gal1 in some but not in other relapses. We analyzed the consequences of increasing ST6Gal1 expression in a diagnosis sample using lentiviral transduction. NSG mice transplanted with these BCP-ALL cells were monitored for survival. Compared to mice transplanted with leukemia cells expressing original ST6Gal1 levels, increased ST6Gal1 expression was associated with significantly reduced survival. A cohort of mice was also treated for 7 weeks with vincristine chemotherapy to induce remission and then allowed to relapse. Upon vincristine discontinuation, relapse was detected in both groups, but mice transplanted with ST6Gal1 overexpressing BCP-ALL cells had an increased leukemia burden and shorter survival than controls. The BCP-ALL cells with higher ST6Gal1 were more resistant to long-term vincristine treatment in an ex vivo tissue co-culture model with OP9 bone marrow stromal cells. Gene expression analysis using RNA-seq showed a surprisingly large number of genes with significantly differential expression, of which approximately 60% increased mRNAs, in the ST6Gal1 overexpressing BCP-ALL cells. Pathways significantly downregulated included those involved in immune cell migration. However, ST6Gal1 knockdown cells also showed increased insensitivity to chemotherapy. Our combined results point to a context-dependent effect of ST6Gal1 expression on BCP-ALL cells, which is discussed within the framework of its activity as an enzyme with many N-linked glycoprotein substrates.
- Published
- 2022
- Full Text
- View/download PDF
5. Improving Chicken Responses to Glycoconjugate Vaccination Against Campylobacter jejuni
- Author
-
Harald Nothaft, Maria Elisa Perez-Muñoz, Tianfu Yang, Abarna V. M. Murugan, Michelle Miller, Daniel Kolarich, Graham S. Plastow, Jens Walter, and Christine M. Szymanski
- Subjects
vaccine ,N-glycan ,Campylobacter ,immune response ,fecal transplant ,Microbiology ,QR1-502 - Abstract
Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduced the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals was still colonized (non-responders). To understand the underlying mechanism, we conducted three vaccination and challenge studies using 135 broiler birds and found a similar responder/non-responder effect. Subsequent genome-wide association studies (GWAS), analyses of bird sex and levels of vaccine-induced IgY responses did not correlate with the responder versus non-responder phenotype. In contrast, antibodies isolated from responder birds displayed a higher Campylobacter-opsonophagocytic activity when compared to antisera from non-responder birds. No differences in the N-glycome of the sera could be detected, although minor changes in IgY glycosylation warrant further investigation. As reported before, the composition of the microbiota, particularly levels of OTU classified as Clostridium spp., Ruminococcaceae and Lachnospiraceae are associated with the response. Transplantation of the cecal microbiota of responder birds into new birds in combination with vaccination resulted in further increases in vaccine-induced antigen-specific IgY responses when compared to birds that did not receive microbiota transplants. Our work suggests that the IgY effector function and microbiota contribute to the efficacy of the E. coli live vaccine, information that could form the basis for the development of improved vaccines targeted at the elimination of C. jejuni from poultry.
- Published
- 2021
- Full Text
- View/download PDF
6. Towards a standardized bioinformatics infrastructure for N- and O-glycomics
- Author
-
Miguel A. Rojas-Macias, Julien Mariethoz, Peter Andersson, Chunsheng Jin, Vignesh Venkatakrishnan, Nobuyuki P. Aoki, Daisuke Shinmachi, Christopher Ashwood, Katarina Madunic, Tao Zhang, Rebecca L. Miller, Oliver Horlacher, Weston B. Struwe, Yu Watanabe, Shujiro Okuda, Fredrik Levander, Daniel Kolarich, Pauline M. Rudd, Manfred Wuhrer, Carsten Kettner, Nicolle H. Packer, Kiyoko F. Aoki-Kinoshita, Frédérique Lisacek, and Niclas G. Karlsson
- Subjects
Science - Abstract
Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.
- Published
- 2019
- Full Text
- View/download PDF
7. Improved strategy for large scale isolation of sialylglycopeptide (SGP) from egg yolk powder
- Author
-
Kathirvel Alagesan and Daniel Kolarich
- Subjects
Science - Abstract
Chicken egg yolk is an easily available source for the isolation of sialylglycopeptides (SGP) carrying homogenous biantennary N-glycans. This approach has gained much attention in the last decade since these SGPs can easily be used for the semi-synthesis of glycoconjugates circumventing laborious full-synthetic methodologies. Here we report an optimised, significantly shorter (one day instead of five) and environmentally friendly procedure for the mg scale isolation of SGP using commercially available egg yolk powder. A single chromatographic step following chloroform/methanol precipitation of proteins and lipids yielded desired approximately 200 mg SGP from 250 g egg yolk powder within a day. • Environmentally friendly procedure for isolation of sialylglycopeptide from Egg yolk powder. • Reduced the protocol from five days down to one. Method name: Improved strategy for large scale isolation and purification of sialylglycopeptide from egg yolk powder, Keywords: Synthetic glycobiology, Glycopeptide isolation, Egg yolk powder
- Published
- 2019
- Full Text
- View/download PDF
8. The cancer cell-derived extracellular vesicle glycocode in immunoevasion
- Author
-
Jenifer P. Goncalves, Vatsal J. Deliwala, Daniel Kolarich, Fernando Souza-Fonseca-Guimaraes, and Joy Wolfram
- Subjects
Extracellular Vesicles ,Neoplasms ,Immunology ,Humans ,Immunology and Allergy - Abstract
Recent evidence suggests that cancer cell-derived extracellular vesicles might facilitate immunoevasion. Glycans are known to play a key role in immunomodulation, especially when tethered to biological membranes. However, the extracellular vesicle glycocode in cancer immunoevasion remains a largely unexplored area with promising potential for new putative diagnostic and therapeutic applications.
- Published
- 2022
9. Head and neck cancer N-glycome traits are cell line and HPV status–dependent
- Author
-
Mohammad Rasheduzzaman, Abarna V. M. Murugan, Xi Zhang, Tiago Oliveira, Riccardo Dolcetti, Liz Kenny, Newell W. Johnson, Daniel Kolarich, and Chamindie Punyadeera
- Subjects
Squamous Cell Carcinoma of Head and Neck ,Polysaccharides ,Head and Neck Neoplasms ,Papillomavirus Infections ,Humans ,Glycomics ,Biochemistry ,Fucose ,Cell Line ,Analytical Chemistry - Abstract
Glycosylation is the most common post-translational modification of proteins, and glycosylation changes at cell surfaces are frequently associated with malignant epithelia including head and neck squamous cell carcinoma (HNSCC). In HNSCC, 5-year survival remains poor, averaging around 50% globally: this is partly related to late diagnosis. Specific protein glycosylation signatures on malignant keratinocytes have promise as diagnostic and prognostic biomarkers and as therapeutic targets. Nevertheless, HNSCC-specific glycome is to date largely unknown. Herein, we tested six established HNSCC cell lines to capture the qualitative and semi-quantitative N-glycome using porous graphitized carbon liquid chromatography coupled to electrospray ionisation tandem mass spectrometry. Oligomannose-type N-glycans were the predominant features in all HNSCC cell lines analysed (57.5–70%). The levels of sialylated N-glycans showed considerable cell line-dependent differences ranging from 24 to 35%. Importantly, α2-6 linked sialylated N-glycans were dominant across most HNSCC cell lines except in SCC-9 cells where similar levels of α2-6 and α2-3 sialylated N-glycans were observed. Furthermore, we found that HPV-positive cell lines contained higher levels of phosphorylated oligomannose N-glycans, which hint towards an upregulation of lysosomal pathways. Almost all fucose-type N-glycans carried core-fucose residues with just minor levels (
- Published
- 2022
10. Supplementary Figure 2 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
EGFR Expression on target cells were evaluated using 1 µg/ml cetuximab and FITC-labeled goat-anti human IgG antibody by indirect immunofluorescence and flow cytometry.
- Published
- 2023
11. Supplementary Table 1 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
Iontrap aquisition Settings according to MIRAGE Guidelines.
- Published
- 2023
12. Supplementary Figure 1 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
SDS-PAGE separated and electroblotted IgA Proteins after staining with direct blue 71. The red boxes indicate the bands cut out for subsequent N-glycan Analysis.
- Published
- 2023
13. Supplementary Table 2 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
N-glycan structures of 225-IgA2-wt and 225-IgA2.0 identified by PGC-LC ESI MS/MS.
- Published
- 2023
14. Data from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
Antibodies of IgA isotype effectively engage myeloid effector cells for cancer immunotherapy. Here, we describe preclinical studies with an Fc engineered IgA2m(1) antibody containing the variable regions of the EGFR antibody cetuximab. Compared with wild-type IgA2m(1), the engineered molecule lacked two N-glycosylation sites (N166 and N337), two free cysteines (C311 and C472), and contained a stabilized heavy and light chain linkage (P221R mutation). This novel molecule displayed improved production rates and biochemical properties compared with wild-type IgA. In vitro, Fab- and Fc-mediated effector functions, such as inhibition of ligand binding, receptor modulation, and engagement of myeloid effector cells for antibody-dependent cell-mediated cytotoxicity, were similar between wild-type and engineered IgA2. The engineered antibody displayed lower levels of terminal galactosylation leading to reduced asialoglycoprotein-receptor binding and to improved pharmacokinetic properties. In a long-term in vivo model against EGFR-positive cancer cells, improved serum half-life translated into higher efficacy of the engineered molecule, which required myeloid cells expressing human FcαRI for its full efficacy. However, Fab-mediated effector functions contributed to the in vivo efficacy because the novel IgA antibody demonstrated therapeutic activity also in non-FcαRI transgenic mice. Together, these results demonstrate that engineering of an IgA antibody can significantly improve its pharmacokinetics and its therapeutic efficacy to inhibit tumor growth in vivo. Cancer Res; 76(2); 403–17. ©2015 AACR.
- Published
- 2023
15. Supplementary Table 3 from An Anti-EGFR IgA That Displays Improved Pharmacokinetics and Myeloid Effector Cell Engagement In Vivo
- Author
-
Thomas Valerius, Jeanette H.W. Leusen, Matthias Peipp, Daniel Kolarich, Sanjay Tiwari, Peter Sondermann, Denis Schewe, Christian Kellner, Thies Rösner, Stefanie Derer, Uwe Möginger, Katja Klausz, Anna Kretschmer, Maaike Nederend, J.H. Marco Jansen, Laura A.P.M. Meulenbroek, Saskia Meyer, and Stefan Lohse
- Abstract
Relative Quantitation of N-glycan structures.
- Published
- 2023
16. Glycomic and sialoproteomic data of gastric carcinoma cells overexpressing ST3GAL4
- Author
-
Stefan Mereiter, Ana Magalhães, Barbara Adamczyk, Chunsheng Jin, Andreia Almeida, Lylia Drici, Maria Ibáñez-Vea, Martin R. Larsen, Daniel Kolarich, Niclas G. Karlsson, and Celso A. Reis
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Science (General) ,Q1-390 - Abstract
Gastric carcinoma MKN45 cells stably transfected with the full-length ST3GAL4 gene were characterised by glycomic and sialoproteomic analysis. Complementary strategies were applied to assess the glycomic alterations induced by ST3GAL4 overexpression. The N- and O-glycome data were generated in two parallel structural analyzes, based on PGC-ESI-MS/MS. Data on glycan structure identification and relative abundance in ST3GAL4 overexpressing cells and respective mock control are presented. The sialoproteomic analysis based on titanium-dioxide enrichment of sialopeptides with subsequent LC-MS/MS identification was performed. This analysis identified 47 proteins with significantly increased sialylation. The data in this article is associated with the research article published in Biochim Biophys Acta “Glycomic analysis of gastric carcinoma cells discloses glycans as modulators of RON receptor tyrosine kinase activation in cancer” [1]. Keywords: N-glycome, O-glycome, Gastric cancer, Sialyltransferase, Sialoproteome
- Published
- 2016
- Full Text
- View/download PDF
17. Profiling the glycome of Cardicola forsteri, a blood fluke parasitic to bluefin tuna
- Author
-
Barbara F. Nowak, Simon Collett, Daniel Kolarich, Lachlan Coff, Jodie L. Abrahams, Nathan J. Bott, Cecilia Power, and Paul A. Ramsland
- Subjects
Glycan ,biology ,Tuna ,Host (biology) ,Lectin ,Trematode Infections ,Tandem mass spectrometry ,Glycome ,Fish Diseases ,Infectious Diseases ,Antigen ,Biochemistry ,Polysaccharides ,Concanavalin A ,Lectins ,Schistosomatidae ,biology.protein ,Animals ,Schistosoma ,Parasites ,Parasitology - Abstract
Infections by blood flukes (Cardicola spp.) are considered the most significant health issue for ranched bluefin tuna, a major aquaculture industry in Japan and Australia. The host-parasite interfaces of trematodes, namely their teguments, are particularly rich in carbohydrates, which function both in evasion and modulation of the host immune system, while some are primary antigenic targets. In this study, histochemistry and mass spectrometry techniques were used to profile the glycans of Cardicola forsteri. Fluorescent lectin staining of adult flukes indicates the presence of oligomannose (Concanavalin A-reactive) and fucosylated (Pisum sativum agglutinin-reactive) N-glycans. Additionally, reactivity of succinylated wheat germ agglutinin (s-WGA) was localised to several internal organs of the digestive and monoecious reproductive systems. Glycan structures were further investigated with tandem mass spectrometry, which revealed structures indicated by lectin reactivity. While O-glycans from these adult specimens were not detectable by mass spectrometry, several oligomannose, paucimannosidic, and complex-type N-glycans were identified, including some carrying hexuronic acid and many carrying core xylose. This is, to our knowledge, the first glycomic characterisation of a marine platyhelminth, with broader implications for research into other trematodes.
- Published
- 2022
18. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
- Author
-
Robert J. Chalkley, Kai Hooi Khoo, Daniel Kolarich, Erdmann Rapp, Yong Zhang, Hung Yi Wu, Miloslav Sanda, Jonas Nilsson, Enes Sakalli, Gun Wook Park, Doron Kletter, Kathirvel Alagesan, Katalin F. Medzihradszky, Rebeca Kawahara, Nathan Edwards, Radoslav Goldman, Nicolle H. Packer, Yehia Mechref, Wantao Ying, Joseph Zaia, Sriram Neelamegham, Bo Meng, Sergey Y. Vakhrushev, Benjamin L. Schulz, Markus Pioch, Benoit Liquet, Jin Young Kim, Johannes Stadlmann, Benjamin L. Parker, Terry Nguyen-Khuong, Jong Shin Yoo, Adam Pap, Nichollas E. Scott, Mingqi Liu, Marcus Hoffmann, Morten Thaysen-Andersen, Jingfu Zhao, Yingwei Hu, Göran Larson, Matthew S F Choo, Pengyuan Yang, Josef M. Penninger, Marshall Bern, Christina M. Woo, Weiqian Cao, Toan K. Phung, Giuseppe Palmisano, Kai Cheng, Anastasia Chernykh, Stuart M. Haslam, Yifan Huang, Hui Zhang, Cassandra L. Pegg, and Georgy Sofronov
- Subjects
Proteomics ,Technology ,Glycosylation ,Informatics ,Proteome ,VARIAÇÃO GENÉTICA ,Computer science ,Glycobiology ,Medical and Health Sciences ,Biochemistry ,Tandem mass spectrum ,Software ,Tandem Mass Spectrometry ,Computational platforms and environments ,Humans ,Community evaluation ,Molecular Biology ,Glycoproteins ,Research data ,business.industry ,Glycopeptides ,Cell Biology ,Biological Sciences ,Data science ,Research Personnel ,Glycoproteomics ,Identification (information) ,business ,Analysis ,Developmental Biology ,Biotechnology - Abstract
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N - and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved ‘high-coverage’ and ‘high-accuracy’ glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics., This analysis presents the results of a community-based evaluation of existing software for large-scale glycopeptide data analysis.
- Published
- 2021
19. A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications
- Author
-
Markus B. Tomek, Daniel Maresch, Markus Windwarder, Valentin Friedrich, Bettina Janesch, Kristina Fuchs, Laura Neumann, Irene Nimeth, Nikolaus F. Zwickl, Juliane C. Dohm, Arun Everest-Dass, Daniel Kolarich, Heinz Himmelbauer, Friedrich Altmann, and Christina Schäffer
- Subjects
carbohydrate-active enzymes ,glycosyltransferase ,immunogenicity ,locus for glycosylation ,methyltransferase ,periodontitis ,Microbiology ,QR1-502 - Abstract
The cell surface of the oral pathogen Tannerella forsythia is heavily glycosylated with a unique, complex decasaccharide that is O-glycosidically linked to the bacterium’s abundant surface (S-) layer, as well as other proteins. The S-layer glycoproteins are virulence factors of T. forsythia and there is evidence that protein O-glycosylation underpins the bacterium’s pathogenicity. To elucidate the protein O-glycosylation pathway, genes suspected of encoding pathway components were first identified in the genome sequence of the ATCC 43037 type strain, revealing a 27-kb gene cluster that was shown to be polycistronic. Using a gene deletion approach targeted at predicted glycosyltransferases (Gtfs) and methyltransferases encoded in this gene cluster, in combination with mass spectrometry of the protein-released O-glycans, we show that the gene cluster encodes the species-specific part of the T. forsythia ATCC 43037 decasaccharide and that this is assembled step-wise on a pentasaccharide core. The core was previously proposed to be conserved within the Bacteroidetes phylum, to which T. forsythia is affiliated, and its biosynthesis is encoded elsewhere on the bacterial genome. Next, to assess the prevalence of protein O-glycosylation among Tannerella sp., the publicly available genome sequences of six T. forsythia strains were compared, revealing gene clusters of similar size and organization as found in the ATCC 43037 type strain. The corresponding region in the genome of a periodontal health-associated Tannerella isolate showed a different gene composition lacking most of the genes commonly found in the pathogenic strains. Finally, we investigated whether differential cell surface glycosylation impacts T. forsythia’s overall immunogenicity. Release of proinflammatory cytokines by dendritic cells (DCs) upon stimulation with defined Gtf-deficient mutants of the type strain was measured and their T cell-priming potential post-stimulation was explored. This revealed that the O-glycan is pivotal to modulating DC effector functions, with the T. forsythia-specific glycan portion suppressing and the pentasaccharide core activating a Th17 response. We conclude that complex protein O-glycosylation is a hallmark of pathogenic T. forsythia strains and propose it as a valuable target for the design of novel antimicrobials against periodontitis.
- Published
- 2018
- Full Text
- View/download PDF
20. Human Mast Cell Tryptase Is a Potential Treatment for Snakebite Envenoming Across Multiple Snake Species
- Author
-
Elizabeth Anderson, Kathrin Stavenhagen, Daniel Kolarich, Christian P. Sommerhoff, Marcus Maurer, and Martin Metz
- Subjects
mast cell ,venom ,proteases ,snakes ,antivenom ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Snake envenoming is a serious and neglected public health crisis that is responsible for as many as 125,000 deaths per year, which is one of the reasons the World Health Organization has recently reinstated snakebite envenoming to its list of category A neglected tropical diseases. Here, we investigated the ability of human mast cell proteases to detoxify six venoms from a spectrum of phylogenetically distinct snakes. To this end, we developed a zebrafish model to assess effects on the toxicity of the venoms and characterized the degradation of venom proteins by mass spectrometry. All snake venoms tested were detoxified by degradation of various venom proteins by the mast cell protease tryptase β, and not by other proteases. Our data show that recombinant human tryptase β degrades and detoxifies a phylogenetically wide range of venoms, indicating that recombinant human tryptase could possibly be developed as a universal antidote to venomous snakebites.
- Published
- 2018
- Full Text
- View/download PDF
21. Alterations of the Human Skin N- and O-Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma
- Author
-
Uwe Möginger, Sonja Grunewald, René Hennig, Chu-Wei Kuo, Falko Schirmeister, Harald Voth, Erdmann Rapp, Kay-Hooi Khoo, Peter H. Seeberger, Jan C. Simon, and Daniel Kolarich
- Subjects
non melanoma skin cancer ,basal cell carcinoma ,squamous cell carcinoma ,skin glycans ,glycosylation ,glycomics ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
The glycome of one of the largest and most exposed human organs, the skin, as well as glycan changes associated with non-melanoma skin cancers have not been studied in detail to date. Skin cancers such as basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are among the most frequent types of cancers with rising incidence rates in the aging population. We investigated the healthy human skin N- and O-glycome and its changes associated with BCC and SCC. Matched patient samples were obtained from frozen biopsy and formalin-fixed paraffin-embedded tissue samples for glycomics analyses using two complementary glycomics approaches: porous graphitized carbon nano-liquid chromatography electro spray ionization tandem mass spectrometry and capillary gel electrophoresis with laser induced fluorescence detection. The human skin N-glycome is dominated by complex type N-glycans that exhibit almost similar levels of α2-3 and α2-6 sialylation. Fucose is attached exclusively to the N-glycan core. Core 1 and core 2 type O-glycans carried up to three sialic acid residues. An increase of oligomannose type N-glycans and core 2 type O-glycans was observed in BCC and SCC, while α2-3 sialylation levels were decreased in SCC but not in BCC. Furthermore, glycopeptide analyses provided insights into the glycoprotein candidates possibly associated with the observed N-glycan changes, with glycoproteins associated with binding events being the most frequently identified class.
- Published
- 2018
- Full Text
- View/download PDF
22. GlycoBioinformatics
- Author
-
Niclas Karlsson, Daniel Kolarich, Kiyoko Aoki-Kinoshita, Nicolle Packer, and Frederique LISACEK
- Subjects
Chemistry ,QD241-441 ,Editorial ,glycoinformatics ,Science ,Organic Chemistry ,bioinformatics ,glycobioinformatics - Published
- 2021
23. Glycomics & Glycoproteomics: From Analytics to Function
- Author
-
Morten Thaysen-Andersen, Daniel Kolarich, and Nicolle H. Packer
- Subjects
Proteomics ,0301 basic medicine ,business.industry ,Chemistry ,media_common.quotation_subject ,010401 analytical chemistry ,Computational biology ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Glycoproteomics ,Glycomics ,03 medical and health sciences ,030104 developmental biology ,Analytics ,Genetics ,Humans ,Function (engineering) ,business ,Molecular Biology ,Glycoproteins ,media_common - Abstract
Morten Thaysen-Andersen, Daniel Kolarich and Nicolle H. Packer introduce the Molecular Omics themed issue on Glycomics & Glycoproteomics: From Analytics to Function.
- Published
- 2021
24. Glycoproteome remodeling in MLL-rearranged B-cell precursor acute lymphoblastic leukemia
- Author
-
Lu Yang, Chun-Wei Chen, Andreia Almeida, Eun Ji Joo, Tiago Oliveira, Mark von Itzstein, Mingfeng Zhang, Kathirvel Alagesan, Francis Jacob, Chih-Hsing Chou, Nicolle H. Packer, Jianjun Chen, Xi Qin, Nora Heisterkamp, Daniel Kolarich, and Hisham Abdel-Azim
- Subjects
Proteomics ,Oncogene Proteins, Fusion ,Gene Expression ,Medicine (miscellaneous) ,Computational biology ,Biology ,Glycomics ,Transcriptome ,Cell Line, Tumor ,Precursor B-Cell Lymphoblastic Leukemia-Lymphoma ,medicine ,Humans ,Transcriptomics ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,B cell ,Fucosylation ,Gene Rearrangement ,Leukemia ,Gene Expression Regulation, Leukemic ,Glycobiology ,Gene Expression Profiling ,Histone-Lysine N-Methyltransferase ,Gene rearrangement ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,multi-omics ,medicine.disease ,Leukemia, Biphenotypic, Acute ,medicine.anatomical_structure ,Research Paper - Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi-omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets. Methods: We have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers. Results: MLL-r cells feature an extensive remodeling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodeling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodeling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology. Conclusions: Apart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.
- Published
- 2021
25. Program and Abstracts for 2020 Annual Meeting of the Society for Glycobiology
- Author
-
Andreia Almeida, Daniel Kolarich, Francis Jacob, Mingfeng Zhang, Kathirvel Alagesan, Hisham Abdel-Azim, Nora Heisterkamp, Mark von Itzstein, Eun Ji Joo, Tiago Oliveira, and Nicolle H. Packer
- Subjects
Transcriptome ,Glycomics ,Acute leukemia ,hemic and lymphatic diseases ,Proteome ,Cancer research ,biology.protein ,Biology ,Proteomics ,Biochemistry ,Pediatric cancer ,Glycome ,Receptor tyrosine kinase - Abstract
Mixed-lineage Acute Leukemia (MLL) is one of the most high-risk forms of pediatric cancer. Although the long-term survival rates of pediatric acute lymphoblastic leukemia have increased over the past 40 years, the current chemotherapeutic treatment schemes often fail in the treatment of MLL. The biological mechanisms resulting in drug resistance, however, are still not fully understood and there is an urgent need to identify novel diagnostic and therapeutical targets. We have established the first integrated multi-omics investigation of primary patient MLL samples and control precursor B bonemarrow cells from healthy donors, mapping their proteome, transcriptome and glycome. 4–6 million cells from 3 normal bone marrow (BM) and 2 MLL samples were used for analysis on our multi-omics platform. Porous-Graphitised Carbon (PGC) nanoLC-ESIMS/MS was used for Glycomics analyses after the enzymatic and chemical release of N- and O-glycans, respectively. The proteome was explored using RP-LC-ESI-MS/MS analyses, performed after offline high-pH fractionation, in addition to RNA-seq analyses. Overall, 4225 proteins were identified across the patient MLL and control BM cells, of which 216 were overexpressed in MLL (p 2). Preliminary analyses of the RNA-seq data matched well with the proteomics findings, revealing significant alterations in expression of glycoprotein signalling receptors and extracellular matrix proteins as well as various transcription factors. High-pH fractionation also allowed us to identify numerous important glycosyltransferases and expression changes thereof on protein and RNA– seq level. N- and O-glycomics revealed overall lower levels of α2–6 sialylated N- and O-glycans in MLL cells (correlating with ST6Gal1 transcript and ST6Gal1 protein levels) as well as an increase in Core 2 type O-glycans (correlating with GCNT1 transcript level). Patient MLL cells exhibit distinct N- and O-glycan fingerprints, along with specific alterations of receptor tyrosine kinase signalling networks. In addition to wellknown MLL glycoprotein markers, our integrated multiomics workflow identified a number of diagnostic/therapeutic protein candidates that have not previously been described.
- Published
- 2020
26. NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies
- Author
-
Miyako Nakano, Alena Wiegandt, Yunli Hu, Viv Lindo, Paulina A. Urbanowicz, Zsuzsanna Lakos, Cassie Caron, Song Klapoetke, Niels Christian Reichardt, Niclas Chiang Tan, Sandra Maier, Rene Hennig, Marton Szigeti, Ju Yeon Lee, Ying Qing Yu, Gregory O. Staples, Sachin Patil, Jolanta Jaworek, Waltraud Evers, Benjamin G. Kremkow, Youngsuk Seo, Kathirvel Alagesan, Yuetian Chen, Gordan Lauc, David L. Duewer, Yang Yang, Daniele Menard, Hyun Joo An, Tim Kelly, Stephen E. Stein, Joseph W. Leone, Anja Wiechmann, Ravi Amunugama, Peng George Wang, Clemens Grunwald-Grube, Maria Lorna A. De Leoz, Göran Larson, Rob Haselberg, Samanta Cajic, Stephanie A. Archer-Hartmann, Maja Pučić-Baković, Edward D. Bodnar, Pauline M. Rudd, Anja Resemann, Daniel Kolarich, Akira Harazono, Jeffrey S. Rohrer, Juan Echevarria Ruiz, Stuart Pengelley, Jong Shin Yoo, Arun V. Everest-Dass, Nicolle H. Packer, Steven W. Mast, William R. Alley, Erika Lattová, Anne Zeck, Corné J.M. Stroop, Radoslaw P. Kozak, Chun Shao, Alain Beck, Joseph Zaia, Erdmann Rapp, Lily Liu, Jennie Truong, Yaojun Wang, Christopher W. Cairo, Roisin O'Flaherty, Radka Saldova, Kudrat Goswami, Emy Komatsu, Jessica Örnros, Taiki Sugiyama, Prachi Bhoskar, Pralima Pradhan, Carlito B. Lebrilla, András Guttman, Christine Merle, Brian Kasper, Oscar G. Potter, Soo Kyung Suh, Li Phing Liew, Ranjan Chakrabarti, Terry D. Cyr, Sohei Funaoka, Masaaki Toyoda, Pui King Amy Leung, Toyin Kasali, Jerko Štambuk, Yanming An, Wolfgang Jabs, Bernd Meyer, Chunxia Zou, John F. Cipollo, Sa Rang Kim, Aaron Shafer, Randy M. Whittal, Jichao Kang, Albert J. R. Heck, Yehia Mechref, Hoi Kei Yau, Guinevere S. M. Lageveen-Kammeijer, Shiwei Sun, Kenichiro Furuki, Richard B. Jones, Béla Reiz, Niclas G. Karlsson, Mohammedazam Lahori, Xu Li, Barbara Adamczyk, Rui Cao, Lauren Wu, Koichi Kato, Detlev Suckau, Paweł Link-Lenczowski, Kelvin H. Lee, Xiaomin Song, Noortje de Haan, Ruth Frenkel, Adam Fung, Friedrich Altmann, Manfred Wuhrer, David Falck, Andreas Bock, Paula Magnelli, Brian Gau, Sachiko Kondo, Robert J. Emery, Chunsheng Jin, Louise Royle, David C. Muddiman, Hélène Perreault, John W. Froehlich, Disha Dadke, Peiqing Zhang, Lara K. Mahal, Takashi Nishikaze, Andrew Saati, Chuncui Huang, Hui Zhang, Carina Sihlbom, Parastoo Azadi, Jonas Nilsson, Yaming Liu, Yannis-Nicolas François, Nassur Said, Jin Young Kim, C. T. Yuen, Shuang Yang, Emmanuelle Leize-Wagner, David Harvey, Xiaofeng Shi, Yan Li, Hirokazu Yagi, Zoran Sosic, Elizabeth M. Hecht, Hua Yuan, Marybeth Creskey, Hyun Kyoung Lee, Sadanori Sekiya, Peter de Vreugd, Len Bell, Sam Tep, BioAnalytical Chemistry, AIMMS, Department of Plant and Microbial Biology, University of California, Laboratory of Infrared Material and Devices, Ningbo University (NBU), University of Natural Resources and Life Sciences (BOKU), Bruker Daltonik GmbH, Bruker Daltonik, Centre d'Immunologie Pierre Fabre, Xinjiang Agriculture University, Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III [Madrid] (ISC)-ministerio de ciencia e innovacion, Complex Carbohydrate Research Center, University of Georgia [USA], GENOS, Universität Duisburg-Essen [Essen], Max Planck Institute for Dynamics of Complex Technical Systems, Max-Planck-Gesellschaft, Section de mathématiques [Genève], Université de Genève (UNIGE), Department of Computer Science [York] (CS-YORK), University of York [York, UK], State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, LeidenUniversity Medical Center, University College Dublin [Dublin] (UCD), Texas A&M University System, College of Engineering and Computer Science, Australian National University (ANU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of Edinburgh, University of Alberta, Department of Biological Sciences, Mass Spectrometry Facility, University of Alberta-Department of Chemistry, Volvo Car Corporation, Centre for Research in Intelligent Systems, Monash University [Clayton], Department of Chemistry [Winnipeg, MB, Canada], University of Manitoba [Winnipeg], Department of Chemistry [Winnipeg, Manitoba, Canada], Université de Strasbourg (UNISTRA), Laboratoire de synthèses métallo-induites, Dynamique et structure moléculaire par spectrométrie de masse (LDSM2), School of Mechanics and Engineering [Chengdu], Southwest Jiaotong University (SWJTU), School of Management and Economics [University of Electronic Science and Technology of China], and University of Electronic Science and Technology of China (UESTC)
- Subjects
Proteomics ,PROTEIN ,fluerescence ,Biochemistry ,reference antibody ,THERAPEUTIC ANTIBODIES ,Biopharmaceutics ,Analytical Chemistry ,chemistry.chemical_compound ,Biological sciences ,Glycomics ,NISTaAb ,Analysis method ,ComputingMilieux_MISCELLANEOUS ,glycoproteins ,mass spectrometry ,chemistry.chemical_classification ,0303 health sciences ,glycan ,interlaboratory study ,030302 biochemistry & molecular biology ,Glycopeptides ,Antibodies, Monoclonal ,3. Good health ,glycomics ,fluorescence ,glycosylation ,glycopeptide ,NISTmAb ,lipids (amino acids, peptides, and proteins) ,Protein glycosylation ,Glycan ,Glycosylation ,QUANTITATION ,medicine.drug_class ,Computational biology ,Biology ,Monoclonal antibody ,03 medical and health sciences ,GLYCOMIC ANALYSIS ,SDG 3 - Good Health and Well-being ,Polysaccharides ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,Report ,medicine ,Humans ,LC-MS/MS ,Molecular Biology ,030304 developmental biology ,Biological Products ,IDENTIFICATION ,MASS-SPECTROMETRY ,PROFILES ,QUANTIFICATION ,carbohydrates (lipids) ,chemistry ,biology.protein ,Laboratories ,Glycoprotein ,Protein Processing, Post-Translational - Abstract
A broad-based interlaboratory study of glycosylation profiles of a reference and modified IgG antibody involving 103 reports from 76 laboratories., Graphical Abstract Highlights A broad-based interlaboratory study of the glycosylation of a reference antibody: NISTmAb. 103 reports were received from 76 diverse laboratories worldwide. Analysis involved two samples, the NISTmAb and an enzymatically modified sample, enabling within-lab separation of random and systematic errors using the “Youden two-sample” method. Consensus values were derived and similar performance across all experimental methods was noted., Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.
- Published
- 2020
27. Exploring the Glycans of Euglena gracilis
- Author
-
Ellis C. O’Neill, Sakonwan Kuhaudomlarp, Martin Rejzek, Jonatan U. Fangel, Kathirvel Alagesan, Daniel Kolarich, William G. T. Willats, and Robert A. Field
- Subjects
algae ,Euglena ,biotechnology ,carbohydrates ,N-glycan ,sugar nucleotide ,Biology (General) ,QH301-705.5 - Abstract
Euglena gracilis is an alga of great biotechnological interest and extensive metabolic capacity, able to make high levels of bioactive compounds, such as polyunsaturated fatty acids, vitamins and β-glucan. Previous work has shown that Euglena expresses a wide range of carbohydrate-active enzymes, suggesting an unexpectedly high capacity for the synthesis of complex carbohydrates for a single-celled organism. Here, we present an analysis of some of the carbohydrates synthesised by Euglena gracilis. Analysis of the sugar nucleotide pool showed that there are the substrates necessary for synthesis of complex polysaccharides, including the unusual sugar galactofuranose. Lectin- and antibody-based profiling of whole cells and extracted carbohydrates revealed a complex galactan, xylan and aminosugar based surface. Protein N-glycan profiling, however, indicated that just simple high mannose-type glycans are present and that they are partially modified with putative aminoethylphosphonate moieties. Together, these data indicate that Euglena possesses a complex glycan surface, unrelated to plant cell walls, while its protein glycosylation is simple. Taken together, these findings suggest that Euglena gracilis may lend itself to the production of pharmaceutical glycoproteins.
- Published
- 2017
- Full Text
- View/download PDF
28. N-Glycosylation in isolated rat nerve terminals
- Author
-
Daniel Kolarich, Jodie L. Abrahams, Martin R. Larsen, Pia Jensen, Inga Matthies, and Tiago Oliveira
- Subjects
Glycan ,Glycosylation ,Biochemistry ,Glycomics ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,N-linked glycosylation ,Tandem Mass Spectrometry ,Genetics ,Animals ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,Synaptosome ,0303 health sciences ,biology ,030302 biochemistry & molecular biology ,Glycopeptides ,Glycome ,Rats ,carbohydrates (lipids) ,chemistry ,biology.protein ,Glycoprotein ,Chromatography, Liquid - Abstract
N-linked glycosylation is a ubiquitous protein modification that is capable of modulating protein structure, function and interactions. Many proteins in the brain associated with the synapse and important for synaptic transmission are highly glycosylated and their glycosylation could be important for learning and memory related molecular processes and synaptic plasticity. In the present study, we extend the knowledge of the synaptic glycome and glycoproteome by performing glycan- and intact glycopeptide-focused analyses of isolated rat nerve terminals (synaptosomes) by LC-MS/MS. Overall, glycomics identified a total of 41N-glycans in isolated synaptosomes. SialylatedN-glycans represented only 7% of the total abundance of the rat synaptosomeN-glycome with oligomannose, neutral hybrid and complex typeN-glycans being the most abundant structures. Using detergent extraction of the active zone proteins from the synaptosomes revealed a change in the active zone glycan abundance in comparison with the rest of the synaptosome glycan content. Characterization of intact sialylatedN-linked glycopeptides enriched by titanium dioxide chromatography revealed more than 85% selectivity of sialylated species and the presence of NeuGc on active zone proteins. In addition, both disialic and trisialic acid modified glycans were present on synaptic glycoproteins, although oxonium ion profiling revealed that trisialic units were only present on glycoproteins in the detergent soluble fraction. However, correct identification of intact sialylatedN-linked glycopeptides using the Byonic program failed, most likely due to the lack of peptide backbone fragmentation during tandem mass spectrometry.
- Published
- 2021
29. Glycoproteome remodelling in MLL-rearranged B-cell precursor acute lymphoblastic leukemia
- Author
-
Kathirvel Alagesan, Hisham Abdel-Azim, Francis Jacob, Tiago Oliveira, Nicolle H. Packer, Chih-Hsing Chou, Xi Qin, Daniel Kolarich, Lu Yang, Nora Heisterkamp, Andreia Almeida, Mark von Itzstein, Chun-Wei Chen, Eun Ji Joo, Mingfeng Zhang, and Jianjun Chen
- Subjects
Transcriptome ,Leukemia ,medicine.anatomical_structure ,Proteome ,medicine ,Cancer research ,Gene rearrangement ,Biology ,medicine.disease ,Proteomics ,Glycome ,B cell ,Fucosylation - Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets.MethodsWe have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers.ResultsMLL-r cells feature an extensive remodelling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodelling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodelling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology.ConclusionsApart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.Graphical abstract
- Published
- 2021
30. 12PG01 - Multi-omics of MLL-rearranged B-cell precursor acute lymphoblastic leukemia reveals broad glycoproteom remodeling
- Author
-
Daniel Kolarich
- Published
- 2021
31. Evolutionary Glycomics: A Comprehensive Study of Vertebrate Host Serum/Plasma Glycome Using Orthogonal Glycomics Techniques
- Author
-
Christine M. Szymanski, Kathirvel Alagesan, Daniel Kolarich, Samantha J. Richardson, Abarna V. M. Murugan, Frédérique Lisacek, Niclas G. Karlsson, Jason P. van de Merwe, Julien Mariethoz, Kimberly A. Finlayson, Harold Nothaft, Catherine A. Hayes, Tiago Oliveira, and Yasin Mojtahedinyazdi
- Subjects
Glycomics ,biology ,Host (biology) ,biology.animal ,Genetics ,Serum plasma ,Vertebrate ,Computational biology ,Molecular Biology ,Biochemistry ,Glycome ,Biotechnology - Published
- 2021
32. The minimum information required for a glycomics experiment (MIRAGE) project: LC guidelines
- Author
-
Carsten Kettner, Rene Ranzinger, Weston B. Struwe, Pauline M. Rudd, Daniel Kolarich, Jodie L. Abrahams, Milos V. Novotny, William S. York, Catherine E. Costello, Erdmann Rapp, and Matthew Campbell
- Subjects
0303 health sciences ,Computer science ,Group method of data handling ,030302 biochemistry & molecular biology ,Scientific literature ,Biochemistry ,Data science ,Data sharing ,Glycomics ,03 medical and health sciences ,Glycan array ,Polysaccharides ,Humans ,Glycoinformatics ,Biological sciences ,Chromatography, Liquid ,030304 developmental biology - Abstract
The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to design guidelines that improve the reporting and reproducibility of glycoanalytical methods. Previously, the MIRAGE Commission has published guidelines for describing sample preparation methods and the reporting of glycan array and mass spectrometry techniques and data collections. Here, we present the first version of guidelines that aim to improve the quality of the reporting of liquid chromatography (LC) glycan data in the scientific literature. These guidelines cover all aspects of instrument setup and modality of data handling and manipulation and is cross-linked with other MIRAGE recommendations. The most recent version of the MIRAGE-LC guidelines is freely available at the MIRAGE project website doi:10.3762/mirage.4.
- Published
- 2019
33. GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical
- Author
-
Daniel Kolarich, Alessandra Gastaldello, Frédérique Lisacek, Elisabeth Gasteiger, Davide Alocci, Nicolle H. Packer, Niclas G. Karlsson, and Julien Mariethoz
- Subjects
Proteomics ,0301 basic medicine ,Glycosylation ,Computer science ,computer.software_genre ,Biochemistry ,Database ,Glycomics ,User-Computer Interface ,03 medical and health sciences ,Software ,Data visualization ,ddc:570 ,Server ,ddc:025.063 ,Glycoproteins ,030102 biochemistry & molecular biology ,Data curation ,business.industry ,Computational Biology ,General Chemistry ,Data science ,Glycoproteomics ,030104 developmental biology ,Glycoinformatics ,Data integration ,business ,computer - Abstract
Knowledge of glycoproteins, their site-specific glycosylation patterns, and the glycan structures that they present to their recognition partners in health and disease is gradually being built on using a range of experimental approaches. The data from these analyses are increasingly being standardized and presented in various sources, from supplemental tables in publications to localized servers in investigator laboratories. Bioinformatics tools are now needed to collect these data and enable the user to search, display, and connect glycomics and glycoproteomics to other sources of related proteomics, genomics, and interactomics information. We here introduce GlyConnect ( https://glyconnect.expasy.org/ ), the central platform of the Glycomics@ExPASy portal for glycoinformatics. GlyConnect has been developed to gather, monitor, integrate, and visualize data in a user-friendly way to facilitate the interpretation of collected glycoscience data. GlyConnect is designed to accommodate and integrate multiple data types as they are increasingly produced.
- Published
- 2018
34. The Hitchhiker's guide to glycoproteomics
- Author
-
Daniel Kolarich, Morten Thaysen-Andersen, Nicolle H. Packer, and Tiago Oliveira
- Subjects
0301 basic medicine ,Proteomics ,Immunology & Inflammation ,Glycosylation ,Computer science ,Glycobiology ,Omics ,Context (language use) ,Computational biology ,01 natural sciences ,Biochemistry ,glycomics ,Glycomics ,03 medical and health sciences ,chemistry.chemical_compound ,Biochemical Techniques & Resources ,Humans ,glycoproteomics ,Review Articles ,Glycoproteins ,Cancer ,mass spectrometry ,Evolutionary Biology ,Post-Translational Modifications ,010401 analytical chemistry ,multi-omics ,Signaling ,0104 chemical sciences ,Glycoproteomics ,030104 developmental biology ,Workflow ,chemistry ,Cardiovascular System & Vascular Biology ,Proteolysis ,Identification (biology) - Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This ‘Hitchhiker's guide to glycoproteomics’ is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins — a class of biomolecules essential in regulating cell function.
- Published
- 2021
35. Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of SerumN- andO-Glycopeptide Data
- Author
-
Wantao Ying, Josef M. Penninger, Yehia Mechref, Gun Wook Park, Weiqian Cao, Morten Thaysen-Andersen, Jingfu Zhao, Rebeca Kawahara, Radoslav Goldman, Kai-Hooi Khoo, Mingqi Liu, Marcus Hoffmann, Nicolle H. Packer, Benjamin L. Schulz, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Yingwei Hu, Hui Zhang, Jonas Nilsson, Doron Kletter, Sriram Neelamegham, Nathan Edwards, Cassandra L. Pegg, Pengyuan Yang, Jong Shin Yoo, Hung-Yi Wu, Daniel Kolarich, Adam Pap, Robert J. Chalkley, Georgy Sofronov, Benjamin L. Parker, Terry Nguyen-Khuong, Kai Cheng, Yong Zhang, Bo Meng, Nichollas E. Scott, Benoit Liquet-Weiland, Joseph Zaia, Sergey Y. Vakhrushev, Markus Pioch, Johannes Stadlmann, Toan K. Phung, Marshall Bern, Christina M. Woo, Katalin F. Medzihradszky, Stuart M. Haslam, Giuseppe Palmisano, Anastasia Chernykh, Göran Larson, Matthew S F Choo, Jin Young Kim, Yifan Huang, and Kathirvel Alagesan
- Subjects
Profiling (computer programming) ,Software ,Computer science ,business.industry ,Informatics ,Human proteome project ,business ,Community evaluation ,Data science ,Tandem mass spectrum ,Glycoproteomics - Abstract
Glycoproteome profiling (glycoproteomics) is a powerful yet analytically challenging research tool. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse software aiding the process have appeared, but their relative performance remains untested. Conducted through the HUPO Human Proteome Project – Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates the performance of informatics solutions for system-wide glycopeptide analysis. Mass spectrometry-based glycoproteomics datasets from human serum were shared with all teams. The relative team performance forN- andO-glycopeptide data analysis was comprehensively established and validated through orthogonal performance tests. Excitingly, several high-performance glycoproteomics informatics solutions were identified. While the study illustrated that significant informatics challenges remain, as indicated by a high discordance between annotated glycopeptides, lists of high-confidence (consensus) glycopeptides were compiled from the standardised team reports. Deep analysis of the performance data revealed key performance-associated search variables and led to recommendations for improved “high coverage” and “high accuracy” glycoproteomics search strategies. This study concludes that diverse software for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies, and specifies key variables that may guide future software developments and assist informatics decision-making in glycoproteomics.
- Published
- 2021
36. Glycoproteomics Technologies in Glycobiotechnology
- Author
-
Kathirvel, Alagesan, Marcus, Hoffmann, Erdmann, Rapp, and Daniel, Kolarich
- Subjects
Glycosylation ,Polysaccharides ,Biosimilar Pharmaceuticals ,Mass Spectrometry - Abstract
Glycosylation is a key factor determining the pharmacological properties of biotherapeutics, including their stability, solubility, bioavailability, pharmacokinetics, and immunogenicity. As such, comprehensive information about glycosylation of biotherapeutics is critical to demonstrate similarity. Regulatory agencies also require extensive documentation of the comprehensive analyses of glycosylation-related critical quality attributes (CQAs) during the development, manufacturing, and release of biosimilars. Mass spectrometry has catalysed tremendous advancements in the characterisation of glycosylation CQAs of biotherapeutics. Here we provide a perspective overview on the MS-based technologies relevant for biotherapeutic product characterisation with an emphasis on the recent developments that allow determination of glycosylation features such as site of glycosylation, sialic acid linkage, glycan structure, and content.
- Published
- 2020
37. Abstract 272: Glycomics: Protein glycosylation changes in the pathogenesis of head and neck cancer
- Author
-
Daniel Kolarich, Riccardo Dolcetti, Newell W. Johnson, Liz Kenny, Mohammad Rasheduzzaman, Xi Zhang, and Chamindie Punyadeera
- Subjects
Glycomics ,Pathogenesis ,Protein glycosylation ,Cancer Research ,Oncology ,business.industry ,Head and neck cancer ,Cancer research ,Medicine ,business ,medicine.disease - Abstract
Background: Glycosylation is the most common post-translational modification of proteins, and glycosylation changes at cell surfaces are frequently associated with malignant epithelia. These affect many functions including proliferation, motility and invasiveness, increasing the propensity to metastasise. Many head & neck squamous cell carcinomata (HNSCC), especially those originating in the lymphoid mucosa of the oropharynx, are driven by so-called high risk genotypes of Human Papillomavirus (HPV). Five-year survival remains poor, averaging around 50% globally: this is partly related to late diagnosis. Specific protein glycosylation signatures on malignant keratinocytes have promise as diagnostic and prognostic markers and as therapeutic targets. Here we begin creation of a glyco-fingerprint library mapping the glyco-space of HNSCC. Materials and methods: Six established HNSCC cell lines were used to capture the qualitative and semi-quantitative profile of the N- and O-glycome using the well-established porous graphitized carbon (PGC) glycomics approach. Furthermore, we attempted to evaluate the effect sialylation has on HNSCC cell migration by enzymatically removing sialic acid residues from cell surface glycoconjugates. Therefore, we used the enzyme neuraminidase to remove sialic acids from HNSCC cells and measured cell proliferation rates by using incucyte. Results: In Human Papillomavirus (HPV) negative HNSCC cell lines, 37-41% of cells carried oligomannoses on their surfaces compared to 45% in HPV+ cell lines. Sialylated N-glycan were the most abundant type of N-glycan, contributing to >40% of the N-glycome in the HPV negative cell lines: but just 32-38% in HPV+ cell lines; di- and tri-sialylated forms were most frequent. The majority of complex type N-glycans (33%) carried core-fucose residues with just minor levels ( Conclusion: This first systematic mapping reveals diverse glycosylation of head and neck cancer cell lines with high levels of core fucosylation and sialylation. Differences between HPV positive and negative cells may partly explain the comparatively good prognosis of HPV-driven HNC. This mapping forms the basis of histopathological profiling of real tumours which might have prognostic potential and suggest targets for immunotherapy. Removal of sialic acids resulted in decreased cell proliferation in vitro, indicating the fundamental role of protein glycosylation in the pathogenesis of HNC. Citation Format: Mohammad Rasheduzzaman, Xi Zhang, Riccardo Dolcetti, Liz Kenny, Newell W. Johnson, Daniel Kolarich, Chamindie Punyadeera. Glycomics: Protein glycosylation changes in the pathogenesis of head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 272.
- Published
- 2021
38. State-of-the-Art Glycomics Technologies in Glycobiotechnology
- Author
-
Alexander, Pralow, Samanta, Cajic, Kathirvel, Alagesan, Daniel, Kolarich, and Erdmann, Rapp
- Subjects
Technology ,Glycosylation ,Polysaccharides ,Biosimilar Pharmaceuticals ,Glycomics ,Mass Spectrometry - Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from RD till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
- Published
- 2020
39. State-of-the-Art Glycomics Technologies in Glycobiotechnology
- Author
-
Kathirvel Alagesan, Alexander Pralow, Daniel Kolarich, Erdmann Rapp, and Samanta Cajic
- Subjects
Glycomics ,Biopharmaceutical ,Emerging technologies ,Computer science ,Complementarity (molecular biology) ,Critical to quality ,Context (language use) ,Biosimilar ,Biochemical engineering ,Glycan Characterization - Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from RD we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
- Published
- 2020
40. Glycoproteomics Technologies in Glycobiotechnology
- Author
-
Kathirvel Alagesan, Daniel Kolarich, Erdmann Rapp, and Marcus Hoffmann
- Subjects
0106 biological sciences ,Glycan ,animal structures ,Glycosylation ,biology ,Biosimilar ,macromolecular substances ,Computational biology ,01 natural sciences ,Glycoproteomics ,carbohydrates (lipids) ,chemistry.chemical_compound ,chemistry ,010608 biotechnology ,biology.protein ,lipids (amino acids, peptides, and proteins) ,Critical quality attributes - Abstract
Glycosylation is a key factor determining the pharmacological properties of biotherapeutics, including their stability, solubility, bioavailability, pharmacokinetics, and immunogenicity. As such, comprehensive information about glycosylation of biotherapeutics is critical to demonstrate similarity. Regulatory agencies also require extensive documentation of the comprehensive analyses of glycosylation-related critical quality attributes (CQAs) during the development, manufacturing, and release of biosimilars. Mass spectrometry has catalysed tremendous advancements in the characterisation of glycosylation CQAs of biotherapeutics. Here we provide a perspective overview on the MS-based technologies relevant for biotherapeutic product characterisation with an emphasis on the recent developments that allow determination of glycosylation features such as site of glycosylation, sialic acid linkage, glycan structure, and content.
- Published
- 2020
41. A novel, ultrasensitive approach for quantitative carbohydrate composition and linkage analysis using LC-ESI ion trap tandem mass spectrometry
- Author
-
Kathirvel Alagesan, Daniel Varon Silva, Peter H Seeberger, and Daniel Kolarich
- Abstract
Glycan identification and characterisation is essential to correlate glycoconjugate structure to biological function. The structural assignment of carbohydrates is often based on MS composition analyses and knowledge on well-studied glycosylation pathways. Nevertheless, many monosaccharide building blocks are indistinguishable by mass alone and detailed linkage information is also not easily obtained by MS/MS analyses, in particular when organisms are studied where the glycosylation pathways are less well defined. Here, we present a novel, simple and sensitive method using Reversed Phase (RP) – Liquid Chromatography Electrospray ionisation tandem mass spectrometry (LC–ESI-MS/MS) for unambiguous identification and linkage determination of monosaccharides including N-acetylneuraminic acids. Sequential permethylation and reductive amination steps are employed prior and after acid hydrolysis to enable separation and differentiation of the various monosaccharides and their respective linkage positions. The well-established, monosaccharide specific methylation patterns allowed for the identification of the various derivatised monosaccharide alditols based on their retention time and tandem mass spectrometry fingerprint. Absolute quantitation can also be accomplished by including a set of internal standards, thus simultaneously providing qualitative and quantitative information on the monosaccharide residues present.
- Published
- 2019
- Full Text
- View/download PDF
42. Flagellin Glycoproteomics of the Periodontitis Associated Pathogen Selenomonas sputigena Reveals Previously Not Described O-glycans and Rhamnose Fragment Rearrangement Occurring on the Glycopeptides
- Author
-
Cornelia B. Rath, Rudolf Figl, Christina Schäffer, Peter H. Seeberger, Falko Schirmeister, and Daniel Kolarich
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,Selenomonas ,Glycan ,Glycosylation ,biology ,Rhamnose ,030106 microbiology ,Biochemistry ,Glycopeptide ,Analytical Chemistry ,Glycoproteomics ,carbohydrates (lipids) ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,biology.protein ,Glycoprotein ,Molecular Biology ,Flagellin - Abstract
Flagellated, Gram-negative, anaerobic, crescent-shaped Selenomonas species are colonizers of the digestive system, where they act at the interface between health and disease. Selenomonas sputigena is also considered a potential human periodontal pathogen, but information on its virulence factors and underlying pathogenicity mechanisms is scarce. Here we provide the first report of a Selenomonas glycoprotein, showing that S. sputigena produces a diversely and heavily O-glycosylated flagellin C9LY14 as a major cellular protein, which carries various hitherto undescribed rhamnose- and N-acetylglucosamine linked O-glycans in the range from mono- to hexasaccharides. A comprehensive glycomic and glycoproteomic assessment revealed extensive glycan macro- and micro-heterogeneity identified from 22 unique glycopeptide species. From the multiple sites of glycosylation, five were unambiguously identified on the 437-amino acid C9LY14 protein (Thr149, Ser182, Thr199, Thr259, and Ser334), the only flagellin protein identified. The O-glycans additionally showed modifications by methylation and putative acetylation. Some O-glycans carried hitherto undescribed residues/modifications as determined by their respective m/z values, reflecting the high diversity of native S. sputigena flagellin. We also found that monosaccharide rearrangement occurred during collision-induced dissociation (CID) of protonated glycopeptide ions. This effect resulted in pseudo Y1-glycopeptide fragment ions that indicated the presence of additional glycosylation sites on a single glycopeptide. CID oxonium ions and electron transfer dissociation, however, confirmed that just a single site was glycosylated, showing that glycan-to-peptide rearrangement can occur on glycopeptides and that this effect is influenced by the molecular nature of the glycan moiety. This effect was most pronounced with disaccharides. This study is the first report on O-linked flagellin glycosylation in a Selenomonas species, revealing that C9LY14 is one of the most heavily glycosylated flagellins described to date. This study contributes to our understanding of the largely under-investigated surface properties of oral bacteria. The data have been deposited to the ProteomeXchange with identifier PXD005859.
- Published
- 2018
43. Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
- Author
-
Rebeca Kawahara, Anastasia Chernykh, Kathirvel Alagesan, Marshall Bern, Weiqian Cao, Robert J. Chalkley, Kai Cheng, Matthew S. Choo, Nathan Edwards, Radoslav Goldman, Marcus Hoffmann, Yingwei Hu, Yifan Huang, Jin Young Kim, Doron Kletter, Benoit Liquet, Mingqi Liu, Yehia Mechref, Bo Meng, Sriram Neelamegham, Terry Nguyen-Khuong, Jonas Nilsson, Adam Pap, Gun Wook Park, Benjamin L. Parker, Cassandra L. Pegg, Josef M. Penninger, Toan K. Phung, Markus Pioch, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Benjamin L. Schulz, Nichollas E. Scott, Georgy Sofronov, Johannes Stadlmann, Sergey Y. Vakhrushev, Christina M. Woo, Hung-Yi Wu, Pengyuan Yang, Wantao Ying, Hui Zhang, Yong Zhang, Jingfu Zhao, Joseph Zaia, Stuart M. Haslam, Giuseppe Palmisano, Jong Shin Yoo, Göran Larson, Kai-Hooi Khoo, Katalin F. Medzihradszky, Daniel Kolarich, Nicolle H. Packer, and Morten Thaysen-Andersen
- Subjects
Computational platforms and environments ,Glycobiology ,Cell Biology ,Author Correction ,GLICOSÍDEOS ,Molecular Biology ,Biochemistry ,Software ,Research data ,Biotechnology - Published
- 2021
44. Nitroimidazole action in Entamoeba histolytica: a central role for thioredoxin reductase.
- Author
-
David Leitsch, Daniel Kolarich, Iain B H Wilson, Friedrich Altmann, and Michael Duchêne
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Metronidazole, a 5-nitroimidazole drug, has been the gold standard for several decades in the treatment of infections with microaerophilic protist parasites, including Entamoeba histolytica. For activation, the drug must be chemically reduced, but little is known about the targets of the active metabolites. Applying two-dimensional gel electrophoresis and mass spectrometry, we searched for protein targets in E. histolytica. Of all proteins visualized, only five were found to form adducts with metronidazole metabolites: thioredoxin, thioredoxin reductase, superoxide dismutase, purine nucleoside phosphorylase, and a previously unknown protein. Recombinant thioredoxin reductase carrying the modification displayed reduced enzymatic activity. In treated cells, essential non-protein thiols such as free cysteine were also affected by covalent adduct formation, their levels being drastically reduced. Accordingly, addition of cysteine allowed E. histolytica to survive in the presence of otherwise lethal metronidazole concentrations and reduced protein adduct formation. Finally, we discovered that thioredoxin reductase reduces metronidazole and other nitro compounds, suggesting a new model of metronidazole activation in E. histolytica with a central role for thioredoxin reductase. By reducing metronidazole, the enzyme renders itself and associated thiol-containing proteins vulnerable to adduct formation. Because thioredoxin reductase is a ubiquitous enzyme, similar processes could occur in other eukaryotic or prokaryotic organisms.
- Published
- 2007
- Full Text
- View/download PDF
45. Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers
- Author
-
Miyako Nakano, Morten Thaysen-Andersen, Manveen K. Sethi, Christopher Ashwood, Uwe Möginger, Zeynep Sumer-Bayraktar, Matthew T. Briggs, Michael Muders, Ian Loke, Saulo Recuero, Sayantani Chatterjee, Ling Y. Lee, Niclas G. Karlsson, Martin K. Oehler, Kathrin Stavenhagen, Jenny H. L. Chik, Katia R. M. Leite, Peter Hoffmann, Daniel Kolarich, Giuseppe Palmisano, Rebeca Kawahara, Miguel Srougi, Sarah Förster, Arun V. Everest-Dass, Katherine Wongtrakul-Kish, Barbara Adamczyk, Jodie L. Abrahams, Edward S. X. Moh, Simone Diestel, Merrina Anugraham, Mark P. Molloy, Vignesh Venkatakrishnan, Hannes Hinneburg, Nicolle H. Packer, Chatterjee, Sayantani, Lee, Ling Y, Kawahara, Rebeca, Abrahams, Jodie L, Briggs, Matthew T, Hoffman, Peter, and Thaysen-Andersen, Morten
- Subjects
Glycosylation ,Colorectal cancer ,Biology ,medicine.disease_cause ,Biochemistry ,Metastasis ,glycomics ,03 medical and health sciences ,Prostate cancer ,chemistry.chemical_compound ,N-linked glycosylation ,Tandem Mass Spectrometry ,Cell Line, Tumor ,Neoplasms ,medicine ,cancer ,Humans ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,glycan ,030302 biochemistry & molecular biology ,Cancer ,protein paucimannosylation ,medicine.disease ,paucimannosidic glycan ,chemistry ,Cancer research ,METÁSTASE NEOPLÁSICA ,Disease Progression ,Carcinogenesis ,Liver cancer ,Mannose ,Chromatography, Liquid - Abstract
While aberrant protein glycosylation is a recognized characteristic of human cancers, advances in glycoanalytics continue to discover new associations between glycoproteins and tumorigenesis. This glycomics-centric study investigates a possible link between protein paucimannosylation, an under-studied class of human N-glycosylation [Man 1-3 GlcNAc 2 Fuc 0-1 ], and cancer. The paucimannosidic glycans (PMGs) of 34 cancer cell lines and 133 tissue samples spanning 11 cancer types and matching non-cancerous specimens are profiled from 467 published and unpublished PGC-LC-MS/MS N-glycome datasets collected over a decade. PMGs, particularly Man 2-3 GlcNAc 2 Fuc 1 , are prominent features of 29 cancer cell lines, but the PMG level varies dramatically across and within the cancer types (1.0-50.2%). Analyses of paired (tumor/non-tumor) and stage-stratified tissues demonstrate that PMGs are significantly enriched in tumor tissues from several cancer types including liver cancer (p = 0.0033) and colorectal cancer (p = 0.0017) and is elevated as a result of prostate cancer and chronic lymphocytic leukaemia progression (p < 0.05). Surface expression of paucimannosidic epitopes is demonstrated on human glioblastoma cells using immunofluorescence while biosynthetic involvement of N-acetyl-β-hexosaminidase is indicated by quantitative proteomics. This intriguing association between protein paucimannosylation and human cancers warrants further exploration to detail the biosynthesis, cellular location(s), protein carriers, and functions of paucimannosylation in tumorigenesis and metastasis.
- Published
- 2019
46. To enrich or not to enrich: Enhancing (glyco)peptide ionization using the CaptiveSpray nanoBooster™
- Author
-
Kathirvel Alagesan and Daniel Kolarich
- Subjects
chemistry.chemical_compound ,chemistry ,Dopant ,Ionization ,Inorganic chemistry ,Acetone ,Ion suppression in liquid chromatography–mass spectrometry ,Methanol ,Acetonitrile ,Glycopeptide ,Adduct - Abstract
The CaptiveSpray source ensures a stable spray and excellent nano ESI performance facilitated by a vortex gas that sweeps around the emitter spray tip to support liquid desolvation and focus the Taylor cone. Enriching the vortex gas with dopant solvents provides tremendous opportunities to increase ionization efficiency, in particular for hydrophilic compounds such as glycopeptides. How this CaptiveSpray nanobooster benefits their analysis, however, has to date not been systematically studied.We evaluated various dopant solvents such as (i) acetone (ii) acetonitrile (iii) methanol (iv) ethanol and (v) isopropanol for their ability to enhance glycopeptide ionization. Using a synthetic IgG2 glycopeptide as a standard, acetonitrile provided a five-fold increase in signal intensities and resulted in an overall charge state increase compared to conventional CaptiveSpray ionization. This trend remained the same when tryptic IgG (glyco)peptides were analyzed and allowed highly sensitive detection of glycopeptides even without any enrichment. While acetone dopant gas enhanced glycopeptide ionization by doubling glycopeptide signal intensities, all other tested solvents resulted either in ion suppression or adduct formation. This is in agreement with and can be explained by their individual physio-chemical properties of the solvents. Finally, by omitting glycopeptide enrichment steps, we established a bias-free human Immunoglobulin G (IgG) subclass specific glycosylation profile applying the optimized CaptiveSpray nanoBooster nano-LC-ESI-MS/MS analysis conditions.
- Published
- 2019
47. Towards a standardized bioinformatics infrastructure for N- and O-glycomics
- Author
-
Christopher Ashwood, Manfred Wuhrer, Shujiro Okuda, Nicolle H. Packer, Carsten Kettner, Peter Andersson, Weston B. Struwe, Kiyoko F. Aoki-Kinoshita, Miguel A. Rojas-Macias, Rebecca L. Miller, Katarina Madunić, Oliver Horlacher, Niclas G. Karlsson, Julien Mariethoz, Pauline M. Rudd, Chunsheng Jin, Tao Zhang, Fredrik Levander, Daniel Kolarich, Nobuyuki P. Aoki, Frédérique Lisacek, Vignesh Venkatakrishnan, Daisuke Shinmachi, and Yu Watanabe
- Subjects
0301 basic medicine ,Glycan ,Bioinformatics analysis ,Databases, Factual ,Computer science ,Science ,General Physics and Astronomy ,02 engineering and technology ,Computational biology ,Review Article ,Data publication and archiving ,General Biochemistry, Genetics and Molecular Biology ,Glycomics ,03 medical and health sciences ,Databases ,Polysaccharides ,ddc:570 ,Animals ,Humans ,ddc:025.063 ,lcsh:Science ,Biological sciences ,Glycoproteins ,Multidisciplinary ,biology ,Mass spectrometry ,Computational Biology ,General Chemistry ,Reference Standards ,021001 nanoscience & nanotechnology ,Public repository ,carbohydrates (lipids) ,030104 developmental biology ,Workflow ,biology.protein ,lcsh:Q ,0210 nano-technology - Abstract
The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase., Glycomics is gaining momentum in basic, translational and clinical research. Here, the authors review current reporting standards and analysis tools for mass-spectrometry-based glycomics, and propose an e-infrastructure for standardized reporting and online deposition of glycomics data.
- Published
- 2019
48. Isomeric Separation and Characterisation of Glycoconjugates
- Author
-
Kathirvel, Alagesan, Arun, Everest-Dass, and Daniel, Kolarich
- Subjects
Polysaccharides ,Glycoconjugates - Abstract
Individual monosaccharides can be linked in a variety of different combinations to form complex glycoconjugates. In contrast to DNA and proteins, glycoconjugate synthesis does not follow any template but is the consequence of the concerted action of various enzymes such as transferases and glycosidases . Thus, tools for glycoconjugate sequencing need to differentiate individual monosaccharide identity, linkage and anomericity to investigate and understand glycoconjugate function. In this chapter we provide a concise overview on the most commonly used and robust tools to separate and characterise glycoconjugate isomers.
- Published
- 2018
49. Protein glycosylation in head and neck cancers: From diagnosis to treatment
- Author
-
Newell W. Johnson, Chamindie Punyadeera, Riccardo Dolcetti, Daniel Kolarich, Mohammad Rasheduzzaman, Arutha Kulasinghe, and Liz Kenny
- Subjects
0301 basic medicine ,Cancer Research ,Glycosylation ,Cell ,Antineoplastic Agents ,Malignancy ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Circulating tumor cell ,Breast cancer ,Biomarkers, Tumor ,Genetics ,medicine ,Humans ,Molecular Targeted Therapy ,Liquid biopsy ,chemistry.chemical_classification ,Regulation of gene expression ,Squamous Cell Carcinoma of Head and Neck ,business.industry ,Liquid Biopsy ,Prognosis ,medicine.disease ,Gene Expression Regulation, Neoplastic ,stomatognathic diseases ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,chemistry ,Head and Neck Neoplasms ,030220 oncology & carcinogenesis ,Cancer research ,Glycoprotein ,business ,Protein Processing, Post-Translational - Abstract
Glycosylation is the most common post-translational modification (PTM) of proteins. Malignant tumour cells frequently undergo an alteration in surface protein glycosylation. This phenomenon is also common in cancers of the head and neck, most of which are squamous cell carcinomas (HNSCC). It affects cell functions, including proliferation, motility and invasiveness, thus increasing the propensity to metastasise. HNSCC represents the sixth most frequent malignancy worldwide. These neoplasms, which arise from the mucous membranes of the various anatomical subsites of the upper aero-digestive tract, are heterogeneous in terms of aetiology and clinico-pathologic features. With current treatments, only about 50% of HNSCC patients survive beyond 5-years. Therefore, there is the pressing need to dissect NHSCC heterogeneity to inform treatment choices. In particular, reliable biomarkers of predictive and prognostic value are eagerly needed. This review describes the current state of the art and bio-pathological meaning of glycosylation signatures associated with HNSCC and explores the possible role of tumour specific glycoproteins as potential biomarkers and attractive therapeutic targets. We have also compiled data relating to altered glycosylation and the nature of glycoproteins as tools for the identification of circulating tumour cells (CTCs) in the new era of liquid biopsy.
- Published
- 2020
50. Emerging roles of protein mannosylation in inflammation and infection
- Author
-
Morten Thaysen-Andersen, Ian Loke, Daniel Kolarich, and Nicolle H. Packer
- Subjects
Models, Molecular ,0301 basic medicine ,Glycosylation ,Clinical Biochemistry ,Mannose ,Biology ,Biochemistry ,Epitope ,03 medical and health sciences ,chemistry.chemical_compound ,C-type lectin ,Neoplasms ,Animals ,Humans ,Lectins, C-Type ,Molecular Biology ,Glycoproteins ,Mannan-binding lectin ,Inflammation ,chemistry.chemical_classification ,Models, Immunological ,Bacterial Infections ,General Medicine ,Cell biology ,030104 developmental biology ,Carbohydrate Sequence ,Immune System Diseases ,Mycoses ,chemistry ,Immunology ,Molecular Medicine ,Protein mannosylation ,Glycoprotein ,Mannose receptor - Abstract
Proteins are frequently modified by complex carbohydrates (glycans) that play central roles in maintaining the structural and functional integrity of cells and tissues in humans and lower organisms. Mannose forms an essential building block of protein glycosylation, and its functional involvement as components of larger and diverse α-mannosidic glycoepitopes in important intra- and intercellular glycoimmunological processes is gaining recognition. With a focus on the mannose-rich asparagine (N-linked) glycosylation type, this review summarises the increasing volume of literature covering human and non-human protein mannosylation, including their structures, biosynthesis and spatiotemporal expression. The review also covers their known interactions with specialised host and microbial mannose-recognising C-type lectin receptors (mrCLRs) and antibodies (mrAbs) during inflammation and pathogen infection. Advances in molecular mapping technologies have recently revealed novel immuno-centric mannose-terminating truncated N-glycans, termed paucimannosylation, on human proteins. The cellular presentation of α-mannosidic glycoepitopes on N-glycoproteins appears tightly regulated; α-mannose determinants are relative rare glycoepitopes in physiological extracellular environments, but may be actively secreted or leaked from cells to transmit potent signals when required. Simultaneously, our understanding of the molecular basis on the recognition of mannosidic epitopes by mrCLRs including DC-SIGN, mannose receptor, mannose binding lectin and mrAb is rapidly advancing, together with the functional implications of these interactions in facilitating an effective immune response during physiological and pathophysiological conditions. Ultimately, deciphering these complex mannose-based receptor-ligand interactions at the detailed molecular level will significantly advance our understanding of immunological disorders and infectious diseases, promoting the development of future therapeutics to improve patient clinical outcomes.
- Published
- 2016
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.