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Godbole S, Voß H, Gocke A, Schlumbohm S, Schumann Y, Peng B, Mynarek M, Rutkowski S, Dottermusch M, Dorostkar MM, Korshunov A, Mair T, Pfister SM, Kwiatkowski M, Hotze M, Neumann P, Hartmann C, Weis J, Liesche-Starnecker F, Guan Y, Moritz M, Siebels B, Struve N, Schlüter H, Schüller U, Krisp C, Neumann JE. Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level. Nat Commun 2024; 15:6237. [PMID: 39043693 PMCID: PMC11266559 DOI: 10.1038/s41467-024-50554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/11/2024] [Indexed: 07/25/2024] Open
Abstract
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies-mainly studying nucleic acids-has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways. We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pG3myc), and synapses/immunological processes (pSHHs, pG3 and pG4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favorable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures.
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Affiliation(s)
- Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Gocke
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schlumbohm
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Bojia Peng
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mario M Dorostkar
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
- German Center for Neurodegenerative Diseases, Munich, Germany
| | - Andrey Korshunov
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Mair
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Madlen Hotze
- Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Philipp Neumann
- Chair for High Performance Computing, Helmut Schmidt University, Hamburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School (MHH), Hannover, Germany
| | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University Hospital, Aachen, Germany
| | | | - Yudong Guan
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Moritz
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Struve
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy & Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christoph Krisp
- Section of Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Hidayah SN, Biabani A, Gaikwad M, Nissen P, Voß H, Riedner M, Schlüter H, Siebels B. Application of sample displacement batch chromatography for fractionation of proteoforms. Proteomics 2024; 24:e2200424. [PMID: 37750450 DOI: 10.1002/pmic.202200424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.
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Affiliation(s)
- Siti Nurul Hidayah
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Sleman, Yogyakarta, Indonesia
| | - Ali Biabani
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manasi Gaikwad
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paula Nissen
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Riedner
- Technology Platform Mass Spectrometry, University of Hamburg, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Shipman J, Sommers C, Keire DA, Chen K, Zhu H. Comprehensive N-Glycan Mapping using Parallel Reaction Monitoring LC-MS/MS. Pharm Res 2023; 40:1399-1410. [PMID: 36513905 DOI: 10.1007/s11095-022-03453-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Glycan composition can impact a biotherapeutic's safety and efficacy. For example, changes in the relative abundance of different glycan attributes like afucosylation, galactosylation or high-mannose content can change the properties or functions of a monoclonal antibody (mAb). While established methods can effectively characterize major glycan species in biotherapeutic drug products, there is still a need for more sensitive and specific methods that can effectively monitor low abundance species which may impact mAb function. METHODS Glycans released from two mAbs, adalimumab and trastuzumab, were derivatized with Rapifluor-MS™. Glycans were separated using HILIC and detected using either fluorescence (FLD) or mass spectrometry (MS). A parallel reaction monitoring (PRM) workflow was used for the MS analysis. RESULTS AND CONCLUSION FLD analysis identified 18 and 19 glycan peaks in adalimumab and trastuzumab, respectively. Glycan identities were determined using MS-analysis and a high number of FLD peaks containing co-eluting glycan species were observed. PRM analysis quantified 38 and 39 glycan species in adalimumab and trastuzumab, respectively, and the increase in glycans that could be identified was due to superior sensitivity and selectivity compared to FLD. Notably, many low abundance glycans identified by PRM included species that were not reported in other studies. PRM also offered several additional advantages; unique structural features could be identified using the collected MS/MS spectra and de-coupling MS acquisition and data processing simplified the transfer of methods between instruments. The results established PRM as a precise, informative tool for glycan analysis and quantitation.
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Affiliation(s)
- Joshua Shipman
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Cynthia Sommers
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Kang Chen
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
| | - Hongbin Zhu
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
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An Efficient and Economical N-Glycome Sample Preparation Using Acetone Precipitation. Metabolites 2022; 12:metabo12121285. [PMID: 36557323 PMCID: PMC9786591 DOI: 10.3390/metabo12121285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Due to the critical role of the glycome in organisms and its close connections with various diseases, much time and effort have been dedicated to glycomics-related studies in the past decade. To achieve accurate and reliable identification and quantification of glycans extracted from biological samples, several analysis methods have been well-developed. One commonly used methodology for the sample preparation of N-glycomics usually involves enzymatic cleavage by PNGase F, followed by sample purification using C18 cartridges to remove proteins. PNGase F and C18 cartridges are very efficient both for cleaving N-glycans and for protein removal. However, this method is most suitable for a limited quantity of samples. In this study, we developed a sample preparation method focusing on N-glycome extraction and purification from large-scale biological samples using acetone precipitation. The N-glycan yield was first tested on standard glycoprotein samples, bovine fetuin and complex biological samples, and human serum. Compared to C18 cartridges, most of the sialylated N-glycans from human serum were detected with higher abundance after acetone precipitation. However, C18 showed a slightly higher efficiency for protein removal. Using the unfiltered human serum as the baseline, around 97.7% of the proteins were removed by acetone precipitation, while more than 99.9% of the proteins were removed by C18 cartridges. Lastly, the acetone precipitation was applied to N-glycome extraction from egg yolks to demonstrate large-scale glycomics sample preparation.
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Guan Y, Zhang M, Gaikwad M, Voss H, Fazel R, Ansari S, Shen H, Wang J, Schlüter H. An Integrated Strategy Reveals Complex Glycosylation of Erythropoietin Using Mass Spectrometry. J Proteome Res 2021; 20:3654-3663. [PMID: 34110173 PMCID: PMC9472269 DOI: 10.1021/acs.jproteome.1c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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The characterization of therapeutic glycoproteins is challenging
due to the structural heterogeneity of the therapeutic protein glycosylation.
This study presents an in-depth analytical strategy for glycosylation
of first-generation erythropoietin (epoetin beta), including a developed
mass spectrometric workflow for N-glycan analysis, bottom-up mass
spectrometric methods for site-specific N-glycosylation, and a LC-MS
approach for O-glycan identification. Permethylated N-glycans, peptides,
and enriched glycopeptides of erythropoietin were analyzed by nanoLC-MS/MS,
and de-N-glycosylated erythropoietin was measured by LC-MS, enabling
the qualitative and quantitative analysis of glycosylation and different
glycan modifications (e.g., phosphorylation and O-acetylation). The
newly developed Python scripts enabled the identification of 140 N-glycan
compositions (237 N-glycan structures) from erythropoietin, especially
including 8 phosphorylated N-glycan species. The site-specificity
of N-glycans was revealed at the glycopeptide level by pGlyco software
using different proteases. In total, 114 N-glycan compositions were
identified from glycopeptide analysis. Moreover, LC-MS analysis of
de-N-glycosylated erythropoietin species identified two O-glycan compositions
based on the mass shifts between non-O-glycosylated and O-glycosylated
species. Finally, this integrated strategy was proved to realize the
in-depth glycosylation analysis of a therapeutic glycoprotein to understand
its pharmacological properties and improving the manufacturing processes.
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Affiliation(s)
- Yudong Guan
- The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
| | - Min Zhang
- Section Mass Spectrometric Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Manasi Gaikwad
- Section Mass Spectrometric Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Hannah Voss
- Section Mass Spectrometric Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Ramin Fazel
- Reasearch and Innovation Center, Livogen Pharmed Co., Tehran 1417755358, Iran
| | - Samira Ansari
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj 3165933155, Iran
| | - Huali Shen
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jigang Wang
- The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen 518055, China
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
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