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Kratochvíl J, Asor R, Helmi S, Struwe WB, Kukura P. Lifting the Concentration Limit of Mass Photometry by PEG Nanopatterning. NANO LETTERS 2024; 24:10032-10039. [PMID: 38950386 PMCID: PMC11342371 DOI: 10.1021/acs.nanolett.4c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
Mass photometry (MP) is a rapidly growing optical technique for label-free mass measurement of single biomolecules in solution. The underlying measurement principle provides numerous advantages over ensemble-based methods but has been limited to low analyte concentrations due to the need to uniquely and accurately quantify the binding of individual molecules to the measurement surface, which results in diffraction-limited spots. Here, we combine nanoparticle lithography with surface PEGylation to substantially lower surface binding, resulting in a 2 orders of magnitude improvement in the upper concentration limit associated with mass photometry. We demonstrate the facile tunability of degree of passivation, enabling measurements at increased analyte concentrations. These advances provide access to protein-protein interactions in the high nanomolar to low micromolar range, substantially expanding the application space of mass photometry.
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Affiliation(s)
- Jiří Kratochvíl
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Roi Asor
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Seham Helmi
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Weston B. Struwe
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Philipp Kukura
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
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2
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Pradita T, Chen YJ, Su TH, Chang KH, Chen PJ, Chen YJ. Data Independent Acquisition Mass Spectrometry Enhanced Personalized Glycosylation Profiling of Haptoglobin in Hepatocellular Carcinoma. J Proteome Res 2024; 23:3571-3584. [PMID: 38994555 PMCID: PMC11301664 DOI: 10.1021/acs.jproteome.4c00227] [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: 03/21/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024]
Abstract
Aberrant glycosylation has gained significant interest for biomarker discovery. However, low detectability, complex glycan structures, and heterogeneity present challenges in glycoprotein assay development. Using haptoglobin (Hp) as a model, we developed an integrated platform combining functionalized magnetic nanoparticles and zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) for highly specific glycopeptide enrichment, followed by a data-independent acquisition (DIA) strategy to establish a deep cancer-specific Hp-glycosylation profile in hepatitis B virus (HBV, n = 5) and hepatocellular carcinoma (HCC, n = 5) patients. The DIA strategy established one of the deepest Hp-glycosylation landscapes (1029 glycopeptides, 130 glycans) across serum samples, including 54 glycopeptides exclusively detected in HCC patients. Additionally, single-shot DIA searches against a DIA-based spectral library outperformed the DDA approach by 2-3-fold glycopeptide coverage across patients. Among the four N-glycan sites on Hp (N-184, N-207, N-211, N-241), the total glycan type distribution revealed significantly enhanced detection of combined fucosylated-sialylated glycans, which were the most dominant glycoforms identified in HCC patients. Quantitation analysis revealed 48 glycopeptides significantly enriched in HCC (p < 0.05), including a hybrid monosialylated triantennary glycopeptide on the N-184 site with nearly none-to-all elevation to differentiate HCC from the HBV group (HCC/HBV ratio: 2462 ± 766, p < 0.05). In summary, DIA-MS presents an unbiased and comprehensive alternative for targeted glycoproteomics to guide discovery and validation of glyco-biomarkers.
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Affiliation(s)
- Tiara Pradita
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Sustainable
Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tung-Hung Su
- Division
of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hepatitis
Research Center, National Taiwan University
Hospital, Taipei 100, Taiwan
| | - Kun-Hao Chang
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Molecular
Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Tsing-Hua University, Hsinchu 300, Taiwan
| | - Pei-Jer Chen
- Division
of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hepatitis
Research Center, National Taiwan University
Hospital, Taipei 100, Taiwan
- Graduate
Institute of Clinical Medicine, National
Taiwan University College of Medicine, Taipei 100, Taiwan
- Department
of Medical Research, National Taiwan University
Hospital, Taipei 100, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Sustainable
Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
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3
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Kalaidopoulou Nteak S, Völlmy F, Lukassen MV, van den Toorn H, den Boer MA, Bondt A, van der Lans SPA, Haas PJ, van Zuilen AD, Rooijakkers SHM, Heck AJR. Longitudinal Fluctuations in Protein Concentrations and Higher-Order Structures in the Plasma Proteome of Kidney Failure Patients Subjected to a Kidney Transplant. J Proteome Res 2024; 23:2124-2136. [PMID: 38701233 PMCID: PMC11165583 DOI: 10.1021/acs.jproteome.4c00064] [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: 02/06/2024] [Revised: 04/09/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Using proteomics and complexome profiling, we evaluated in a year-long study longitudinal variations in the plasma proteome of kidney failure patients, prior to and after a kidney transplantation. The post-transplant period was complicated by bacterial infections, resulting in dramatic changes in the proteome, attributed to an acute phase response (APR). As positive acute phase proteins (APPs), being elevated upon inflammation, we observed the well-described C-reactive protein and Serum Amyloid A (SAA), but also Fibrinogen, Haptoglobin, Leucine-rich alpha-2-glycoprotein, Lipopolysaccharide-binding protein, Alpha-1-antitrypsin, Alpha-1-antichymotrypsin, S100, and CD14. As negative APPs, being downregulated upon inflammation, we identified the well-documented Serotransferrin and Transthyretin, but added Kallistatin, Heparin cofactor 2, and interalpha-trypsin inhibitor heavy chain H1 and H2 (ITIH1, ITIH2). For the patient with the most severe APR, we performed plasma complexome profiling by SEC-LC-MS on all longitudinal samples. We observed that several plasma proteins displaying alike concentration patterns coelute and form macromolecular complexes. By complexome profiling, we expose how SAA1 and SAA2 become incorporated into high-density lipid particles, replacing largely Apolipoprotein (APO)A1 and APOA4. Overall, our data highlight that the combination of in-depth longitudinal plasma proteome and complexome profiling can shed further light on correlated variations in the abundance of several plasma proteins upon inflammatory events.
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Affiliation(s)
- Sofia Kalaidopoulou Nteak
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Franziska Völlmy
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Marie V. Lukassen
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Henk van den Toorn
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Albert Bondt
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
| | - Sjors P. A. van der Lans
- Department
of Medical Microbiology, University Medical
Center Utrecht, Utrecht 3584 CH, The Netherlands
| | - Pieter-Jan Haas
- Department
of Medical Microbiology, University Medical
Center Utrecht, Utrecht 3584 CH, The Netherlands
| | - Arjan D. van Zuilen
- Department
of Nephrology and Hypertension, University
Medical Center Utrecht, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Suzan H. M. Rooijakkers
- Department
of Medical Microbiology, University Medical
Center Utrecht, Utrecht 3584 CH, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Utrecht 3584 CH, The Netherlands
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4
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Delanghe JR, Delrue C, Speeckaert R, Speeckaert MM. Unlocking the link between haptoglobin polymorphism and noninfectious human diseases: insights and implications. Crit Rev Clin Lab Sci 2024; 61:275-297. [PMID: 38013410 DOI: 10.1080/10408363.2023.2285929] [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: 07/21/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Haptoglobin (Hp) is a polymorphic protein that was initially described as a hemoglobin (Hb)-binding protein. The major functions of Hp are to scavenge Hb, prevent iron loss, and prevent heme-based oxidation. Hp regulates angiogenesis, nitric oxide homeostasis, immune responses, and prostaglandin synthesis. Genetic polymorphisms in the Hp gene give rise to different phenotypes, including Hp 1-1, Hp 2-1, and Hp 2-2. Extensive research has been conducted to investigate the association between Hp polymorphisms and several medical conditions including cardiovascular disease, inflammatory bowel disease, cancer, transplantation, and hemoglobinopathies. Generally, the Hp 2-2 phenotype is associated with increased disease risk and poor outcomes. Over the years, the Hp 2 allele has spread under genetic pressures. Individuals with the Hp 2-2 phenotype generally exhibit lower levels of CD163 expression in macrophages. The decreased expression of CD163 may be associated with the poor antioxidant capacity in the serum of subjects carrying the Hp 2-2 phenotype. However, the Hp 1-1 phenotype may confer protection in some cases. The Hp1 allele has strong antioxidant, anti-inflammatory, and immunomodulatory properties. It is important to note that the benefits of the Hp1 allele may vary depending on genetic and environmental factors as well as the specific disease or condition under consideration. Therefore, the Hp1 allele may not necessarily confer advantages in all situations, and its effects may be context-dependent. This review highlights the current understanding of the role of Hp polymorphisms in cardiovascular disease, inflammatory bowel disease, cancer, transplantation, hemoglobinopathies, and polyuria.
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Affiliation(s)
- Joris R Delanghe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Charlotte Delrue
- Department of Nephrology, Ghent University Hospital, Ghent, Belgium
| | | | - Marijn M Speeckaert
- Department of Nephrology, Ghent University Hospital, Ghent, Belgium
- Research Foundation-Flanders (FWO), Brussels, Belgium
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He K, Baniasad M, Kwon H, Caval T, Xu G, Lebrilla C, Hommes DW, Bertozzi C. Decoding the glycoproteome: a new frontier for biomarker discovery in cancer. J Hematol Oncol 2024; 17:12. [PMID: 38515194 PMCID: PMC10958865 DOI: 10.1186/s13045-024-01532-x] [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: 12/02/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.
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Affiliation(s)
- Kai He
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA.
| | | | - Hyunwoo Kwon
- James Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | | | - Gege Xu
- InterVenn Biosciences, South San Francisco, USA
| | - Carlito Lebrilla
- Department of Biochemistry and Molecular Medicine, UC Davis Health, Sacramento, USA
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6
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Kohansal-Nodehi M, Swiatek-de Lange M, Kroeniger K, Rolny V, Tabarés G, Piratvisuth T, Tanwandee T, Thongsawat S, Sukeepaisarnjaroen W, Esteban JI, Bes M, Köhler B, Chan HLY, Busskamp H. Discovery of a haptoglobin glycopeptides biomarker panel for early diagnosis of hepatocellular carcinoma. Front Oncol 2023; 13:1213898. [PMID: 37920152 PMCID: PMC10619681 DOI: 10.3389/fonc.2023.1213898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023] Open
Abstract
Background There is a need for new serum biomarkers for early detection of hepatocellular carcinoma (HCC). Haptoglobin (Hp) N-glycosylation is altered in HCC, but the diagnostic value of site-specific Hp glycobiomarkers is rarely reported. We aimed to determine the site-specific glycosylation profile of Hp for early-stage HCC diagnosis. Method Hp glycosylation was analyzed in the plasma of patients with liver diseases (n=57; controls), early-stage HCC (n=50) and late-stage HCC (n=32). Hp phenotype was determined by immunoblotting. Hp was immunoisolated and digested into peptides. N-glycopeptides were identified and quantified using liquid chromatography-mass spectrometry. Cohort samples were compared using Wilcoxon rank-sum (Mann-Whitney U) tests. Diagnostic performance was assessed using receiver operating characteristic (ROC) curves and area under curve (AUC). Results Significantly higher fucosylation, branching and sialylation of Hp glycans, and expression of high-mannose glycans, was observed as disease progressed from cirrhosis to early- and late-stage HCC. Several glycopeptides demonstrated high values for early diagnosis of HCC, with an AUC of 93% (n=1), >80% (n=3), >75% (n=13) and >70% (n=11), compared with alpha-fetoprotein (AFP; AUC of 79%). The diagnostic performance of the identified biomarkers was only slightly affected by Hp phenotype. Conclusion We identified a panel of Hp glycopeptides that are significantly differentially regulated in early- and late-stage HCC. Some glycobiomarkers exceeded the diagnostic value of AFP (the most commonly used biomarker for HCC diagnosis). Our findings provide evidence that glycobiomarkers can be effective in the diagnosis of early HCC - individually, as a panel of glycopeptides or combined with conventional serological biomarkers.
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Affiliation(s)
| | | | | | - Vinzent Rolny
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
| | - Glòria Tabarés
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
| | - Teerha Piratvisuth
- NKC Institute of Gastroenterology and Hepatology, Songklanagarind Hospital, Prince of Songkla University, Hat Yai, Thailand
| | - Tawesak Tanwandee
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Satawat Thongsawat
- Department of Internal Medicine, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Marta Bes
- Transfusion Safety Laboratory, Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Bruno Köhler
- Department of Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Liver Cancer Center Heidelberg, Heidelberg, Germany
| | - Henry Lik-Yuen Chan
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Holger Busskamp
- Roche Diagnostics GmbH, Research and Development Core Lab, Penzberg, Germany
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7
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Di Marco F, Blümel G, Blöchl C, Wuhrer M, Huber CG. A semi-automated hybrid HPLC-MS approach for in-depth characterization of intact non-covalent heterodimer glycoforms of gonadotropin biopharmaceuticals. Anal Chim Acta 2023; 1274:341574. [PMID: 37455084 DOI: 10.1016/j.aca.2023.341574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/07/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Gonadotropins are a class of heavily glycosylated protein hormones, thus extremely challenging to characterize by mass spectrometry. As biopharmaceuticals, gonadotropins are prescribed for the treatment of infertility and are derived from different sources: either from pooled urine of pregnant women or upon production in genetically modified Chinese Hamster Ovary cells. Human chorionic gonadotropin (hCG) is sold as a biopharmaceutical under the name Pregnyl® (urinary hCG, u-hCG) and Ovitrelle® (recombinant hCG, r-hCG), and recombinant human follicle stimulating hormone (r-hFSH) is marketed as Gonal-f®. Recently, we reported the exhaustive characterization of r-hCG at different structural levels. RESULTS We implement size exclusion (SE) HPLC-MS to automatize the acquisition of native mass spectra of r-hCG dimer, but also u-hCG and r-hFSH, comparing the drug products up to intact heterodimer level. A hybrid HPLC-MS approach was employed for the characterization of r-hCG, u-hCG and r-hFSH drug products at different structural levels. Released glycans were analyzed by porous graphitized carbon (PGC)-HPLC-MS/MS, glycopeptides by reversed-phase (RP)-HPLC-MS/MS, subunits by RP-HPLC-MS and finally the intact native heterodimers by semi-automated online buffer exchange SE-HPLC-MS. The data were integrated using bioinformatic tools, to finally unravel the composition of 1481 co-existing dimeric glycoforms for r-hCG, 1167 glycoforms for u-hCG, and 1440 glycoforms for r-hFSH, and to compare critical quality attributes of the different drug products such as their degree of sialylation and O-glycosylation. SIGNIFICANCE AND NOVELTY The strong alliance of bioanalytics and bioinformatics data integration at the different structural levels allowed the identification of more than thousand different glycoforms of r-hCG, u-hCG, and r-hFSH. The results showed that these biopharmaceuticals differ considerably in their glycosylation patterns and highlight the importance of in-depth characterization of biopharmaceuticals for quality control. © 2017 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Fiammetta Di Marco
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - Gabriele Blümel
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - Constantin Blöchl
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria; Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Christian G Huber
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria.
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Oh MJ, Lee SH, Kim U, An HJ. In-depth investigation of altered glycosylation in human haptoglobin associated cancer by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:496-518. [PMID: 34037272 DOI: 10.1002/mas.21707] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 05/08/2023]
Abstract
Serum haptoglobin (Hp), a highly sialylated biomolecule with four N-glycosylation sites, is a positive acute-phase response glycoprotein that acts as an immunomodulator. Hp has gained considerable attention due to its potential as a signature molecule that exhibits aberrant glycosylation in inflammatory disorders and malignancies. Its glycosylation can be analyzed qualitatively and quantitatively by various methods using mass spectrometry. In this review, we have provided a brief overview of Hp structure and biological function and described mass spectrometry-based techniques for analyzing glycosylation ranging from macroheterogeneity to microheterogeneity of Hp in diseases and cancer. The sugars on haptoglobin can be a sweet bridge to link the potential of cancer-specific biomarkers to clinically relevant applications.
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Affiliation(s)
- Myung Jin Oh
- Asia-Pacific Glycomics Reference Site, Daejeon, South Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Sung Hyeon Lee
- Department of Biomedical Research Center, Korea University Guro Hospital, Seoul, South Korea
| | - Unyoung Kim
- Division of Bioanalysis, Biocomplete Inc., Seoul, South Korea
| | - Hyun Joo An
- Asia-Pacific Glycomics Reference Site, Daejeon, South Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
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9
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Dingess KA, Hoek M, van Rijswijk DMH, Tamara S, den Boer MA, Veth T, Damen MJA, Barendregt A, Romijn M, Juncker HG, van Keulen BJ, Vidarsson G, van Goudoever JB, Bondt A, Heck AJR. Identification of common and distinct origins of human serum and breastmilk IgA1 by mass spectrometry-based clonal profiling. Cell Mol Immunol 2023; 20:26-37. [PMID: 36447030 PMCID: PMC9707141 DOI: 10.1038/s41423-022-00954-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
The most abundant immunoglobulin present in the human body is IgA. It has the highest concentrations at the mucosal lining and in biofluids such as milk and is the second most abundant class of antibodies in serum. We assessed the structural diversity and clonal repertoire of IgA1-containing molecular assemblies longitudinally in human serum and milk from three donors using a mass spectrometry-based approach. IgA-containing molecules purified from serum or milk were assessed by the release and subsequent analysis of their Fab fragments. Our data revealed that serum IgA1 consists of two distinct structural populations, namely monomeric IgA1 (∼80%) and dimeric joining (J-) chain coupled IgA1 (∼20%). Also, we confirmed that IgA1 in milk is present solely as secretory (S)IgA, consisting of two (∼50%), three (∼33%) or four (∼17%) IgA1 molecules assembled with a J-chain and secretory component (SC). Interestingly, the serum and milk IgA1-Fab repertoires were distinct between monomeric, and J-chain coupled dimeric IgA1. The serum dimeric J-chain coupled IgA1 repertoire contained several abundant clones also observed in the milk IgA1 repertoire. The latter repertoire had little to no overlap with the serum monomeric IgA1 repertoire. This suggests that human IgA1s have (at least) two distinct origins; one of these produces dimeric J-chain coupled IgA1 molecules, shared in human serum and milk, and another produces monomeric IgA1 ending up exclusively in serum.
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Affiliation(s)
- Kelly A Dingess
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Amsterdam UMC, Vrije Universiteit, University of Amsterdam, Emma Children's Hospital, Amsterdam Reproduction & Development Research Institute, Department of Pediatrics, Amsterdam, the Netherlands
| | - Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Danique M H van Rijswijk
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Tim Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Mirjam J A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Michelle Romijn
- Amsterdam UMC, Vrije Universiteit, University of Amsterdam, Emma Children's Hospital, Amsterdam Reproduction & Development Research Institute, Department of Pediatrics, Amsterdam, the Netherlands
| | - Hannah G Juncker
- Amsterdam UMC, Vrije Universiteit, University of Amsterdam, Emma Children's Hospital, Amsterdam Reproduction & Development Research Institute, Department of Pediatrics, Amsterdam, the Netherlands
| | - Britt J van Keulen
- Amsterdam UMC, Vrije Universiteit, University of Amsterdam, Emma Children's Hospital, Amsterdam Reproduction & Development Research Institute, Department of Pediatrics, Amsterdam, the Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Johannes B van Goudoever
- Amsterdam UMC, Vrije Universiteit, University of Amsterdam, Emma Children's Hospital, Amsterdam Reproduction & Development Research Institute, Department of Pediatrics, Amsterdam, the Netherlands
| | - Albert Bondt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, The Netherlands.
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10
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Chen YH, Tian W, Yasuda M, Ye Z, Song M, Mandel U, Kristensen C, Povolo L, Marques ARA, Čaval T, Heck AJR, Sampaio JL, Johannes L, Tsukimura T, Desnick R, Vakhrushev SY, Yang Z, Clausen H. A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution. Front Bioeng Biotechnol 2023; 11:1128371. [PMID: 36911201 PMCID: PMC9999025 DOI: 10.3389/fbioe.2023.1128371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 03/14/2023] Open
Abstract
Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due in part to short circulation times and suboptimal biodistribution of the therapeutic enzymes. We previously engineered Chinese hamster ovary (CHO) cells to produce α-galactosidase A (GLA) with various N-glycan structures and demonstrated that elimination of mannose-6-phosphate (M6P) and conversion to homogeneous sialylated N-glycans prolonged circulation time and improved biodistribution of the enzyme following a single-dose infusion into Fabry mice. Here, we confirmed these findings using repeated infusions of the glycoengineered GLA into Fabry mice and further tested whether this glycoengineering approach, Long-Acting-GlycoDesign (LAGD), could be implemented on other lysosomal enzymes. LAGD-engineered CHO cells stably expressing a panel of lysosomal enzymes [aspartylglucosamine (AGA), beta-glucuronidase (GUSB), cathepsin D (CTSD), tripeptidyl peptidase (TPP1), alpha-glucosidase (GAA) or iduronate 2-sulfatase (IDS)] successfully converted all M6P-containing N-glycans to complex sialylated N-glycans. The resulting homogenous glycodesigns enabled glycoprotein profiling by native mass spectrometry. Notably, LAGD extended the plasma half-life of all three enzymes tested (GLA, GUSB, AGA) in wildtype mice. LAGD may be widely applicable to lysosomal replacement enzymes to improve their circulatory stability and therapeutic efficacy.
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Affiliation(s)
- Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,GlycoDisplay ApS, Copenhagen, Denmark
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ming Song
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tomislav Čaval
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Julio Lopes Sampaio
- Institut Curie, PSL Research University, Cellular and Chemical Biology, U1143 INSERM, UMR3666 CNRS, Paris, France
| | - Ludger Johannes
- Institut Curie, PSL Research University, Cellular and Chemical Biology, U1143 INSERM, UMR3666 CNRS, Paris, France
| | - Takahiro Tsukimura
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Functional Bioanalysis, Meiji Pharmaceutical University, Tokyo, Japan
| | - Robert Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk AS, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Cramer DAT, Franc V, Caval T, Heck AJR. Charting the Proteoform Landscape of Serum Proteins in Individual Donors by High-Resolution Native Mass Spectrometry. Anal Chem 2022; 94:12732-12741. [PMID: 36074704 PMCID: PMC9494300 DOI: 10.1021/acs.analchem.2c02215] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Most proteins in serum are glycosylated, with several
annotated
as biomarkers and thus diagnostically important and of interest for
their role in disease. Most methods for analyzing serum glycoproteins
employ either glycan release or glycopeptide centric mass spectrometry-based
approaches, which provide excellent tools for analyzing known glycans
but neglect previously undefined or unknown glycosylation and/or other
co-occurring modifications. High-resolution native mass spectrometry
is a relatively new technique for the analysis of intact glycoproteins,
providing a “what you see is what you get” mass profile
of a protein, allowing the qualitative and quantitative observation
of all modifications present. So far, a disadvantage of this approach
has been that it centers mostly on just one specific serum glycoprotein
at the time. To address this issue, we introduce an ion-exchange chromatography-based
fractionation method capable of isolating and analyzing, in parallel,
over 20 serum (glyco)proteins, covering a mass range between 30 and
190 kDa, from 150 μL of serum. Although generating data in parallel
for all these 20 proteins, we focus the discussion on the very complex
proteoform profiles of four selected proteins, i.e., α-1-antitrypsin,
ceruloplasmin, hemopexin, and complement protein C3. Our analyses
provide an insight into the extensive proteoform landscape of serum
proteins in individual donors, caused by the occurrence of various N- and O-glycans, protein cysteinylation,
and co-occurring genetic variants. Moreover, native mass intact mass
profiling also provided an edge over alternative approaches revealing
the presence of apo- and holo-forms of ceruloplasmin and the endogenous
proteolytic processing in plasma of among others complement protein
C3. We also applied our approach to a small cohort of serum samples
from healthy and diseased individuals. In these, we qualitatively
and quantitatively monitored the changes in proteoform profiles of
ceruloplasmin and revealed a substantial increase in fucosylation
and glycan occupancy in patients with late-stage hepatocellular carcinoma
and pancreatic cancer as compared to healthy donor samples.
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Affiliation(s)
- Dario A T Cramer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Tomislav Caval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
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12
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Specific electrolyte effects on hemoglobin in denaturing medium investigated through electro spray ionization mass spectrometry. J Inorg Biochem 2022; 234:111872. [DOI: 10.1016/j.jinorgbio.2022.111872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/29/2022] [Accepted: 05/19/2022] [Indexed: 12/14/2022]
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13
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Kohansal-Nodehi M, Swiatek-de Lange M, Tabarés G, Busskamp H. Haptoglobin polymorphism affects its N-glycosylation pattern in serum. J Mass Spectrom Adv Clin Lab 2022; 25:61-70. [PMID: 35938056 PMCID: PMC9352458 DOI: 10.1016/j.jmsacl.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
Polymorphism affects glycosylation pattern of haptoglobin in healthy population. Sample phenotype classification was done based on the number and type of α-chains. Glycoproteomic analyses of haptoglobin were done using enzyme-assisted LC-MS/MS. Significant differences were obseerved in branching, sialylation and fucosylation.
Introduction Haptoglobin (Hp) is an abundant acute-phase protein secreted mainly by the liver into the bloodstream. There are three Hp protein phenotypes (Hp type 1–1, 2–1, and 2–2), which differ in the number of α- and β-chains, type of α-chain (the β-chain type remains the same in all the Hp phenotypes), and the polymers that they form via disulfide bonds. Hp has four N-glycosylation sites on the β-chain. Glycosylation of Hp has been reported frequently as a potential glycobiomarker for many diseases; however, whether Hp polymorphism affects its glycosylation has not yet been addressed extensively or in depth. Objectives This study investigated the differences between the glycosylation patterns of Hp phenotypes using serum from 12 healthy individuals (four for each Hp phenotype). Method An efficient method for isolating Hp from serum was established and subsequently the Hp phenotype of each sample was characterized by immunoblotting. Then, LC-MS/MS analysis of isolated Hp after treatment with three exoglycosidases (sialidase, α2-3 neuraminidase, Endo F3) was performed to characterize the glycosylation pattern of Hp for each individual sample. Results The data reveal significant differences among the branching, sialylation, and fucosylation of Hp types, documenting the effect of Hp polymorphism on its glycosylation. Conclusion Overall, the study suggests that Hp phenotype characterization should be considered during the investigation of Hp glycosylation.
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14
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Wu D, Robinson CV. Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry. Curr Opin Struct Biol 2022; 74:102351. [DOI: 10.1016/j.sbi.2022.102351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
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15
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Characterising biomolecular interactions and dynamics with mass photometry. Curr Opin Chem Biol 2022; 68:102132. [DOI: 10.1016/j.cbpa.2022.102132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/22/2022] [Indexed: 12/25/2022]
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16
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Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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17
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Ivanov DG, Yang Y, Pawlowski JW, Carrick IJ, Kaltashov IA. Rapid Evaluation of the Extent of Haptoglobin Glycosylation Using Orthogonal Intact-Mass MS Approaches and Multivariate Analysis. Anal Chem 2022; 94:5140-5148. [PMID: 35285615 PMCID: PMC11232314 DOI: 10.1021/acs.analchem.1c05585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intact-mass measurements are becoming increasingly popular in mass spectrometry (MS) based protein characterization, as they allow the entire complement of proteoforms to be evaluated within a relatively short time. However, applications of this approach are currently limited to systems exhibiting relatively modest degrees of structural diversity, as the high extent of heterogeneity frequently prevents straightforward MS measurements. Incorporation of limited charge reduction into electrospray ionization (ESI) MS is an elegant way to obtain meaningful information on most heterogeneous systems, yielding not only the average mass of the protein but also the mass range populated by the entire complement of proteoforms. Application of this approach to characterization of two different phenotypes of haptoglobin (1-1 and 2-1) provides evidence of a significant difference in their extent of glycosylation (with the glycan load of phenotype 2-1 being notably lighter) despite a significant overlap of their ionic signals. More detailed characterization of their glycosylation patterns is enabled by the recently introduced technique of cross-path reactive chromatography (XP-RC) with online MS detection, which combines chromatographic separation with in-line reduction of disulfide bonds to generate metastable haptoglobin subunits. Application of XP-RC to both haptoglobin phenotypes confirms that no modifications are present within their light chains and provides a wealth of information on glycosylation patterns of the heavy chains. N-Glycosylation patterns of both haptoglobin phenotypes were found to be consistent with bi- and triantennary structures of complex type that exhibit significant level of fucosylation and sialylation. However, multivariate analysis of haptoglobin 1-1 reveals higher number of the triantennary structures, in comparison to haptoglobin 2-1, as well as a higher extent of fucosylation. The glycosylation patterns deduced from the XP-RC/MS measurements are in agreement with the conclusions of the intact-mass analysis supplemented by limited charge reduction, suggesting that the latter technique can be employed in situations when fast assessment of protein heterogeneity is needed (e.g., process analytical technology applications).
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Yang Yang
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Jake W Pawlowski
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Ian J Carrick
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
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18
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Clinical Interest of Serum Alpha-2 Macroglobulin, Apolipoprotein A1, and Haptoglobin in Patients with Non-Alcoholic Fatty Liver Disease, with and without Type 2 Diabetes, before or during COVID-19. Biomedicines 2022; 10:biomedicines10030699. [PMID: 35327501 PMCID: PMC8945355 DOI: 10.3390/biomedicines10030699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 02/04/2023] Open
Abstract
In patients with non-alcoholic fatty liver disease (NAFLD) with or without type 2 diabetes mellitus (T2DM), alpha-2 macroglobulin (A2M), apolipoprotein A1 (ApoA1), and haptoglobin are associated with the risk of liver fibrosis, inflammation (NASH), and COVID-19. We assessed if these associations were worsened by T2DM after adjustment by age, sex, obesity, and COVID-19. Three datasets were used: the “Control Population”, which enabled standardization of protein serum levels according to age and sex (N = 27,382); the “NAFLD-Biopsy” cohort for associations with liver features (N = 926); and the USA “NAFLD-Serum” cohort for protein kinetics before and during COVID-19 (N = 421,021). The impact of T2DM was assessed by comparing regression curves adjusted by age, sex, and obesity for the liver features in “NAFLD-Biopsy”, and before and during COVID-19 pandemic peaks in “NAFLD-Serum”. Patients with NAFLD without T2DM, compared with the values of controls, had increased A2M, decreased ApoA1, and increased haptoglobin serum levels. In patients with both NAFLD and T2DM, these significant mean differences were magnified, and even more during the COVID-19 pandemic in comparison with the year 2019 (all p < 0.001), with a maximum ApoA1 decrease of 0.21 g/L in women, and a maximum haptoglobin increase of 0.17 g/L in men. In conclusion, T2DM is associated with abnormal levels of A2M, ApoA1, and haptoglobin independently of NAFLD, age, sex, obesity, and COVID-19.
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19
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Gazi I, Franc V, Tamara S, van Gool MP, Huppertz T, Heck AJ. Identifying glycation hot-spots in bovine milk proteins during production and storage of skim milk powder. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P. Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140735. [PMID: 34742912 DOI: 10.1016/j.bbapap.2021.140735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
Methods of structural mass spectrometry have become more popular to study protein structure and dynamics. Among them, fast photochemical oxidation of proteins (FPOP) has several advantages such as irreversibility of modifications and more facile determination of the site of modification with single residue resolution. In the present study, FPOP analysis was applied to study the hemoglobin (Hb) - haptoglobin (Hp) complex allowing identification of respective regions altered upon the complex formation. FPOP footprinting using a timsTOF Pro mass spectrometer revealed structural information for 84 and 76 residues in Hp and Hb, respectively, including statistically significant differences in the modification extent below 0.3%. The most affected residues upon complex formation were Met76 and Tyr140 in Hbα, and Tyr280 and Trp284 in Hpβ. The data allowed determination of amino acids directly involved in Hb - Hp interactions and those located outside of the interaction interface yet affected by the complex formation. Also, previously modeled interaction between Hb βTrp37 and Hp βPhe292 was not confirmed by our data. Data are available via ProteomeXchange with identifier PXD021621.
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Affiliation(s)
- Dmitry S Loginov
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Orekhovich Institute of Biomedical Chemistry, Pogodinskaja str. 10, 119191 Moscow, Russia.
| | - Jan Fiala
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic; Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Peter Brechlin
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Gary Kruppa
- Bruker s.r.o., Prazakova 60, 619 00, Brno, Czech Republic
| | - Petr Novak
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic.
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21
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Lai SH, Tamara S, Heck AJ. Single-particle mass analysis of intact ribosomes by mass photometry and Orbitrap-based charge detection mass spectrometry. iScience 2021; 24:103211. [PMID: 34712917 PMCID: PMC8529500 DOI: 10.1016/j.isci.2021.103211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022] Open
Abstract
Standard methods for mass analysis measure ensembles of thousand to millions of molecules. This approach enables analysis of monodisperse recombinant proteins, whereas some heterogeneous protein assemblies pose a significant challenge, whereby co-occurring stoichiometries, sub-complexes, and modifications hamper analysis using native mass spectrometry. To tackle the challenges posed by mass heterogeneity, single-particle methods may come to the rescue. Recently, two such approaches have been introduced, namely, mass photometry (MP) and Orbitrap-based charge detection mass spectrometry (CDMS). Both methods assess masses of individual molecules, albeit adhering to distinct physical principles. To evaluate these methods side by side, we analyzed a set of ribosomal particles, representing polydisperse ribonucleoprotein assemblies in the MDa range. MP and CDMS provide accurate masses for intact ribosomes and enable quantitative analysis of concomitant distinct particles within each ribosome sample. Here, we discuss pros and cons of these single-molecule techniques, also in the context of other techniques used for mass analysis.
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Affiliation(s)
- Szu-Hsueh Lai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Podzolkov VI, Dragomiretskaya NA, Beliaev IG, Kucherova JS, Kazadaeva AV. Endothelial Microvascular Dysfunction and Its Relationship with Haptoglobin Levels in Patients with Different Phenotypes of Chronic Heart Failure. RATIONAL PHARMACOTHERAPY IN CARDIOLOGY 2021. [DOI: 10.20996/1819-6446-2021-10-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aim. To study the relationship between the level of haptoglobin and the main indicators of microcirculation (MC) in patients with different phenotypes of chronic heart failure (CHF).Materials and methods. Patients with different phenotypes of functional class II-IV chronic heart failure according to NYHA (n=80) underwent a general clinical examination, determination of the serum haptoglobin level by enzyme-linked immunosorbent assay, as well as an assessment of the MC state on the medial surface of the upper third of the leg by laser Doppler flowmetry (LDF).Results. Patients with CHF included patients with preserved left ventricular ejection fraction (HFpEF; n=27, intermediate ejection fraction (HFmrEF; n=25) and reduced ejection fraction (HFrEF; n=28). The median value of haptoglobin in the HFpEF group was 1387.6 [ 747.5; 1946.9] mg/l, in the HFmrEF group was 1583.4 [818.9; 2201.4] mg/l, in the HFrEF group was 968.5 [509.5; 1324.4] mg/l. Correlation analysis revealed statistically significant relationships between haptoglobin and the amplitudes of the endothelial frequency range (Ae) in the groups of HFmrEF (r=-0.628, 95% confidence interval [CI] -0.256; -0.825, p=0.003) and HFrEF (r=-0.503, 95% CI -0.089; -0.803, p=0.02). A negative relationship between the haptoglobin level and Kv and σ was revealed, as well as a formula for calculating the value of haptoglobin was obtained, which is predicted on the basis of the amplitude index of the endothelial frequency range: [haptoglobin]=1787-(4053×Ae).Conclusion. The multifactorial effect of haptoglobin is realized in the central and peripheral mechanisms of MC regulation. Low values of haptoglobin in blood plasma should be considered as a potential marker for the development of complications and used in a comprehensive assessment of the state of patients with CHF. Evaluation of the diagnostic and prognostic significance of haptoglobin, especially in patients with HFmrEF, requires further study.
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Affiliation(s)
- V. I. Podzolkov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | | | - I. G. Beliaev
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - Ju. S. Kucherova
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - A. V. Kazadaeva
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
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23
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Priest L, Peters JS, Kukura P. Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins. Chem Rev 2021; 121:11937-11970. [PMID: 34587448 PMCID: PMC8517954 DOI: 10.1021/acs.chemrev.1c00271] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 02/02/2023]
Abstract
Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.
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Affiliation(s)
| | | | - Philipp Kukura
- Physical and Theoretical
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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24
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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25
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Soltermann F, Struwe WB, Kukura P. Label-free methods for optical in vitro characterization of protein-protein interactions. Phys Chem Chem Phys 2021; 23:16488-16500. [PMID: 34342317 PMCID: PMC8359934 DOI: 10.1039/d1cp01072g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
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26
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Lebede M, Di Marco F, Esser-Skala W, Hennig R, Wohlschlager T, Huber CG. Exploring the Chemical Space of Protein Glycosylation in Noncovalent Protein Complexes: An Expedition along Different Structural Levels of Human Chorionic Gonadotropin by Employing Mass Spectrometry. Anal Chem 2021; 93:10424-10434. [PMID: 34288669 PMCID: PMC8340079 DOI: 10.1021/acs.analchem.1c02199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Modern analytical
approaches employing high-resolution mass spectrometry
(MS) facilitate the generation of a vast amount of structural data
of highly complex glycoproteins. Nevertheless, systematic interpretation
of this data at different structural levels remains an analytical
challenge. The glycoprotein utilized as a model system in this study,
human chorionic gonadotropin (hCG), exists as a heterodimer composed
of two heavily glycosylated subunits. In order to unravel the multitude
of glycoforms of recombinant hCG (drug product Ovitrelle), we combine
established techniques, such as released glycan and glycopeptide analysis,
with novel approaches employing high-performance liquid chromatography-mass
spectrometry (HPLC-MS) to characterize protein subunits and native
MS to analyze the noncovalent hCG complex. Starting from the deconvoluted
mass spectrum of dimeric hCG comprising about 50 signals, it was possible
to explore the chemical space of hCG glycoforms and elucidate the
complexity that hides behind just 50 signals. Systematic, stepwise
integration of data obtained at the levels of released glycans, glycopeptides,
and subunits using a computational annotation tool allowed us to reveal
1031 underlying glycoforms. Additionally, critical quality attributes
such as sialylation and core fucosylation were compared for two batches
of Ovitrelle to assess the potential product variability.
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Affiliation(s)
- Maximilian Lebede
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Fiammetta Di Marco
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Wolfgang Esser-Skala
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Department of Biosciences, Computational Systems Biology Group, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - René Hennig
- glyXera GmbH, Brenneckestraße 20 - ZENIT, 39120 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Therese Wohlschlager
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G Huber
- Department of Biosciences, Bioanalytical Research Labs, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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27
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Abstract
Haptoglobin (Hp) is a blood plasma glycoprotein that binds free hemoglobin (Hb) and plays a critical role in tissue protection and the prevention of oxidative damage. In addition, it has a number of regulatory functions. Haptoglobin is an acute phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. Only in humans, the Hp gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of Hp, homozygous Hp1-1 and Hp2-2, and heterozygous Hp2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual's predisposition to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting of the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the Hp β-chain has become the main direction in the study of pathological processes, including malignant neoplasms. Many studies are focused on the identification of PTM and changes in the level of the α2-chain of this protein in pathology. These characteristics of Hp indicate the possibility of the existence of this protein as different proteoforms, probably with different functions. This review is devoted to the description of the structural and functional diversity of Hp and its potential use as a biomarker of various pathologies.
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Affiliation(s)
- S N Naryzhny
- Institute of Biomedical Chemistry, Moscow, Russia; Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
| | - O K Legina
- Petersburg Institute of Nuclear Physics B.P. Konstantinova National Research Center "Kurchatov Institute", Gatchina, Russia
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28
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Yang Y, Niu C, Bobst CE, Kaltashov IA. Charge Manipulation Using Solution and Gas-Phase Chemistry to Facilitate Analysis of Highly Heterogeneous Protein Complexes in Native Mass Spectrometry. Anal Chem 2021; 93:3337-3342. [PMID: 33566581 PMCID: PMC8514162 DOI: 10.1021/acs.analchem.0c05249] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity is a significant challenge complicating (and in some cases making impossible) electrospray ionization mass spectrometry (ESI MS) analysis of noncovalent complexes comprising structurally heterogeneous biopolymers. The broad mass distribution exhibited by such species inevitably gives rise to overlapping ionic signals representing different charge states, resulting in a continuum spectrum with no discernible features that can be used to assign ionic charges and calculate their masses. This problem can be circumvented by using limited charge reduction, which utilizes gas-phase chemistry to induce charge-transfer reactions within ionic populations selected within narrow m/z windows, thereby producing well-defined and readily interpretable charge ladders. However, the ionic signal in native MS typically populates high m/z regions of mass spectra, which frequently extend beyond the precursor ion isolation limits of most commercial mass spectrometers. While the ionic signal of single-chain proteins can be shifted to lower m/z regions simply by switching to a denaturing solvent, this approach cannot be applied to noncovalent assemblies due to their inherent instability under denaturing conditions. An alternative approach explored in this work relies on adding supercharging reagents to protein solutions as a means of increasing the extent of multiple charging of noncovalent complexes in ESI MS without compromising their integrity. This shifts the ionic signal down the m/z scale to the region where ion selection and isolation can be readily accomplished with a front-end quadrupole, followed by limited charge reduction of the isolated ionic population. The feasibility of the new approach is demonstrated using noncovalent complexes formed by hemoglobin with structurally heterogeneous haptoglobin.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
| | | | - Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
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29
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Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V. Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Res 2021; 49:444-457. [PMID: 33330919 PMCID: PMC7797070 DOI: 10.1093/nar/gkaa1187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Steffi Jimmy
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Pavel Kudrin
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Fabio Trebini
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, Akita, 010-0874, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium.,WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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30
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Čaval T, Lin YH, Varkila M, Reiding KR, Bonten MJM, Cremer OL, Franc V, Heck AJR. Glycoproteoform Profiles of Individual Patients' Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode. Front Immunol 2021; 11:608466. [PMID: 33519818 PMCID: PMC7840657 DOI: 10.3389/fimmu.2020.608466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/24/2020] [Indexed: 01/08/2023] Open
Abstract
Sepsis and septic shock remain the leading causes of death in intensive care units (ICUs), yet the pathogenesis originating from the inflammatory response during sepsis remains ambiguous. Acute-phase proteins are typically highly glycosylated, and the nature of the glycans have been linked to the incidence and severity of such inflammatory responses. To further build upon these findings we here monitored, the longitudinal changes in the plasma proteome and, in molecular detail, glycoproteoform profiles of alpha-1-antichymotrypsin (AACT) extracted from plasma of ten individual septic patients. For each patient we included four different time-points, including post-operative (before sepsis) and following discharge from the ICU. We isolated AACT from plasma depleted for albumin, IgG and serotransferrin and used high-resolution native mass spectrometry to qualitatively and quantitatively monitor the multifaceted glycan microheterogeneity of desialylated AACT, which allowed us to monitor how changes in the glycoproteoform profiles reflected the patient's physiological state. Although we observed a general trend in the remodeling of the AACT glycoproteoform profiles, e.g. increased fucosylation and branching/LacNAc elongation, each patient exhibited unique features and responses, providing a resilient proof-of-concept for the importance of personalized longitudinal glycoproteoform profiling. Importantly, we observed that the AACT glycoproteoform changes induced by sepsis did not readily subside after discharge from ICU.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Yu-Hsien Lin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Meri Varkila
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Karli R. Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Marc J. M. Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Olaf L. Cremer
- Department of Intensive Care Medicine, University Medical Center Utrecht, Utrecht, Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
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31
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Naryzny SN, Legina OK. Haptoglobin as a Biomarker. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES B, BIOMEDICAL CHEMISTRY 2021; 15:184-198. [PMID: 34422226 PMCID: PMC8365284 DOI: 10.1134/s1990750821030069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
Haptoglobin (Hp) is a glycoprotein that binds free hemoglobin (Hb) in plasma and plays a critical role in tissue protection and prevention of oxidative damage. Besides, it has some regulatory functions. Haptoglobin is an acute-phase protein, its concentration in plasma changes in pathology, and the test for its concentration is part of normal clinical practice. Haptoglobin is a conservative protein synthesized mainly in the liver and lungs and is the subject of research as a potential biomarker of many diseases, including various forms of malignant neoplasms. Haptoglobin has several unique biophysical characteristics. The human Нр gene is polymorphic, has three structural alleles that control the synthesis of three major phenotypes of haptoglobin: homozygous Нр1-1 and Нр2-2, and heterozygous Нр2-1, determined by a combination of allelic variants that are inherited. Numerous studies indicate that the phenotype of haptoglobin can be used to judge the individual predisposition of a person to various diseases. In addition, Hp undergoes various post-translational modifications (PTMs). These are structural transformations (removal of the signal peptide, cutting off the Pre-Hp precursor molecule into two subunits, α and β, limited proteolysis of α-chains, formation of disulfide bonds, multimerization), as well as chemical modifications of α-chains and glycosylation of the β-chain. Glycosylation of the β-chain of haptoglobin at four Asn sites is the most important variable PTM that regulates the structure and function of the glycoprotein. The study of modified oligosaccharides of the β-chain of Hp has become the main direction in the study of pathological processes, including malignant neoplasms. These characteristics indicate the possibility of the existence of Hp in the form of a multitude of proteoforms, probably performing different functions. This review is devoted to the description of the structural and functional diversity and the potential use of Hp as a biomarker of various pathologies.
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Affiliation(s)
- S. N. Naryzny
- Institute of Biomedical Chemistry, ul. Pogodinskaya 10, 119121 Moscow, Russia ,St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
| | - O. K. Legina
- St-Petersburg Nuclear Physics Institute (PNPI) NRC Kurchatov Institute, Orlova Roshcha 1, 188300 Gatchina, Leningrad oblast Russia
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