1
|
McDonald AG, Mariethoz J, Davey GP, Lisacek F. In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis. Sci Rep 2022; 12:10846. [PMID: 35760821 DOI: 10.1038/s41598-022-14260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/03/2022] [Indexed: 11/09/2022] Open
Abstract
Human milk oligosaccharides (HMOs) form the third most abundant component of human milk and are known to convey several benefits to the neonate, including protection from viral and bacterial pathogens, training of the immune system, and influencing the gut microbiome. As HMO production during lactation is driven by enzymes that are common to other glycosylation processes, we adapted a model of mucin-type GalNAc-linked glycosylation enzymes to act on free lactose. We identified a subset of 11 enzyme activities that can account for 206 of 226 distinct HMOs isolated from human milk and constructed a biosynthetic reaction network that identifies 5 new core HMO structures. A comparison of monosaccharide compositions demonstrated that the model was able to discriminate between two possible groups of intermediates between major subnetworks, and to assign possible structures to several previously uncharacterised HMOs. The effect of enzyme knockouts is presented, identifying β-1,4-galactosyltransferase and β-1,3-N-acetylglucosaminyltransferase as key enzyme activities involved in the generation of the observed HMO glycosylation patterns. The model also provides a synthesis chassis for the most common HMOs found in lactating mothers.
Collapse
|
2
|
Puranik A, Saldanha M, Chirmule N, Dandekar P, Jain R. Advanced strategies in glycosylation prediction and control during biopharmaceutical development: Avenues toward Industry 4.0. Biotechnol Prog 2022; 38:e3283. [PMID: 35752935 DOI: 10.1002/btpr.3283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/31/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022]
Abstract
Glycosylation has been shown to define the safety and efficacy of biopharmaceuticals, thus classified as a critical quality attribute. However, controlling glycan heterogeneity has always been a major challenge owing to the multi-variate factors that govern the glycosylation process. Conventional approaches for controlling glycosylation such as gene editing and metabolic control have succeeded in obtaining desired glycan profiles in accordance with the Quality by Design paradigm. Nonetheless, the development of smart algorithms and omics-enabled complete cell characterization have made it possible to predict glycan profiles beforehand, and manipulate process variables accordingly. This review thus discusses the various approaches available for control and prediction of glycosylation in biopharmaceuticals. Further, the futuristic goal of integrating such technologies is discussed in order to attain an automated and digitized continuous bioprocess for control of glycosylation. Given, control of a process as complex as glycosylation requires intense monitoring intervention, we examine the current technologies that enable automation. Finally, we discuss the challenges and the technological gap that currently limits incorporation of an automated process in routine bio-manufacturing, with a glimpse into the economic bearing. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Amita Puranik
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Marianne Saldanha
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
| | | | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai, India
| |
Collapse
|
3
|
Zhang L, Wang M, Castan A, Hjalmarsson H, Chotteau V. Probabilistic model by Bayesian network for the prediction of antibody glycosylation in perfusion and fed-batch cell cultures. Biotechnol Bioeng 2021; 118:3447-3459. [PMID: 33788254 DOI: 10.1002/bit.27769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/01/2023]
Abstract
Glycosylation is a critical quality attribute of therapeutic monoclonal antibodies (mAbs). The glycan pattern can have a large impact on the immunological functions, serum half-life and stability. The medium components and cultivation parameters are known to potentially influence the glycosylation profile. Mathematical modelling provides a strategy for rational design and control of the upstream bioprocess. However, the kinetic models usually contain a very large number of unknown parameters, which limit their practical applications. In this article, we consider the metabolic network of N-linked glycosylation as a Bayesian network (BN) and calculate the fluxes of the glycosylation process as joint probability using the culture parameters as inputs. The modelling approach is validated with data of different Chinese hamster ovary cell cultures in pseudo perfusion, perfusion, and fed batch cultures, all showing very good predictive capacities. In cases where a large number of cultivation parameters is available, it is shown here that principal components analysis can efficiently be employed for a dimension reduction of the inputs compared to Pearson correlation analysis and feature importance by decision tree. The present study demonstrates that BN model can be a powerful tool in upstream process and medium development for glycoprotein productions.
Collapse
Affiliation(s)
- Liang Zhang
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH Royal Institute of Technology, Stockholm, Sweden
| | - MingLiang Wang
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH Royal Institute of Technology, Stockholm, Sweden.,Division of Decision and Control System, School of Electrical Engineering and Computer Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Håkan Hjalmarsson
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH Royal Institute of Technology, Stockholm, Sweden.,Division of Decision and Control System, School of Electrical Engineering and Computer Science, KTH-Royal Institute of Technology, Stockholm, Sweden.,Digital Futures - KTH Royal Institute of Technology, Stockholm, Sweden
| | - Veronique Chotteau
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH Royal Institute of Technology, Stockholm, Sweden.,Digital Futures - KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
4
|
Stach CS, McCann MG, O’Brien CM, Le TS, Somia N, Chen X, Lee K, Fu HY, Daoutidis P, Zhao L, Hu WS, Smanski M. Model-Driven Engineering of N-Linked Glycosylation in Chinese Hamster Ovary Cells. ACS Synth Biol 2019; 8:2524-2535. [PMID: 31596566 DOI: 10.1021/acssynbio.9b00215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chinese hamster ovary (CHO) cells are used for industrial production of protein-based therapeutics (i.e., "biologics"). Here we describe a method for combining systems-level kinetic models with a synthetic biology platform for multigene overexpression to rationally perturb N-linked glycosylation. Specifically, we sought to increase galactose incorporation on a secreted Immunoglobulin G (IgG) protein. We rationally design, build, and test a total of 23 transgenic cell pools that express single or three-gene glycoengineering cassettes comprising a total of 100 kilobases of engineered DNA sequence. Through iterative engineering and model refinement, we rationally increase the fraction of bigalactosylated glycans five-fold from 11.9% to 61.9% and simultaneously decrease the glycan heterogeneity on the secreted IgG. Our approach allows for rapid hypothesis testing and identification of synergistic behavior from genetic perturbations by bridging systems and synthetic biology.
Collapse
Affiliation(s)
| | | | | | | | | | - Xinning Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
| | | | | | | | - Liang Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
| | | | | |
Collapse
|
5
|
Arigoni-Affolter I, Scibona E, Lin CW, Brühlmann D, Souquet J, Broly H, Aebi M. Mechanistic reconstruction of glycoprotein secretion through monitoring of intracellular N-glycan processing. Sci Adv 2019; 5:eaax8930. [PMID: 31807707 PMCID: PMC6881162 DOI: 10.1126/sciadv.aax8930] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/18/2019] [Indexed: 05/06/2023]
Abstract
N-linked glycosylation plays a fundamental role in determining the thermodynamic stability of proteins and is involved in multiple key biological processes. The mechanistic understanding of the intracellular machinery responsible for the stepwise biosynthesis of N-glycans is still incomplete due to limited understanding of in vivo kinetics of N-glycan processing along the secretory pathway. We present a glycoproteomics approach to monitor the processing of site-specific N-glycans in CHO cells. On the basis of a model-based analysis of structure-specific turnover rates, we provide a kinetic description of intracellular N-glycan processing along the entire secretory pathway. This approach refines and further extends the current knowledge on N-glycans biosynthesis and provides a basis to quantify alterations in the glycoprotein processing machinery.
Collapse
Affiliation(s)
| | - Ernesto Scibona
- Institute for Chemical and Bioengineering, Department of Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - David Brühlmann
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Jonathan Souquet
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Hervé Broly
- Merck Healthcare, Biotech Process Sciences, Route de Fenil 25, 1804 Corsier-sur-Vevey, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
- Corresponding author.
| |
Collapse
|
6
|
Le T, O’Brien C, Gupta U, Sousa G, Daoutidis P, Hu W. An integrated platform for mucin‐type
O
‐glycosylation network generation and visualization. Biotechnol Bioeng 2019; 116:1341-1354. [DOI: 10.1002/bit.26952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 12/19/2018] [Accepted: 02/08/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Tung Le
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| | - Conor O’Brien
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| | - Udit Gupta
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| | - Guilherme Sousa
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| | - Prodromos Daoutidis
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| | - Wei‐Shou Hu
- Department of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis Minnesota
| |
Collapse
|
7
|
Sumit M, Dolatshahi S, Chu AHA, Cote K, Scarcelli JJ, Marshall JK, Cornell RJ, Weiss R, Lauffenburger DA, Mulukutla BC, Figueroa B. Dissecting N-Glycosylation Dynamics in Chinese Hamster Ovary Cells Fed-batch Cultures using Time Course Omics Analyses. iScience 2019; 12:102-120. [PMID: 30682623 PMCID: PMC6352710 DOI: 10.1016/j.isci.2019.01.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/24/2022] Open
Abstract
N-linked glycosylation affects the potency, safety, immunogenicity, and pharmacokinetic clearance of several therapeutic proteins including monoclonal antibodies. A robust control strategy is needed to dial in appropriate glycosylation profile during the course of cell culture processes accurately. However, N-glycosylation dynamics remains insufficiently understood owing to the lack of integrative analyses of factors that influence the dynamics, including sugar nucleotide donors, glycosyltransferases, and glycosidases. Here, an integrative approach involving multi-dimensional omics analyses was employed to dissect the temporal dynamics of glycoforms produced during fed-batch cultures of CHO cells. Several pathways including glycolysis, tricarboxylic citric acid cycle, and nucleotide biosynthesis exhibited temporal dynamics over the cell culture period. The steps involving galactose and sialic acid addition were determined as temporal bottlenecks. Our results show that galactose, and not manganese, is able to mitigate the temporal bottleneck, despite both being known effectors of galactosylation. Furthermore, sialylation is limited by the galactosylated precursors and autoregulation of cytidine monophosphate-sialic acid biosynthesis. Major glycosylated species exhibit temporal dynamics during fed-batch processes Key metabolic pathways linked to N-glycosylation exhibit significant temporal dynamics Dynamics in nucleotide sugar donors (NSDs) directly influences glycoform heterogeneity Glycoform heterogeneity can be mitigated by supplementing NSD biosynthetic precursors
Collapse
Affiliation(s)
- Madhuresh Sumit
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Sepideh Dolatshahi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - An-Hsiang Adam Chu
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Kaffa Cote
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - John J Scarcelli
- Cell Line Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Jeffrey K Marshall
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Richard J Cornell
- Analytical Research and Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bhanu Chandra Mulukutla
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA.
| | - Bruno Figueroa
- Culture Process Development, Bio Therapeutics Pharmaceutical Sciences, Pfizer, 1 Burtt Road, Andover, MA 01810, USA
| |
Collapse
|
8
|
Zhang L, Castan A, Stevenson J, Chatzissavidou N, Vilaplana F, Chotteau V. Combined effects of glycosylation precursors and lactate on the glycoprofile of IgG produced by CHO cells. J Biotechnol 2019; 289:71-79. [DOI: 10.1016/j.jbiotec.2018.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 12/29/2022]
|
9
|
Gupta U, Le T, Hu WS, Bhan A, Daoutidis P. Automated network generation and analysis of biochemical reaction pathways using RING. Metab Eng 2018; 49:84-93. [DOI: 10.1016/j.ymben.2018.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
|
10
|
Hossler P, Chumsae C, Racicot C, Ouellette D, Ibraghimov A, Serna D, Mora A, McDermott S, Labkovsky B, Scesney S, Grinnell C, Preston G, Bose S, Carrillo R. Arabinosylation of recombinant human immunoglobulin-based protein therapeutics. MAbs 2017; 9:715-734. [PMID: 28375048 PMCID: PMC5419081 DOI: 10.1080/19420862.2017.1294295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein glycosylation is arguably the paramount post-translational modification on recombinant glycoproteins, and highly cited in the literature for affecting the physiochemical properties and the efficacy of recombinant glycoprotein therapeutics. Glycosylation of human immunoglobulins follows a reasonably well-understood metabolic pathway, which gives rise to a diverse range of asparagine-linked (N-linked), or serine/threonine-linked (O-linked) glycans. In N-linked glycans, fucose levels have been shown to have an inverse relationship with the degree of antibody-dependent cell-mediated cytotoxicity, and high mannose levels have been implicated in potentially increasing immunogenicity and contributing to less favorable pharmacokinetic profiles. Here, we demonstrate a novel approach to potentially reduce the presence of high-mannose species in recombinant human immunoglobulin preparations, as well as facilitate an approximate 100% replacement of fucosylation with arabinosylation in Chinese hamster ovary cell culture through media supplementation with D-arabinose, an uncommonly used mammalian cell culture sugar substrate. The replacement of fucose with arabinose was very effective and practical to implement, since no cell line engineering or cellular adaptation strategies were required. Arabinosylated recombinant IgGs and the accompanying reduction in high mannose glycans, facilitated a reduction in dendritic cell uptake, increased FcγRIIIa signaling, and significantly increased the levels of ADCC. These aforementioned effects were without any adverse changes to various structural or functional attributes of multiple recombinant human antibodies and a bispecific DVD-Ig. Protein arabinosylation represents an expansion of the N-glycan code in mammalian expressed glycoproteins.
Collapse
Affiliation(s)
- Patrick Hossler
- a Process Sciences, AbbVie Bioresearch Center , Worcester , MA , USA
| | | | | | - David Ouellette
- a Process Sciences, AbbVie Bioresearch Center , Worcester , MA , USA
| | | | - Daniel Serna
- b Preclinical Safety, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Alessandro Mora
- a Process Sciences, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Sean McDermott
- a Process Sciences, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Boris Labkovsky
- c Discovery-Biologics, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Susanne Scesney
- b Preclinical Safety, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Christine Grinnell
- d Drug Metabolism and Pharmacokinetics, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Gregory Preston
- d Drug Metabolism and Pharmacokinetics, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Sahana Bose
- c Discovery-Biologics, AbbVie Bioresearch Center , Worcester , MA , USA
| | - Ralf Carrillo
- e Preformulation, AbbVie Bioresearch Center , Worcester , MA , USA
| |
Collapse
|
11
|
Galleguillos SN, Ruckerbauer D, Gerstl MP, Borth N, Hanscho M, Zanghellini J. What can mathematical modelling say about CHO metabolism and protein glycosylation? Comput Struct Biotechnol J 2017; 15:212-221. [PMID: 28228925 PMCID: PMC5310201 DOI: 10.1016/j.csbj.2017.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 11/15/2022] Open
Abstract
Chinese hamster ovary cells have been in the spotlight for process optimization in recent years, due to being the major, long established cell factory for the production of recombinant proteins. A deep, quantitative understanding of CHO metabolism and mechanisms involved in protein glycosylation has proven to be attainable through the development of high throughput technologies. Here we review the most notable accomplishments in the field of modelling CHO metabolism and protein glycosylation.
Collapse
Affiliation(s)
- Sarah N Galleguillos
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - David Ruckerbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Matthias P Gerstl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Michael Hanscho
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Jürgen Zanghellini
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre of Industrial Biotechnology, Vienna, Austria
| |
Collapse
|
12
|
Hossler P, Racicot C, Chumsae C, Mcdermott S, Cochran K. Cell culture media supplementation of infrequently used sugars for the targeted shifting of protein glycosylation profiles. Biotechnol Prog 2017; 33:511-22. [DOI: 10.1002/btpr.2429] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/10/2016] [Indexed: 11/07/2022]
|
13
|
Zhang P, Woen S, Wang T, Liau B, Zhao S, Chen C, Yang Y, Song Z, Wormald MR, Yu C, Rudd PM. Challenges of glycosylation analysis and control: an integrated approach to producing optimal and consistent therapeutic drugs. Drug Discov Today 2016; 21:740-65. [DOI: 10.1016/j.drudis.2016.01.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/22/2015] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
|
14
|
Abstract
The presence of α2,6-sialic acids on the Fc N-glycan provides anti-inflammatory properties to the IgGs through a mechanism that remains unclear. Fc-sialylated IgGs are rare in humans as well as in industrial host cell lines such as Chinese hamster ovary (CHO) cells. Facilitated access to well-characterized α2,6-sialylated IgGs would help elucidate the mechanism of this intriguing IgG's effector function. This study presents a method for the efficient Fc glycan α2,6-sialylation of a wild-type and a F243A IgG1 mutant by transient co-expression with the human α2,6-sialyltransferase 1 (ST6) and β1,4-galactosyltransferase 1 (GT) in CHO cells. Overexpression of ST6 alone only had a moderate effect on the glycoprofiles, whereas GT alone greatly enhanced Fc-galactosylation, but not sialylation. Overexpression of both GT and ST6 was necessary to obtain a glycoprofile dominated by α2,6-sialylated glycans in both antibodies. The wild-type was composed of the G2FS(6)1 glycan (38%) with remaining unsialylated glycans, while the mutant glycoprofile was essentially composed of G2FS(6)1 (25%), G2FS(3,6)2 (16%) and G2FS(6,6)2 (37%). The α2,6-linked sialic acids represented over 85% of all sialic acids in both antibodies. We discuss how the limited sialylation level in the wild-type IgG1 expressed alone or with GT results from the glycan interaction with Fc's amino acid residues or from intrinsic galactosyl- and sialyl-transferases substrate specificities.
Collapse
Key Words
- B4GALT1
- CHO cells
- ECL, Erythrina Cristagalli lectin
- GT, β1,4-galactosyltransferase 1
- HILIC, hydrophilic interaction liquid chromatography
- IgG1
- LC-ESI-MS, liquid chromatography coupled to electrospray ionization mass spectrometry
- MAL-II, Maackia Amurensis lectin II
- N-glycosylation
- PEI, polyethylenimine
- SIAT1
- SNA, Sambucus Nigra agglutinin
- ST6, α2,6-sialyltransferase 1
- TZM, trastuzumab (Herceptin®)
- cIEF, capillary zone electrophoresis isoelectric focusing
- mAbs, monoclonal antibodies
- sialylation
- transfection
- α2,3SA, α2,3-linked sialic acid
- α2,6SA, α2,6-linked sialic acid
Collapse
Affiliation(s)
- Céline Raymond
- a Human Health Therapeutics Portfolio; National Research Council of Canada ; Montreal , Canada
| | | | | | | | | | | |
Collapse
|
15
|
Sha S, Agarabi C, Brorson K, Lee DY, Yoon S. N-Glycosylation Design and Control of Therapeutic Monoclonal Antibodies. Trends Biotechnol 2016; 34:835-846. [PMID: 27016033 DOI: 10.1016/j.tibtech.2016.02.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/31/2022]
Abstract
The N-linked glycan profiles on recombinant monoclonal antibody therapeutics significantly affect antibody biological functions and are largely determined by host cell genotypes and culture conditions. A key step in bioprocess development for monoclonal antibodies (mAbs) involves optimization and control of N-glycan profiles. With pressure from pricing and biosimilars looming, more efficient and effective approaches are sought in the field of glycoengineering. Metabolic studies and mathematical modeling are two such approaches that optimize bioprocesses by better understanding and predicting glycosylation. In this review, we summarize a group of strategies currently used for glycan profile modulation and control. Metabolic analysis and mathematical modeling are then explored with an emphasis on how these two techniques can be utilized to advance glycoengineering.
Collapse
Affiliation(s)
- Sha Sha
- Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01850, USA
| | - Cyrus Agarabi
- Division of Biotechnology Review and Research II, Office of Biotechnology Products, OPQ, CDER, FDA, Silver Spring, MD, USA
| | - Kurt Brorson
- Division of Biotechnology Review and Research II, Office of Biotechnology Products, OPQ, CDER, FDA, Silver Spring, MD, USA
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, Singapore 117585, Singapore
| | - Seongkyu Yoon
- Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01850, USA.
| |
Collapse
|
16
|
Ling WL. Development of protein-free medium for therapeutic protein production in mammalian cells: recent advances and perspectives. ACTA ACUST UNITED AC 2015; 3:215-26. [DOI: 10.4155/pbp.15.8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
17
|
Le H, Vishwanathan N, Jacob NM, Gadgil M, Hu WS. Cell line development for biomanufacturing processes: recent advances and an outlook. Biotechnol Lett 2015; 37:1553-64. [PMID: 25971160 DOI: 10.1007/s10529-015-1843-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/29/2015] [Indexed: 12/20/2022]
Abstract
At the core of a biomanufacturing process for recombinant proteins is the production cell line. It influences the productivity and product quality. Its characteristics also dictate process development, as the process is optimized to complement the producing cell to achieve the target productivity and quality. Advances in the past decade, from vector design to cell line screening, have greatly expanded our capability to attain producing cell lines with certain desired traits. Increasing availability of genomic and transcriptomic resources for industrially important cell lines coupled with advances in genome editing technology have opened new avenues for cell line development. These developments are poised to help biosimilar manufacturing, which requires targeting pre-defined product quality attributes, e.g., glycoform, to match the innovator's range. This review summarizes recent advances and discusses future possibilities in this area.
Collapse
|
18
|
Hossler P, McDermott S, Racicot C, Chumsae C, Raharimampionona H, Zhou Y, Ouellette D, Matuck J, Correia I, Fann J, Li J. Cell culture media supplementation of uncommonly used sugars sucrose and tagatose for the targeted shifting of protein glycosylation profiles of recombinant protein therapeutics. Biotechnol Prog 2014; 30:1419-31. [DOI: 10.1002/btpr.1968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/04/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Patrick Hossler
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - Sean McDermott
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | | | | | | | - Yu Zhou
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - David Ouellette
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - Joseph Matuck
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - Ivan Correia
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - John Fann
- Process Sciences-Cell Culture; AbbVie Inc.; Worcester MA 01605
| | - Jianmin Li
- Oncology Biologics; AbbVie Inc.; Redwood City CA 94063
| |
Collapse
|
19
|
Aghamohseni H, Ohadi K, Spearman M, Krahn N, Moo-Young M, Scharer JM, Butler M, Budman HM. Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody. J Biotechnol 2014; 186:98-109. [PMID: 25014402 DOI: 10.1016/j.jbiotec.2014.05.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/08/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Abstract
The impact of operating conditions on the glycosylation pattern of humanized camelid monoclonal antibody, EG2-hFc produced by Chinese hamster ovary (CHO) cells has been evaluated by a combination of experiments and modeling. Cells were cultivated under different levels of glucose and glutamine concentrations with the goal of investigating the effect of nutrient depletion levels and ammonia build up on the cell growth and the glycoprofiles of the monoclonal antibody (Mab). The effect of average pH reduction on glycosylation level during the entire culture time or during a specific time span was also investigated. The relative abundance of glycan structures was quantified by hydrophilic interaction liquid chromatography (HILIC) and the galactosylation index (GI) and the sialylation index (SI) were determined. Lower initial concentrations of glutamine resulted in lower glucose consumption and lower cell yield but increased GI and SI levels when compared to cultures started with higher initial glutamine levels. Similarly, reducing the average pH of culture resulted in lower growth but higher SI and GI levels. These findings indicate that there is a tradeoff between cell growth, resulting Mab productivity and the achievement of desirable higher glycosylation levels. A dynamic model, based on a metabolic flux analysis (MFA), is proposed to describe the metabolism of nutrients, cell growth and Mab productivity. Finally, existing software (GLYCOVIS) that describes the glycosylation pathways was used to illustrate the impact of extracellular species on the glycoprofiles.
Collapse
Affiliation(s)
| | - Kaveh Ohadi
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Maureen Spearman
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Natalie Krahn
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Murray Moo-Young
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Jeno M Scharer
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| | - Mike Butler
- Microbiology Department, University of Manitoba, Winnipeg, MB, Canada.
| | - Hector M Budman
- Chemical Engineering Department, University of Waterloo, Waterloo, ON, Canada.
| |
Collapse
|
20
|
Dall'Olio GM, Laayouni H, Luisi P, Sikora M, Montanucci L, Bertranpetit J. Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation. BMC Evol Biol 2012; 12:98. [PMID: 22731960 PMCID: PMC3426484 DOI: 10.1186/1471-2148-12-98] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 06/25/2012] [Indexed: 01/11/2023] Open
Abstract
Background Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment and innate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection are frequent on genes that are known to be at bifurcation points, and that are identified as being in key position by a network-level analysis such as MGAT3 and GCS1. Conclusions These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.
Collapse
Affiliation(s)
- Giovanni Marco Dall'Olio
- IBE, Institut de Biologia Evolutiva (UPF-CSIC), Parc de Recerca Biomèdica de Barcelona (PRBB), Dr, Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | | | | | | | | | | |
Collapse
|
21
|
Dall'Olio GM, Jassal B, Montanucci L, Gagneux P, Bertranpetit J, Laayouni H. The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. Glycobiology 2011; 21:1395-400. [PMID: 21199820 DOI: 10.1093/glycob/cwq215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Asparagine N-linked glycosylation is one of the most important forms of protein post-translational modification in eukaryotes and is one of the first metabolic pathways described at a biochemical level. Here, we report a new annotation of this pathway for the Human species, published after passing a peer-review process in Reactome. The new annotation presented here offers a high level of detail and provides references and descriptions for each reaction, along with integration with GeneOntology and other databases. The open-source approach of Reactome toward annotation encourages feedback from its users, making it easier to keep the annotation of this pathway updated with future knowledge. Reactome's web interface allows easy navigation between steps involved in the pathway to compare it with other pathways and resources in other scientific databases and to export it to BioPax and SBML formats, making it accessible for computational studies. This new entry in Reactome expands and complements the annotations already published in databases for biological pathways and provides a common reference to researchers interested in studying this important pathway in the human species. Finally, we discuss the status of the annotation of this pathway and point out which steps are worth further investigation or need better experimental validation.
Collapse
|
22
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006. Mass Spectrom Rev 2011; 30:1-100. [PMID: 20222147 DOI: 10.1002/mas.20265] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.
Collapse
Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
| |
Collapse
|
23
|
Hossler P. Protein glycosylation control in mammalian cell culture: past precedents and contemporary prospects. Adv Biochem Eng Biotechnol 2011; 127:187-219. [PMID: 22015728 DOI: 10.1007/10_2011_113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein glycosylation is a post-translational modification of paramount importance for the function, immunogenicity, and efficacy of recombinant glycoprotein therapeutics. Within the repertoire of post-translational modifications, glycosylation stands out as having the most significant proven role towards affecting pharmacokinetics and protein physiochemical characteristics. In mammalian cell culture, the understanding and controllability of the glycosylation metabolic pathway has achieved numerous successes. However, there is still much that we do not know about the regulation of the pathway. One of the frequent conclusions regarding protein glycosylation control is that it needs to be studied on a case-by-case basis since there are often conflicting results with respect to a control variable and the resulting glycosylation. In attempts to obtain a more multivariate interpretation of these potentially controlling variables, gene expression analysis and systems biology have been used to study protein glycosylation in mammalian cell culture. Gene expression analysis has provided information on how glycosylation pathway genes both respond to culture environmental cues, and potentially facilitate changes in the final glycoform profile. Systems biology has allowed researchers to model the pathway as well-defined, inter-connected systems, allowing for the in silico testing of pathway parameters that would be difficult to test experimentally. Both approaches have facilitated a macroscopic and microscopic perspective on protein glycosylation control. These tools have and will continue to enhance our understanding and capability of producing optimal glycoform profiles on a consistent basis.
Collapse
Affiliation(s)
- Patrick Hossler
- Abbott Laboratories, Abbott Bioresearch Center, Worcester, MA, 01605, USA,
| |
Collapse
|
24
|
Feng HT, Wong NSC, Sim LC, Wati L, Ho Y, Lee MM. Rapid characterization of high/low producer CHO cells using matrix-assisted laser desorption/ionization time-of-flight. Rapid Commun Mass Spectrom 2010; 24:1226-1230. [PMID: 20391592 DOI: 10.1002/rcm.4506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
An intact-cell mass spectrometry (ICM) method using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) was evaluated for the screening of stable recombinant Chinese hamster ovary (CHO) cell lines, an important mammalian cell line in bioprocessing. With rapid and simple cell pretreatments, viabilities of cells could be rapidly distinguished on the different fingerprints of mass spectra. Detectable m/z values on cell surfaces and their relative intensities were processed by two biostatistical methods, principle components analysis (PCA) and partial least squares (PLS), with promising results. Discrimination among cell lines with different expressed recombinant proteins or different productivities could be achieved. The ICM method has the advantage of providing multiple parameters simultaneously and possesses the potential to become a powerful method for routine monitoring of bioprocesses.
Collapse
Affiliation(s)
- Hua-Tao Feng
- Bioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way, Centros, Singapore 138668.
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering.
Collapse
Affiliation(s)
- Pan-Jun Kim
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (DYL); (HJ)
| | - Hawoong Jeong
- Institute for the BioCentury, KAIST, Daejeon, South Korea
- Department of Physics, KAIST, Daejeon, South Korea
- * E-mail: (DYL); (HJ)
| |
Collapse
|
26
|
|
27
|
Abstract
Motivation: Recent research underlines the importance of finegrained knowledge on protein localization. In particular, subcompartmental localization in the Golgi apparatus is important, for example, for the order of reactions performed in glycosylation pathways or the sorting functions of SNAREs, but is currently poorly understood. Results: We assemble a dataset of type II transmembrane proteins with experimentally determined sub-Golgi localizations and use this information to develop a predictor based on the transmembrane domain of these proteins, making use of a dedicated proteinstructure based kernel in an SVM. Various applications demonstrate the power of our approach. In particular, comparison with a large set of glycan structures illustrates the applicability of our predictions on a ‘glycomic’ scale and demonstrates a significant correlation between sub-Golgi localization and the ordering of different steps in glycan biosynthesis. Contact:roeland.vanham@wur.nl Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- A D J van Dijk
- Applied Bioinformatics, PRI, Wageningen UR, Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|
28
|
Yusufi FNK, Park W, Lee MM, Lee DY. An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioprocess Biosyst Eng 2008; 32:97-107. [PMID: 18458952 DOI: 10.1007/s00449-008-0226-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 04/16/2008] [Indexed: 11/25/2022]
Abstract
Advances in high-throughput techniques have led to the creation of increasing amounts of glycome data. The storage and analysis of this data would benefit greatly from a compact notation for describing glycan structures that can be easily stored and interpreted by computers. Towards this end, we propose a fixed-length alpha-numeric code for representing N-linked glycan structures commonly found in secreted glycoproteins from mammalian cell cultures. This code, GlycoDigit, employs a pre-assigned alpha-numeric index to represent the monosaccharides attached in different branches to the core glycan structure. The present branch-centric representation allows us to visualize the structure while the numerical nature of the code makes it machine readable. In addition, a difference operator can be defined to quantitatively differentiate between glycan structures for further analysis. The usefulness and applicability of GlycoDigit were demonstrated by constructing and visualizing an N-linked glycosylation network.
Collapse
Affiliation(s)
- Faraaz Noor Khan Yusufi
- Bioprocessing Technology Institute, Biomedical Sciences Institutes, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | | | | |
Collapse
|
29
|
Abstract
N-glycosylation plays a key role in the quality of many therapeutic glycoprotein biologics. The biosynthesis reactions of these oligosaccharides are a type of network in which a relatively small number of enzymes give rise to a large number of N-glycans as the reaction intermediates and terminal products. Multiple glycans appear on the glycoprotein molecules and give rise to a heterogeneous product. Controlling the glycan distribution is critical to the quality control of the product. Understanding N-glycan biosynthesis and the etiology of microheterogeneity would provide physiological insights, and facilitate cellular engineering to enhance glycoprotein quality. We developed a mathematical model of glycan biosynthesis in the Golgi and analyzed the various reaction variables on the resulting glycan distribution. The Golgi model was modeled as four compartments in series. The mechanism of protein transport across the Golgi is still controversial. From the viewpoint of their holding time distribution characteristics, the two main hypothesized mechanisms, vesicular transport and Golgi maturation models, resemble four continuous mixing-tanks (4CSTR) and four plug-flow reactors (4PFR) in series, respectively. The two hypotheses were modeled accordingly and compared. The intrinsic reaction kinetics were first evaluated using a batch (or single PFR) reactor. A sufficient holding time is needed to produce terminally-processed glycans. Altering enzyme concentrations has a complex effect on the final glycan distribution, as the changes often affect many reaction steps in the network. Comparison of the glycan profiles predicted by the 4CSTR and 4PFR models points to the 4PFR system as more likely to be the true mechanism. To assess whether glycan heterogeneity can be eliminated in the biosynthesis of biotherapeutics the 4PFR model was further used to assess whether a homogeneous glycan profile can be created through metabolic engineering. We demonstrate by the spatial localization of enzymes to specific compartments all terminally processed N-glycans can be synthesized as homogeneous products with a sufficient holding time in the Golgi compartments. The model developed may serve as a guide to future engineering of glycoproteins.
Collapse
Affiliation(s)
- Patrick Hossler
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Bhanu Chandra Mulukutla
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|