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Luo C, Xu X, Liu C, He S, Chen J, Feng Y, Liu S, Peng W, Zhou Y, Liu Y, Wei P, Li B, Mai H, Xia X, Bei J. RBFOX2/GOLIM4 Splicing Axis Activates Vesicular Transport Pathway to Promote Nasopharyngeal Carcinogenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004852. [PMID: 34180133 PMCID: PMC8373120 DOI: 10.1002/advs.202004852] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/29/2021] [Indexed: 05/05/2023]
Abstract
20-30% of patients with nasopharyngeal carcinoma (NPC) develop distant metastasis or recurrence leading to poor survival, of which the underlying key molecular events have yet to be addressed. Here alternative splicing events in 85 NPC samples are profiled using transcriptome analysis and it is revealed that the long isoform of GOLIM4 (-L) with exon-7 is highly expressed in NPC and associated with poor prognosis. Lines of evidence demonstrate the pro-tumorigenic function of GOLIM4-L in NPC cells. It is further revealed that RBFOX2 binds to a GGAA motif in exon-7 and promotes its inclusion forming GOLIM4-L. RBFOX2 knockdown suppresses the tumorigenesis of NPC cells, phenocopying GOLIM4-L knockdown, which is significantly rescued by GOLIM4-L overexpression. High expression of RBFOX2 is correlated with the exon-7 inclusion of GOLIM4 in NPC biopsies and associated with worse prognosis. It is observed that RBFOX2 and GOLIM4 can influence vesicle-mediated transport through maintaining the organization of Golgi apparatus. Finally, it is revealed that RAB26 interacts with GOLIM4 and mediates its tumorigenic potentials in NPC cells. Taken together, the findings provide insights into how alternative splicing contributes to NPC development, by highlighting a functional link between GOLIM4-L and its splicing regulator RBFOX2 activating vesicle-mediated transport involving RAB26.
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Affiliation(s)
- Chun‐Ling Luo
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Xiao‐Chen Xu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Chu‐Jun Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Shuai He
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Jie‐Rong Chen
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Yan‐Chun Feng
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Shu‐Qiang Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Wan Peng
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Ya‐Qing Zhou
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Yu‐Xiang Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Pan‐Pan Wei
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Bo Li
- Department of Biochemistry and Molecular BiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080P. R. China
- RNA Biomedical InstituteSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhou510120P. R. China
| | - Hai‐Qiang Mai
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Xiao‐Jun Xia
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jin‐Xin Bei
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of Medical OncologyNational Cancer Centre of SingaporeSingapore169610Singapore
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Le NQK, Yapp EKY, Nagasundaram N, Chua MCH, Yeh HY. Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture. Comput Struct Biotechnol J 2019; 17:1245-1254. [PMID: 31921391 PMCID: PMC6944713 DOI: 10.1016/j.csbj.2019.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/07/2019] [Accepted: 09/11/2019] [Indexed: 11/20/2022] Open
Abstract
Protein function prediction is one of the most well-studied topics, attracting attention from countless researchers in the field of computational biology. Implementing deep neural networks that help improve the prediction of protein function, however, is still a major challenge. In this research, we suggested a new strategy that includes gated recurrent units and position-specific scoring matrix profiles to predict vesicular transportation proteins, a biological function of great importance. Although it is difficult to discover its function, our model is able to achieve accuracies of 82.3% and 85.8% in the cross-validation and independent dataset, respectively. We also solve the problem of imbalance in the dataset via tuning class weight in the deep learning model. The results generated showed sensitivity, specificity, MCC, and AUC to have values of 79.2%, 82.9%, 0.52, and 0.861, respectively. Our strategy shows superiority in results on the same dataset against all other state-of-the-art algorithms. In our suggested research, we have suggested a technique for the discovery of more proteins, particularly proteins connected with vesicular transport. In addition, our accomplishment could encourage the use of gated recurrent units architecture in protein function prediction.
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Affiliation(s)
- Nguyen Quoc Khanh Le
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
- Professional Master Program in Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan
| | - Edward Kien Yee Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, #08-04, Innovis, 138634, Singapore
| | - N. Nagasundaram
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
| | - Matthew Chin Heng Chua
- Institute of Systems Science, 25 Heng Mui Keng Terrace, National University of Singapore, 119615, Singapore
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639818, Singapore
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4
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Au CE, Hermo L, Byrne E, Smirle J, Fazel A, Simon PHG, Kearney RE, Cameron PH, Smith CE, Vali H, Fernandez-Rodriguez J, Ma K, Nilsson T, Bergeron JJM. Expression, sorting, and segregation of Golgi proteins during germ cell differentiation in the testis. Mol Biol Cell 2015; 26:4015-32. [PMID: 25808494 PMCID: PMC4710233 DOI: 10.1091/mbc.e14-12-1632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/19/2015] [Indexed: 12/14/2022] Open
Abstract
A total of 1318 proteins characterized in the male germ cell Golgi apparatus reveal a new germ cell–specific Golgi marker and a new pan-Golgi marker for all cells. The localization of these and other Golgi proteins reveals differential expression linked to mitosis, meiosis, acrosome formation, and postacrosome Golgi migration and destination in the late spermatid. The molecular basis of changes in structure, cellular location, and function of the Golgi apparatus during male germ cell differentiation is unknown. To deduce cognate Golgi proteins, we isolated germ cell Golgi fractions, and 1318 proteins were characterized, with 20 localized in situ. The most abundant protein, GL54D of unknown function, is characterized as a germ cell–specific Golgi-localized type II integral membrane glycoprotein. TM9SF3, also of unknown function, was revealed to be a universal Golgi marker for both somatic and germ cells. During acrosome formation, several Golgi proteins (GBF1, GPP34, GRASP55) localize to both the acrosome and Golgi, while GL54D, TM9SF3, and the Golgi trafficking protein TMED7/p27 are segregated from the acrosome. After acrosome formation, GL54D, TM9SF3, TMED4/p25, and TMED7/p27 continue to mark Golgi identity as it migrates away from the acrosome, while the others (GBF1, GPP34, GRASP55) remain in the acrosome and are progressively lost in later steps of differentiation. Cytoplasmic HSP70.2 and the endoplasmic reticulum luminal protein-folding enzyme PDILT are also Golgi recruited but only during acrosome formation. This resource identifies abundant Golgi proteins that are expressed differentially during mitosis, meiosis, and postacrosome Golgi migration, including the last step of differentiation.
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Affiliation(s)
- Catherine E Au
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Louis Hermo
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
| | - Elliot Byrne
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Jeffrey Smirle
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Ali Fazel
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Paul H G Simon
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Robert E Kearney
- Department of Biomedical Engineering Department, McGill University, Montreal, QC H3A 2B4, Canada
| | - Pamela H Cameron
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Charles E Smith
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
| | - Hojatollah Vali
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kewei Ma
- Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - Tommy Nilsson
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
| | - John J M Bergeron
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada Division of Endocrinology and Metabolism, McGill University Health Centre Research Institute, Montreal, QC H3A 1A1, Canada
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Abstract
Proteins synthesised at the endoplasmic reticulum (ER) have to undergo a number of consecutive and coordinated steps to reach the Golgi complex. To understand the dynamic complexity of ER-to-Golgi transport at the structural and molecular level, light microscopy approaches are fundamental tools that allow in vivo observations of protein dynamics and interactions of fluorescent proteins in living cells. Imaging protein and organelle dynamics close to the ultra-structural level became possible by combining light microscopy with electron microscopy analyses or super-resolution light microscopy methods. Besides, increasing evidence suggests that the early secretory pathway is tightly connected to other cellular processes, such as signal transduction, and quantitative information at the systems level is fundamental to achieve a comprehensive molecular understanding of these connections. High-throughput microscopy in fixed and living cells in combination with systematic perturbation of gene expression by, e.g. RNA interference, will open new avenues to gain such an understanding of the early secretory pathway at the systems level. In this Commentary, we first outline examples that revealed the dynamic organisation of ER-to-Golgi transport in living cells. Next, we discuss the use of advanced imaging methods in studying ER-to-Golgi transport and, finally, delineate the efforts in understanding ER-to-Golgi transport at the systems level.
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Affiliation(s)
- Fatima Verissimo
- European Molecular Biology Laboratory, Cell Biology and Cell Biophysics Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
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6
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Ispolatov I, Müsch A. A model for the self-organization of vesicular flux and protein distributions in the Golgi apparatus. PLoS Comput Biol 2013; 9:e1003125. [PMID: 23874173 PMCID: PMC3715413 DOI: 10.1371/journal.pcbi.1003125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/20/2013] [Indexed: 01/19/2023] Open
Abstract
The generation of two non-identical membrane compartments via exchange of vesicles is considered to require two types of vesicles specified by distinct cytosolic coats that selectively recruit cargo, and two membrane-bound SNARE pairs that specify fusion and differ in their affinities for each type of vesicles. The mammalian Golgi complex is composed of 6-8 non-identical cisternae that undergo gradual maturation and replacement yet features only two SNARE pairs. We present a model that explains how distinct composition of Golgi cisternae can be generated with two and even a single SNARE pair and one vesicle coat. A decay of active SNARE concentration in aging cisternae provides the seed for a cis[Formula: see text]trans SNARE gradient that generates the predominantly retrograde vesicle flux which further enhances the gradient. This flux in turn yields the observed inhomogeneous steady-state distribution of Golgi enzymes, which compete with each other and with the SNAREs for incorporation into transport vesicles. We show analytically that the steady state SNARE concentration decays exponentially with the cisterna number. Numerical solutions of rate equations reproduce the experimentally observed SNARE gradients, overlapping enzyme peaks in cis, medial and trans and the reported change in vesicle nature across the Golgi: Vesicles originating from younger cisternae mostly contain Golgi enzymes and SNAREs enriched in these cisternae and extensively recycle through the Endoplasmic Reticulum (ER), while the other subpopulation of vesicles contains Golgi proteins prevalent in older cisternae and hardly reaches the ER.
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Affiliation(s)
- Iaroslav Ispolatov
- Departamento de Física, Universidad de Santiago de Chile, Santiago, Chile.
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7
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Smirle J, Au CE, Jain M, Dejgaard K, Nilsson T, Bergeron J. Cell biology of the endoplasmic reticulum and the Golgi apparatus through proteomics. Cold Spring Harb Perspect Biol 2013; 5:a015073. [PMID: 23284051 DOI: 10.1101/cshperspect.a015073] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enriched endoplasmic reticulum (ER) and Golgi membranes subjected to mass spectrometry have uncovered over a thousand different proteins assigned to the ER and Golgi apparatus of rat liver. This, in turn, led to the uncovering of several hundred proteins of poorly understood function and, through hierarchical clustering, showed that proteins distributed in patterns suggestive of microdomains in cognate organelles. This has led to new insights with respect to their intracellular localization and function. Another outcome has been the critical testing of the cisternal maturation hypothesis showing overwhelming support for a predominant role of COPI vesicles in the transport of resident proteins of the ER and Golgi apparatus (as opposed to biosynthetic cargo). Here we will discuss new insights gained and also highlight new avenues undertaken to further explore the cell biology of the ER and the Golgi apparatus through tandem mass spectrometry.
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Affiliation(s)
- Jeffrey Smirle
- The Research Institute of the McGill University Health Centre and the Department of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
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8
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Orme CM, Bogan JS. The ubiquitin regulatory X (UBX) domain-containing protein TUG regulates the p97 ATPase and resides at the endoplasmic reticulum-golgi intermediate compartment. J Biol Chem 2011; 287:6679-92. [PMID: 22207755 DOI: 10.1074/jbc.m111.284232] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
p97/VCP is a hexameric ATPase that is coupled to diverse cellular processes, such as membrane fusion and proteolysis. How p97 activity is regulated is not fully understood. Here we studied the potential role of TUG, a widely expressed protein containing a UBX domain, to control mammalian p97. In HEK293 cells, the vast majority of TUG was bound to p97. Surprisingly, the TUG UBX domain was neither necessary nor sufficient for this interaction. Rather, an extended sequence, comprising three regions of TUG, bound to the p97 N-terminal domain. The TUG C terminus resembled the Arabidopsis protein PUX1. Similar to the previously described action of PUX1 on AtCDC48, TUG caused the conversion of p97 hexamers into monomers. Hexamer disassembly was stoichiometric rather than catalytic and was not greatly affected by the p97 ATP-binding state or by TUG N-terminal regions in vitro. In HeLa cells, TUG localized to the endoplasmic reticulum-to-Golgi intermediate compartment and endoplasmic reticulum exit sites. Although siRNA-mediated TUG depletion had no marked effect on total ubiquitylated proteins or p97 localization, TUG overexpression caused an accumulation of ubiquitylated substrates and targeted both TUG and p97 to the nucleus. A physiologic role of TUG was revealed by siRNA-mediated depletion, which showed that TUG is required for efficient reassembly of the Golgi complex after brefeldin A removal. Together, these data support a model in which TUG controls p97 oligomeric status at a particular location in the early secretory pathway and in which this process regulates membrane trafficking in various cell types.
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Affiliation(s)
- Charisse M Orme
- Section of Endocrinology and Metabolism, Department of Internal Medicine, University School of Medicine, New Haven, Connecticut 06520-8020, USA
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9
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Puri A, Neelamegham S. Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks. Ann Biomed Eng 2011; 40:816-27. [PMID: 22090146 DOI: 10.1007/s10439-011-0464-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 11/05/2011] [Indexed: 01/07/2023]
Abstract
Following the footsteps of genomics and proteomics, recent years have witnessed the growth of large-scale experimental methods in the field of glycomics. In parallel, there has also been growing interest in developing Systems Biology based methods to study the glycome. The combined goals of these endeavors is to identify glycosylation-dependent mechanisms regulating human physiology, check points that can control the progression of pathophysiology, and modifications to reaction pathways that can result in more uniform biopharmaceutical processes. In these efforts, mathematical models of N- and O-linked glycosylation have emerged as paradigms for the field. While these are relatively few in number, nevertheless, the existing models provide a basic framework that can be used to develop more sophisticated analysis strategies for glycosylation in the future. The current review surveys these computational models with focus on the underlying mathematics and assumptions, and with respect to their ability to generate experimentally testable hypotheses.
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Affiliation(s)
- Apurv Puri
- Department of Chemical and Biological Engineering, and The New York State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
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