A Markov model of glycosylation elucidates isozyme specificity and glycosyltransferase interactions for glycoengineering

Chenguang Liang, Austin W. T. Chiang, Anders H. Hansen, Johnny Arnsdorf, Sanne Schoffelen, James T. Sorrentino, Benjamin P. Kellman, Bokan Bao, Bjørn G. Voldborg, Nathan E. Lewis*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Glycosylated biopharmaceuticals are important in the global pharmaceutical market. Despite the importance of their glycan structures, our limited knowledge of the glycosylation machinery still hinders controllability of this critical quality attribute. To facilitate discovery of glycosyltransferase specificity and predict glycoengineering efforts, here we extend the approach to model N-linked protein glycosylation as a Markov process. Our model leverages putative glycosyltransferase (GT) specificity to define the biosynthetic pathways for all measured glycans, and the Markov chain modelling is used to learn glycosyltransferase isoform activities and predict glycosylation following glycosyltransferase knock-in/knockout. We apply our methodology to four different glycoengineered therapeutics (i.e., Rituximab, erythropoietin, Enbrel, and alpha-1 antitrypsin) produced in CHO cells. Our model accurately predicted N-linked glycosylation following glycoengineering and further quantified the impact of glycosyltransferase mutations on reactions catalyzed by other glycosyltransferases. By applying these learned GT-GT interaction rules identified from single glycosyltransferase mutants, our model further predicts the outcome of multi-gene glycosyltransferase mutations on the diverse biotherapeutics. Thus, this modeling approach enables rational glycoengineering and the elucidation of relationships between glycosyltransferases, thereby facilitating biopharmaceutical research and aiding the broader study of glycosylation to elucidate the genetic basis of complex changes in glycosylation.
Original languageEnglish
JournalCurrent Research in Biotechnology
Volume2
Pages (from-to)22-36
ISSN2590-2628
DOIs
Publication statusPublished - 2020

Bibliographical note

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Keywords

  • Glycosylation model
  • Glycomics
  • Systems glycobiology
  • Glycoengineering
  • Isozyme specificity
  • Glycosyltransferase interactions

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