Off-target glycans encountered along the synthetic biology route towards humanized N-glycans in Pichia pastoris

Laukens, B.; Jacobs, P. P.; Geysens, K.; Martins, J.; De Wachter, C.; Ameloot, P.; Morelle, W.; Haustraete, J.; Renauld, J.-C.; Samyn, B.; Contreras, R.; Devos, S.; Callewaert, N.

doi:10.1101/2020.01.28.923631

bioRxiv · 10.1101/2020.01.28.923631

Off-target glycans encountered along the synthetic biology route towards humanized N-glycans in Pichia pastoris

Laukens, B.·Jacobs, P. P.·Geysens, K.·Martins, J.·De Wachter, C.·Ameloot, P.·Morelle, W.·Haustraete, J.·Renauld, J.-C.·Samyn, B.·Contreras, R.·Devos, S.·Callewaert, N.

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Abstract

BackgroundThe glycosylation pathways of several eukaryotic protein expression hosts are being engineered to enable the production of therapeutic glycoproteins with humanized application-customized glycan structures. In several expression hosts, this has been quite successful, but one caveat is that the new N-glycan structures inadvertently might be substrates for one or more of the multitude of endogenous glycosyltransferases in such heterologous background. This then results in the formation of novel, undesired glycan structures, which often remain insufficiently characterized. ResultsWhen expressing mouse interleukin-22 (mIL-22) in a Pichia pastoris (syn. Komagataella phaffi) GlycoSwitchM5 strain which had been optimized to produce Man5GlcNAc2 N-glycans, glycan profiling revealed two major species: Man5GlcNAc2 and an unexpected, partially -mannosidase-resistant structure. A detailed structural analysis using exoglycosidase sequencing, mass spectrometry, linkage analysis and NMR, revealed that this novel glycan was Man5GlcNAc2 modified with a Glc-1,2-Man{beta}-1,2-Man{beta}-1,3-Glc-1,3-R tetra-saccharide. Also the biosynthetic intermediates of this off-target modification were detected. Expression of a Golgi-targeted GlcNAc Transferase-I strongly inhibited the formation of this novel modification, resulting in more homogeneous modification with the targeted GlcNAcMan5GlcNAc2 structure. We have also observed the off-target glycan on other glycoproteins produced in the GlycoSwitchM5 strain. This illustrates the intricacies of Golgi glycosylation pathways and cautions that the use of glyco-engineered expression host cells should always be accompanied by detailed glycan analysis of the particular therapeutic proteins being produced. ConclusionsOur findings reinforce accumulating evidence that robustly customizing the N-glycosylation pathway in Pichia pastoris to produce particular human-type structures is still an incompletely solved synthetic biology challenge, which will require further innovation to enable safe glycoprotein pharmaceutical production.

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Laukens, B., Jacobs, P. P., Geysens, K., Martins, J., De Wachter, C., Ameloot, P., Morelle, W., Haustraete, J., Renauld, J.-C., Samyn, B., Contreras, R., Devos, S., Callewaert, N.. 2020-01-29. Off-target glycans encountered along the synthetic biology route towards humanized N-glycans in Pichia pastoris. https://doi.org/10.1101/2020.01.28.923631

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