Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy

Muthu, Manikandan; Chun, Se Chul; Gopal, Judy; Anthonydhason, Vimala; Haga, Steve; Devadoss, Anna Jacintha Prameela; Oh, Jae-Wook

doi:10.3390/ijms21249336

Cited by 8 publications

(3 citation statements)

References 174 publications

(162 reference statements)

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“…The site-specific glycosylation data from bottom-up analyses, and the glycan composition data from glycomics analyses, enable assignment of putative glycan compositions to observed proteoform 29,30 molecular weights. These assignments are represented in graphical form 34,35 as a monosaccharide 'fingerprint' and a glycan 'barcode' to facilitate streamlined multi-attribute assessment of glycoprotein-related CQAs. 36,37 The 'monosaccharide fingerprint' was introduced in the development of microarray libraries to measure glycan molecular similarity.…”

Section: Introductionmentioning

confidence: 99%

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Schachner,

Mullen,

Phung

et al. 2023

Preprint

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Glycosylated biotherapeutics are an emerging class of drugs with high molecular heterogeneity, which can affect their safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins. Here, we present a new approach to glycoform fingerprinting that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact glycoproteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment and offers insights into glycoform composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug's pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.

show abstract

Section: Introductionmentioning

confidence: 99%

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Schachner,

Mullen,

Phung

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We use site-specific glycosylation data from bottom-up analyses and glycan composition data from glycomics analyses to decipher putative glycan compositions corresponding to observed proteoform molecular weights 30,31 . The outcomes of this analytical approach are graphically represented 35,36 as a monosaccharide fingerprint and a glycan barcode [37][38][39] . These visual tools delineate the monosaccharide composition of the biotherapeutic per molecular weight and the percent abundance of each glycan per site.…”

mentioning

confidence: 99%

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Schachner,

Mullen,

Phung

et al. 2024

Nat Commun

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The heterogeneity inherent in today’s biotherapeutics, especially as a result of heavy glycosylation, can affect a molecule’s safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins or other heterogeneous biotherapeutics. Here, we present an approach to the molecular assessment of biotherapeutics that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact heterogeneous and/or glycosylated proteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment. For glycoproteins in particular, the method may offer insights into glycan composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug’s pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.

show abstract

“…The site-speci c glycosylation data from bottom-up analyses, and the glycan composition data from glycomics analyses, enable assignment of putative glycan compositions to observed proteoform 29,30 molecular weights. These assignments are represented in graphical form 34,35 as a monosaccharide ' ngerprint' and a glycan 'barcode' to facilitate streamlined multi-attribute assessment of glycoprotein-related CQAs. 36,37 The 'monosaccharide ngerprint' was introduced in the development of microarray libraries to measure glycan molecular similarity.…”

mentioning

confidence: 99%

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Schachner,

Mullen,

Phung

et al. 2023

Preprint

View full text Add to dashboard Cite

Glycosylated biotherapeutics are an emerging class of drugs with high molecular heterogeneity, which can affect their safety and efficacy. Characterizing this heterogeneity is crucial for drug development and quality assessment, but existing methods are limited in their ability to analyze intact glycoproteins. Here, we present a new approach to glycoform fingerprinting that uses proton-transfer charge-reduction with gas-phase fractionation to analyze intact glycoproteins by mass spectrometry. The method provides a detailed landscape of the intact molecular weights present in biotherapeutic protein preparations in a single experiment and offers insights into glycoform composition when coupled with a suitable bioinformatic strategy. We tested the approach on various biotherapeutic molecules, including Fc-fusion, VHH-fusion, and peptide-bound MHC class II complexes to demonstrate efficacy in measuring the proteoform-level diversity of biotherapeutics. Notably, we inferred the glycoform distribution for hundreds of molecular weights for the eight-times glycosylated fusion drug IL22-Fc, enabling correlations between glycoform sub-populations and the drug’s pharmacological properties. Our method is broadly applicable and provides a powerful tool to assess the molecular heterogeneity of emerging biotherapeutics.

show abstract

Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy

Cited by 8 publications

References 174 publications

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Exposing the molecular heterogeneity of glycosylated biotherapeutics

Exposing the molecular heterogeneity of glycosylated biotherapeutics

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