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Glycopeptide analysis of A549 cells after influenza A infection

ABSTRACT: Influenza A virus (IAV) hijacks host cellular machinery, but many virus–IAV interactions and contacting protein sites remain uncharacterised, particularly those dependent on intact cellular architecture, such as membrane-associated or phase-separated compartments. Here, we applied in-cell cross-linking mass spectrometry (XL-MS), integrated with AlphaFold-based structural modelling and functional assays, to map protein-protein contact sites in IAV-infected human cells.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Influenza A Virus (a/india/p063078/2006(h3n2))

SUBMITTER: Frank Stein

LAB HEAD: Jan Kosinski

PROVIDER: PXD072851 | Pride | 2026-04-23

REPOSITORIES: Pride

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			Action	DRS
	Bert_251120_S4781_MB_IB_JS_Kosinski_Influenza_knockdowns_set1_FP_F1.raw	Raw
	Bert_251120_S4781_MB_IB_JS_Kosinski_Influenza_knockdowns_set1_FP_F10.raw	Raw
	Bert_251120_S4781_MB_IB_JS_Kosinski_Influenza_knockdowns_set1_FP_F11.raw	Raw
	Bert_251120_S4781_MB_IB_JS_Kosinski_Influenza_knockdowns_set1_FP_F12.raw	Raw
	Bert_251120_S4781_MB_IB_JS_Kosinski_Influenza_knockdowns_set1_FP_F13.raw	Raw

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Project description:Influenza A virus (IAV) mutates rapidly, preventing a single seasonal vaccine from targeting more than one strain, and year-to-year vaccine effectiveness is low. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information is likely to improve the ability to design vaccines with broader effectiveness against evolved strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between wild-type IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though no N-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.

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Glycopeptide analysis of A549 cells after influenza A infection

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