Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks

Huang, Qiu Yu; Song, Kangkang; Chen, Xu; Bolon, Daniel N.; Wang, Jennifer; Finberg, Robert W.; Schiffer, Celia A.; Somasundaran, Mohan

doi:10.1016/j.str.2022.02.014

Cited by 10 publications

(6 citation statements)

References 53 publications

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“…Using influenza HA as a model, we reoriented the full-length HA ectodomain in an “upside-down” configuration facilitated by its binding to alum, to redirect antibody responses away from the variable HA-head and toward the highly conserved HA-stem. We envisioned that this approach could increase the exposure of the poorly accessible HA-stem that was originally occluded by HA-head on influenza virions 31,32 , while simultaneously sterically decreasing the exposure of HA-head – in the context of an intact HA trimer that preserves the native structure of HA-stem.…”

Section: Discussionmentioning

confidence: 99%

“…Interestingly, stem-directed (but not head-directed) mAbs isolated from vaccinated individuals exhibit significantly reduced binding to the whole virus as compared to recombinant HA proteins 31 . We hypothesize that steric occlusion leads to poor accessibility of HA-stem 32 , thereby biasing antibody responses toward HA-head during natural infection 31 .…”

Section: Introductionmentioning

confidence: 99%

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Designing epitope-focused vaccinesviaantigen reorientation

Utz

et al. 2022

Preprint

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A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an 'upside down' configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Designing epitope-focused vaccinesviaantigen reorientation

Utz

et al. 2022

Preprint

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show abstract

“…Interestingly, stem-directed (but not head-directed) mAbs isolated from vaccinated individuals exhibit significantly reduced binding to the whole virus as compared to recombinant HA proteins 30 . We hypothesize that steric occlusion leads to poor accessibility of HA-stem 31 , thereby biasing antibody responses toward HA-head during natural infection 30 .…”

Section: Oligod-modified Antigens Stimulate Robust Gc Responsesmentioning

confidence: 99%

Vaccine design via antigen reorientation

Xu,

Carter,

et al. 2024

Nat Chem Biol

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A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an ‘upside-down’ configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines.

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“…Quantitative cryo-ET has also been performed in non-cellular samples. Recent studies characterize morphological differences of influenza virus by measuring size, glycoprotein spacing, and capsid organization and structure ( Huang et al, 2022 ). Quantitative characterization of ice thickness, 3D shape, and particle distribution has also helped assessing issues (e.g., air-water interface) when performing SPA tomography ( Noble et al, 2018a ; Noble et al, 2018b ).…”

Section: Quantitative Cryo-electron Tomographymentioning

confidence: 99%

Quantitative Cryo-Electron Tomography

Navarro

2022

Front. Mol. Biosci.

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The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.

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Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks

Cited by 10 publications

References 53 publications

Designing epitope-focused vaccinesviaantigen reorientation

Designing epitope-focused vaccinesviaantigen reorientation

Vaccine design via antigen reorientation

Quantitative Cryo-Electron Tomography

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