Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning

Radford, Caelan E.; Schommers, Philipp; Gieselmann, Lutz; Crawford, Katharine H.D.; Dadonaite, Bernadeta; Yu, Timothy C.; Dingens, Adam S.; Overbaugh, Julie; Klein, Florian; Bloom, Jesse D.

doi:10.1016/j.chom.2023.05.025

Cited by 14 publications

(6 citation statements)

References 72 publications

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“…To study the impacts of mutations to the Lassa virus GPC, we utilized a pseudovirus deep mutational scanning platform that we previously developed and applied to HIV envelope 43 and SARS-CoV-2 spike. 42,44 This platform enabled us to create large libraries of GPC-pseudotyped lentiviruses that have a genotype-phenotype link between a barcode in the lentivirus genomes and the GPC variant on the surface of each virion (Figure 1A,B).…”

Section: Resultsmentioning

confidence: 99%

“…We created deep mutational scanning libraries using a PCR-based mutagenesis method that introduces all amino acid mutations at each site in GPC. 42,43,53,54 The GPC variants in our libraries contained an average ∼2 nonsynonymous mutations each (Figure S1B), with the number of amino-acid mutations per variant roughly following a Poisson distribution (Figure S1C). We generated two independent GPC mutant libraries each containing ∼50,000 variants that covered ∼99% of all 9,820 possible amino-acid mutations to GPC (Figure S1D).…”

Section: Resultsmentioning

confidence: 99%

“…To do this, we incubated the pseudovirus libraries with increasing concentrations of antibody before infecting target cells, using a non-neutralized VSV-G-pseudotyped “standard” virus to convert sequencing counts to absolute neutralization values (Figure 3A). 42,43 We then analyzed the data using a biophysical model 75 that computes an escape value for each mutation that is roughly proportional to the log fold change in antibody inhibitory concentration 50% (IC 50 ) caused by the mutation.…”

Section: Resultsmentioning

confidence: 99%

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Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Carr,

Crawford,

Murphy

et al. 2024

Preprint

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Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host,Mastomysrodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus’s glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Carr,

Crawford,

Murphy

et al. 2024

Preprint

Self Cite

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“…First, using the command line tool configure-dms-viz, available as a Python package on PyPI (https://pypi.org/project/configure-dms-viz/), the user formats their data into a JSON specification file. Then, the user uploads this specification file to dms-viz.github.io, a web-based interface written in Javascript, D3.js, and NGL.js (Rose et al 2018). Finally, the specification file can either be shared directly or hosted remotely to generate a shareable URL link (Figure 2).…”

Section: Design and Usagementioning

confidence: 99%

“…Radford et al ( 2023) mapped mutations to HIV envelope (Env) that affect neutralization by polyclonal human serum using a pseudotyping-based deep mutational scanning platform (Radford et al 2023).…”

Section: Examples 1 Mapping the Neutralization Profile Of Antibodies ...mentioning

confidence: 99%

dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets

Hannon,

Bloom

2023

Preprint

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Summary and PurposeUnderstanding how mutations impact a protein’s functions is valuable for many types of biological questions. High-throughput techniques such as deep-mutational scanning (DMS) have greatly expanded the number of mutation-function datasets. For instance, DMS has been used to determine how mutations to viral proteins affect antibody escape (Dadonaite et al. 2023), receptor affinity (Starr et al. 2020), and essential functions such as viral genome transcription and replication (Li et al. 2023). With the growth of sequence databases, in some cases the effects of mutations can also be inferred from phylogenies of natural sequences (Bloom and Neher 2023) (Figure 1).The mutation-based data generated by these approaches is often best understood in the context of a protein’s 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a protein’s structure are often cumbersome and require multiple steps and softwares. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool,dms-viz. Withdms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format. Seehttps://dms-viz.github.io/to usedms-viz.

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High throughput profiling identified PA-L106R amino acid substitution in A(H1N1)pdm09 influenza virus that confers reduced susceptibility to baloxavir in vitro

Chen,

Su,

Choy

et al. 2024

Antiviral Research

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Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning

Cited by 14 publications

References 72 publications

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets

High throughput profiling identified PA-L106R amino acid substitution in A(H1N1)pdm09 influenza virus that confers reduced susceptibility to baloxavir in vitro

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