VirScan: High-throughput Profiling of Antiviral Antibody Epitopes

Shrock, Ellen; Shrock, Christine; Elledge, Stephen J.

doi:10.21769/bioprotoc.4464

Cited by 14 publications

(16 citation statements)

References 18 publications

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“…Given the challenge of mapping antibody epitopes at high resolution, it has been unclear how common recurrent antibody responses are and how widely they are shared across human populations. Recently, we developed VirScan, a phage display platform programmed to display peptides spanning the human virome, which enabled the high-throughput identification of antiviral antibody epitopes (14)(15)(16)(17)(18). We used VirScan to profile hundreds of human serum samples (14) and found that although many viral peptides recognized by an individual were relatively specific to that person, many other viral peptides-which we termed "public epitopes"-were recognized by a substantial percentage (≤98%) of individuals seropositive for the given virus (14).…”

Section: Resultsmentioning

confidence: 99%

“…We performed VirScan ( 14 – 16 ), which is based on the phage immunoprecipitation and sequencing (PhIP-Seq) methodology ( 17 ), as described previously ( 14 – 16 , 18 ) or with slight modifications. For the light chain isotype-specific IPs, we substituted magnetic protein A and protein G Dynabeads (Invitrogen) with 5 μg of biotinylated goat anti-human kappa (Southern Biotech) or 4 μg of biotinylated goat anti-human lambda (Southern Biotech) antibodies.…”

Section: Methodsmentioning

confidence: 99%

“…VirScan data generated with the human virome library and the CoV 56-AA library were analyzed as previously described ( 15 , 16 , 18 ).…”

Section: Methodsmentioning

confidence: 99%

“…The day after establishing the phage and serum mixtures, we added these antibodies and incubated the reactions overnight at 4°C. Afterward, we added 20 ml of Pierce streptavidin magnetic beads (Thermo Fisher Scientific), incubated the reactions for 4 hours at room temperature, then continued with the washing steps and the remainder of the protocol, as previously described (14)(15)(16)18).…”

Section: Virscanmentioning

confidence: 99%

“…We then added 60 ml (for kappa depletions) or 40 ml (for lambda depletions) of Pierce streptavidin magnetic beads, incubated the reactions for 4 hours at room temperature, then moved the supernatants into new plates. We added 40 ml of mixed protein A and protein G Dynabeads to the supernatants, incubated the reactions for 4 hours at room temperature, and continued with the IPs and library preparation for multiplexed Illumina sequencing as described previously (14)(15)(16)18).…”

Section: Virscanmentioning

confidence: 99%

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Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

Shrock

Timms

Kula

et al. 2023

Science

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Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant “public epitopes” at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid–binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system’s architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…VirScan data generated with the human virome library and the CoV 56-AA library were analyzed as previously described ( 15 , 16 , 18 ).…”

Section: Methodsmentioning

confidence: 99%

Section: Virscanmentioning

confidence: 99%

Section: Virscanmentioning

confidence: 99%

See 3 more Smart Citations

Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

Shrock

Timms

Kula

et al. 2023

Science

View full text Add to dashboard Cite

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Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens

Filimonova,

Innocenti,

Vogl

2023

Methods in Molecular Biology

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Chronic inflammation, neutrophil activity, and autoreactivity splits long COVID

Woodruff,

Bonham,

Anam

et al. 2023

Nat Commun

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While immunologic correlates of COVID-19 have been widely reported, their associations with post-acute sequelae of COVID-19 (PASC) remain less clear. Due to the wide array of PASC presentations, understanding if specific disease features associate with discrete immune processes and therapeutic opportunities is important. Here we profile patients in the recovery phase of COVID-19 via proteomics screening and machine learning to find signatures of ongoing antiviral B cell development, immune-mediated fibrosis, and markers of cell death in PASC patients but not in controls with uncomplicated recovery. Plasma and immune cell profiling further allow the stratification of PASC into inflammatory and non-inflammatory types. Inflammatory PASC, identifiable through a refined set of 12 blood markers, displays evidence of ongoing neutrophil activity, B cell memory alterations, and building autoreactivity more than a year post COVID-19. Our work thus helps refine PASC categorization to aid in both therapeutic targeting and epidemiological investigation of PASC.

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VirScan: High-throughput Profiling of Antiviral Antibody Epitopes

Cited by 14 publications

References 18 publications

Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens

Chronic inflammation, neutrophil activity, and autoreactivity splits long COVID

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