Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.
Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
Pubmed ID: 38670113 RIS Download
Research resources used in this publication
- Agilent 4150 TapeStation System (RRID:SCR_019393) (instrument resource)
- Illumina NextSeq 2000 system (RRID:SCR_023614) (instrument resource)
- Thermo Fisher Qubit fluorimeter (RRID:SCR_018095) (instrument resource)
- BD FACS Aria II (RRID:SCR_018091) (instrument resource)
- MDCK (RRID:CVCL_0422) (cell line)
- Sartorius Octet BLI systems (RRID:SCR_023267) (instrument resource)
- Cytiva AKTA pure 25 L chromatography system (RRID:SCR_023461) (instrument resource)
- Illumina MiSeq System (RRID:SCR_016379) (portal)
- Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) (software resource)
- MOE (RRID:SCR_014882) (software resource)
- XDS Program Package (RRID:SCR_015652) (software resource)
- Rosetta (RRID:SCR_015701) (software resource)
- Phenix (RRID:SCR_014224) (software resource)
- Coot (RRID:SCR_014222) (software resource)
- UCSF ChimeraX (RRID:SCR_015872) (software resource)
- MEGA (RRID:SCR_023017) (software resource)
- R Project for Statistical Computing (RRID:SCR_001905) (software resource)
- PANDAseq (RRID:SCR_002705) (software resource)
- Pandas (RRID:SCR_018214) (software resource)
- tidyverse (RRID:SCR_019186) (software resource)
- Seurat (RRID:SCR_016341) (software resource)
- WEBLOGO (RRID:SCR_010236) (service resource)
- Cell Ranger (RRID:SCR_017344) (software resource)
- Geneious (RRID:SCR_010519) (software resource)
- Python Programming Language (RRID:SCR_008394) (software resource)
- IMGT/V-QUEST (RRID:SCR_010749) (service resource)
- Bash (RRID:SCR_021268) (software resource)
- GraphPad Prism (RRID:SCR_002798) (software resource)
- FlowJo (RRID:SCR_008520) (software resource)
- C57BL/6J (RRID:IMSR_JAX:000664) (organism)
- circlize (RRID:SCR_002141) (software resource)
-
B6.SJL-Ptprca Pepc
- HEK293-F (RRID:CVCL_6642) (cell line)
- Expi293F (RRID:CVCL_D615) (cell line)
- FreeStyle 293-F (RRID:CVCL_D603) (cell line)
Additional research tools detected in this publication
Antibodies used in this publication
- Alkaline Phosphatase-AffiniPure Goat Anti-Mouse IgG, Fc_ Fragment Specific (min X Hu,Bov,Hrs Sr Prot) (RRID:AB_2338535)
- F4/80 Monoclonal Antibody (BM8), APC-eFluor™ 780, eBioscience (RRID:AB_2637188)
- CD8a Monoclonal Antibody (53-6.7), APC-eFluor™ 780, eBioscience (RRID:AB_1272221)
- Ly-6G/Ly-6C Monoclonal Antibody (RB6-8C5), APC-eFluor™ 780, eBioscience (RRID:AB_1518805)
- CD4 Monoclonal Antibody (RM4-5), APC-eFluor™ 780, eBioscience (RRID:AB_1272219)
- CD38 Monoclonal Antibody (90), Alexa Fluor™ 700, eBioscience (RRID:AB_657740)
- TotalSeq(TM)-C0306 anti-mouse Hashtag 6 (RRID:AB_2819910)
- TotalSeq(TM)-C0310 anti-mouse Hashtag 10 (RRID:AB_2819914)
- TotalSeq(TM)-C0309 anti-mouse Hashtag 9 (RRID:AB_2819913)
- TotalSeq(TM)-C0308 anti-mouse Hashtag 8 (RRID:AB_2819912)
- TotalSeq(TM)-C0307 anti-mouse Hashtag 7 (RRID:AB_2819911)
- TotalSeq(TM)-C0302 anti-mouse Hashtag 2 (RRID:AB_2800694)
- TotalSeq(TM)-C0301 anti-mouse Hashtag 1 (RRID:AB_2800693)
- Alexa Fluor(R) 594 anti-mouse CD3 (RRID:AB_2563427)
- Alexa Fluor(R) 488 anti-mouse CD45.2 (RRID:AB_492868)
- TotalSeq(TM)-C0305 anti-mouse Hashtag 5 (RRID:AB_2800697)
- Rat Anti-CD16 / CD32 Monoclonal Antibody, Unconjugated, Clone 2.4G2 (RRID:AB_394657)
- TotalSeq(TM)-C0304 anti-mouse Hashtag 4 (RRID:AB_2800696)
- Brilliant Violet 510(TM) anti-mouse CD4 (RRID:AB_2562608)
- PE anti-mouse CD24 (RRID:AB_312840)
- APC anti-mouse CD23 (RRID:AB_2563438)
- TotalSeq(TM)-C0303 anti-mouse Hashtag 3 (RRID:AB_2800695)
- PerCP/Cyanine5.5 anti-mouse/human CD45R/B220 (RRID:AB_893354)
- FITC anti-mouse CD21/CD35 (CR2/CR1) (RRID:AB_940403)
- Alexa Fluor(R) 700 anti-mouse TCR beta chain (RRID:AB_1027654)
- APC/Cyanine7 anti-mouse CD21/CD35 (CR2/CR1) (RRID:AB_1953275)
- APC anti-mouse CD43 (RRID:AB_11149685)
- FITC anti-mouse/human CD45R/B220 (RRID:AB_312991)
- CD249 (BP-1) Monoclonal Antibody (6C3), FITC, eBioscience (RRID:AB_465295)
- IgM (RRID:AB_2741430)
- IgG1 (RRID:AB_2737664)
- BV421 Rat Anti-Mouse CD24 (RRID:AB_2737002)
- CD45R (B220) (RRID:AB_2738007)
- Brilliant Violet 421(TM) anti-mouse IgD (RRID:AB_2562743)
- CD45R (B220) (RRID:AB_2738383)
- BV510 Rat Anti-Mouse IgD (RRID:AB_2737003)
- PE anti-mouse CD138 (Syndecan-1) (RRID:AB_10915989)
- IgM (RRID:AB_2741424)
- Ig, κ light chain (RRID:AB_2741090)
- Ig, λ1, λ2, & λ3 Light Chain (RRID:AB_2742301)
- CD38 (RRID:AB_2739886)
- IgD (RRID:AB_2738322)
- PE anti-mouse CD45.2 (RRID:AB_313445)
- Brilliant Violet 785(TM) anti-mouse CD45.2 (RRID:AB_2562604)
- PE-Cy™7 Hamster Anti-Mouse CD95 (RRID:AB_396768)
- PerCP/Cyanine5.5 anti-mouse CD45.1 (RRID:AB_893348)
- PE/Cyanine7 anti-mouse IgD (RRID:AB_2561875)
Associated grants
- Agency: NIAID NIH HHS, United States
Id: R01 AI155447 - Agency: NIAID NIH HHS, United States
Id: U19 AI057229 - Agency: NIAID NIH HHS, United States
Id: R01 AI146779 - Agency: NIAID NIH HHS, United States
Id: R01 AI124378 - Agency: Bill & Melinda Gates Foundation, United States
Id: INV-004923 - Agency: NIAID NIH HHS, United States
Id: P30 AI060354 - Agency: NIAID NIH HHS, United States
Id: R01 AI137057 - Agency: NIAID NIH HHS, United States
Id: R01 AI153098 - Agency: NIAID NIH HHS, United States
Id: P01 AI089618
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
This is a list of tools and resources that we have found mentioned in this publication.
GenScript (tool)
RRID:SCR_002891
Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.
View all literature mentionsZENODO (tool)
RRID:SCR_004129
Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.
View all literature mentionsSTAR (tool)
RRID:SCR_004463
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
View all literature mentionsPRISM (tool)
RRID:SCR_005375
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role.
View all literature mentionsResearch Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (tool)
RRID:SCR_012820
Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.
View all literature mentionsAlkaline Phosphatase-AffiniPure Goat Anti-Mouse IgG, Fc_ Fragment Specific (min X Hu,Bov,Hrs Sr Prot) (antibody)
RRID:AB_2338535
This unknown targets Mouse IgG, Fc? Fragment Specific
View all literature mentionsF4/80 Monoclonal Antibody (BM8), APC-eFluor™ 780, eBioscience (antibody)
RRID:AB_2637188
This monoclonal targets F4/80
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RRID:AB_1272221
This monoclonal targets CD8a
View all literature mentionsLy-6G/Ly-6C Monoclonal Antibody (RB6-8C5), APC-eFluor™ 780, eBioscience (antibody)
RRID:AB_1518805
This monoclonal targets Ly-6G/Ly-6C
View all literature mentionsCD4 Monoclonal Antibody (RM4-5), APC-eFluor™ 780, eBioscience (antibody)
RRID:AB_1272219
This monoclonal targets CD4
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RRID:AB_657740
This monoclonal targets CD38
View all literature mentionsTotalSeq(TM)-C0306 anti-mouse Hashtag 6 (antibody)
RRID:AB_2819910
This monoclonal targets H-2/CD45
View all literature mentionsTotalSeq(TM)-C0310 anti-mouse Hashtag 10 (antibody)
RRID:AB_2819914
This monoclonal targets H-2/CD45
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RRID:AB_2819913
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RRID:AB_2819912
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RRID:AB_2819911
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RRID:AB_2800694
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RRID:AB_2800693
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RRID:AB_2563427
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RRID:AB_492868
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RRID:AB_2800697
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RRID:AB_394657
This monoclonal targets CD16 / CD32
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RRID:AB_2800696
This monoclonal targets H-2/CD45
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RRID:AB_2562608
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RRID:AB_312840
This monoclonal targets CD24
View all literature mentionsAPC anti-mouse CD23 (antibody)
RRID:AB_2563438
This monoclonal targets CD23
View all literature mentionsTotalSeq(TM)-C0303 anti-mouse Hashtag 3 (antibody)
RRID:AB_2800695
This monoclonal targets H-2/CD45
View all literature mentionsPerCP/Cyanine5.5 anti-mouse/human CD45R/B220 (antibody)
RRID:AB_893354
This monoclonal targets CD45R
View all literature mentionsFITC anti-mouse CD21/CD35 (CR2/CR1) (antibody)
RRID:AB_940403
This monoclonal targets CD21/CD35
View all literature mentionsAlexa Fluor(R) 700 anti-mouse TCR beta chain (antibody)
RRID:AB_1027654
This monoclonal targets TCR beta chain
View all literature mentionsAPC/Cyanine7 anti-mouse CD21/CD35 (CR2/CR1) (antibody)
RRID:AB_1953275
This monoclonal targets CD21/CD35
View all literature mentionsAPC anti-mouse CD43 (antibody)
RRID:AB_11149685
This monoclonal targets CD43
View all literature mentionsFITC anti-mouse/human CD45R/B220 (antibody)
RRID:AB_312991
This monoclonal targets CD45R
View all literature mentionsCD249 (BP-1) Monoclonal Antibody (6C3), FITC, eBioscience (antibody)
RRID:AB_465295
This monoclonal targets CD249 (BP-1)
View all literature mentionsBV421 Rat Anti-Mouse CD24 (antibody)
RRID:AB_2737002
This monoclonal targets CD24
View all literature mentionsCD45R (B220) (antibody)
RRID:AB_2738007
This monoclonal targets CD45R (B220)
View all literature mentionsBrilliant Violet 421(TM) anti-mouse IgD (antibody)
RRID:AB_2562743
This monoclonal targets IgD
View all literature mentionsCD45R (B220) (antibody)
RRID:AB_2738383
This monoclonal targets CD45R (B220)
View all literature mentionsBV510 Rat Anti-Mouse IgD (antibody)
RRID:AB_2737003
This monoclonal targets IgD
View all literature mentionsPE anti-mouse CD138 (Syndecan-1) (antibody)
RRID:AB_10915989
This monoclonal targets CD138
View all literature mentionsIg, κ light chain (antibody)
RRID:AB_2741090
This monoclonal targets Ig, κ light chain
View all literature mentionsIg, λ1, λ2, & λ3 Light Chain (antibody)
RRID:AB_2742301
This monoclonal targets Ig, λ1, λ2, & λ3 Light Chain
View all literature mentionsPE anti-mouse CD45.2 (antibody)
RRID:AB_313445
This monoclonal targets CD45.2
View all literature mentionsBrilliant Violet 785(TM) anti-mouse CD45.2 (antibody)
RRID:AB_2562604
This monoclonal targets CD45.2
View all literature mentionsPE-Cy™7 Hamster Anti-Mouse CD95 (antibody)
RRID:AB_396768
This monoclonal targets CD95
View all literature mentionsPerCP/Cyanine5.5 anti-mouse CD45.1 (antibody)
RRID:AB_893348
This monoclonal targets CD45.1
View all literature mentionsPE/Cyanine7 anti-mouse IgD (antibody)
RRID:AB_2561875
This monoclonal targets IgD
View all literature mentionsAgilent 4150 TapeStation System (instrument resource)
RRID:SCR_019393
System is automated electrophoresis platform for nucleic acid sample quality control. Allows analysis of DNA and RNA samples for up to 16 samples per run. Used for quality control of RNA and DNA samples in next-generation sequencing, biobank, or vaccine development workflows.
View all literature mentionsIllumina NextSeq 2000 system (instrument resource)
RRID:SCR_023614
Sequencing system supports range of methods such as exome sequencing, target enrichment, single-cell profiling.
View all literature mentionsThermo Fisher Qubit fluorimeter (instrument resource)
RRID:SCR_018095
Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds.
View all literature mentionsBD FACS Aria II (instrument resource)
RRID:SCR_018091
Fluorescence activated cell sorting instrument by BD Biosciences. Flow cytometer as high speed fixed alignment benchtop cell sorter. Cytometer can be operated at varied pressures and can acquire up to 70,000 events per second. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.
View all literature mentionsMDCK (cell line)
RRID:CVCL_0422
Cell line MDCK is a Spontaneously immortalized cell line with a species of origin Canis lupus familiaris
View all literature mentionsSartorius Octet BLI systems (instrument resource)
RRID:SCR_023267
Octet BLI systems enable real-time, label-free analysis for determination of kinetics, affinity and antibody/protein quantitation. Includes Octet Analysis Studio for analysis of assays measuring kinetics and affinity values for drug-target binding and high-throughput kinetic screening for lead identification. Typical applications include kinetic analysis of protein-protein, protein-small molecules, antibody-antigen, antibody-VLP, antibody-Fc gamma receptors, including antibody-neonatal receptor (FcRn) interactions. Additional applications supported include lot release and stability analysis of drug molecules based on binding kinetics and affinity.
View all literature mentionsCytiva AKTA pure 25 L chromatography system (instrument resource)
RRID:SCR_023461
Chromatography system for purification in research applications. Allows for customization due to its modular design with flow rate. Available with flow rate of up to 25 mL/min or flow rate of up to 150 mL/min. Offers more than 20 hardware options for custom system, including new UV monitor.Includes Air sensor L9;CELL 2 U KPL;Conductivity monitor C9n Cpl;Injection valve V9-Inj;Instrument control unit, I9, Äkta pure; Mixer M9;Pressure monitor R9-2 with pump restrictor; Pump P9 Cpl 2x; UV Monitor U9-L Cpl;Fraction collector F9-R, Cytiva, CAT# 29011362;Superdex 200 increase 10/300 GL, Cytiva, CAT# 28-9909-44.
View all literature mentionsIllumina MiSeq System (portal)
RRID:SCR_016379
MiSeq System offers wide range of sequencing applications. Capable of automated paired end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits are optimized for variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics.
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RRID:SCR_014230
Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website.
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RRID:SCR_014882
Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis.
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RRID:SCR_015652
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RRID:SCR_015701
Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
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RRID:SCR_014224
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RRID:SCR_014222
Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.
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RRID:SCR_015872
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RRID:SCR_023017
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RRID:SCR_001905
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RRID:SCR_002705
Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
View all literature mentionsPandas (software resource)
RRID:SCR_018214
Software Python package for data analysis providing labeled data structures similar to R data. Provides data structures designed to make working with relational or labeled data. Software as building block for doing practical, real world open source data analysis and manipulation tool.
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RRID:SCR_019186
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RRID:SCR_016341
Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
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RRID:SCR_010236
Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.
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RRID:SCR_017344
Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics.
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RRID:SCR_010519
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
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RRID:SCR_008394
Programming language for all operating systems that lets users work more quickly and integrate their systems more effectively. Often compared to Tcl, Perl, Ruby, Scheme or Java. Some of its key distinguishing features include very clear and readable syntax, strong introspection capabilities, intuitive object orientation, natural expression of procedural code, full modularity, exception-based error handling, high level dynamic data types, extensive standard libraries and third party modules for virtually every task, extensions and modules easily written in C, C (or Java for Python, or .NET languages for IronPython), and embeddable within applications as a scripting interface.
View all literature mentionsIMGT/V-QUEST (service resource)
RRID:SCR_010749
Data analysis service for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. It identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ''Detailed view'', the results and alignments for each submitted sequence individually and, in ''Synthesis view'', the alignments of the sequences that, in a given run, express the same V gene and allele.
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RRID:SCR_021268
GNU Project shell. Sh-compatible shell that incorporates useful features from Korn shell (ksh) and the C shell (csh). Improvements offered by Bash include command-line editing, unlimited size command history,job control,shell functions and aliases,indexed arrays of unlimited size,integer arithmetic in any base from two to sixty four.
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RRID:SCR_002798
Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
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RRID:SCR_008520
Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsC57BL/6J (organism)
RRID:IMSR_JAX:000664
Mus musculus with name C57BL/6J from IMSR.
View all literature mentionscirclize (software resource)
RRID:SCR_002141
Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.
View all literature mentions
B6.SJL-Ptprca Pepc/BoyJ (organism)
RRID:IMSR_JAX:002014
Mus musculus with name B6.SJL-Ptprca Pepc
HEK293-F (cell line)
RRID:CVCL_6642
Cell line HEK293-F is a Transformed cell line with a species of origin Homo sapiens (Human)
View all literature mentionsExpi293F (cell line)
RRID:CVCL_D615
Cell line Expi293F is a Transformed cell line with a species of origin Homo sapiens (Human)
View all literature mentionsFreeStyle 293-F (cell line)
RRID:CVCL_D603
Cell line FreeStyle 293-F is a Transformed cell line with a species of origin Homo sapiens (Human)
View all literature mentions
