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Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn
Open accessPublished version of a preprint
Abstract
We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%. We find that the immune system develops antibodies to human gut bacteria-infecting viruses, particularly E.coli -infecting Myoviridae . Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 26
- Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. Massive expansion of human gut bacteriophage diversity. Cell 184, 1098–1109.e9 (2021). · DOI · Paper page
- Andreu-Sánchez, S. et al. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 56, 1376–1392.e8 (2023). · DOI
- Bourgonje, A. R. et al. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 56, 1393–1409.e6 (2023). · DOI
- Venkataraman, T. et al. Comprehensive profiling of antibody responses to the human anellome using programmable phage display. Cell Rep. 41, 111754 (2022). · DOI
- Grant-McAuley, W. et al. Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment. BMC Infect. Dis. 22, 838 (2022). · DOI
- Larman, H. B. et al. Autoantigen discovery with a synthetic human peptidome. Nat. Biotechnol. 29, 535–541 (2011). · DOI
- Xu, G. J. et al. Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. Science 348, aaa0698 (2015). · DOI
- Monaco, D. R. et al. Profiling serum antibodies with a pan allergen phage library identifies key wheat allergy epitopes. Nat. Commun. 12, 379 (2021). · DOI
- Leviatan, S. et al. Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 55, 2454–2469.e6 (2022). · DOI
- Vogl, T. et al. Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nat. Med. 27, 1442–1450 (2021). · DOI
- Angkeow, J. W. et al. Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses. Immunity 55, 1051–1066.e4 (2022). · DOI
- Mohan, D. et al. PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes. Nat. Protoc. 13, 1958–1978 (2018). · DOI
- Vita, R. et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47, D339–D343 (2019). · DOI
- Shrock, E. L. et al. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 380, eadc9498 (2023). · DOI
- Clifford, J. N. et al. BepiPred-3.0: Improved B-cell epitope prediction using protein language models. Protein Sci. 31, e4497 (2022). · DOI · Paper page
- Singh, H., Ansari, H. R. & Raghava, G. P. S. Improved method for linear B-cell epitope prediction using antigen’s primary sequence. PLoS One 8, e62216 (2013). · DOI
- Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015). · DOI · Paper page
- Jespersen, M. C., Peters, B., Nielsen, M. & Marcatili, P. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 45, W24–W29 (2017). · DOI
- Bernhofer, M. et al. PredictProtein - predicting protein structure and function for 29 years. Nucleic Acids Res. 49, W535–W540 (2021). · DOI
- Arvin, A. M. et al. (eds) Human herpesviruses (Cambridge University Press, Cambridge, England, 2007).
- Monaco, D. R. et al. Deconvoluting virome-wide antibody epitope reactivity profiles. EBioMedicine 75, 103747 (2022). · DOI
- Venkataraman, T. et al. Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait. Immunity 55, 174–184.e5 (2022). · DOI
- Morrison, C. S. et al. Hormonal contraceptive use and HIV disease progression among women in Uganda and Zimbabwe. J. Acquir. Immune Defic. Syndr. 57, 157–164 (2011). · DOI
- Shrock, E. L., Shrock, C. L. & Elledge, S. J. VirScan: High-throughput profiling of antiviral antibody epitopes. Bio Protoc. 12, e4464 (2022). · DOI
- Chen, A., Kammers, K., Larman, H. B., Scharpf, R. B. & Ruczinski, I. Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data. BMC Genomics 23, 654 (2022). · DOI
- Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010). · DOI · Paper page
Metadata
- Authors
- Liebhoff, A.-M., Venkataraman, T., Morgenlander, W. R., Na, M., Kula, T., Waugh, K., Morrison, C., Rewers, M., Longman, R., Round, J., Elledge, S., Ruczinski, I., Langmead, B., & Larman, H. B.
- Affiliations
- Johns Hopkins University (US)
- Brigham and Women's Hospital (US)
- University of Colorado Denver (US)
- Family Health International 360 (US)
- Weill Cornell Medicine (US)
- University of Utah (US)
- Corresponding author
- Larman, H. Benjamin
- ORCID
- Venue
- Nature Communications
- Published
- 2024-02-21
- Volume
- 15
- Issue
- 1
- Pages
- 1577-1577
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10881494
- OpenAlex
- W4391998003
- Cited by
- 10
- References
- 1
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 3
- FWCI
- 1.36
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Leona M. and Harry B. Helmsley Charitable Trust
- National Institutes of Health (DK032493)
- National Institute of General Medical Sciences (R01GM136724, GM136724, T32GM136577, R35GM139602)
- National Institute of Allergy and Infectious Diseases (UM1AI068613)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK032493, R37DK032493, P30DK116073)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- phage immunoprecipitation sequencing, Myoviridae, gut-immune axis
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