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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. Nat Commun 2024; 15:1577. [PMID: 38383452 PMCID: PMC10881494 DOI: 10.1038/s41467-024-45601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
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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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - William R Morgenlander
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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