Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.

Autor: Liebhoff AM; 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., Venkataraman T; Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA., Morgenlander WR; Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA., Na M; Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA., Kula T; 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., Waugh K; Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA., Morrison C; Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA., Rewers M; Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA., Longman R; Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA., Round J; Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA., Elledge S; 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., Ruczinski I; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA., Langmead B; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA., Larman HB; Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA. hlarman1@jhmi.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Feb 21; Vol. 15 (1), pp. 1577. Date of Electronic Publication: 2024 Feb 21.
DOI: 10.1038/s41467-024-45601-8
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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