1. Immunology and Inflammation

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding

  1. Brooke D Huisman
  2. Zheng Dai
  3. David K Gifford
  4. Michael E Birnbaum  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
https://doi.org/10.7554/eLife.78589
Share this article
Cite this article
  1. Brooke D Huisman
  2. Zheng Dai
  3. David K Gifford
  4. Michael E Birnbaum
(2022)
A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding
eLife 11:e78589.
https://doi.org/10.7554/eLife.78589
  2. Download BibTeX
  3. Download .RIS

Abstract

T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. While the peptide datasets show broad agreement with previously described MHC-binding motifs, they additionally reveal experimentally validated computational false positives and false negatives. We therefore present this approach as able to complement current experimental datasets and computational predictions. Further, our yeast display approach underlines design considerations for epitope identification experiments and serves as a framework for examining relationships between viral conservation and MHC binding, which can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of our approach to determine peptide-MHC binding interactions in a manner that can supplement and potentially enhance current algorithm-based approaches.

Data availability

All deep sequencing data are deposited on the Sequence Read Archive (SRA), with accession codes PRJNA806475 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA806475] and PRJNA708266 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA708266]. Processed peptide data is provided as a supplemental dataset with this submission. Source data for FP measurements listed in Figure 4 is provided with this submission.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Brooke D Huisman

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6229-6498

  2. Zheng Dai

    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.

  3. David K Gifford

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    David K Gifford, is a founder of ThinkTx..

  4. Michael E Birnbaum

    Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    mbirnb@mit.edu
    Competing interests
    Michael E Birnbaum, is an equity holder in 3T Biosciences, and is a co-founder, equity holder, and consultant of Viralogic Therapeutics and Abata Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2281-3518

Funding

National Institutes of Health (P30-CA14051)

  • Michael E Birnbaum

David and Lucile Packard Foundation

  • Michael E Birnbaum

Schmidt Futures

  • David K Gifford
  • Michael E Birnbaum

National Science Foundation

  • Brooke D Huisman

National Institutes of Health (U19-AI110495)

  • Michael E Birnbaum

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Huisman et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,769
    views
  • 465
    downloads
  • 14
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Brooke D Huisman
  2. Zheng Dai
  3. David K Gifford
  4. Michael E Birnbaum
(2022)
A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding
eLife 11:e78589.
https://doi.org/10.7554/eLife.78589

Share this article

https://doi.org/10.7554/eLife.78589

Categories and tags

Research organisms

Further reading

    1. Immunology and Inflammation

    Adipocyte microRNA-802 promotes adipose tissue inflammation and insulin resistance by modulating macrophages in obesity

    Yue Yang, Bin Huang ... Fangfang Zhang
    Research Article

    Adipose tissue inflammation is now considered to be a key process underlying metabolic diseases in obese individuals. However, it remains unclear how adipose inflammation is initiated and maintained or the mechanism by which inflammation develops. We found that microRNA-802 (Mir802) expression in adipose tissue is progressively increased with the development of dietary obesity in obese mice and humans. The increasing trend of Mir802 preceded the accumulation of macrophages. Adipose tissue-specific knockout of Mir802 lowered macrophage infiltration and ameliorated systemic insulin resistance. Conversely, the specific overexpression of Mir802 in adipose tissue aggravated adipose inflammation in mice fed a high-fat diet. Mechanistically, Mir802 activates noncanonical and canonical NF-κB pathways by targeting its negative regulator, TRAF3. Next, NF-κB orchestrated the expression of chemokines and SREBP1, leading to strong recruitment and M1-like polarization of macrophages. Our findings indicate that Mir802 endows adipose tissue with the ability to recruit and polarize macrophages, which underscores Mir802 as an innovative and attractive candidate for miRNA-based immune therapy for adipose inflammation.

    1. Immunology and Inflammation

    T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells

    Josep Garnica, Patricia Sole ... Pere Santamaria
    Research Article

    Chronic antigenic stimulation can trigger the formation of interleukin 10 (IL-10)-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that murine T-follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process. At the single-cell level, the TFH-to-TR1 cell transition is accompanied by both, downregulation of TFH cell-specific gene expression due to loss of chromatin accessibility, and upregulation of TR1 cell-specific genes linked to chromatin regions that remain accessible throughout the transdifferentiation process, with minimal generation of new open chromatin regions. By interrogating the epigenetic status of accessible TR1 genes on purified TFH and conventional T-cells, we find that most of these genes, including Il10, are already poised for expression at the TFH cell stage. Whereas these genes are closed and hypermethylated in Tconv cells, they are accessible, hypomethylated, and enriched for H3K27ac-marked and hypomethylated active enhancers in TFH cells. These enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors TOX-2, IRF4, and c-MAF. Together, these data suggest that the TR1 gene expression program is genetically imprinted at the TFH cell stage.

    1. Genetics and Genomics
    2. Immunology and Inflammation

    ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis

    Stephanie Guillet, Tomi Lazarov ... Frédéric Geissmann
    Research Article

    Systemic lupus erythematosus (SLE) is an autoimmune disease, the pathophysiology and genetic basis of which are incompletely understood. Using a forward genetic screen in multiplex families with SLE, we identified an association between SLE and compound heterozygous deleterious variants in the non-receptor tyrosine kinases (NRTKs) ACK1 and BRK. Experimental blockade of ACK1 or BRK increased circulating autoantibodies in vivo in mice and exacerbated glomerular IgG deposits in an SLE mouse model. Mechanistically, NRTKs regulate activation, migration, and proliferation of immune cells. We found that the patients’ ACK1 and BRK variants impair efferocytosis, the MERTK-mediated anti-inflammatory response to apoptotic cells, in human induced pluripotent stem cell (hiPSC)-derived macrophages, which may contribute to SLE pathogenesis. Overall, our data suggest that ACK1 and BRK deficiencies are associated with human SLE and impair efferocytosis in macrophages.