A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines

  1. Sara Feola
  2. Jacopo Chiaro
  3. Beatriz Martins
  4. Salvatore Russo
  5. Manlio Fusciello
  6. Erkko Ylösmäki
  7. Chiara Bonini
  8. Eliana Ruggiero
  9. Firas Hamdan
  10. Michaela Feodoroff
  11. Gabriella Antignani
  12. Tapani Viitala
  13. Sari Pesonen
  14. Mikaela Grönholm
  15. Rui MM Branca
  16. Janne Lehtiö
  17. Vincenzo Cerullo  Is a corresponding author
  1. University of Helsinki, Finland
  2. University Vita e Salute San Raffaele, Italy
  3. University of Helsinki, Finland
  4. Valo Therapeutics Oy, Finland
  5. Karolinska Institutet, Sweden
  6. Karolinska Institute, Sweden

Abstract

Beside the isolation and identification of MHC-I restricted peptides from the surface of cancer cells, one of the challenges is eliciting an effective anti-tumor CD8+ T cell mediated response as part of therapeutic cancer vaccine. Therefore, the establishment of a solid pipeline for the downstream selection of clinically relevant peptides and the subsequent creation of therapeutic cancer vaccines are of utmost importance. Indeed, the use of peptides for eliciting specific anti-tumor adaptive immunity is hindered by two main limitations: the efficient selection of the most optimal candidate peptides and the use of a highly immunogenic platform to combine with the peptides to induce effective tumor-specific adaptive immune responses. Here, we describe for the first time a streamlined pipeline for the generation of personalized cancer vaccines starting from the isolation and selection of the most immunogenic peptide candidates expressed on the tumor cells and ending in the generation of efficient therapeutic oncolytic cancer vaccines. This immunopeptidomics-based pipeline was carefully validated in a murine colon tumor model CT26. Specifically, we used state-of-the-art immunoprecipitation and mass spectrometric methodologies to isolate >8000 peptide targets from the CT26 tumor cell line. The selection of the target candidates was then based on two separate approaches: RNAseq analysis and the HEX software. The latter is a tool previously developed by Chiaro et al. (1), able to identify tumor antigens similar to pathogen antigens, in order to exploit molecular mimicry and tumor pathogen cross-reactive T-cells in cancer vaccine development. The generated list of candidates (twenty-six in total) was further tested in a functional characterization assay using interferon-g ELISpot (Enzyme-Linked Immunospot), reducing the number of candidates to six. These peptides were then tested in our previously described oncolytic cancer vaccine platform PeptiCRAd, a vaccine platform that combines an immunogenic oncolytic adenovirus (OAd) coated with tumor antigen peptides. In our work, PeptiCRAd was successfully used for the treatment of mice bearing CT26, controlling the primary malignant lesion and most importantly a secondary, non-treated, cancer lesion. These results confirmed the feasibility of applying the described pipeline for the selection of peptide candidates and generation of therapeutic oncolytic cancer vaccine, filling a gap in the field of cancer immunotherapy, and paving the way to translate our pipeline into human therapeutic approach.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD026463. The ligandome dataset is currently hidden but will be made public upon eventual acceptance of the current manuscript.Reviewer Account details for ligandome data accessing: https://www.ebi.ac.uk/pride/login PXD026463Username: reviewer_pxd026463@ebi.ac.ukPassword: oMUWIAw3

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

Article and author information

Author details

  1. Sara Feola

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4012-4310
  2. Jacopo Chiaro

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  3. Beatriz Martins

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  4. Salvatore Russo

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  5. Manlio Fusciello

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  6. Erkko Ylösmäki

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  7. Chiara Bonini

    Experimental Hematology Unit, University Vita e Salute San Raffaele, Milan, Italy
    Competing interests
    No competing interests declared.
  8. Eliana Ruggiero

    Experimental Hematology Unit, University Vita e Salute San Raffaele, Milan, Italy
    Competing interests
    No competing interests declared.
  9. Firas Hamdan

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  10. Michaela Feodoroff

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6094-9838
  11. Gabriella Antignani

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  12. Tapani Viitala

    Pharmaceutical Biophysics Research Group, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9074-9450
  13. Sari Pesonen

    Valo Therapeutics Oy, Helsinki, Finland
    Competing interests
    Sari Pesonen, is an employee and a shareholder at VALO Therapeutics.
  14. Mikaela Grönholm

    Drug Research Program (DRP) ImmunoViroTherapy Lab, University of Helsinki, Helsinki, Finland
    Competing interests
    No competing interests declared.
  15. Rui MM Branca

    Department of Oncology-Pathology, Karolinska Institutet, stockholm, Sweden
    Competing interests
    No competing interests declared.
  16. Janne Lehtiö

    Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8100-9562
  17. Vincenzo Cerullo

    ImmunoVirothearpy Lab, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
    For correspondence
    vincenzo.cerullo@helsinki.fi
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4901-3796

Funding

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

Ethics

Animal experimentation: All animal experiments were reviewed and approved by the Experimental Animal Committee of the University of Helsinki and the Provincial Government of Southern Finland (license number ESAVI/11895/2019).4-6 weeks old female Balb/cOlaHsd mice were obtained from Envigo (Laboratory, Bar Harbor, Maine UK).

Reviewing Editor

  1. Ping-Chih Ho, Ludwig Institute for Cancer Research, Switzerland

Publication history

  1. Preprint posted: June 9, 2021 (view preprint)
  2. Received: June 11, 2021
  3. Accepted: March 1, 2022
  4. Accepted Manuscript published: March 22, 2022 (version 1)
  5. Version of Record published: April 7, 2022 (version 2)

Copyright

© 2022, Feola 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.

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  1. Sara Feola
  2. Jacopo Chiaro
  3. Beatriz Martins
  4. Salvatore Russo
  5. Manlio Fusciello
  6. Erkko Ylösmäki
  7. Chiara Bonini
  8. Eliana Ruggiero
  9. Firas Hamdan
  10. Michaela Feodoroff
  11. Gabriella Antignani
  12. Tapani Viitala
  13. Sari Pesonen
  14. Mikaela Grönholm
  15. Rui MM Branca
  16. Janne Lehtiö
  17. Vincenzo Cerullo
(2022)
A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines
eLife 11:e71156.
https://doi.org/10.7554/eLife.71156
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