PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification

Sara Feola, Markus Haapala, Karita Peltonen, Cristian Capasso, Beatriz Martins, Gabriella Antignani, Antonio Federico, Vilja Pietiäinen, Jacopo Chiaro, Michaela Feodoroff, Salvatore Russo, Antti Rannikko, Manlio Fusciello, Satu Koskela, Jukka Partanen, Firas Hamdan, Sari M. Tähkä, Erkko Ylösmäki, Dario Greco, Mikaela GrönholmTuija Kekarainen, Masoumeh Eshaghi, Olga L. Gurvich, Seppo Ylä-Herttuala, Rui M. Rui, Janne Lehtiö, Tiina M. Sikanen, Vincenzo Cerullo

Research output: Contribution to journalArticleScientificpeer-review


Identification of HLA class I ligands from the tumor surface (ligandome or immunopeptidome) is essential for designing T-cell mediated cancer therapeutic approaches. However, the sensitivity of the process for isolating MHC-I restricted tumor-specific peptides has been the major limiting factor for reliable tumor antigen characterization, making clear the need for technical improvement. Here, we describe our work from the fabrication and development of a microfluidic-based chip (PeptiCHIP) and its use to identify and characterize tumor-specific ligands on clinically relevant human samples. Specifically, we assessed the potential of immobilizing a pan-HLA antibody on solid surfaces via well-characterized streptavidin-biotin chemistry, overcoming the limitations of the cross-linking chemistry used to prepare the affinity matrix with the desired antibodies in the immunopeptidomics workflow. Furthermore, to address the restrictions related to the handling and the limited availability of tumor samples, we further developed the concept toward the implementation of a microfluidic through-flow system. Thus, the biotinylated pan-HLA antibody was immobilized on streptavidin-functionalized surfaces, and immune-affinity purification (IP) was carried out on customized microfluidic pillar arrays made of thiol-ene polymer. Compared to the standard methods reported in the field, our methodology reduces the amount of antibody and the time required for peptide isolation. In this work, we carefully examined the specificity and robustness of our customized technology for immunopeptidomics workflows. We tested this platform by immunopurifying HLA-I complexes from 1 × 106 cells both in a widely studied B-cell line and in patients-derived ex vivo cell cultures, instead of 5 × 108 cells as required in the current technology. After the final elution in mild acid, HLA-I-presented peptides were identified by tandem mass spectrometry and further investigated by in vitro methods. These results highlight the potential to exploit microfluidics-based strategies in immunopeptidomics platforms and in personalized immunopeptidome analysis from cells isolated from individual tumor biopsies to design tailored cancer therapeutic vaccines. Moreover, the possibility to integrate multiple identical units on a single chip further improves the throughput and multiplexing of these assays with a view to clinical needs.

Original languageEnglish
Pages (from-to)15992–16010
JournalACS Nano
Issue number10
Publication statusPublished - 2021
Publication typeA1 Journal article-refereed


  • affinity purification
  • HLA peptides
  • ligandome
  • microfluidics
  • thiol-enes

Publication forum classification

  • Publication forum level 3

ASJC Scopus subject areas

  • Materials Science(all)
  • Engineering(all)
  • Physics and Astronomy(all)


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