{
  "abstract": "Background Protein-protein interactions (PPIs) act as a crucial communication system between cells and their local surrounding environment to maintain cellular homeostasis. The dysregulation of this process is involved in affecting the course of several pathogenesis, including cancer. Notably, the interaction of Programmed cell Death Ligand 1 (PD-L1) on tumor cells binding to the Programmed cell Death Protein 1 (PD-1) receptor on immune cells is a key mechanism employed by cancer cells to evade the immune response. Regardless of the success of PD-1/PD-L1 checkpoint inhibitor immunotherapies, a correct patient stratification for these therapies has been challenging. The spatial investigation of PD-1/PD-L1 and other PPIs in the multiomics data framework holds the potential to deeply reveal the interplay of cellular components for a better understanding and forecasting of the clinical outcomes.Methods We developed a fully automated multiplex workflow on the COMETTM platform capable of staining and imaging protein-protein interactions, mRNA and protein biomarkers on the same FFPE tissue slide, at subcellular resolution. RNAscopeTM HiPlex Pro and sequential immunofluorescence (seqIFTM), for RNA and protein marker detection respectively, were combined with an assay exploiting oligonucleotide-conjugated antibodies and the specificity and sensitivity of RNAscopeTM technology for efficient protein proximity detection.Results As a proof-of-concept for our spatial multiomics assay, we showed the co-detection of PD-1 and PD-L1 protein interaction, alongside RNA targets and protein biomarkers in their spatial context in FFPE human tissues. The specificity of the PPI signal was validated by comparing it with sequential immunofluorescence staining of individual PD-1 and PD-L1 antibodies on the same tissue section. Additionally, the cell phenotyping of the surrounding region was investigated by a panel of RNA targets and protein biomarkers specific to diverse immune and stromal cell populations.Conclusions The integration of PPI assays on the multiomics workflow of the COMETTM platform is a powerful strategy to investigate protein interactions directly in their spatial settings. The flexibility of the technique in the choice of the markers under investigation opens a large potential for new biomarker discovery and validation of new clinically relevant interactions, for improving patient stratification and development of novel immunotherapies.",
  "authors": [
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Alice Comberlato"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Pino Bordignon"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Arec Manoukian"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Ge-Ah Kim"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Sonali A Deshpande"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Li-Chong Wang"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Alexandre Kehren"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Maithreyan Srinivasan"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Saška Brajkovic"
    }
  ],
  "title": "61 Fully automated multiomics assay for co-detection of protein-protein interactions, RNA and protein markers on the same tissue section",
  "uid": "ef8c79a9-ac27-54d1-8e4c-bb6efe994f5b"
}