{
  "abstract": "Background Despite advances in immunotherapy, durable patient responses remain a minority. This is partly due to the limitations of single-biomarker assays in capturing the full complexity of the TME. Here we present a multi-omics approach leveraging Vizgen’s spatial transcriptomics and proteomics platforms to better investigate the TME. The MERSCOPE® Ultra™ Platform enables high-resolution, spatially resolved analysis of up to 1000 genes, while InSituPlex mIF assays allow for ultrasensitive, high-throughput spatial detection of proteins governing immune-tumor interactions and cell functions. By developing new methods for multi-omics integration, we demonstrate the complementary strength of these assays in revealing the impact of local immune environments on tumor and immune dynamics.Methods Formalin-fixed paraffin-embedded (FFPE) specimens from lung, colon, and breast tumor indications were cut into 5µm sections for both technologies. The MERSCOPE workflow was run using the 815-plex Immune-Oncology (IO) Panel for lung and colon cancer, and the 815-plex Breast Cancer Panel for breast cancer samples. The resulting spatial transcriptomic data was processed for single cell spatial analyses. For mIF experiments, serial sections were stained with 12 primary antibodies using a Leica Biosystems BOND RX autostainer, then imaged on the Zeiss AxioScan.Z1 and analyzed using Vizgen’s STARVUETM platform. To enable joint spatial analyses, MERSCOPE and InSituPlex images were co-registered.Results Spatial transcriptomics revealed enriched immune cell populations in several tumors, guiding the selection of 12 protein biomarkers to validate immune cell subtypes. Concordance between RNA and protein results was established by correlating the expression of shared markers across the 815-gene and InSituPlex panels. To enable high-resolution spatial analysis of both data types within the TME, spatial transcriptomics and proteomics images were co-registered. The resulting multi-omics datasets were then used to explore immune cell infiltration patterns, cell-cell interactions and cytokine landscapes in addition to mapping functional immune cell subsets in multiple tumor indications. This integrative approach allowed for mapping of the transcriptional landscape of immune cell subsets, such as cytotoxic T cells and tumor-associated macrophages, while simultaneously assessing the expression and localization of key functional proteins, including immune checkpoints.Conclusions Integrating gene expression profiling and mIF assays results in a comprehensive, spatially resolved understanding of the TME. This combined approach supports biomarker discovery and interrogation of immune-oncology pathways simultaneously with single cell-based spatial validation. These technologies offer synergistic insights into immune pathways and the immune contexture’s role in modulating the TME.",
  "authors": [
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Angela Vasaturo"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Sudhir Tattikota"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Cassandra R Kysilovsky"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Kevin Hwang"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Renchao Chen"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Manisha Ray"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Chen Chengyi"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Jiang He"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "George Emanuel"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Michael Downing"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Ruben Cardenes"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Lorenz Rognoni"
    }
  ],
  "title": "101 Combining Vizgen’s MERSCOPE gene expression profiling and InSituPlex multiplex immunofluorescence (mIF) to unravel the complexity of the tumor microenvironment (TME)",
  "uid": "00b2f313-1c83-5227-adf9-72785b8c97dc"
}