{
  "abstract": "Background Despite remarkable results for many patients, the response rate for immunotherapy varies from one patient to the next. While technological advances have made it possible to study single cells in their native context, samples with lower RNA quality remain challenging for capturing the full complexity and dynamic nature of the tumor-immune microenvironment. Vizgen’s MERSCOPE® Ultra™ platform allows for high-plex, high-resolution, spatially resolved spatial transcriptomic analysis of up to 1000 genes, enabling the study of whole transcriptomic signatures associated with tumor status and the immune system. The Multiplexed Error-Robust Fluorescence in Situ Hybridization (MERFISH) technology facilitates direct RNA profiling in situ with high sensitivity and sub-cellular resolution. With MERFISH 2.0, an enhanced MERFISH workflow that substantially improves the sensitivity of RNA detection, we profiled multiple tumor samples from patients and elucidated how the local immune environment influences gene expression and protein activity in the tumors.Methods Formalin-fixed paraffin-embedded (FFPE) specimens from multiple tumor indications were cut into 5µm sections for spatial transcriptomic measurement. An 815-plex Human Immune-Oncology (IO) Panel was used for lung and colon cancer, and an 815-plex Human Breast Cancer Panel was used for breast cancer samples using the MERFISH 2.0 workflow. The resulting data was used for single cell and spatial analyses.Results MERFISH data was used to map and annotate all cell types in each tumor, showing a significant enrichment of immune cells for certain samples. We showed that in all samples, particularly those with lower RNA quality, MERFISH 2.0 shows excellent detection efficiency for RNA transcripts and subsequent quality of downstream data analysis. Specifically, MERFISH 2.0 allowed for deeper profiling of cellular sub-types and offered enhanced insights into cell-cell communication within the tumor microenvironment. Inter- and intra-tumor immune profiling benefited from increased sensitivity to low-expressing markers, enabling a more comprehensive analysis of the TME. Additionally, evaluating T cell functional states alongside the spatial organization of tumor and immune cells helped define distinct infiltration-driven tumor profiles.Conclusions Spatially resolved transcriptomic profiling of tumor samples at single-cell level offers significant opportunities for understanding how cancers develop and evolve in situ. These improvements enable detailed characterization of tumor heterogeneity and will unlock new insights and new avenues for therapeutic research.",
  "authors": [
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Manisha Ray"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Angela Vasaturo"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Sudhir Tattikota"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Renchao Chen"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Kevin Hwang"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Chen Chengyi"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "George Emanuel"
    },
    {
      "affiliations": [
        "Ultivue by Vizgen, Cambridge, MA, USA"
      ],
      "name": "Lorenz Rognoni"
    },
    {
      "affiliations": [
        "Vizgen, Cambridge, MA, USA"
      ],
      "name": "Jiang He"
    }
  ],
  "title": "102 New developments in spatial transcriptomics using MERFISH 2.0 unlock insights into the tumor microenvironment",
  "uid": "0f2c5bc8-097f-50db-8863-0d79a75a4ca0"
}