{
  "abstract": "Background The tumor microenvironment (TME) is a complex and dynamic ecosystem playing a crucial role in tumor development, progression, immune evasion, and therapeutic response. Integrating protein expression with complementary outputs, such as mapping cytokine and chemokine-expressing cells, is crucial to unveiling functional cell states and mechanisms of cancer progression. 1 2 However, accurately visualizing secreted molecules while preserving spatial context still remains a significant challenge in spatial biology.In this study, we employed an automated hyperplex multiomics approach to simultaneously detect protein and RNA expression, providing an in-depth cellular profiling of the TME across a variety of cancer types.Methods We analyzed a formalin-fixed paraffin-embedded Tissue Microarray (TMA) comprising specimens of multiple human cancer types, namely prostate cancer, lung cancer, breast cancer, colorectal cancer, melanoma, and lymphoma. A TMA section was stained and imaged on the COMET™ automated platform, integrating RNAscope™ 3 HiPlex Pro and sequential immunofluorescence (seqIF™).4 This multiomics approach enabled concomitant detection of up to 12 RNA and over 50 protein targets on the same tissue section. The resulting image was analyzed using the HORIZON™ software to reveal in situ single-cell level features and spatially map their distribution.Results The high-plex proteomic panel enabled detailed characterization of the TME composition, including tumor cells, a large variety of immune cell subsets, cancer-associated fibroblasts, vasculature, and markers of cell state and activation, including cell division and immune checkpoints. The combined detection of transcripts encoding secreted molecules, such as cytokines and chemokines, provided insight into local immune activity and cell-cell communication within the tumor and surrounding stromal compartments.Conclusions This automated multiomics workflow enables comprehensive analysis of the TME across multiple cancer types, while significantly reducing the experimental turnover and sample consumption. Multiomics spatial profiling at single-cell resolution opens new opportunities to explore the cellular interactions at the tumor-immune interface and identify functional states relevant to immunotherapy and disease progression.References Ferri-Borgogno S, et al. Molecular, metabolic, and subcellular mapping of the tumor immune microenvironment via 3D targeted and non-targeted multiplex multi-omics analyses. Cancers (Basel). 2024 Feb 20;16(5):846. doi: 10.3390/cancers16050846.Yi M, et al. Targeting cytokine and chemokine signaling pathways for cancer therapy. Signal Transduct Target Ther. 2024 Jul 22;9(1):176. doi: 10.1038/s41392-024-01868-3.Wang F et al. RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues. J Mol Diagn. 2012 Jan;14(1):22–9. doi: 10.1016/j.jmoldx.2011.08.002.Rivest F, et al. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci Rep. 2023;13(1):16994. doi: 10.1038/s41598-023-43435-w.",
  "authors": [
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Marion Bonnet"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Cansaran Saygili Demir"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Kim Van Den Handel"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Pedro Machado Almeida"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Lionel Arn"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Lorenzo Bruno"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Debia Wakhloo"
    },
    {
      "affiliations": [
        "Advanced Cell Diagnostics, a Bio-Techne Brand, Newark, CA, USA"
      ],
      "name": "Anushka Dikshit"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Maria-Giuseppina Procopio"
    },
    {
      "affiliations": [
        "Lunaphore Technologies, Tolochenaz, Switzerland"
      ],
      "name": "Saška Brajkovic"
    }
  ],
  "title": "1241 Spatial multiomics approach for comprehensive characterization of the tumor microenvironment across various cancer types",
  "uid": "98f5dc0d-64a6-5f4e-9c99-f3df8f7bb17e"
}