SPATIAL TRANSCRIPTOMICS FOR MOLECULAR DISSECTING OF THE TUMOR IMMUNE MICROENVIRONMENT: COMPARISON OF COMMERCIALLY AVAILABLE PLATFORMS

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Abstract
Tumor is complex tissue where cancer cell fate strongly depends of multicellular component of the tumor microenvironment (TME). The principal control of cancer cell proliferation, oxygen and nutrient supply, and metastatic potential is provided by intratumor immune components. Cancer cells develop multiple strategies to program intratumor immunity, and to escape the host defense. Single-cell RNA-sequencing (scRNA-seq) methods enable identification of singe cell transcriptome of individual cells in the tumor tissue. However, scRNA-seq analyses single cells in suspension where tumor architecture is damaged. In order to identify the essential and potentially targetable molecular interaction of cancer cells and immune cells in the TME, analysis of the single cell transcriptome in the spatial context is critical. Spatial transcriptomics (ST) methods proved the necessary precision for the understanding tumor tissue architecture and heterogeneity, and allow to examine intercellular molecular communications in the TME. In our review, we have summarized the results of the studies which applied the most popular and commercially available ST technologies in cancer research (10x Genomics Visium, 10x Genomics Xenium, Nanostring GeoMx-DSP, Nanostring CosMx, STOmics, and Vizgen MERSCOPE). We elucidated how these studies were able to decipher the new molecular mechanisms of cancer progression controlled by the immune components of the TME. We focused on the new venues for anti-cancer therapy based on immune cell transcriptomics. We discussed the benefits and limitations of the currently used ST approaches. We also summarized how ST technologies can contribute valuable findings for the tissue and cell atlases of cancer.

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