Fig. 6: Application of TACIT in a Multimodal Single-Slide of a Tertiary Lymphoid Structure.

a Spatial transcriptomics and proteomics assays use segmentation to extract single-cell data, transferring the segmentation mask between experiments. This can lead to marker bleed-through, where in proteomics, immunofluorescence markers stain the edges of adjacent B cells. Similarly, in transcriptomics, probes like the MS4A1 gene are observed outside B cell boundaries in a TLS from a minor salivary gland affected by GVHD. b TACIT and Louvain perform differently when analyzing high-density immune areas, such as TLS. TACIT identifies a more detailed and expected population of immune cells within the TLS compared to Louvain. c A heatmap shows the genes and proteins used by TACIT to define cell signatures. d Voronoi plots illustrate how varying cell assignments lead to different analytical outcomes. TACIT’s reconstruction reveals a diverse mix of immune cells, small vessels, and antigen-presenting cells characteristic of a TLS. e A heatmap displays the genes and proteins used by Louvain to define cell signatures. f Voronoi plots with Louvain show a broad categorization of immune cells, merging them into generalized innate and adaptive groups. g The choice of tools for cell assignment in multi-omics spatial assays impacts downstream analysis. The neighborhood analysis with TACIT illustrates expected cell proximities in a TLS, showing B cells and dendritic cells near small vessels and T cells. Conversely, Louvain shows unilateral interactions, focusing solely on the most abundant structural cell types in the analyzed ROI. h Using a single slide for spatial proteomics and transcriptomics allows for the identification of cell types and the assignment of specific biomolecules like chemokines, interleukins, and immune checkpoints to cells. This method not only reveals cellular patterns but also aids in studying spatial cell-cell communication. ROI reconstruction with TACIT assigned CD247 to T cells, B cells, and macrophages, highlighting diverse interactions. Conversely, the Clustering signature was exclusive to B cells, concentrated around capillaries, with no further interactions. Source data are provided as a Source Data file.