Spatial transcriptomics reveals differential inflammatory pathways in discoid lupus erythematosus and lichen planus

Here, we performed spatial transcriptomics using GeoMx® Digital Spatial Profiling, a highly multiplex method for detection of proteins and RNA in fixed tissue (Merritt et al., 2020) to broadly profile immune response pathways in keratinocytes and immune cells between patients with DLE and LP. Specifically, we used the Cancer Transcriptome Atlas (1868 genes) on archived biopsies from patients with DLE (n=9) and LP (n=10) and control skin (n=4). First, tissues were initially stained with morphological markers CD45 and pan-cytokeratin (Pan-CK) to identify regions of interest (ROIs) for subsequent analysis. Cell-masking was used to select mRNA in either keratinocytes (Pan-CK+) or CD45+ immune cells, but no other cells that may have been present in the geometric ROI. A total of 311 segments (CD45+ cells or PanCK+ cells) from 153 ROIs across 23 unique patient samples for a total of 95,823 cells were included in this analysis.