Comparison of skin spatial transciptomics before and after IL-1-targeted biological treatment in Pityriasis rubra pilaris

Pityriasis rubra pilaris (PRP) is a rare inflammatory skin disease with a poorly understood pathogenesis. Through a molecularly-driven precision medicine approach and an extensive mechanistic pathway analysis we identified IL-1ß as a key mediator, orchestrating an NF-?B-mediated IL-1ß-CCL20 axis. Treatment with the IL-1-antagonists anakinra and canakinumab in patients resulted in rapid clinical improvement. Here we show by spatial profiling that in skin samples after treatment the molecular signature of the PRP was reversed: positive DEGs before treatment showed significant negative enrichment after treatment; the same accounts for GSEA analysis of selected pathways of interest, such as TNF-alpha signaling via NF-kB; predicted activation scores of IPA annotations for disease, pathways, and upstream regulator exhibited a significant negative correlation between active PRP and after treatment; and finally IPA mechanistic network analysis showed that gene regulation arising from IL1B was reversed with treatment. Overall design: Skin biopsies from active PRP lesions were taken from two patients before and at week 8 of anakinra treatment. The biopsies were processed using the GeoMx Human Whole Transcriptome Atlas (WTA). This technique utilizes mRNA-specific in situ hybridization probes linked to distinct DNA barcodes. Upon selection of a "region of interest" (ROI), these barcodes are detached using UV cleavage. Subsequently, the extracted RNA undergoes sequencing on an Illumina system, generating a transcriptome for each designated ROI. Specific ROIs targeted were the epidermis (Pan-CK), CD3+ and CD68+ cells, but due to low overall counts in ROIs, the samples were all pooled together, to increase statistical power. This resulted in 24 technical replicates for patient 1 (13 pre-treatment, 11 during treatment) and 26 for patient 2 (13 pre-treatment, 13 during treatment).