252 The spatial transcriptomic landscape of SCCIS in immunocompetent and immunosuppressed patients

This study defined the in situ transcriptomics of cellular subsets in the epidermis and dermis of lesional and perilesional skin in squamous cell carcinoma in situ (SCCIS), a precursor to cutaneous squamous cell carcinoma (cSCC), to identify novel prognostic and therapeutic biomarkers. Solid organ transplant patients are 65-250 times more likely to develop cSCC and have an 8-fold increased risk of developing metastatic disease compared to non-immunosuppresed cSCC patients. The nanoString GeoMx Digital Spatial Profiler was used to interrogate the whole transcriptome of lesional and perilesional epidermal (CK+) and dermal (CD68+, CD45+ and SYTO13+) cellular subsets in 34 FFPE SCCIS specimens from 18 immunocompetent patients and 12 immunosuppressed, solid organ transplant patients. 664 unique transcriptomic libraries were collected from these two cohorts of specimens. Gene set enrichment analysis and differential expression analysis identified enriched genes (average: 2,939 and 1,295, FDR<0.05) and gene pathways (average: 379 and 398, FDR<0.05) in the lesional vs perilesional epidermis and dermis, respectively. Expected upregulation of Cell Cycle, DNA Replication, nucleotide metabolism and Kinase signaling was seen in the lesional epidermis along with downregulation of Hedgehog signaling. Ubiquitin conjugating enzymes were upregulated including NEURL1B,which has been shown to inhibit Notch signaling. Inter-cohort variabilities were seen that may explain biologic differences in the immunosuppressed patient population. These include downregulation of CXC chemokine signaling including CXCL9 and other immunoregulatory molecules such as MHC class II clusters in the immunosuppressed cohort. These data provide insights into the spatial transcriptomic landscape of cellular subcompartments in SCCIS. While identifying putative novel mechanisms underlying disease biology including post-translational downregulation of Notch and immunoregulatory differences that may contribute to the propensity for disease progression in immunosuppressed patients.