Spatial transcriptomics reveals heterogeneous schwann cell activity and poor immune infiltration in cutaneous neurofibromas

Summary: Abstract Body: Cutaneous neurofibromas (CNs) are benign skin neoplasms that characterize neurofibromatosis type 1 (NF1) and can cause psychological distress as well as physical pain and discomfort. The spatial organization and function of cell types within CN pathogenesis remains unclear. Better understanding of spatially divergent molecular pathogenesis is needed to inform treatment. Here, we perform spatial transcriptomic analysis on 5 CNs from NF1 patients–capturing transcripts from 970,224 8µm-wide wells–representing, to our knowledge, the largest spatial transcriptomics study of CNs to date. Unsupervised clustering of transcriptional data yielded 13 clusters corresponding to fibroblasts, Schwann-lineage cells, antigen-presenting cells (APCs), lymphocytes, endothelial cells, keratinocytes, and sebaceous glands. Expression of both MTOR (MTOR, AKT1, PIK3CA) and RAS/MAPK (HRAS, KRAS, RAF1) pathways, known to be upregulated in NF1, was found in all CNs. Gene set enrichment of clusters identified upregulation of vascular development (p=1.08e-05) by fibroblasts and APCs throughout superficial areas of the tumors, suggesting attempted vasculature redirection to CNs. Spatially-aware clusters identified a deep apoptotic core of Schwann cells (enriched for apoptosis, p=1.05e-19) surrounded by superficial tumor regions with Schwann cells and proliferative infiltrating cells such as fibroblasts and endothelial cells (upregulated cell motility, p=8.82e-06), along with a peripheral grenz zone and epidermis. Immune cells largely clustered around superficial CN layers and the periphery, demonstrating little infiltration. This suggests that deep and poorly perfused regions of CNs lead to Schwann cell apoptosis, and lack of vasculature may inhibit deep infiltration of tumor-targeting immune mechanisms. Therapies aimed at improving immune infiltration of CNs may facilitate tumor regression. Benjamin D. Hu¹, Hannah Verma¹, Carina Seah¹, Jeremy Orloff¹, Shaan Lalvani¹, Raphaella Lambert¹, Grace Rabinowitz¹, Swaroop Bose¹, Monali NandyMazumdar¹, Yeriel Estrada¹, Joel Correa da Rosa¹, Emma Guttman-Yassky¹, Andrew Ji¹, Kristin Beaumont¹, Rebecca Brown¹, Nicholas Gulati¹ 1. Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, United States. Bioinformatics, Computational Biology, and Imaging