Spatial transcriptomics identifies immunomodulation and vasculogenesis as pathways distinguishing NF1-associated vs a sporadic cutaneous neurofibroma

Summary: Abstract Body: Cutaneous neurofibromas (CNs) are benign tumors associated with neurofibromatosis type 1 (NF1). Although the presence of multiple CNs is highly specific for NF1 (NF1-CN), non-NF1-associated, single sporadic CNs (sp-CN) are far more common, and histologically identical. NF1-CN develop secondary to mutations in the NF1 gene, leading to RAS/MAPK pathway overactivation. Whole-exome sequencing studies have identified a different mechanism, KIR2DL5 mutation, leading to the development of sp-CN, suggesting that tailored therapeutic approaches may be required for NF1-CN vs sp-CN. Here, we perform, to our knowledge, the first spatial transcriptomics study of NF1-CN and sp-CN, identifying distinctive molecular processes underlying NF1-CN and sp-CN across over 1 million cells. Five NF1-CN from patients with documented NF1 diagnoses and one sp-CN from an adult male patient with no other signs or symptoms of NF1, were assayed with the Visium HD system (10x Genomics). Unsupervised clustering identified 15 transcriptional clusters, 13 of which were shared between all 6 tumor samples. Two additional B-cell subtype clusters unique to NF1-CN were identified, suggesting greater adaptive immunoreactivity in NF1-CN. Overall, NF1-CNs demonstrated greater immune infiltration (i.e., upregulating C3 (p=1.42e-11) and CXCL14 (p=1.35e-08)) and decreased vasculogenesis (i.e., vascular development, p=2.46x10-19) on pathway analysis. Despite this, NF1-CNs comparatively overexpressed APOD (p=2.49e-18), a known regulator of neurofibroma progression that could underlie the increased growth potential of NF1-CN compared with sp-CN. These data suggest that despite histological similarities, NF1-CNs and sp-CNs may have distinct microenvironments that confer differential susceptibility for vasculogenic and immunomodulatory therapeutics. Carina Seah¹, Jeremy Orloff¹, Benjamin D. Hu¹, Hannah Verma¹, Shaan Lalvani¹, Yeriel Estrada¹, Emma Guttman-Yassky¹, Rebecca Brown², Nicholas Gulati¹ 1. Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, United States. 2. Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States. Genetic Disease, Gene Regulation, Gene Therapy & Epigenetics