Cell-type expression deconvolution of bulk RNA-seq demonstrates an immune response to topical diphencyprone in cutaneous neurofibromas

Summary: Abstract Body: Cutaneous neurofibromas (CNs) are benign tumors associated with neurofibromatosis type 1 (NF1) that pose significant psychosocial and physical burdens to patients. There are currently no effective pharmacologic treatments for CNs. Topical diphencyprone (DPCP) is a hapten that induces hypersensitivity reactions in the skin and has been used therapeutically for cutaneous melanoma metastases. In this clinical trial, DPCP was applied to CNs for 10 weeks after a sensitization period. 36 CN samples of biopsies from day 0, 17 (after first DPCP application), and 107 (30 days after final DPCP application) were assessed by RNA-seq and immunohistochemistry. Single-cell RNA sequencing (scRNA-seq) of 7 CNs was performed to deconvolute bulk RNA-seq data. Cell-type-specific expression profiles were leveraged to impute the cellular composition of the bulk samples. Using Wilcoxon signed rank tests, there was a significant increase in the proportion of the population of macrophages and dendritic cells when comparing day 0 (4.1% of cells) to day 17 (8.1%) (p<0.05). Immunohistochemistry of CD68 and CD11c, markers for macrophages and dendritic cells, respectively, demonstrated significant increases in intensity of staining from day 0 to day 17 (p<0.05). From day 17 to day 107, macrophages and dendritic cells decreased to 4.9%, still higher than baseline (p<0.05). There were no significant proportion changes in vascular endothelial cells, keratinocytes, lymphocytes, neuronal/glial cells, or fibroblasts. These findings indicate a strong influx of immune cells after the first DPCP application, which was largely not sustained 30 days after the final application. DPCP is a promising immunotherapy for CNs, but the optimal application schedule is to be determined. Hannah Verma¹, Benjamin D. Hu¹, Jeremy Orloff¹, Carina Seah¹, Shaan Lalvani¹, Raphaella Lambert¹, Grace Rabinowitz¹, Swaroop Bose¹, Monali NandyMazumdar¹, Joel Correa da Rosa¹, Yeriel Estrada¹, Emma Guttman-Yassky¹, Andrew Ji¹, Rebecca Brown¹, Nicholas Gulati¹ 1. Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, United States. Clinical Research: Interventional Research