Abstract

Pathways involved in Merkel Cell Carcinoma (MCC) metastasis are poorly understood.  Herein, we leverage spatial transcriptomics with a tumor cell (TC) centric approach to investigate this and uncover possible novel therapeutic targets. Four patients with matched primary and metastatic MCC were selected (8 samples total). Digital spatial profiling was performed after selection of 181 regions of interest (ROI) via Nanostring GeoMX Digital Spatial Profiler (GMX-DSP-1Y). The GeoMx Cancer Transcriptome Atlas assay using RNA expression of 1,800 genes was used. Unsupervised clustering, Gene Set Enrichment Analysis (GSEA) and Differential Gene Expression (DGE) analysis were performed (Cutoffs FDR<0.05, Lg2Fc >2;<-2) comparing Tumor vs TME in primary and metastasis, and primary vs metastasis in Tumor and TME. Pathway analysis showed enrichment for NADH dehydrogenase 1 alpha and beta in primary and metastatic TC (FDR=0.005).  Glycolysis and cholesterol metabolism pathways (FOS/AP-1) upregulation was identified in metastatic TCs (Lg2FC =2.09, FDR=0.02). GSEA identified depleted antigen processing and presentation in both pMCC and mMCC TCs (NES=-1.66, FDR= 0.02; NES=-1.65, FDR= 0.02). DGE corroborated the findings, showing downregulation of Major Histocompatibility Complex (MHC) class I and II in primary and metastatic TCs (Lg2FC= -3.01, FDR= 1.5E-25). pMCC shows downregulation of MHC-I and -II. Glycolysis and lipid metabolomic pathways appear to play a key role in mMCC. The findings provide a rationale to investigate combinational regimens with interferon gamma (to restore the MHC-II expression) along with metabolomic drugs and or immunotherapy in advanced cases.