Spatial lipidomic profiling of cutaneous melanoma using electroporation-based biopsy reveals subtype-specific metabolic alterations

Cutaneous melanoma is a highly aggressive skin cancer with rising global incidence. Although understanding melanoma metabolism requires spatially resolved molecular information, conventional excisional sampling offers limited access to spatial gradients within tumors. Here, we introduce a handheld electroporation-based biopsy (e-biopsy) device, a newly engineered tool that delivers controlled pulsed electric fields to transiently permeabilize cells and extract intracellular molecules directly from tissue. This minimally invasive, probe-based approach enables rapid, localized molecular harvesting without surgical excision, offering a fundamentally new route for in situ tumor profiling. Using this handheld system, we obtained paired molecular samples from tumor centers and margins in 44 locations across 21 melanoma patients, including superficial spreading melanoma and malignant melanoma in situ. Mass-spectrometry analysis of e-biopsy extracts identified 85 lipid species and revealed reproducible spatial metabolic patterns. While the device enabled consistent extraction across regions, tumor centers displayed a reduced presence of select triacylglycerols (TG), ether-linked lysophosphatidylcholines (LPCs), and phosphatidylcholine (PC) PC(32:1). Certain species, including LPC(16:0e) and TG(15:0_16:1_18:1), were absent or markedly diminished centrally. Subtype comparisons showed limited differences at tumor cores but margin-specific TG variations. This study demonstrates that the handheld e-biopsy device provides a novel, minimally invasive platform for spatial metabolic characterization of melanoma.