Nanostraw Electroporation for Temporal RNA Sampling from Living 2D and 3D Cell Culture Systems

Traditional gene expression studies extract RNA through destructive cell lysis, restricting analysis to single time points and necessitating parallel samples. This prevents temporal tracking in the same cells and poses challenges for scarce primary samples. To overcome this, we present nanoelectroextraction (NEE), a minimally perturbative, unbiased RNA sampling technique compatible with both 2D and 3D culture systems. NEE utilizes hollow nanostraw membranes with mild electroporation to extract intracellular RNA without compromising cell viability or gene expression, as confirmed by RNA sequencing. The method is compatible with multiple detection platforms, including qPCR and bulk RNA sequencing. We validate NEE across 2D A549 cells, primary normal human lung fibroblasts, human monocyte-derived macrophages, and 3D cancer spheroids. Over 3 days, NEE enables longitudinal tracking of gene expression dynamics, capturing cytokine-induced reprogramming and siRNA-mediated knockdown with strong agreement to lysis controls. NEE thus provides a powerful platform for studying dynamic gene expression in both conventional and complex biological models.