Droplet Microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape

Abstract Development of novel chemically- and physically-defined surfaces and environments for cell culture and screening is important for various biological applications. The Droplet Microarray (DMA) platform based on hydrophilic-superhydrophobic patterning enables high-throughput cellular screening in nanoliter volumes and on various biocompatible surfaces. Here we performed phenotypic and transcriptomic analysis of HeLa-CCL2 cells cultured on DMA, with a goal to analyze cellular response on different surfaces and culture volumes down to 3 nL, compared to conventional cell culture platforms. Our results indicate that cells cultured on four tested substrates: nanostructured non-polymer, rough and smooth variants of poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) polymer and poly(thioether) dendrimer, are compatible with cells grown in Petri dish. Cells cultured on nanostructured non-polymer coating exhibited the closet transcriptomic resemblance to that of cells grown in Petri dish. Analysis of cells cultured in 100, 9 and 3 nL media droplets on DMA indicated that all but cells grown in 3 nL volumes had unperturbed viability with minimal alterations in transcriptome compared to 96-well plate. Our findings demonstrate the applicability of DMA for cell-based assays and highlight the possibility of establishing regular cell culture on various biomaterial-coated substrates and in nanoliter volumes, along with routinely used cell culture platforms.