Development of a custom spatial -omics platform using a photolithographic DNA printer

BACKGROUND: High-risk neuroblastoma tumors respond differently to therapy due to their unique molecular makeup and tumor microenvironment. Therefore, molecularly profiling of these tumors helps tailoring treatment. Spatial transcriptomics enables detailed transcriptional profiling while preserving spatial context. We are working on a customized version of this technology using a DNA microarray printer and an in-house developed library preparation protocol.

AIMS: We aim to develop a novel, cost-effective spatial transcriptomics platform, providing an unbiased transcriptome view at single-cell resolution. Designed in-house, the platform is highly versatile, supporting applications such as mRNA profiling (transcriptome-wide or targeted) and targeted (methylated) DNA analyses.

METHODS: Currently in its final developmental stage, the platform features up to four subarrays of 85 000, 14x14 µm spots with a 15 µm pitch distance and a 5x5 mm tissue capture area, offering single-cell resolution. Custom-printed microarrays cost under €100 each, significantly reducing costs compared to commercial alternatives. A working version of a whole transcriptome 3’ end RNA-seq protocol is operational, with modifications under development.

RESULTS: Currently, we can generate fluorescent cDNA footprints on glass slides and have optimized a library preparation method, achieving results comparable to commercial bulk RNA-seq library preparation methods. Regarding the in situ synthesized probe sequence quality, the barcode recall is 75% at 99% precision. Upon integrating all workflow elements, our spatial transcriptomics platform is nearly ready to deliver results.

CONCLUSIONS: Molecular profiling refines neuroblastoma treatment. Our affordable, customizable spatial transcriptomics platform enables single-cell resolution and supports diverse research goals fostering advances in precision medicine in neuroblastoma.