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, such tumors should be carefully molecularly examined to select and adjust the treatment scheme. Spatial transcriptomics is a promising technology enabling detailed molecular profiling at the transcriptional level, while preserving spatial information within the tumor microenvironment. We are working on establishing a customized version of this technology using a purposely built DNA microarray printer and an in-house developed library preparation protocol.
AIMS: We aim to develop a novel, cost-effective spatial transcriptomics platform that provides an unbiased transcriptome view at single-cell resolution. Designed entirely 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, 10 x 10 μm squared spots with an 11 μm pitch distance and a 5x5 mm tissue capture area, offering single-cell resolution. Custom-printed microarrays, using micromirror-guided photolithography, 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 a glass slide and have optimized a library preparation method, achieving results comparable to commercially available 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. We anticipate the first results on neuroblastoma tissue at ANR 2025.
CONCLUSIONS: Molecular profiling is vital for refining neuroblastoma treatments. Our cost-effective and customizable spatial transcriptomics platform provides single-cell resolution and adapts to diverse research goals, fostering collaborations and advancing precision medicine in neuroblastoma.
