Sequencing-free spatial profiling of post-transcriptional regulation in fresh tissues using nanoneedle arrays

Spatial transcriptomics has transformed tissue analysis but remains constrained by high cost, complex workflows, sequencing dependence and limited access to post-transcriptional regulation in fresh tissues. Here we present a sequencing-free and amplification-free approach for the spatial profiling of post-transcriptional regulation across large tissue sections. The method operates on fresh, minimally processed tissue slices using a nanoneedle array to extract RNA molecules from individual cells while preserving spatial organization. Messenger RNAs, microRNAs and N⁶-methyladenosine-modified RNAs are quantified by multiplexed fluorescence encoding and imaging-based decoding at subcellular resolution. Benchmarking against fluorescence in situ hybridization, immunostaining and bulk measurements demonstrates sensitivity and spatial fidelity comparable to established spatial transcriptomics methods, with reduced cost and workflow complexity. We validate the approach by mapping patterned messenger RNA expression in developing mouse neural tissue and applying it to the olfactory bulb, a layered brain region that provides a stringent test of spatial heterogeneity. Finally, we demonstrate applicability to human biopsy specimens, enabling low cost spatial multi-omics analysis relevant to disease stratification and prognosis.