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

A nanoneedle array extracts RNA from individual cells of a fresh tissue slice while preserving spatial organisation, with messenger RNAs, microRNAs and N6-methyladenosine-modified RNAs quantified by multiplexed fluorescence encoding and imaging-based decoding at subcellular resolution.

Spatial transcriptomics remains constrained by cost, workflow complexity, dependence on sequencing and limited access to post-transcriptional regulation in fresh tissues. The authors describe a sequencing-free and amplification-free approach applied to minimally processed fresh tissue slices: a nanoneedle array extracts RNA from individual cells while preserving spatial organisation, and 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 hybridisation, immunostaining and bulk measurements showed sensitivity and spatial fidelity comparable to established spatial transcriptomics methods, at reduced cost and workflow complexity. The method was validated by mapping patterned messenger RNA expression in developing mouse neural tissue and then in the olfactory bulb, a layered region providing a stringent test of spatial heterogeneity, and applicability was demonstrated on human biopsy specimens.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

This is plainly upstream of clinical use: the demonstration is largely murine, the human component is limited to biopsy specimens, and no patient cohort with measured diagnostic or prognostic performance is presented. What deserves attention is the economics, since dispensing with sequencing and amplification would bring spatial transcriptomics within reach of platforms that cannot currently afford it, together with access to the post-transcriptional layer, microRNAs and N6-methyladenosine, that current approaches capture poorly. No consequence for constitutional genetic diagnosis at this stage: the audience is translational research in pathology.

Analysis by Dr Thibaut Benquey