Sequencing-free Tissue-wide Spatial Profiling of Post-transcriptional Regulations

Abstract

The importance of genetic or epi-genetic heterogeneity has been increasingly recognized, but it has been challenging to profile intracellular post-transcriptional targets with sufficient throughput and resolution at across large-scale tissue samples. This study describes a technique, Spectrum-FISH, for high-throughput, sequencing-free, and tissue-wide spatial profiling of various post-transcriptional targets in acute tissue sections with subcellular resolution. The platform uses a biochip with an array of vertically aligned nanoprobes to effectively extract intracellular molecules for downstream analysis in the coordinates of the large-scale of cells within a tissue slice. As a proof-of-concept, the Spectrum-FISH is used to profile the spatial dynamics of 24 miRNAs and 9 m6A-modified messenger RNAs (m6A-mRNA) in acute olfactory bulb (OB) slices of millimeter scale. The results showed potentially multiomics spatial heterogeneity for the examined post-transcriptional regulations in rodent OB, especially in the outer plexiform layer and granule layer, where highly correlated miRNAs and m6A-mRNAs groups were identified, indicating a potential cooperative involvement of different post-transcriptional regulations at these OB regions.