Application of microRNA In Situ Hybridization on Long-term Stored Human Formalin-fixed Paraffin-embedded Brain...

Here, we report that long-term stored human brain samples, formalin-fixed paraffin-embedded (FFPE) from The Brain Collection, University of Southern Denmark, Denmark ( https://www.sdu.dk/en/forskning/bridge/the-brain-collection ), can be used for in situ hybridization (ISH) analysis of selected microRNAs (miRNAs). The Human Brain Collection consists of brains from 9479 subjects who died at a Danish State Mental Hospital in the period of 1945-1982. In the present study we included tissue specimens from prefrontal cortex (PFC) and hippocampus (HIP) from 163 patients diagnosed with schizophrenia, bipolar disorder, or major depressive disorder. Initially, the Nanostring nCounter platform was used to identify miRNA candidates for ISH analysis using the miRNAscope technology. Based on the Nanostring nCounter quantifications with bulk tissue, we identified and selected 10 miRNAs from PFC (miR-9-5p, miR-29b-3p, miR-30c-5p, miR-124-3p, miR-125b-5p, miR-138-5p, miR-181a-5p, miR-224-5p, miR-302d-3p, and miR-432-5p) and 6 miRNAs from HIP (let-7a-5p, miR-7-5p, miR-124-3p, miR-127-3p, miR-145-5p and miR-149-5p). miRNAscope ISH analysis was then performed with the respective probes on 30 PFC and 30 HIP samples, respectively. In the PFC six miRNAs (miR-9-5p, miR-29b-3p, miR-124-3p, miR-125b-5p, miR-138-5p, and miR-181a-5p) were detected and four (miR-145-5p, let-7a-5p, miR-124-3p and miR-7-5p) in the HIP samples. In both brain regions miR-124-3p was the most abundantly expressed. We conclude, that the combination of the Nanostring nCounter technology and the miRNAscope analysis is a valid approach to study spatial expression of specific miRNAs in these up to 76 years old FFPE blocks. This opens a new avenue of possibilities for studying the underlying epigenetic mechanisms in mental disorders.