Base by Base9 Okt 2025

162: Spatial miRNomics: technologies, challenges, and opportunities

Robles-Remacho A et al., Trends in Genetics - A concise review of emerging methods to map microRNA (miRNA) expression in tissues with spatial context, covering imaging and sequencing approaches, technical barriers, bioinformatics needs, and clinical implications. Key terms: spatial miRNomics, microRNA, spatial transcriptomics, in situ polyadenylation, Patho-DBiT.

Study Highlights:
Spatial miRNA profiling is an emerging field with established singleplex imaging methods and new sequencing-based strategies that use in situ polyadenylation to capture nonpolyadenylated RNAs. STRS and Patho-DBiT demonstrated the feasibility of detecting hundreds to thousands of miRNAs in tissue sections, including FFPE samples, while imaging-based multiplexing remains limited. Bioinformatic tools such as miTEA-HiRes enable inference of miRNA activity from spatial transcriptomics, but challenges persist in sample fixation, retention, sensitivity for low-abundance miRNAs, and rRNA interference.

Conclusion:
Spatial miRNomics is now technically feasible and has revealed tissue- and disease-specific miRNA patterns, but further advances in multiplexed imaging, single-cell resolution, standardized workflows, and tailored bioinformatics are required to make spatial miRNA profiling routine and clinically actionable.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities

First author:
Robles-Remacho A

Journal:
Trends in Genetics

DOI:
10.1016/j.tig.2025.06.005

Reference:
Robles-Remacho A., Zou Y., Grillo M., Nilsson M. Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities. Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.06.005

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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