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/ Support:Base by Base is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming:❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/spatially-resolved-microrna-expression-in-tissues-technologies-challenges-and-opportunities