162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities

️ Episode 162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities In this episode of PaperCast Base by Base, we explore how emerging “spatial miRNomics” methods map microRNA expression directly within intact tissues, revealing cell- and region-specific regulatory patterns that bulk and even single-cell assays can miss. Study Highlights:This review charts the field from established singleplex imaging with LNA probes and miRNAscope to early multiplex strategies and sequencing-based workflows that add poly(A) tails in situ to capture small RNAs. It explains how spatial total RNA sequencing (STRS) and Patho-DBiT adapt commercial spatial transcriptomics to detect miRNAs, reporting tissue- and disease-specific signatures in FFPE and fresh-frozen samples. The authors detail fixation chemistry, probe design, and sensitivity constraints unique to short RNAs, and they outline bioinformatic needs including isomiR-aware alignment, rRNA depletion strategies, and target-based activity inference such as miTEA‑HiRes. They close with a roadmap to scale from low-plex detection toward omics-level profiling and clinical translation across oncology, neurology, cardiology, and immune pathology. Conclusion:Spatial miRNomics is poised to unlock the location-specific layer of post-transcriptional regulation, but robust chemistry, higher multiplexing, single-cell resolution, and standardized pipelines are essential for clinical impact. Reference:Robles‑Remacho, A., Zou, Y., Grillo, M., & Nilsson, M. (2025). Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities. Trends in Genetics. 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:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/