Spatial transcriptomics tools enable the detection and localization of hundreds to thousands of transcripts in biological tissues. However, most technologies are not designed to detect microRNAs. Existing technologies should be expanded to incorporate these key molecular regulators and enable more-comprehensive transcriptomic studies that will shape the new field of spatial miRNomics.
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References
Wienholds, E. et al. MicroRNA expression in zebrafish embryonic development. Science 309, 310–311 (2005).
Moses, L. & Pachter, L. Museum of spatial transcriptomics. Nat. Methods 19, 534–546 (2022).
Nemeth, K. et al. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat. Rev. Genet. 25, 211–232 (2024).
Rishik, S. et al. miRNATissueAtlas 2025: an update to the uniformly processed and annotated human and mouse non-coding RNA tissue atlas. Nucleic Acids Res. 53, D129–D137 (2025).
Yi, M. et al. The role of cancer-derived microRNAs in cancer immune escape. J. Hematol. Oncol. 13, 25 (2020).
Telonis, A. G. et al. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res. 45, 2973–2985 (2017).
McKellar, D. et al. Spatial mapping of the total transcriptome by in situ polyadenylation. Nat. Biotechnol. 41, 513–520 (2023).
Bai, Z. et al. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 187, 6760–6779 (2024).
Stark, R., Grzelak, M. & Hadfield, J. RNA sequencing: the teenage years. Nat. Rev. Genet. 20, 631–656 (2019).
Pena, J. T. G. et al. miRNA in situ hybridization in formaldehyde and EDC - Fixed tissues. Nat. Methods 6, 139–141 (2009).
Acknowledgements
The authors acknowledge funding from the Swedish Research Council (2024-02533) and Cancerfonden (24-3457). A. R.-R. thanks the Alfonso Martín Escudero Foundation for supporting his postdoctoral grant.
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Robles-Remacho, A., Nilsson, M. Spatial miRNomics: towards the integration of microRNAs in spatial biology. Nat Rev Genet 26, 291–292 (2025). https://doi.org/10.1038/s41576-025-00819-0
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DOI: https://doi.org/10.1038/s41576-025-00819-0
