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Deciphering the RNA landscapes on mammalian cell surfaces.

Xiao Jiang1, Chu Xu1, Enzhuo Yang1

  • 1Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Protein & Cell
|September 19, 2025
PubMed
Summary

This study introduces novel methods to profile and image cell surface RNAs, revealing diverse non-coding RNAs beyond glycoRNAs on mammalian cells. These techniques confirm membrane localization and abundance of various RNAs, expanding the understanding of cell surface RNA landscapes.

Keywords:
high-throughput sequencinglive cell imaging and quantificationmammalian blood cellssurface RNA landscapes

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • Genomics

Background:

  • Cell surface RNAs, including glycoRNAs, are known but their composition across cell types is poorly understood.
  • Existing methods lack the specificity and sensitivity to comprehensively profile surface RNAs.

Purpose of the Study:

  • To develop and validate a suite of methodologies for profiling, imaging, and quantifying cell surface RNAs.
  • To characterize the diverse landscape of non-coding RNAs present on mammalian cell surfaces.

Main Methods:

  • Developed AMOUR (Amplification-based Method for Unbiased RNA profiling) utilizing T7-based linear amplification.
  • Integrated fluorescently labeled DNA probes with live cell imaging and flow cytometry.
  • Utilized techniques to confirm membrane anchorage and quantify RNA abundance.

Main Results:

  • Identified diverse non-coding RNAs on mammalian cell surfaces, extending beyond previously known glycoRNAs.
  • Confirmed membrane localization and quantified abundance of specific RNAs including Y family RNAs, U5 snRNA, MTRNR2, MT-TA, VTRNA1-1, and XIST.
  • Detailed the surface RNA landscapes of human umbilical cord blood mononuclear cells (hUCB-MNCs) and murine blood cells.

Conclusions:

  • The developed methodologies provide effective approaches for investigating cell surface RNAs.
  • The study expands the known repertoire of cell surface RNAs and provides a detailed characterization of their presence on specific cell types.
  • This work lays the foundation for future research into the functional roles of cell surface RNAs.