2. Academic Validation
  3. Deciphering the RNA Landscapes on Mammalian Cell Surfaces

Deciphering the RNA Landscapes on Mammalian Cell Surfaces

  • Protein Cell. 2025 Sep 18:pwaf079. doi: 10.1093/procel/pwaf079.
Xiao Jiang 1,  Chu Xu 1,  Enzhuo Yang 1,  Danhua Xu 2,  Yong Peng 3,  Xue Han 1,  Jingwen Si 4 5,  Qixin Shao 1,  Zhuo Liu 1,  Qiuxiao Chen 1,  Weizhi He 1,  Shuang He 1,  Yanhui Xu 1,  Chuan He 6 7,  Xinxin Huang 2,  Lulu Hu 1 4
Affiliations

Affiliations

  • 1 Cancer 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.
  • 2 Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
  • 3 Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
  • 4 Sycamore Research Institute of Life Sciences, Shanghai, 201203, China.
  • 5 Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
  • 6 Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
  • 7 Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.
PMID: 40973153 DOI: 10.1093/procel/pwaf079
Abstract

Cell surface RNAs, notably glycoRNAs, have been reported, yet the precise compositions of surface RNAs across different primary cell types remain unclear. Here, we introduce a comprehensive suite of methodologies for profiling, imaging, and quantifying specific surface RNAs. We present AMOUR, a method leveraging T7-based linear amplification, to accurately profile surface RNAs while preserving plasma membrane integrity. By integrating fluorescently labeled DNA probes with live primary cells, and employing imaging along with flow cytometry analysis, we can effectively image and quantify representative surface RNAs. Utilizing these techniques, we have identified diverse non-coding RNAs present on mammalian cell surfaces, expanding beyond the known glycoRNAs. We confirm the membrane anchorage and quantify the abundance of several representative surface RNA molecules in cultured HeLa cells and human umbilical cord blood mononuclear cells (hUCB-MNCs). Our imaging and flow cytometry analyses unequivocally confirm the membrane localization of Y family RNAs, spliceosomal snRNA U5, mitochondrial rRNA MTRNR2, mitochondrial tRNA MT-TA, VTRNA1-1, and the long non-coding RNA XIST. Our study not only introduces effective approaches for investigating surface RNAs but also provides a detailed portrayal of the surface RNA landscapes of hUCB-MNCs and murine blood cells, paving the way for future research in the field of surface RNAs.

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