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Nanopore approaches for single-molecule temporal omics: promises and challenges

Nature Methods volume 22, pages 241–253 (2025)Cite this article

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Abstract

The great molecular heterogeneity within single cells demands omics analysis from a single-molecule perspective. Moreover, considering the perpetual metabolism and communication within cells, it is essential to determine the time-series changes of the molecular library, rather than obtaining data at only one time point. Thus, there is an urgent need to develop a single-molecule strategy for this omics analysis to elucidate the biosystem heterogeneity and temporal dynamics. In this Perspective, we explore the potential application of nanopores for single-molecule temporal omics to characterize individual molecules beyond mass, in both a single-molecule and high-throughput manner. Accordingly, recent advances in nanopores available for single-molecule temporal omics are reviewed from the view of single-molecule mass identification, revealing single-molecule heterogeneity and illustrating temporal evolution. Furthermore, we discuss the primary challenges associated with using nanopores for single-molecule temporal omics in complex biological samples, and present the potential strategies and notes to respond to these challenges.

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Fig. 1: Recent advances in the spatial and temporal study of omics analysis.
Fig. 2: Single-molecule mass identification at the single-unit level using nanopores.
Fig. 3: Revealing the heterogeneity within the same molecules via confinement, the chemical environment and the interactions inside nanopores.
Fig. 4: Recording and illustrating the temporal evolution of multiple species in real time.
Fig. 5: Integration of protein nanopores and nanopipettes for single-cell temporal omics.

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Acknowledgements

This research was supported by the National Natural Science Foundation of China (22334006 to Y.-T.L., 22304077 to J.J., 22027806 to Y.-T.L. and 22125403 to R.T.).

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  1. These authors contributed equally: Meng-Yin Li, Jie Jiang.

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  1. State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China

    Meng-Yin Li, Jie Jiang, Jun-Ge Li, Hongyan Niu, Yi-Lun Ying & Yi-Tao Long

  2. Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China

    Meng-Yin Li, Hongyan Niu & Yi-Lun Ying

  3. Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, China

    Ruijun Tian

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M.-Y.L. and J.J. contributed equally to this work. M.-Y.L., J.J. and Y.-T.L. researched data and wrote the manuscript. M.-Y.L., J.-G.L. and Y.-L.Y. designed the figures. M.-Y.L., J.J., H.N., R.T. and Y.-T.L. contributed substantially to the discussion of the content of the paper.

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Li, MY., Jiang, J., Li, JG. et al. Nanopore approaches for single-molecule temporal omics: promises and challenges. Nat Methods 22, 241–253 (2025). https://doi.org/10.1038/s41592-024-02492-3

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