Omics have revolutionized biology and medicine. From genomics and transcriptomics to proteomics and metabolomics, these approaches have provided critical insights into the networks of molecular actions, enabling breakthroughs in understanding cellular differentiation, disease mechanisms, and targeted therapies. However, conventional omics studies typically rely on large-scale sample analysis, which yields averaged information from cell populations, obscuring heterogeneity at the single-cell or even single-molecule level, key factors in many biological processes.
Recently, advancements in single-cell and spatial omics have significantly improved resolution of omics studies, enabling the studying of the molecular distributions and functions at the single-cell or subcellular level. Despite these advancements, such approaches remain largely limited to static snapshots. Considering the extensive single-molecule conformation or modification heterogeneity as well as the highly ephemeral metabolites and hormones present in biological organisms, we propose that the temporal evolution of the biomolecular libraries and their states is as significant as the heterogeneity between cells, as biological processes occur one molecule at a time and are thus inherently dynamic. Therefore, increasing the understanding of the complexity of life requires considering the single-molecule and temporal perspectives, which calls for an innovative approach applied to single-molecule temporal omics.
Nanopore was developed as a single-molecule approach mainly for nucleic acid sequencing and their epigenetic modification detection. In principle, nanopores characterize a large quantity of individual molecules one by one without labeling or modification, and indeed offer an intrinsic advantage for satisfying the requirements of obtaining the temporal evolution of diverse molecular types and states needed for single-molecule temporal omics. First, nanopores are extremely sensitive for single-unit/group identification within individual biomolecules (such as DNA, RNA, proteins and polysaccharides), a method that is regarded as ‘mass spectrometry’ (MS) at the single-molecule level. Second, nanopores own the intrinsic capability to identify single-molecule heterogeneity, enabling detection of conformational or modification-state differences in individual molecules. Third, by continuously reading individual molecules, nanopores can quantify multiple species in real time with a temporal resolution of less than half a minute. In particular, nanopore offers a nondestructive approach with the ability to further determine the biomolecule functional characteristics, including substrate binding and product release. Therefore, nanopores could potentially be applied to develop a single-molecule temporal omics approach, although there would be considerable challenges.
While nanopore holds immense promise for single-molecule temporal omics, it faces several key challenges: Signal Specificity: Similar signals from diverse molecules in complex biological samples would reduce detection accuracy; Capture Efficiency: Detecting low-concentration molecules is challenging; Temporal Resolution: Biological molecular dynamics often occur on a second to millisecond scale that are hard to resolve.
The related paper entitled “Nanopore approaches for single-molecule temporal omics: promises and challenges” has been published on Nature Methods on November 18, 2024 (Paper link: https://doi.org/10.1038/s41592-024-02492-3). Dr. Meng-Yin Li and Prof. Yi-Tao Long from our department are the co-corresponding authors. Dr. Meng-Yin Li and Dr. Jie Jiang are the co-first authors. Thanks for Prof. Ruijun Tian from Southern University of Science and Technology for kind discussions on omics studies. This research was supported by the National Natural Science Foundation of China.
Figure 1. Recent advances in the spatial and temporal study of omics analysis.
Figure 2. Single-molecule mass identification at the single-unit level using nanopores.
Figure 3. Revealing the heterogeneity within the same molecules via confinement, the chemical environment and the interactions inside nanopores.
Figure 4. Recording and illustrating the temporal evolution of multiple species in real time.
Figure 5. Integration of protein nanopores and nanopipettes for single-cell temporal omics.
