Kamei Ken-Ichiro F, Wakamoto Yuichi
Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
Research Center for Complex Systems Biology, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
Microscopy (Oxf). 2025 Jun 26;74(3):189-200. doi: 10.1093/jmicro/dfaf020.
Genome-wide profiling of gene expression levels in cells, such as transcriptomics and proteomics, is a powerful experimental approach in modern biology, allowing not only efficient exploration of the genetic elements responsible for biological phenomena of interest, but also characterization of the global constraints behind plastic phenotypic changes of cells that accompany large-scale remodeling of omics profiles. To understand how individual cells change their molecular profiles to achieve specific phenotypic changes in phenomena such as differentiation, cancer metastasis and adaptation, it is crucial to characterize the dynamics of cellular phenotypes and omics profiles simultaneously at the single-cell level. Especially in the last decade, significant technical progress has been made in the in situ identification of omics profiles of cells on the microscope. However, most approaches still remain destructive and cannot unravel the post-measurement dynamics. In recent years, Raman spectroscopy-based methods for omics inference have emerged, allowing the characterization of genome-wide molecular profile dynamics in living cells. In this review, we give a brief overview of the recent development of imaging-based omics profiling methods. We then present the approach to infer omics profiles from single-cell Raman spectra. Since Raman spectra can be obtained from living cells in a non-destructive and non-staining manner, this method may open the door to live-cell omics.
对细胞中的基因表达水平进行全基因组分析，如转录组学和蛋白质组学，是现代生物学中一种强大的实验方法，它不仅能有效地探索导致感兴趣的生物学现象的遗传因素，还能刻画伴随组学图谱大规模重塑的细胞可塑性表型变化背后的全局限制因素。为了理解单个细胞如何改变其分子图谱以在分化、癌症转移和适应等现象中实现特定的表型变化，在单细胞水平上同时刻画细胞表型和组学图谱的动态变化至关重要。特别是在过去十年中，在显微镜下对细胞的组学图谱进行原位鉴定方面取得了重大技术进展。然而，大多数方法仍然具有破坏性，无法揭示测量后的动态变化。近年来，基于拉曼光谱的组学推断方法出现了，它能够刻画活细胞中全基因组分子图谱的动态变化。在这篇综述中，我们简要概述了基于成像的组学分析方法的最新进展。然后我们介绍了从单细胞拉曼光谱推断组学图谱的方法。由于拉曼光谱可以以非破坏性和非染色的方式从活细胞中获得，这种方法可能为活细胞组学打开大门。
