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Kobayashi-Kirschvink KJ, Nakaoka H, Oda A, Kamei KIF, Nosho K, Fukushima H, Kanesaki Y, Yajima S, Masaki H, Ohta K, Wakamoto Y. Linear Regression Links Transcriptomic Data and Cellular Raman Spectra. Cell Syst 2018; 7:104-117.e4. [PMID: 29936183 DOI: 10.1016/j.cels.2018.05.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/10/2018] [Accepted: 05/21/2018] [Indexed: 10/28/2022]
Abstract
Raman microscopy is an imaging technique that has been applied to assess molecular compositions of living cells to characterize cell types and states. However, owing to the diverse molecular species in cells and challenges of assigning peaks to specific molecules, it has not been clear how to interpret cellular Raman spectra. Here, we provide firm evidence that cellular Raman spectra and transcriptomic profiles of Schizosaccharomyces pombe and Escherichia coli can be computationally connected and thus interpreted. We find that the dimensions of high-dimensional Raman spectra and transcriptomes measured by RNA sequencing can be reduced and connected linearly through a shared low-dimensional subspace. Accordingly, we were able to predict global gene expression profiles by applying the calculated transformation matrix to Raman spectra, and vice versa. Highly expressed non-coding RNAs contributed to the Raman-transcriptome linear correspondence more significantly than mRNAs in S. pombe. This demonstration of correspondence between cellular Raman spectra and transcriptomes is a promising step toward establishing spectroscopic live-cell omics studies.
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Affiliation(s)
- Koseki J Kobayashi-Kirschvink
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan.
| | - Hidenori Nakaoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Research Center for Complex Systems Biology, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Arisa Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Ken-Ichiro F Kamei
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Kazuki Nosho
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroko Fukushima
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan; Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kunihiro Ohta
- Research Center for Complex Systems Biology, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Research Center for Complex Systems Biology, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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