Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace
Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace
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DOI：
10.1101/235580
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发表时间：
2017-12
期刊：
影响因子：
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通讯作者：
Koseki J. Kobayashi-Kirschvink;Hidenori Nakaoka;Arisa H. Oda;Ken-ichiro F. Kamei;Kazuki Nosho;Hiroko Fukushima;Y. Kanesaki;S. Yajima;Haruhiko Masaki;K. Ohta;Y. Wakamoto
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文献类型：
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作者：
Koseki J. Kobayashi-Kirschvink;Hidenori Nakaoka;Arisa H. Oda;Ken-ichiro F. Kamei;Kazuki Nosho;Hiroko Fukushima;Y. Kanesaki;S. Yajima;Haruhiko Masaki;K. Ohta;Y. Wakamoto
拉曼光谱是一种能够反映体内全细胞分子组成的成像技术，近年来在细胞生物学中得到了应用，用于表征不同的细胞类型和状态。然而，由于复杂的分子组成和光谱重叠，细胞拉曼光谱的解释仍然不清楚。在本报告中，我们将细胞拉曼光谱与裂糖菌和大肠杆菌的转录组进行了比较，并提供了确凿的证据，证明它们可以在计算上联系和解释。具体来说，我们发现RNA-seq测量的高维拉曼光谱和转录组的维度可以有效地降低并通过共享的低维子空间线性连接。因此，我们能够通过将计算的变换矩阵应用于拉曼光谱来重建全局基因表达谱，反之亦然。引人注目的是，在S. pombe中，高表达的ncRNAs比mrna更显著地促进了拉曼-转录组线性对应，这意味着它们在协调分子组成方面发挥了主要作用。全细胞拉曼光谱和转录组之间的这种兼容性标志着建立光谱活细胞组学研究的重要和有希望的一步。
Raman spectroscopy is an imaging technique that can reflect whole-cell molecular compositions in vivo, and has been applied recently in cell biology to characterize different cell types and states. However, due to the complex molecular compositions and spectral overlaps, the interpretation of cellular Raman spectra have remained unclear. In this report, we compared cellular Raman spectra to transcriptomes of Schizosaccharomyces pombe and Escherichia coli, and provide firm evidence that they can be computationally connected and interpreted. Specifically, we find that the dimensions of high-dimensional Raman spectra and transcriptomes measured by RNA-seq can be effectively reduced and connected linearly through a shared low-dimensional subspace. Accordingly, we were able to reconstruct global gene expression profiles by applying the calculated transformation matrix to Raman spectra, and vice versa. Strikingly, highly expressed ncRNAs contributed to the Raman-transcriptome linear correspondence more significantly than mRNAs in S. pombe, which implies their major role in coordinating molecular compositions. This compatibility between whole-cell Raman spectra and transcriptomes marks an important and promising step towards establishing spectroscopic live-cell omics studies.