Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells
Abstract This work combines single cell Raman spectroscopy (RS) with group and basis restricted non-negative matrix factorisation (GBR-NMF) to identify individual biochemical changes associated with radiation exposure in three human cancer cell lines. The cell lines analysed were derived from lung (...
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| Format: | Article |
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Nature Portfolio
2021-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-83343-5 |
| _version_ | 1818683856308404224 |
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| author | Kirsty Milligan Xinchen Deng Phillip Shreeves Ramie Ali-Adeeb Quinn Matthews Alexandre Brolo Julian J. Lum Jeffrey L. Andrews Andrew Jirasek |
| author_facet | Kirsty Milligan Xinchen Deng Phillip Shreeves Ramie Ali-Adeeb Quinn Matthews Alexandre Brolo Julian J. Lum Jeffrey L. Andrews Andrew Jirasek |
| author_sort | Kirsty Milligan |
| collection | DOAJ |
| description | Abstract This work combines single cell Raman spectroscopy (RS) with group and basis restricted non-negative matrix factorisation (GBR-NMF) to identify individual biochemical changes associated with radiation exposure in three human cancer cell lines. The cell lines analysed were derived from lung (H460), breast (MCF7) and prostate (LNCaP) tissue and are known to display varying degrees of radio sensitivity due to the inherent properties of each cell type. The GBR-NMF approach involves the deconstruction of Raman spectra into component biochemical bases using a library of Raman spectra of known biochemicals present in the cells. Subsequently, scores are obtained on each of these bases which can be directly correlated with the contribution of each chemical to the overall Raman spectrum. We validated GBR-NMF through the correlation of GBR-NMF-derived glycogen scores with scores that were previously observed using principal component analysis (PCA). Phosphatidylcholine, glucose, arginine and asparagine showed a distinct differential score pattern between radio-resistant and radio-sensitive cell types. In summary, the GBR-NMF approach allows for the monitoring of individual biochemical radiation-response dynamics previously unattainable with more traditional PCA-based approaches. |
| first_indexed | 2024-12-17T10:41:23Z |
| format | Article |
| id | doaj.art-be7d93b845f34652a78ac742d2abbcae |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-17T10:41:23Z |
| publishDate | 2021-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-be7d93b845f34652a78ac742d2abbcae2022-12-21T21:52:15ZengNature PortfolioScientific Reports2045-23222021-02-0111111110.1038/s41598-021-83343-5Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cellsKirsty Milligan0Xinchen Deng1Phillip Shreeves2Ramie Ali-Adeeb3Quinn Matthews4Alexandre Brolo5Julian J. Lum6Jeffrey L. Andrews7Andrew Jirasek8Department of Physics, The University of British ColumbiaDepartment of Physics, The University of British ColumbiaDepartment of Statistics, The University of British ColumbiaDepartment of Physics, The University of British ColumbiaBC Cancer, Centre for the NorthDepartment of Chemistry, University of VictoriaDepartment of Biochemistry and Microbiology, University of VictoriaDepartment of Statistics, The University of British ColumbiaDepartment of Physics, The University of British ColumbiaAbstract This work combines single cell Raman spectroscopy (RS) with group and basis restricted non-negative matrix factorisation (GBR-NMF) to identify individual biochemical changes associated with radiation exposure in three human cancer cell lines. The cell lines analysed were derived from lung (H460), breast (MCF7) and prostate (LNCaP) tissue and are known to display varying degrees of radio sensitivity due to the inherent properties of each cell type. The GBR-NMF approach involves the deconstruction of Raman spectra into component biochemical bases using a library of Raman spectra of known biochemicals present in the cells. Subsequently, scores are obtained on each of these bases which can be directly correlated with the contribution of each chemical to the overall Raman spectrum. We validated GBR-NMF through the correlation of GBR-NMF-derived glycogen scores with scores that were previously observed using principal component analysis (PCA). Phosphatidylcholine, glucose, arginine and asparagine showed a distinct differential score pattern between radio-resistant and radio-sensitive cell types. In summary, the GBR-NMF approach allows for the monitoring of individual biochemical radiation-response dynamics previously unattainable with more traditional PCA-based approaches.https://doi.org/10.1038/s41598-021-83343-5 |
| spellingShingle | Kirsty Milligan Xinchen Deng Phillip Shreeves Ramie Ali-Adeeb Quinn Matthews Alexandre Brolo Julian J. Lum Jeffrey L. Andrews Andrew Jirasek Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells Scientific Reports |
| title | Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| title_full | Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| title_fullStr | Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| title_full_unstemmed | Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| title_short | Raman spectroscopy and group and basis-restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| title_sort | raman spectroscopy and group and basis restricted non negative matrix factorisation identifies radiation induced metabolic changes in human cancer cells |
| url | https://doi.org/10.1038/s41598-021-83343-5 |
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