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Daum R, Brauchle EM, Berrio DAC, Jurkowski TP, Schenke-Layland K. Non-invasive detection of DNA methylation states in carcinoma and pluripotent stem cells using Raman microspectroscopy and imaging. Sci Rep 2019; 9:7014. [PMID: 31065074 PMCID: PMC6504883 DOI: 10.1038/s41598-019-43520-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of gene expression. Global DNA methylation changes occur in carcinogenesis as well as early embryonic development. However, the current methods for studying global DNA methylation levels are invasive and require sample preparation. The present study was designed to investigate the potential of Raman microspectroscopy and Raman imaging as non-invasive, marker-independent and non-destructive tools for the detection of DNA methylation in living cells. To investigate global DNA methylation changes, human colon carcinoma HCT116 cells, which were hypomorphic for DNA methyltransferase 1, therefore showing a lower global DNA methylation (DNMT1−/− cells), were compared to HCT116 wildtype cells. As a model system for early embryogenesis, murine embryonic stem cells were adapted to serum-free 2i medium, leading to a significant decrease in DNA methylation. Subsequently, 2i medium -adapted cells were compared to cells cultured in serum-containing medium. Raman microspectroscopy and imaging revealed significant differences between high- and low-methylated cell types. Higher methylated cells demonstrated higher relative intensities of Raman peaks, which can be assigned to the nucleobases and 5-methylcytosine. Principal component analysis detected distinguishable populations of high- and low-methylated samples. Based on the provided data we conclude that Raman microspectroscopy and imaging are suitable tools for the real-time, marker-independent and artefact-free investigation of the DNA methylation states in living cells.
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Affiliation(s)
- Ruben Daum
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Eva M Brauchle
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Daniel Alejandro Carvajal Berrio
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany. .,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany. .,Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive South, MRL 3645, Los Angeles, CA, USA.
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Ahlawat S, Chowdhury A, Uppal A, Kumar N, Gupta PK. Use of Raman optical tweezers for cell cycle analysis. Analyst 2017; 141:1339-46. [PMID: 26738697 DOI: 10.1039/c5an00971e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the results of our investigations on the use of Raman optical tweezers for label free analysis of cells in different phases of their cell cycle. The studies performed on human colon adenocarcinoma (Colo-205) cells synchronized in G0/G1 and G2/M phases showed that the DNA Raman band at 783 cm(-1) in the Raman spectra of optically trapped cells can provide information about the DNA content in the nucleus of the cell without the need for the isolation of the nucleus. The histograms of intensity of this band among the cell populations were found to corroborate the results obtained from fluorescence image cytometry performed on DAPI stained cells.
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Affiliation(s)
- Sunita Ahlawat
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Centre for Advanced Technology, Indore, 452013, India.
| | - Aniket Chowdhury
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Centre for Advanced Technology, Indore, 452013, India.
| | - Abha Uppal
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Centre for Advanced Technology, Indore, 452013, India.
| | - Nitin Kumar
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Centre for Advanced Technology, Indore, 452013, India.
| | - Pradeep Kumar Gupta
- Laser Biomedical Applications and Instrumentation Division, Raja Ramanna Centre for Advanced Technology, Indore, 452013, India.
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Overstall AM, Woods DC. A strategy for Bayesian inference for computationally expensive models with application to the estimation of stem cell properties. Biometrics 2013; 69:458-68. [PMID: 23421643 DOI: 10.1111/biom.12017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 10/01/2012] [Accepted: 12/01/2012] [Indexed: 11/28/2022]
Abstract
Bayesian inference is considered for statistical models that depend on the evaluation of a computationally expensive computer code or simulator. For such situations, the number of evaluations of the likelihood function, and hence of the unnormalized posterior probability density function, is determined by the available computational resource and may be extremely limited. We present a new example of such a simulator that describes the properties of human embryonic stem cells using data from optical trapping experiments. This application is used to motivate a novel strategy for Bayesian inference which exploits a Gaussian process approximation of the simulator and allows computationally efficient Markov chain Monte Carlo inference. The advantages of this strategy over previous methodology are that it is less reliant on the determination of tuning parameters and allows the application of model diagnostic procedures that require no additional evaluations of the simulator. We show the advantages of our method on synthetic examples and demonstrate its application on stem cell experiments.
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Affiliation(s)
- Antony M Overstall
- School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9SS, UK.
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