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Urbańska M, Sofińska K, Czaja M, Szymoński K, Skirlińska-Nosek K, Seweryn S, Lupa D, Szymoński M, Lipiec E. Molecular alterations in metaphase chromosomes induced by bleomycin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124026. [PMID: 38368817 DOI: 10.1016/j.saa.2024.124026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 12/22/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Chromosomes are intranuclear structures, their main function is to store and transmit genetic information during cell division. They are composed of tightly packed DNA in the form of chromatin, which is constantly exposed to various damaging factors. The resulting changes in DNA can have serious consequences (e.g. mutations) if they are not repaired or repaired incorrectly. In this article, we studied chromosomes isolated from human cervical cancer cells (HeLa) exposed to a genotoxic drug causing both single- and double-strand breaks. Specifically, we used bleomycin to induce DNA damage. We followed morphological and chemical changes in chromosomes upon damage induction. Atomic force microscopy was used to visualize the morphology of chromosomes, while Raman microspectroscopy enabled the detection of changes in the chemical structure of chromatin with the resolution close to the diffraction limit. Additionally, we extracted spectra corresponding to chromosome I or chromatin from hyperspectral Raman maps with convolutional neural networks (CNN), which were further analysed with the principal component analysis (PCA) algorithm to reveal molecular markers of DNA damage in chromosomes. The applied multimodal approach revealed simultaneous morphological and molecular changes, including chromosomal aberrations, alterations in DNA conformation, methylation pattern, and increased protein expression upon the bleomycin treatment at the level of the single chromosome.
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Affiliation(s)
- Marta Urbańska
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland; Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Kamila Sofińska
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Michał Czaja
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland; Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Krzysztof Szymoński
- Jagiellonian University Medical College, Department of Pathomorphology, Grzegorzecka 16, 31-531, Krakow, Poland; University Hospital, Department of Pathomorphology, Krakow, Poland
| | - Katarzyna Skirlińska-Nosek
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland; Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Sara Seweryn
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland; Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Dawid Lupa
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Marek Szymoński
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Ewelina Lipiec
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
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Lipiec E, Ruggeri FS, Benadiba C, Borkowska AM, Kobierski JD, Miszczyk J, Wood BR, Deacon GB, Kulik A, Dietler G, Kwiatek WM. Infrared nanospectroscopic mapping of a single metaphase chromosome. Nucleic Acids Res 2019; 47:e108. [PMID: 31562528 PMCID: PMC6765102 DOI: 10.1093/nar/gkz630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 07/07/2019] [Accepted: 07/13/2019] [Indexed: 01/27/2023] Open
Abstract
The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.
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Affiliation(s)
- Ewelina Lipiec
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Francesco S Ruggeri
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Chemistry, University of Cambridge, CB21EW, UK
| | - Carine Benadiba
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anna M Borkowska
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Jan D Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy Jagiellonian University Medical College, PL-31007 Cracow, Poland
| | - Justyna Miszczyk
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Glen B Deacon
- School of Chemistry, Faculty of Science, Monash University, 3800 Victoria, Australia
| | - Andrzej Kulik
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
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Müller D, Geiger D, Stark J, Kienle A. Angle-resolved light scattering of single human chromosomes: experiments and simulations. Phys Med Biol 2019; 64:045016. [PMID: 30630136 DOI: 10.1088/1361-6560/aafd6f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Angle-resolved light scattering measurements of human metaphase chromosomes were compared to the results of numerical light scattering simulations with geometrical models based on atomic force microscopy (AFM) measurements of the same chromosomes. The simulations were conducted using the discrete dipole approximation method (DDA), which solves Maxwell's equations for induced dipoles, positioned in a discrete lattice. A remarkable agreement between the light scattering simulations and measurements of all 6 studied chromosomes was found. Additionally, the influence of small changes in the orientation of a complex scatterer geometry on its angle-resolved scattering pattern is shown. A method is presented to approximate such variations in the scatterer's orientation by a linear shift of the angular scattering pattern. This method provides an initial guess on the scatterers orientation, reducing the amount of simulations needed considerably. It was validated on simulations of a cuboid and successfully applied in the evaluation of the chromosome measurements.
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Affiliation(s)
- Dennis Müller
- Institute for Lasertechnologies in Medicine and Metrology (ILM), Helmholtzstr. 12, 89081 Ulm, Germany. Author to whom any correspondence should be addressed
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