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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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Agrawal T, Paul D, Saroj S, Ali A, Choubey V, Mukherjee D, Pal S, Rakshit T. Label-Free Physical-Analytical Techniques Reveal Epigenetic Modifications of Breast Cancer Chromosomes. J Phys Chem B 2023; 127:3534-3542. [PMID: 37036757 DOI: 10.1021/acs.jpcb.3c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Epigenetic dysregulation including DNA methylation and histone modifications is being increasingly recognized as a promising biomarker for the diagnosis and prognosis of cancer. Herein, we devised a label-free analytical toolbox comprising IR, UV-vis, CD spectroscopy, and cyclic voltammetry, which is capable to differentiate significantly hyper-methylated breast cancer chromosomes from the normal breast epithelial counterparts.
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Affiliation(s)
- Tanya Agrawal
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Debashish Paul
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Saroj Saroj
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Akbar Ali
- Department of Chemistry, Indian Institute of Technology, Bhilai, Chhattisgarh 492015, India
| | - Vivekanand Choubey
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
| | - Dipanjan Mukherjee
- Laboratory of Bioimaging and Pathologies, University of Strasbourg, F-67081 Strasbourg CEDEX, France
| | - Suchetan Pal
- Department of Chemistry, Indian Institute of Technology, Bhilai, Chhattisgarh 492015, India
| | - Tatini Rakshit
- Department of Chemistry, Shiv Nadar IoE, Delhi-NCR, Uttar Pradesh 201314, India
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