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Bhuiyan AH, Clément JE, Ferdous Z, Mochizuki K, Tabata K, Taylor JN, Kumamoto Y, Harada Y, Bocklitz T, Fujita K, Komatsuzaki T. Differentiability of cell types enhanced by detrending a non-homogeneous pattern in a line-illumination Raman microscope. Analyst 2023. [PMID: 37403759 DOI: 10.1039/d3an00516j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
A line illumination Raman microscope extracts the underlying spatial and spectral information of a sample, typically a few hundred times faster than raster scanning. This makes it possible to measure a wide range of biological samples such as cells and tissues - that only allow modest intensity illumination to prevent potential damage - within feasible time frame. However, a non-uniform intensity distribution of laser line illumination may induce some artifacts in the data and lower the accuracy of machine learning models trained to predict sample class membership. Here, using cancerous and normal human thyroid follicular epithelial cell lines, FTC-133 and Nthy-ori 3-1 lines, whose Raman spectral difference is not so large, we show that the standard pre-processing of spectral analyses widely used for raster scanning microscopes introduced some artifacts. To address this issue, we proposed a detrending scheme based on random forest regression, a nonparametric model-free machine learning algorithm, combined with a position-dependent wavenumber calibration scheme along the illumination line. It was shown that the detrending scheme minimizes the artifactual biases arising from non-uniform laser sources and significantly enhances the differentiability of the sample states, i.e., cancerous or normal epithelial cells, compared to the standard pre-processing scheme.
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Affiliation(s)
- Abdul Halim Bhuiyan
- Graduate School of Chemical Sciences and Engineering, Materials Chemistry and Engineering Course, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, 060-8628, Hokkaido, Japan.
- Department of Mathematics, Bangladesh University of Engineering and Technology, Dhaka-1000, Bangladesh
| | - Jean-Emmanuel Clément
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan
| | - Zannatul Ferdous
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan
| | - Kentaro Mochizuki
- Department of Pathology and Cell Regulation, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo, Kyoto, 602-8566, Kyoto, Japan
| | - Koji Tabata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, 001-0020, Hokkaido, Japan
| | - James Nicholas Taylor
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, 001-0020, Hokkaido, Japan
| | - Yasuaki Kumamoto
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Yoshinori Harada
- Department of Pathology and Cell Regulation, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo, Kyoto, 602-8566, Kyoto, Japan
| | - Thomas Bocklitz
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC/ACP), Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany
- Institute of Computer Science, Faculty of Mathematics, Physics & Computer Science, University Bayreuth, Universitaetsstraße 30, 95447 Bayreuth, Germany
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka, Suita, 565-0871, Osaka, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Yamadaoka, Suita, 565-0871, Osaka, Japan
| | - Tamiki Komatsuzaki
- Graduate School of Chemical Sciences and Engineering, Materials Chemistry and Engineering Course, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, 060-8628, Hokkaido, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, 001-0021, Hokkaido, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, 001-0020, Hokkaido, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka, Suita, 565-0871, Osaka, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, Ibaraki, 8-1, Osaka, 567-0047, Japan
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Ferdous Z, Clément JE, Gong JP, Tanaka S, Komatsuzaki T, Tsuda M. Geometrical analysis identified morphological features of hydrogel-induced cancer stem cells in synovial sarcoma model cells. Biochem Biophys Res Commun 2023; 642:41-49. [PMID: 36549099 DOI: 10.1016/j.bbrc.2022.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Cancer stem cells (CSCs) has been a key target to cure cancer patients completely. Although many CSC markers have been identified, they are frequently cancer type-specific and those expressions are occasionally variable, which becomes an obstacle to elucidate the characteristics of the CSCs. Here we scrutinized the relationship between stemness elevation and geometrical features of single cells. The PAMPS hydrogel was utilized to create the CSCs from mouse myoblast C2C12 and its synovial sarcoma model cells. qRT-PCR analysis confirmed the significant increase in expression levels of Sox2, Nanog, and Oct3/4 on the PAMPS gel, which was higher in the synovial sarcoma model cells. Of note, the morphological heterogeneity was appeared on the PAMPS gel, mainly including flat spreading, elongated spindle, and small round cells, and the Sox2 expression was highest in the small round cells. To examine the role of morphological differences in the elevation of stemness, over 6,400 cells were segmented along with the Sox2 intensity, and 12 geometrical features were extracted at single cell level. A nonlinear mapping of the geometrical features by using uniform manifold approximation and projection (UMAP) clearly revealed the existence of relationship between morphological differences and the stemness elevation, especially for C2C12 and its synovial sarcoma model on the PAMPS gel in which the small round cells possess relatively high Sox2 expression on the PAMPS gel, which supports the strong relationship between morphological changes and the stemness elevation. Taken together, these geometrical features can be useful for morphological profiling of CSCs to classify and distinguish them for understanding of their role in disease progression and drug discovery.
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Affiliation(s)
- Zannatul Ferdous
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jean-Emmanuel Clément
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan; World Premier International Research Center Initiative, Institute for Chemical Reaction, Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Jian Ping Gong
- World Premier International Research Center Initiative, Institute for Chemical Reaction, Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan; Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; World Premier International Research Center Initiative, Institute for Chemical Reaction, Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Tamiki Komatsuzaki
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo, Japan; World Premier International Research Center Initiative, Institute for Chemical Reaction, Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Masumi Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan; World Premier International Research Center Initiative, Institute for Chemical Reaction, Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
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Hirota A, Clément JE, Tanikawa S, Nonoyama T, Komatsuzaki T, Gong JP, Tanaka S, Imajo M. ERK MAP Kinase Signaling Regulates RAR Signaling to Confer Retinoid Resistance on Breast Cancer Cells. Cancers (Basel) 2022; 14:cancers14235890. [PMID: 36497371 PMCID: PMC9739577 DOI: 10.3390/cancers14235890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Retinoic acid (RA) and its synthetic derivatives, retinoids, have been established as promising anticancer agents based on their ability to regulate cell proliferation and survival. Clinical trials, however, have revealed that cancer cells often acquire resistance to retinoid therapy. Therefore, elucidation of underlying mechanisms of retinoid resistance has been considered key to developing more effective use of retinoids in cancer treatment. In this study, we show that constitutive activation of ERK MAP kinase signaling, which is often caused by oncogenic mutations in RAS or RAF genes, suppresses RA receptor (RAR) signaling in breast cancer cells. We show that activation of the ERK pathway suppresses, whereas its inhibition promotes, RA-induced transcriptional activation of RAR and the resultant upregulation of RAR-target genes in breast cancer cells. Importantly, ERK inhibition potentiates the tumor-suppressive activity of RA in breast cancer cells. Moreover, we also reveal that suppression of RAR signaling and activation of ERK signaling are associated with poor prognoses in breast cancer patients and represent hallmarks of specific subtypes of breast cancers, such as basal-like, HER2-enriched and luminal B. These results indicate that ERK-dependent suppression of RAR activity underlies retinoid resistance and is associated with cancer subtypes and patient prognosis in breast cancers.
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Affiliation(s)
- Akira Hirota
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Jean-Emmanuel Clément
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Satoshi Tanikawa
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Takayuki Nonoyama
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Tamiki Komatsuzaki
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0020, Japan
| | - Jian Ping Gong
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Shinya Tanaka
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Masamichi Imajo
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Correspondence: ; Tel.: +81-11-706-9683
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Leray A, Clément JE, Bouhélier A, Finot E. Conformational Changes and Charge Transfer in Biomolecules Resolved Using Dynamic Enhanced Raman Correlation Spectroscopy. J Phys Chem B 2019; 123:1931-1938. [PMID: 30715883 DOI: 10.1021/acs.jpcb.8b10803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this contribution, we report that conformational changes of molecules that are often buried in a wide-distributed Gaussian distribution can be discerned by analyzing the dynamics of specific Raman lines. We investigate the pertinence of the auto- and cross-correlation functions applied to the dynamics of three Raman lines of an amino acid, the tryptophan. The cross-correlation between intensity and the Raman band is an indicator of the charge transfer during the diffusion limited reaction of tryptophan and the gold surface. The Péclet number Pe can provide a valuable indicator of the convective and/or diffusive features of each Raman band. Adsorption induced conformation changes can be identified using the autocorrelation of the multiples states within the Raman band centered at 1550 cm-1.
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Affiliation(s)
- Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS , Université de Bourgogne Franche Comté , F-21078 Dijon , France
| | - Jean-Emmanuel Clément
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS , Université de Bourgogne Franche Comté , F-21078 Dijon , France
| | - Alexandre Bouhélier
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS , Université de Bourgogne Franche Comté , F-21078 Dijon , France
| | - Eric Finot
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS , Université de Bourgogne Franche Comté , F-21078 Dijon , France
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