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Dong T, Wan S, Wang Y, Fu Y, Wang P. Effects of Chemical Fixatives on Kinetic Measurements of Biomolecular Interaction on Cell Membrane. J Membr Biol 2024; 257:131-142. [PMID: 38206377 DOI: 10.1007/s00232-024-00305-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
Understanding the interaction between ligands and membrane proteins is important for drug design and optimization. Although investigation using live cells is desirable, it is not feasible in some circumstances and cell fixation is performed to reduce cell motion and degradation. This study compared the effects of five fixatives, i.e., formaldehyde vapor (FV), paraformaldehyde (PFA), acetone, methanol, and ethanol, on kinetic measurements via the LigandTracer method. We found that all five fixatives exerted insignificant effects on lectin-glycan interaction. However, antibody-receptor interaction is markedly perturbed by coagulant fixatives. The acetone fixation changed the binding of the anti-human epidermal growth factor receptor 2 (HER2) antibody to HER2 on the cell membrane from a 1:2 to a 1:1 binding model, while methanol and ethanol abolished the antibody binding possibly by removal of the HER2 receptors on the cell membrane. The capability of binding was retained when methanol fixation was performed at lower temperatures, albeit with a binding model of 1:1 instead. Moreover, whereas cell morphology does not exert a substantial impact on lectin-glycan interaction, it can indeed modify the binding model of antibody-receptor interaction. Our results provided insights into the selection of fixatives for cell-based kinetic studies.
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Affiliation(s)
- Tianbao Dong
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Shengyang Wan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Yanhui Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Yaru Fu
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Pengcheng Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China.
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2
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Abstract
Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.
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Affiliation(s)
- Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
| | | | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
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3
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Xu Y, Hou X, Zhu Q, Mao S, Ren J, Lin J, Xu N. Phenotype Identification of HeLa Cells Knockout CDK6 Gene Based on Label-Free Raman Imaging. Anal Chem 2022; 94:8890-8898. [PMID: 35704426 DOI: 10.1021/acs.analchem.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identifying cell phenotypes is essential for understanding the function of biological macromolecules and molecular biology. We developed a noninvasive, label-free, single-cell Raman imaging analysis platform to distinguish between the cell phenotypes of the HeLa cell wild type (WT) and cyclin-dependent kinase 6 (CDK6) gene knockout (KO) type. Via large-scale Raman spectral and imaging analysis, two phenotypes of the HeLa cells were distinguished by their intrinsic biochemical profiles. A significant difference was found between the two cell lines: large lipid droplets formed in the knockout HeLa cells but were not observed in the WT cells, which was confirmed by Oil Red O staining. The band ratio of the Raman spectrum of saturated/unsaturated fatty acids was identified as the Raman spectral marker for HeLa cell WT or gene knockout type differentiation. The interaction between organelles involved in lipid metabolism was revealed by Raman imaging and Lorentz fitting, where the distribution intensity of the mitochondria and the endoplasmic reticulum membrane decreased. At the same time, lysosomes increased after the CDK6 gene knockout. The parameters obtained from Raman spectroscopy are based on hierarchical cluster analysis and one-way ANOVA, enabling highly accurate cell classification.
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Affiliation(s)
- Ying Xu
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
| | - Xiaoli Hou
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, People's Republic of China
| | - Qiaoqiao Zhu
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
| | - Shijie Mao
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
| | - Jie Ren
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
| | - Jidong Lin
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
| | - Ning Xu
- Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China
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4
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Härkönen T, Roininen L, Moores MT, Vartiainen EM. Bayesian Quantification for Coherent Anti-Stokes Raman Scattering Spectroscopy. J Phys Chem B 2020; 124:7005-7012. [PMID: 32673491 PMCID: PMC7458428 DOI: 10.1021/acs.jpcb.0c04378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
We
propose a Bayesian statistical model for analyzing coherent
anti-Stokes Raman scattering (CARS) spectra. Our quantitative analysis
includes statistical estimation of constituent line-shape parameters,
the underlying Raman signal, the error-corrected CARS spectrum, and
the measured CARS spectrum. As such, this work enables extensive uncertainty
quantification in the context of CARS spectroscopy. Furthermore, we
present an unsupervised method for improving spectral resolution of
Raman-like spectra requiring little to no a priori information. Finally, the recently proposed wavelet prism method
for correcting the experimental artifacts in CARS is enhanced by using interpolation techniques for
wavelets. The method is validated using CARS spectra of adenosine
mono-, di-, and triphosphate in water, as well as equimolar aqueous
solutions of d-fructose, d-glucose, and their disaccharide
combination sucrose.
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Affiliation(s)
- Teemu Härkönen
- LUT School of Engineering Science, LUT University, FI-53851 Lappeenranta, Finland
| | - Lassi Roininen
- LUT School of Engineering Science, LUT University, FI-53851 Lappeenranta, Finland
| | - Matthew T Moores
- National Institute for Applied Statistics Research Australia, University of Wollongong, Keiraville NSW 2500, Australia
| | - Erik M Vartiainen
- LUT School of Engineering Science, LUT University, FI-53851 Lappeenranta, Finland
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5
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Yamato N, Matsuya M, Niioka H, Miyake J, Hashimoto M. Nerve Segmentation with Deep Learning from Label-Free Endoscopic Images Obtained Using Coherent Anti-Stokes Raman Scattering. Biomolecules 2020; 10:biom10071012. [PMID: 32650539 PMCID: PMC7407310 DOI: 10.3390/biom10071012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 01/04/2023] Open
Abstract
Semantic segmentation with deep learning to extract nerves from label-free endoscopic images obtained using coherent anti-Stokes Raman scattering (CARS) for nerve-sparing surgery is described. We developed a CARS rigid endoscope in order to identify the exact location of peripheral nerves in surgery. Myelinated nerves are visualized with a CARS lipid signal in a label-free manner. Because the lipid distribution includes other tissues as well as nerves, nerve segmentation is required to achieve nerve-sparing surgery. We propose using U-Net with a VGG16 encoder as a deep learning model and pre-training with fluorescence images, which visualize the lipid distribution similar to CARS images, before fine-tuning with a small dataset of CARS endoscopy images. For nerve segmentation, we used 24 CARS and 1,818 fluorescence nerve images of three rabbit prostates. We achieved label-free nerve segmentation with a mean accuracy of 0.962 and an F1 value of 0.860. Pre-training on fluorescence images significantly improved the performance of nerve segmentation in terms of the mean accuracy and F1 value (p<0.05). Nerve segmentation of label-free endoscopic images will allow for safer endoscopic surgery, while reducing dysfunction and improving prognosis after surgery.
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Affiliation(s)
- Naoki Yamato
- Graduate School/Faculty of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan; (N.Y.); (M.M.)
| | - Mana Matsuya
- Graduate School/Faculty of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan; (N.Y.); (M.M.)
| | - Hirohiko Niioka
- Institute for Datability Science, Osaka University, Suita 565-0871, Japan
- Correspondence: (H.N.); (M.H.); Tel.: +81-6-6105-6074 (H.N.); +81-11-706-6857 (M.H.)
| | - Jun Miyake
- Hitz Research Alliance Laboratory, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan;
| | - Mamoru Hashimoto
- Faculty of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
- Correspondence: (H.N.); (M.H.); Tel.: +81-6-6105-6074 (H.N.); +81-11-706-6857 (M.H.)
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6
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Payne TD, Moody AS, Wood AL, Pimiento PA, Elliott JC, Sharma B. Raman spectroscopy and neuroscience: from fundamental understanding to disease diagnostics and imaging. Analyst 2020; 145:3461-3480. [PMID: 32301450 DOI: 10.1039/d0an00083c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neuroscience would directly benefit from more effective detection techniques, leading to earlier diagnosis of disease. The specificity of Raman spectroscopy is unparalleled, given that a molecular fingerprint is attained for each species. It also allows for label-free detection with relatively inexpensive instrumentation, minimal sample preparation, and rapid sample analysis. This review summarizes Raman spectroscopy-based techniques that have been used to advance the field of neuroscience in recent years.
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Affiliation(s)
- Taylor D Payne
- University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN 37996, USA.
| | - Amber S Moody
- National Center of Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA
| | - Avery L Wood
- University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN 37996, USA.
| | - Paula A Pimiento
- University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN 37996, USA.
| | - James C Elliott
- University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN 37996, USA.
| | - Bhavya Sharma
- University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN 37996, USA.
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7
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Rangan S, Schulze HG, Vardaki MZ, Blades MW, Piret JM, Turner RFB. Applications of Raman spectroscopy in the development of cell therapies: state of the art and future perspectives. Analyst 2020; 145:2070-2105. [DOI: 10.1039/c9an01811e] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This comprehensive review article discusses current and future perspectives of Raman spectroscopy-based analyses of cell therapy processes and products.
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Affiliation(s)
- Shreyas Rangan
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- School of Biomedical Engineering
| | - H. Georg Schulze
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
| | - Martha Z. Vardaki
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
| | - Michael W. Blades
- Department of Chemistry
- The University of British Columbia
- Vancouver
- Canada
| | - James M. Piret
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- School of Biomedical Engineering
| | - Robin F. B. Turner
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
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8
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Levchenko SM, Kuzmin AN, Pliss A, Ohulchanskyy TY, Prasad PN, Qu J. Cellular transformations in near-infrared light-induced apoptosis in cancer cells revealed by label-free CARS imaging. JOURNAL OF BIOPHOTONICS 2019; 12:e201900179. [PMID: 31339662 DOI: 10.1002/jbio.201900179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/24/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Photobiomodulation (PBM) involves light to activate cellular signaling pathways leading to cell proliferation or death. In this work, fluorescence and Coherent anti-Stokes Raman Scattering (CARS) imaging techniques were applied to assess apoptosis in human cervical cancer cells (HeLa) induced by near infrared (NIR) laser light (808 nm). Using the Caspase 3/7 fluorescent probe to identify apoptotic cells, we found that the pro-apoptotic effect is significantly dependent of irradiation dose. The highest apoptosis rate was noted for the lower irradiation doses, that is, 0.3 J/cm2 (~58%) and 3 J/cm2 (~28%). The impact of light doses on proteins/lipids intracellular metabolism and distribution was evaluated using CARS imaging, which revealed apoptosis-associated reorganization of nuclear proteins and cytoplasmic lipids after irradiation with 0.3 J/cm2 . Doses of NIR light causing apoptosis (0.3, 3 and 30 J/cm2 ) induced a gradual increase in the nuclear protein level over time, in contrast to proteins in cells non-irradiated and irradiated with 10 J/cm2 . Furthermore, irradiation of the cells with the 0.3 J/cm2 dose resulted in lipid droplets (LDs) accumulation, which was apparently caused by an increase in reactive oxygen species (ROS) generation. We suggest that PBM induced apoptosis could be caused by the ability of NIR light to trigger excessive LDs formation which, in turn, induces cellular cytotoxicity.
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Affiliation(s)
- Svitlana M Levchenko
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Andrey N Kuzmin
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York
- Advanced Cytometry Instrumentation Systems, LLC, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York
- Advanced Cytometry Instrumentation Systems, LLC, Buffalo, New York
| | - Tymish Y Ohulchanskyy
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, New York
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
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