1
|
Rugiel M, Janik-Olchawa N, Kowalczyk J, Pomorska K, Sitarz M, Bik E, Horak D, Babic M, Setkowicz Z, Chwiej J. Raman microscopy allows to follow internalization, subcellular accumulation and fate of iron oxide nanoparticles in cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124888. [PMID: 39116589 DOI: 10.1016/j.saa.2024.124888] [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: 05/13/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
An important issue in the context of both potenial toxicity of iron oxide nanoparticles (IONP) and their medical applications is tracking of the internalization process of these nanomaterials into living cells, as well as their localization and fate within them. The typical methods used for this purpose are transmission electron microscopy, confocal fluorescence microscopy as well as light-scattering techniques including dark-field microscopy and flow cytometry. All the techniques mentioned have their advantages and disadvantages. Among the problems it is necessary to mention complicated sample preparation, difficult interpretation of experimental data requiring qualified and experienced personnel, different behavior of fluorescently labeled IONP comparing to those label-free or finally the lack of possibility of chemical composition characteristics of nanomaterials. The purpose of the present investigation was the assessment of the usefulness of Raman microscopy for the tracking of the internalization of IONP into cells, as well as the optimization of this process. Moreover, the study focused on identification of the potential differences in the cellular fate of superparamagnetic nanoparticles having magnetite and maghemite core. The Raman spectra of U87MG cells which internalized IONP presented additional bands which position depended on the used laser wavelength. They occurred at the wavenumber range 1700-2400 cm-1 for laser 488 nm and below the wavenumber of 800 cm-1 in case of laser 532 nm. The intensity of the mentioned Raman bands was higher for the green laser (532 nm) and their position, was independent and not characteristic on the primary core material of IONP (magnetite, maghemite). The obtained results showed that Raman microscopy is an excellent, non-destructive and objective technique that allows monitoring the process of internalization of IONP into cells and visualizing such nanoparticles and/or their metabolism products within them at low exposure levels. What is more, the process of tracking IONP using the technique may be further improved by using appropriate wavelength and power of the laser source.
Collapse
Affiliation(s)
- Marzena Rugiel
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Natalia Janik-Olchawa
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Julia Kowalczyk
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Karolina Pomorska
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Maciej Sitarz
- Faculty of Materials Science and Ceramics, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Ewelina Bik
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland
| | - Daniel Horak
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského 2, 162 00, Prague 6, Czech Republic
| | - Michal Babic
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského 2, 162 00, Prague 6, Czech Republic
| | - Zuzanna Setkowicz
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Joanna Chwiej
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Mickiewicza 30, 30-059 Krakow, Poland.
| |
Collapse
|
2
|
Xia Q, Perera HA, Bolarinho R, Piskulich ZA, Guo Z, Yin J, He H, Li M, Ge X, Cui Q, Ramström O, Yan M, Cheng JX. Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe. SCIENCE ADVANCES 2024; 10:eadq0294. [PMID: 39167637 PMCID: PMC11338237 DOI: 10.1126/sciadv.adq0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.
Collapse
Affiliation(s)
- Qing Xia
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Harini A. Perera
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Rylie Bolarinho
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | | | - Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Hongjian He
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Mingsheng Li
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Xiaowei Ge
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Olof Ramström
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Chemistry, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| |
Collapse
|
3
|
He M, Zhou X, Wang X. Glycosylation: mechanisms, biological functions and clinical implications. Signal Transduct Target Ther 2024; 9:194. [PMID: 39098853 PMCID: PMC11298558 DOI: 10.1038/s41392-024-01886-1] [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: 10/21/2023] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 08/06/2024] Open
Abstract
Protein post-translational modification (PTM) is a covalent process that occurs in proteins during or after translation through the addition or removal of one or more functional groups, and has a profound effect on protein function. Glycosylation is one of the most common PTMs, in which polysaccharides are transferred to specific amino acid residues in proteins by glycosyltransferases. A growing body of evidence suggests that glycosylation is essential for the unfolding of various functional activities in organisms, such as playing a key role in the regulation of protein function, cell adhesion and immune escape. Aberrant glycosylation is also closely associated with the development of various diseases. Abnormal glycosylation patterns are closely linked to the emergence of various health conditions, including cancer, inflammation, autoimmune disorders, and several other diseases. However, the underlying composition and structure of the glycosylated residues have not been determined. It is imperative to fully understand the internal structure and differential expression of glycosylation, and to incorporate advanced detection technologies to keep the knowledge advancing. Investigations on the clinical applications of glycosylation focused on sensitive and promising biomarkers, development of more effective small molecule targeted drugs and emerging vaccines. These studies provide a new area for novel therapeutic strategies based on glycosylation.
Collapse
Affiliation(s)
- Mengyuan He
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Xiangxiang Zhou
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
- Branch of National Clinical Research Center for Hematologic Diseases, Jinan, Shandong, 250021, China.
| |
Collapse
|
4
|
Li Y, Sun Y, Shi L. Viewing 3D spatial biology with highly-multiplexed Raman imaging: from spectroscopy to biotechnology. Chem Commun (Camb) 2024. [PMID: 39041798 DOI: 10.1039/d4cc02319f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Understansding complex biological systems requires the simultaneous characterization of a large number of interacting components in their native 3D environment with high spatial resolution. Highly-multiplexed Raman imaging is an emerging general strategy for detecting biomarkers with scalable multiplexity and ultra-sensitivity based on a series of stimulated Raman scattering (SRS) techniques. Here we review recent advances in highly-multiplexed Raman imaging and how they contribute to the technological revolution in 3D spatial biology, focusing on the developmental pathway from spectroscopy study to biotechnology invention. We envision highly-multiplexed Raman imaging is taking off, which will greatly facilitate our understanding in biological and medical research fields.
Collapse
Affiliation(s)
- Yingying Li
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yuchen Sun
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| |
Collapse
|
5
|
Min W, Gao X. The Duality of Raman Scattering. Acc Chem Res 2024; 57:1896-1905. [PMID: 38916989 DOI: 10.1021/acs.accounts.4c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
ConspectusFirst predicted more than 100 years ago, Raman scattering is a cornerstone of photonics, spectroscopy, and imaging. The conventional framework of understanding Raman scattering was built on Raman cross section σRaman. Carrying a dimension of area, σRaman characterizes the interaction strength between light and molecules during inelastic scattering. The numerical values of σRaman turn out to be many orders of magnitude smaller in comparison to the linear absorption cross sections σAbsorption of similar molecular systems. Such an enormous gap has been the reason for researchers to believe the extremely feeble Raman scattering ever since its discovery. However, this prevailing picture is conceptually problematic or at least incomplete due to the fact that Raman scattering and linear absorption belong to different orders of light-matter interaction.In this Account, we will summarize an alternate way to think about Raman scattering, which we term stimulated response formulation. To capture the third-order interaction nature of Raman scattering, we introduced stimulated Raman cross section, σSRS, defined as the intrinsic molecular property in response to the external photon fluxes. Foremost, experimental measurement of σSRS turns out to be not weak at all or even larger when fairly compared with electronic counterparts of the same order. The analytical expression for σSRS derived from quantum electrodynamics also supports the measurement and proves that σSRS is intrinsically strong. Hence, σRaman and σSRS can be extremely small and large, respectively, for the same molecule at the same time. Our subsequent theoretical studies show that stimulated response formulation can unify spontaneous emission, stimulated emission, spontaneous Raman, and stimulated Raman via eq 10, in a coherent and symmetric way. In particular, an Einstein-coefficient-like equation, eq 12a, was derived, showing that σRaman can be explicitly expressed as σSRS multiplied by an effective photon flux arising from zero-point fluctuation of the vacuum. The feeble vacuum fluctuation hence explains how σSRS can be intrinsically strong while, at the same time, σRaman ends up being many orders of magnitude smaller when both compared to the electronic counterparts. These two sides of the same coin prompted us to propose "the duality of Raman scattering" (Table 1). Finally, this formulation naturally leads to a quantitative treatment of stimulated Raman scattering (SRS) microscopy, providing an intuitive, molecule-centric explanation as to how SRS microscopy can outperform regular Raman microscopy. Hence, as unveiled by the new formulation, a duality of Raman scattering has emerged, with implications for both fundamental science and practical technology.
Collapse
Affiliation(s)
- Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Xin Gao
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
6
|
Raghunathan R, Vasquez M, Zhang K, Zhao H, Wong STC. Label-free optical imaging for brain cancer assessment. Trends Cancer 2024; 10:557-570. [PMID: 38575412 PMCID: PMC11168891 DOI: 10.1016/j.trecan.2024.03.005] [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: 01/01/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Advances in label-free optical imaging offer a promising avenue for brain cancer assessment, providing high-resolution, real-time insights without the need for radiation or exogeneous agents. These cost-effective and intricately detailed techniques overcome the limitations inherent in magnetic resonance imaging (MRI), computed tomography (CT), and positron emission tomography (PET) scans by offering superior resolution and more readily accessible imaging options. This comprehensive review explores a variety of such methods, including photoacoustic imaging (PAI), optical coherence tomography (OCT), Raman imaging, and IR microscopy. It focuses on their roles in the detection, diagnosis, and management of brain tumors. By highlighting recent advances in these imaging techniques, the review aims to underscore the importance of label-free optical imaging in enhancing early detection and refining therapeutic strategies for brain cancer.
Collapse
Affiliation(s)
- Raksha Raghunathan
- Department of Systems Medicine and Bioengineering and T.T. and W.F. Chao Center for BRAIN, Houston Methodist Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA; Advanced Cellular and Tissue Microscopy Core, Houston Methodist Neal Cancer Center and Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Matthew Vasquez
- Department of Systems Medicine and Bioengineering and T.T. and W.F. Chao Center for BRAIN, Houston Methodist Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA; Advanced Cellular and Tissue Microscopy Core, Houston Methodist Neal Cancer Center and Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Katherine Zhang
- Department of Systems Medicine and Bioengineering and T.T. and W.F. Chao Center for BRAIN, Houston Methodist Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA; Advanced Cellular and Tissue Microscopy Core, Houston Methodist Neal Cancer Center and Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Hong Zhao
- Department of Systems Medicine and Bioengineering and T.T. and W.F. Chao Center for BRAIN, Houston Methodist Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA; Advanced Cellular and Tissue Microscopy Core, Houston Methodist Neal Cancer Center and Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Stephen T C Wong
- Department of Systems Medicine and Bioengineering and T.T. and W.F. Chao Center for BRAIN, Houston Methodist Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA; Advanced Cellular and Tissue Microscopy Core, Houston Methodist Neal Cancer Center and Houston Methodist Research Institute, Houston, TX 77030, USA; Departments of Radiology, Pathology, and Laboratory Medicine and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
7
|
Dunnington EL, Wong BS, Fu D. Innovative Approaches for Drug Discovery: Quantifying Drug Distribution and Response with Raman Imaging. Anal Chem 2024; 96:7926-7944. [PMID: 38625100 PMCID: PMC11108735 DOI: 10.1021/acs.analchem.4c01413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
| | | | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
8
|
Xia Q, Perera HA, Bolarinho R, Piskulich ZA, Guo Z, Yin J, He H, Li M, Ge X, Cui Q, Ramström O, Yan M, Cheng JX. Click-free imaging of carbohydrate trafficking in live cells using an azido photothermal probe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584185. [PMID: 38559219 PMCID: PMC10979903 DOI: 10.1101/2024.03.08.584185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Real-time tracking of intracellular carbohydrates remains challenging. While click chemistry allows bio-orthogonal tagging with fluorescent probes, the reaction permanently alters the target molecule and only allows a single snapshot. Here, we demonstrate click-free mid-infrared photothermal (MIP) imaging of azide-tagged carbohydrates in live cells. Leveraging the micromolar detection sensitivity for 6-azido-trehalose (TreAz) and the 300-nm spatial resolution of MIP imaging, the trehalose recycling pathway in single mycobacteria, from cytoplasmic uptake to membrane localization, is directly visualized. A peak shift of azide in MIP spectrum further uncovers interactions between TreAz and intracellular protein. MIP mapping of unreacted azide after click reaction reveals click chemistry heterogeneity within a bacterium. Broader applications of azido photothermal probes to visualize the initial steps of the Leloir pathway in yeasts and the newly synthesized glycans in mammalian cells are demonstrated.
Collapse
Affiliation(s)
- Qing Xia
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
- Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Harini A. Perera
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Rylie Bolarinho
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Zeke A. Piskulich
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Hongjian He
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mingsheng Li
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Xiaowei Ge
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Olof Ramström
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts, Lowell, Massachusetts 01854, United States
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
- Photonics Center, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| |
Collapse
|
9
|
Shen J, Zhang J, Fu Z, Pan Y, Li X, Wu S, Shan Y, Liu L. Dynamic repulsive interaction enables an asymmetric electron-phonon coupling for improving Raman scattering. Phys Chem Chem Phys 2024; 26:7343-7350. [PMID: 38369913 DOI: 10.1039/d3cp05835b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Two-dimensional (2D) materials are an excellent platform for surface-enhanced Raman spectroscopy (SERS). For ReS2, the Raman enhancement effect can be highly improved through the dipole-dipole interactions and synergistic resonance effects in the phase-engineering ReS2 films. However, the performance of the substrate can be improved further through regulating the electronic interaction between the ReS2 and probe molecules. Herein, a dynamic coulomb repulsion strategy is proposed to trigger an electronic state redistribution by asymmetric electrostatic interactions. With the phase-engineering ReS2/graphene heterostructure as a prototype, under laser excitation, the generated hot electrons in graphene and ReS2 can repel each other due to Coulomb interaction, which breaks the symmetrical distribution of hot electrons in ReS2, and increases the electronic concentration at the interface between ReS2 and the probe molecule. With R6G as the probe molecule, the asymmetric electron distribution and synergistic resonance effects on their interface improve the limit of detection to 10-12 M with an EF of 2.15 × 108. Meanwhile, the heterostructure also shows good uniformity, stability as well as unique anisotropy. This strategy can be generalized to other 2D heterostructures to obtain the ultrasensitive SERS substrates.
Collapse
Affiliation(s)
- Jiawei Shen
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Jiaxin Zhang
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Zirui Fu
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Yan Pan
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Xiaowan Li
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Shuyi Wu
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application, School of Physical Science and Technology, Suzhou University of Science and Technology, Suzhou, 215009, People's Republic of China.
| | - Yun Shan
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, People's Republic of China.
| | - Lizhe Liu
- National Laboratory of Solid State Microstructures and School of Physics, Nanjing University, Nanjing 210093, People's Republic of China.
| |
Collapse
|
10
|
Streu K, Hunsberger S, Patel J, Wan X, Daly CA. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch. J Chem Phys 2024; 160:074106. [PMID: 38364010 DOI: 10.1063/5.0185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024] Open
Abstract
The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.
Collapse
Affiliation(s)
- Kristina Streu
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Sara Hunsberger
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Jeanette Patel
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Xiang Wan
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, Illinois 60660, USA
| | - Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| |
Collapse
|
11
|
Robertson JL, Dervisis N, Rossmeisl J, Nightengale M, Fields D, Dedrick C, Ngo L, Issa AS, Guruli G, Orlando G, Senger RS. Cancer detection in dogs using rapid Raman molecular urinalysis. Front Vet Sci 2024; 11:1328058. [PMID: 38384948 PMCID: PMC10879274 DOI: 10.3389/fvets.2024.1328058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction The presence of cancer in dogs was detected by Raman spectroscopy of urine samples and chemometric analysis of spectroscopic data. The procedure created a multimolecular spectral fingerprint with hundreds of features related directly to the chemical composition of the urine specimen. These were then used to detect the broad presence of cancer in dog urine as well as the specific presence of lymphoma, urothelial carcinoma, osteosarcoma, and mast cell tumor. Methods Urine samples were collected via voiding, cystocentesis, or catheterization from 89 dogs with no history or evidence of neoplastic disease, 100 dogs diagnosed with cancer, and 16 dogs diagnosed with non-neoplastic urinary tract or renal disease. Raman spectra were obtained of the unprocessed bulk liquid urine samples and were analyzed by ISREA, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were applied using the Rametrix®Toolbox software. Results and discussion The procedure identified a spectral fingerprint for cancer in canine urine, resulting in a urine screening test with 92.7% overall accuracy for a cancer vs. cancer-free designation. The urine screen performed with 94.0% sensitivity, 90.5% specificity, 94.5% positive predictive value (PPV), 89.6% negative predictive value (NPV), 9.9 positive likelihood ratio (LR+), and 0.067 negative likelihood ratio (LR-). Raman bands responsible for discerning cancer were extracted from the analysis and biomolecular associations were obtained. The urine screen was more effective in distinguishing urothelial carcinoma from the other cancers mentioned above. Detection and classification of cancer in dogs using a simple, non-invasive, rapid urine screen (as compared to liquid biopsies using peripheral blood samples) is a critical advancement in case management and treatment, especially in breeds predisposed to specific types of cancer.
Collapse
Affiliation(s)
- John L. Robertson
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, VA, United States
- Rametrix Technologies Inc., Blacksburg, VA, United States
| | - Nikolas Dervisis
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - John Rossmeisl
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Marlie Nightengale
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Daniel Fields
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Cameron Dedrick
- Virginia Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Lacey Ngo
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Amr Sayed Issa
- Rametrix Technologies Inc., Blacksburg, VA, United States
| | - Georgi Guruli
- Department of Surgery, VCU Health, Richmond, VA, United States
| | - Giuseppe Orlando
- Department of General Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Ryan S. Senger
- Rametrix Technologies Inc., Blacksburg, VA, United States
- Department of Biological Systems Engineering, College of Agriculture & Life Sciences and College of Engineering, Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|
12
|
Chen C, Qi J, Li Y, Li D, Wu L, Li R, Chen Q, Sun N. Applications of Raman spectroscopy in the diagnosis and monitoring of neurodegenerative diseases. Front Neurosci 2024; 18:1301107. [PMID: 38370434 PMCID: PMC10869569 DOI: 10.3389/fnins.2024.1301107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Raman scattering is an inelastic light scattering that occurs in a manner reflective of the molecular vibrations of molecular structures and chemical conditions in a given sample of interest. Energy changes in the scattered light can be assessed to determine the vibration mode and associated molecular and chemical conditions within the sample, providing a molecular fingerprint suitable for sample identification and characterization. Raman spectroscopy represents a particularly promising approach to the molecular analysis of many diseases owing to clinical advantages including its instantaneous nature and associated high degree of stability, as well as its ability to yield signal outputs corresponding to a single molecule type without any interference from other molecules as a result of its narrow peak width. This technology is thus ideally suited to the simultaneous assessment of multiple analytes. Neurodegenerative diseases represent an increasingly significant threat to global public health owing to progressive population aging, imposing a severe physical and social burden on affected patients who tend to develop cognitive and/or motor deficits beginning between the ages of 50 and 70. Owing to a relatively limited understanding of the etiological basis for these diseases, treatments are lacking for the most common neurodegenerative diseases, which include Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. The present review was formulated with the goal of briefly explaining the principle of Raman spectroscopy and discussing its potential applications in the diagnosis and evaluation of neurodegenerative diseases, with a particular emphasis on the research prospects of this novel technological platform.
Collapse
Affiliation(s)
- Chao Chen
- Central Laboratory, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
| | - Jinfeng Qi
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ying Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ding Li
- Department of Clinical Laboratory, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
| | - Lihong Wu
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ruihua Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Qingfa Chen
- Institute of Tissue Engineering and Regenerative Medicine, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
- Research Center of Basic Medicine, Jinan Central Hospital, Jinan, China
| | - Ning Sun
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| |
Collapse
|
13
|
Li K, Yang M. Activatable organic probes for in situ imaging of biomolecules. Chem Asian J 2024; 19:e202301037. [PMID: 38116891 DOI: 10.1002/asia.202301037] [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: 11/23/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Biomolecules are fundamental for various chemical and biological processes of living organisms. High-resolution in situ imaging of the dynamics and local distribution of biomolecules may facilitate better interpretation of diverse complex cell events in the biomedicine field. In different advanced imaging tools, fluorescence imaging-based activatable organic probes can be noninvasively and effortlessly internalized into cells and can be easily modified, which is essential for the in situ imaging of targets in living organisms. We here briefly summarize the existing general design strategies of activatable organic probes for retaining the fluorescence signal inside cells. We particularly describe the bioapplication of these probes for the in situ bioimaging. This review is expected to promote the development of new molecular tools for extending the application of these in situ imaging strategies to other biomolecules.
Collapse
Affiliation(s)
- Ke Li
- College of Chemistry & Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, China
| | - Minghui Yang
- College of Chemistry & Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, China
| |
Collapse
|
14
|
Eleni Karakatsani M, Estrada H, Chen Z, Shoham S, Deán-Ben XL, Razansky D. Shedding light on ultrasound in action: Optical and optoacoustic monitoring of ultrasound brain interventions. Adv Drug Deliv Rev 2024; 205:115177. [PMID: 38184194 PMCID: PMC11298795 DOI: 10.1016/j.addr.2023.115177] [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: 10/09/2023] [Revised: 12/27/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Monitoring brain responses to ultrasonic interventions is becoming an important pillar of a growing number of applications employing acoustic waves to actuate and cure the brain. Optical interrogation of living tissues provides a unique means for retrieving functional and molecular information related to brain activity and disease-specific biomarkers. The hybrid optoacoustic imaging methods have further enabled deep-tissue imaging with optical contrast at high spatial and temporal resolution. The marriage between light and sound thus brings together the highly complementary advantages of both modalities toward high precision interrogation, stimulation, and therapy of the brain with strong impact in the fields of ultrasound neuromodulation, gene and drug delivery, or noninvasive treatments of neurological and neurodegenerative disorders. In this review, we elaborate on current advances in optical and optoacoustic monitoring of ultrasound interventions. We describe the main principles and mechanisms underlying each method before diving into the corresponding biomedical applications. We identify areas of improvement as well as promising approaches with clinical translation potential.
Collapse
Affiliation(s)
- Maria Eleni Karakatsani
- Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Switzerland; Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland
| | - Héctor Estrada
- Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Switzerland; Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland
| | - Zhenyue Chen
- Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Switzerland; Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland
| | - Shy Shoham
- Department of Ophthalmology and Tech4Health and Neuroscience Institutes, NYU Langone Health, NY, USA
| | - Xosé Luís Deán-Ben
- Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Switzerland; Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland.
| | - Daniel Razansky
- Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Switzerland; Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Switzerland.
| |
Collapse
|
15
|
Zhou L, Feng RR, Zhang W, Gai F. Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences. J Phys Chem Lett 2024; 15:187-200. [PMID: 38156972 DOI: 10.1021/acs.jpclett.3c02619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.
Collapse
Affiliation(s)
- Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
16
|
Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
Collapse
Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
17
|
Min W, Gao X. Raman scattering and vacuum fluctuation: An Einstein-coefficient-like equation for Raman cross sections. J Chem Phys 2023; 159:194103. [PMID: 37965998 PMCID: PMC10653873 DOI: 10.1063/5.0171382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 11/16/2023] Open
Abstract
Since it was first predicted 100 years ago, Raman scattering has been a cornerstone of molecular spectroscopy with a widespread impact on science and technology. Nearly all theoretical frameworks have employed Raman cross sections (σRaman) to characterize and quantify molecular Raman response. The recently introduced absolute stimulated Raman scattering cross section (σSRS), on the other hand, provides an alternative way of interpreting molecular responses under two coherent laser sources. However, the theoretical connection between σRaman and σSRS remains unclear. Herein, we are inspired by Einstein's A and B coefficients for spontaneous and stimulated emissions and derived an analogous equation [Eq. (16)] for Raman scattering from an approach along quantum electrodynamics. Equation (16) decomposes Raman cross sections into a contribution from the vacuum electromagnetic field and an underlying molecular response captured by stimulated Raman cross sections (in the unit of Göppert-Mayer). This theoretical relation is supported by recent experimental measurements on methanol as a model compound. Foremost, it provides a connection between experimentally defined σRaman and σSRS under certain approximations. In addition, it quantitatively shows that it is the weak vacuum field of the Stokes channel that makes Raman cross sections appear so small, corroborating the conventional Raman theory. Moreover, it suggests stimulated Raman cross sections to be a vacuum-decoupled intrinsic quantity for characterizing molecular response during Raman scattering. Remarkably, stimulated Raman cross sections turn out to be not weak when compared to two-photon absorption, narrowing the conventional gap of cross sections between spontaneous Raman and UV-vis absorption by more than 1010 folds.
Collapse
Affiliation(s)
- Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Xin Gao
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| |
Collapse
|
18
|
Liu Y, Li M, Liu H, Kang C, Yu X. Strategies and Progress of Raman Technologies for Cellular Uptake Analysis of the Drug Delivery Systems. Int J Nanomedicine 2023; 18:6883-6900. [PMID: 38026519 PMCID: PMC10674749 DOI: 10.2147/ijn.s435087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Nanoparticle (NP)-based drug delivery systems have the potential to significantly enhance the pharmacological and therapeutic properties of drugs. These systems enhance the bioavailability and biocompatibility of pharmaceutical agents via enabling targeted delivery to specific tissues or organs. However, the efficacy and safety of these systems are largely dependent on the cellular uptake and intracellular transport of NPs. Thus, it is crucial to monitor the intracellular behavior of NPs within a single cell. Yet, it is challenging due to the complexity and size of the cell. Recently, the development of the Raman instrumentation offers a versatile tool to allow noninvasive cellular measurements. The primary objective of this review is to highlight the most recent advancements in Raman techniques (spontaneous Raman scattering, bioorthogonal Raman scattering, coherence Raman scattering, and surface-enhanced Raman scattering) when it comes to assessing the internalization of NP-based drug delivery systems and their subsequent movement within cells.
Collapse
Affiliation(s)
- Yajuan Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology, and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People’s Republic of China
| | - Mei Li
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, 550025, People’s Republic of China
| | - Haisha Liu
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, 550025, People’s Republic of China
| | - Chao Kang
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang, 550025, People’s Republic of China
| | - Xiyong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology, and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People’s Republic of China
| |
Collapse
|
19
|
Chaloupková Z, Žárská L, Belza J, Poláková K. Label-free detection and mapping of graphene oxide in single HeLa cells based on MCR-Raman spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5582-5588. [PMID: 37917034 DOI: 10.1039/d3ay01122d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
GO is a 2D nanomaterial that has attracted attention in many industries in recent years, such as the chemical industry, electronics or medicine. Due to its unique properties such as strength, hydrophilicity and large specific surface area with the possibility of functionalization, GO is a particularly attractive material in biomedicine as a candidate for use in targeted drug delivery. In such a case, we need information on whether graphene oxide penetrates into cells and whether we are able to detect and monitor GO in these cells during and also after the treatment to evaluate possible degradation process of GO and its interaction within the cell compartements. This work introduces the Raman spectroscopy as label-free detection method showing the advantages of combining Raman spectroscopy with MCR (Multivariate Curve Resolution) analysis for advanced detection of GO in cervical cancer (HeLa) cells. Our synthesized GO is characterized firstly by AFM, SEM and Raman spectroscopy and then MCR-Raman spectroscopy is used to detect internalized GO in individual HeLa cells. Moreover, by using our methodology, distribution of GO as well as its chemical stability inside the cell for up to six months is investigated without using any additional labeling or tracing the GO. Thus, MCR-Raman spectroscopy may become a new analytical tool in preclinical and clinical applications of graphene-based nanotheranostics.
Collapse
Affiliation(s)
- Zuzana Chaloupková
- CATRIN - Regional Center of Advanced Technologies and Materials, Palacky University Olomouc, Olomouc, Czechia.
| | - Ludmila Žárská
- CATRIN - Regional Center of Advanced Technologies and Materials, Palacky University Olomouc, Olomouc, Czechia.
| | - Jan Belza
- CATRIN - Regional Center of Advanced Technologies and Materials, Palacky University Olomouc, Olomouc, Czechia.
- Department of Physcial Chemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czechia
| | - Kateřina Poláková
- CATRIN - Regional Center of Advanced Technologies and Materials, Palacky University Olomouc, Olomouc, Czechia.
| |
Collapse
|
20
|
Liu X, Zhang Y, Li X, Xu J, Zhao C, Yang J. Raman Spectroscopy Combined with Malaria Protein for Early Capture and Recognition of Broad-Spectrum Circulating Tumor Cells. Int J Mol Sci 2023; 24:12072. [PMID: 37569448 PMCID: PMC10419290 DOI: 10.3390/ijms241512072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Early identification of tumors can significantly reduce the mortality rate. Circulating tumor cells (CTCs) are a type of tumor cell that detaches from the primary tumor and circulates through the bloodstream. Monitoring CTCs may allow the early identification of tumor progression. However, due to their rarity and heterogeneity, the enrichment and identification of CTCs is still challenging. Studies have shown that Raman spectroscopy could distinguish CTCs from metastatic cancer patients. VAR2CSA, a class of malaria proteins, has a strong broad-spectrum binding effect on various tumor cells and is a promising candidate biomarker for cancer detection. Here, recombinant malaria VAR2CSA proteins were synthesized, expressed, and purified. After confirming that various types of tumor cells can be isolated from blood by recombinant malaria VAR2CSA proteins, we further proved that the VAR2CSA combined with Raman spectroscopy could be used efficiently for tumor capture and type recognition using A549 cell lines spiked into the blood. This would allow the early screening and detection of a broad spectrum of CTCs. Finally, we synthesized and purified the malaria protein fusion antibody and confirmed its in vitro tumor-killing activity. Herein, this paper exploits the theoretical basis of a novel strategy to capture, recognize, and kill broad-spectrum types of CTCs from the peripheral blood.
Collapse
Affiliation(s)
- Xinning Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Yidan Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Xunrong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100000, China
| | - Chenyang Zhao
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao Marine Biomedical Research Institute, Ocean University of China, Qingdao 266071, China; (X.L.)
- Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Marine Science and Technology Center, Qingdao 266100, China
| |
Collapse
|
21
|
Abstract
Cellular membranes are essential components of all living organisms. They are composed of a complex mixture of lipids with diverse chemical structures and crucial biological functions. The dynamic and heterogeneous nature of cellular membranes presents a challenge for studying their biophysical properties and organization in vivo. Raman imaging, particularly coherent Raman scattering techniques such as stimulated Raman scattering (SRS) microscopy, have emerged as powerful tools for studying cellular membranes with high spatial and temporal resolution and minimal perturbation. In this Review, we discuss the scientific importance and technical challenges of characterizing membrane composition in cellular contexts and how the advances of Raman imaging can provide unique insights into membrane phase behavior and organization. We also highlight recent applications of Raman imaging in studying cellular membranes and implications in diseases. In particular, the discovery of phase separation and a solid-phase intracellular membrane on endoplasmic reticulum is reviewed in detail, shedding light on the biology of lipotoxicity.
Collapse
Affiliation(s)
- Yihui Shen
- Chemistry and Lewis Sigler Institute of Genomics, Princeton University, Princeton, NJ, 08540, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States, 91125
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| |
Collapse
|
22
|
von Krusenstiern AN, Robson RN, Qian N, Qiu B, Hu F, Reznik E, Smith N, Zandkarimi F, Estes VM, Dupont M, Hirschhorn T, Shchepinov MS, Min W, Woerpel KA, Stockwell BR. Identification of essential sites of lipid peroxidation in ferroptosis. Nat Chem Biol 2023; 19:719-730. [PMID: 36747055 PMCID: PMC10238648 DOI: 10.1038/s41589-022-01249-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2023]
Abstract
Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, provides a potential treatment avenue for drug-resistant cancers and may play a role in the pathology of some degenerative diseases. Identifying the subcellular membranes essential for ferroptosis and the sequence of their peroxidation will illuminate drug discovery strategies and ferroptosis-relevant disease mechanisms. In this study, we employed fluorescence and stimulated Raman scattering imaging to examine the structure-activity-distribution relationship of ferroptosis-modulating compounds. We found that, although lipid peroxidation in various subcellular membranes can induce ferroptosis, the endoplasmic reticulum (ER) membrane is a key site of lipid peroxidation. Our results suggest an ordered progression model of membrane peroxidation during ferroptosis that accumulates initially in the ER membrane and later in the plasma membrane. Thus, the design of ER-targeted inhibitors and inducers of ferroptosis may be used to optimally control the dynamics of lipid peroxidation in cells undergoing ferroptosis.
Collapse
Affiliation(s)
| | - Ryan N Robson
- Department of Chemistry, New York University, New York, NY, USA
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Baiyu Qiu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Eduard Reznik
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nailah Smith
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Verna M Estes
- Department of Chemistry, New York University, New York, NY, USA
| | - Marcel Dupont
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Tal Hirschhorn
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
| | - K A Woerpel
- Department of Chemistry, New York University, New York, NY, USA.
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, USA.
- Department of Chemistry, Columbia University, New York, NY, USA.
| |
Collapse
|
23
|
Borisjuk L, Horn P, Chapman K, Jakob PM, Gündel A, Rolletschek H. Seeing plants as never before. THE NEW PHYTOLOGIST 2023; 238:1775-1794. [PMID: 36895109 DOI: 10.1111/nph.18871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 05/04/2023]
Abstract
Imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. While optical microscopy remains the core tool for imaging, a suite of novel technologies is now beginning to make a significant contribution to visualize plant metabolism. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility. In addition to providing a description of the basic principles underlying these technologies, the review discusses their various advantages and limitations, reveals the current state of the art, and suggests their potential application to experimental practice. Finally, a view is presented as to how the technologies will likely develop, how these developments may encourage the formulation of novel experimental strategies, and how the enormous potential of these technologies can contribute to progress in plant science.
Collapse
Affiliation(s)
- Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Patrick Horn
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Kent Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Peter M Jakob
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| |
Collapse
|
24
|
Yang WS. Ferroptosis: whERe is the critical site of lipid peroxidation? Front Cell Dev Biol 2023; 11:1179245. [PMID: 37274745 PMCID: PMC10232733 DOI: 10.3389/fcell.2023.1179245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
|
25
|
Li J, Yan P, Li Y, Han M, Zeng Q, Li J, Yu Z, Zhang D, Chen X. Harnessing the power of Raman spectroscopic imaging for ophthalmology. Front Chem 2023; 11:1211121. [PMID: 37252371 PMCID: PMC10213270 DOI: 10.3389/fchem.2023.1211121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Eye diseases can cause great inconvenience to people's daily life; therefore, it is necessary to study the causes of ocular diseases and related physiological processes. Raman spectroscopic imaging (RSI) is a non-destructive, non-contact detection technique with the advantages of label-free, non-invasive and highly specific. Compared with other mature imaging technologies, RSI can provide real-time molecular information and high-resolution imaging at relatively low cost, making it very suitable for quantitative detection of biological molecules. RSI can reflect the overall situation of the sample, revealing the content distribution of the same substance in different areas of the sample. This review focuses on the recent advances in ophthalmology, with particular emphasis on the powerful use of RSI techniques, as well as its combination with other imaging techniques. Finally, we prospect the wider application and future potential of RSI approaches in ophthalmology.
Collapse
Affiliation(s)
- Jing Li
- Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated People’s Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Peirao Yan
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| | - Yong Li
- Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated People’s Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Ming Han
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| | - Qi Zeng
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| | - Juan Li
- Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated People’s Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Zhe Yu
- Shaanxi Eye Hospital, Xi’an People’s Hospital (Xi’an Fourth Hospital), Affiliated People’s Hospital of Northwest University, Xi’an, Shaanxi, China
| | - Dongjie Zhang
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| | - Xueli Chen
- Center for Biomedical-photonics and Molecular Imaging, Xi’an Key Laboratory of Intelligent Sensing and Regulation of Trans-Scale Life Information, School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, China
| |
Collapse
|
26
|
Chen X, Wu Z, He Y, Hao Z, Wang Q, Zhou K, Zhou W, Wang P, Shan F, Li Z, Ji J, Fan Y, Li Z, Yue S. Accurate and Rapid Detection of Peritoneal Metastasis from Gastric Cancer by AI-Assisted Stimulated Raman Molecular Cytology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2300961. [PMID: 37114845 PMCID: PMC10375130 DOI: 10.1002/advs.202300961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Peritoneal metastasis (PM) is the mostcommon form of distant metastasis and one of the leading causes of death in gastriccancer (GC). For locally advanced GC, clinical guidelines recommend peritoneal lavage cytology for intraoperative PM detection. Unfortunately, current peritoneal lavage cytology is limited by low sensitivity (<60%). Here the authors established the stimulated Raman molecular cytology (SRMC), a chemical microscopy-based intelligent cytology. The authors firstly imaged 53 951 exfoliated cells in ascites obtained from 80 GC patients (27 PM positive, 53 PM negative). Then, the authors revealed 12 single cell features of morphology and composition that are significantly different between PM positive and negative specimens, including cellular area, lipid protein ratio, etc. Importantly, the authors developed a single cell phenotyping algorithm to further transform the above raw features to feature matrix. Such matrix is crucial to identify the significant marker cell cluster, the divergence of which is finally used to differentiate the PM positive and negative. Compared with histopathology, the gold standard of PM detection, their SRMC method could reach 81.5% sensitivity, 84.9% specificity, and the AUC of 0.85, within 20 minutes for each patient. Together, their SRMC method shows great potential for accurate and rapid detection of PM from GC.
Collapse
Affiliation(s)
- Xun Chen
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
- School of Engineering Medicine, Beihang University, 100191, Beijing, China
| | - Zhouqiao Wu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Yexuan He
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| | - Zhe Hao
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| | - Qi Wang
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Keji Zhou
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| | - Wanhui Zhou
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| | - Pu Wang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| | - Fei Shan
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Jiafu Ji
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
- School of Engineering Medicine, Beihang University, 100191, Beijing, China
| | - Ziyu Li
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, 100142, Beijing, China
| | - Shuhua Yue
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100191, Beijing, China
| |
Collapse
|
27
|
Wang H, Lee D, Wei L. Toward the Next Frontiers of Vibrational Bioimaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:3-17. [PMID: 37122829 PMCID: PMC10131268 DOI: 10.1021/cbmi.3c00004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 05/02/2023]
Abstract
Chemical imaging based on vibrational contrasts can extract molecular information entangled in complex biological systems. To this end, nonlinear Raman scattering microscopy, mid-infrared photothermal (MIP) microscopy, and atomic force microscopy (AFM)-based force-detected photothermal microscopies are emerging with better chemical sensitivity, molecular specificity, and spatial resolution than conventional vibrational methods. Their utilization in bioimaging applications has provided biological knowledge in unprecedented detail. This Perspective outlines key methodological developments, bioimaging applications, and recent technical innovations of the three techniques. Representative biological demonstrations are also highlighted to exemplify the unique advantages of obtaining vibrational contrasts. With years of effort, these three methods compose an expanding vibrational bioimaging toolbox to tackle specific bioimaging needs, benefiting many biological investigations with rich information in both label-free and labeling manners. Each technique will be discussed and compared in the outlook, leading to possible future directions to accommodate growing needs in vibrational bioimaging.
Collapse
Affiliation(s)
- Haomin Wang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Dongkwan Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
28
|
Fernández-Galiana Á, Bibikova O, Vilms Pedersen S, Stevens MM. Fundamentals and Applications of Raman-Based Techniques for the Design and Development of Active Biomedical Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2210807. [PMID: 37001970 DOI: 10.1002/adma.202210807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Raman spectroscopy is an analytical method based on light-matter interactions that can interrogate the vibrational modes of matter and provide representative molecular fingerprints. Mediated by its label-free, non-invasive nature, and high molecular specificity, Raman-based techniques have become ubiquitous tools for in situ characterization of materials. This review comprehensively describes the theoretical and practical background of Raman spectroscopy and its advanced variants. The numerous facets of material characterization that Raman scattering can reveal, including biomolecular identification, solid-to-solid phase transitions, and spatial mapping of biomolecular species in bioactive materials, are highlighted. The review illustrates the potential of these techniques in the context of active biomedical material design and development by highlighting representative studies from the literature. These studies cover the use of Raman spectroscopy for the characterization of both natural and synthetic biomaterials, including engineered tissue constructs, biopolymer systems, ceramics, and nanoparticle formulations, among others. To increase the accessibility and adoption of these techniques, the present review also provides the reader with practical recommendations on the integration of Raman techniques into the experimental laboratory toolbox. Finally, perspectives on how recent developments in plasmon- and coherently-enhanced Raman spectroscopy can propel Raman from underutilized to critical for biomaterial development are provided.
Collapse
Affiliation(s)
- Álvaro Fernández-Galiana
- Department of Materials, Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
| | - Olga Bibikova
- Department of Materials, Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
| | - Simon Vilms Pedersen
- Department of Materials, Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
| |
Collapse
|
29
|
Spratt SJ, Mizuguchi T, Akaboshi H, Kosakamoto H, Okada R, Obata F, Ozeki Y. Imaging the uptake of deuterated methionine in Drosophila with stimulated Raman scattering. Front Chem 2023; 11:1141920. [PMID: 37065821 PMCID: PMC10090404 DOI: 10.3389/fchem.2023.1141920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
Introduction: Visualizing small individual biomolecules at subcellular resolution in live cells and tissues can provide valuable insights into metabolic activity in heterogeneous cells, but is challenging.Methods: Here, we used stimulated Raman scattering (SRS) microscopy to image deuterated methionine (d-Met) incorporated into Drosophila tissues in vivo.Results: Our results demonstrate that SRS can detect a range of previously uncharacterized cell-to-cell differences in d-Met distribution within a tissue at the subcellular level.Discussion: These results demonstrate the potential of SRS microscopy for metabolic imaging of less abundant but important amino acids such as methionine in tissue.
Collapse
Affiliation(s)
- Spencer J. Spratt
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takaha Mizuguchi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hikaru Akaboshi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yasuyuki Ozeki,
| |
Collapse
|
30
|
Jia H, Yue S. Stimulated Raman Scattering Imaging Sheds New Light on Lipid Droplet Biology. J Phys Chem B 2023; 127:2381-2394. [PMID: 36897936 PMCID: PMC10042165 DOI: 10.1021/acs.jpcb.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/05/2023] [Indexed: 03/11/2023]
Abstract
A lipid droplet (LD) is a dynamic organelle closely associated with cellular functions and energy homeostasis. Dysregulated LD biology underlies an increasing number of human diseases, including metabolic disease, cancer, and neurodegenerative disorder. Commonly used lipid staining and analytical tools have difficulty providing the information regarding LD distribution and composition at the same time. To address this problem, stimulated Raman scattering (SRS) microscopy uses the intrinsic chemical contrast of biomolecules to achieve both direct visualization of LD dynamics and quantitative analysis of LD composition with high molecular selectivity at the subcellular level. Recent developments of Raman tags have further enhanced sensitivity and specificity of SRS imaging without perturbing molecular activity. With these advantages, SRS microscopy has offered great promise for deciphering LD metabolism in single live cells. This article overviews and discusses the latest applications of SRS microscopy as an emerging platform to dissect LD biology in health and disease.
Collapse
Affiliation(s)
- Hao Jia
- Key Laboratory of Biomechanics and
Mechanobiology (Beihang University), Ministry of Education, Institute
of Medical Photonics, Beijing Advanced Innovation Center for Biomedical
Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shuhua Yue
- Key Laboratory of Biomechanics and
Mechanobiology (Beihang University), Ministry of Education, Institute
of Medical Photonics, Beijing Advanced Innovation Center for Biomedical
Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
31
|
Wang W, Shi B, He C, Wu S, Zhu L, Jiang J, Wang L, Lin L, Ye J, Zhang H. Euclidean distance-based Raman spectroscopy (EDRS) for the prognosis analysis of gastric cancer: A solution to tumor heterogeneity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122163. [PMID: 36462319 DOI: 10.1016/j.saa.2022.122163] [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: 09/01/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The prognosis analysis of gastric cancer is critical for selection of treatments and development of advanced therapeutic methods. A prognosis approach that is accurate, fast, convenient, and of low cost for gastric cancers is in high demand. Raman spectroscopy is a label-free and non-destructive technique to provide molecular fingerprints of biological samples, holding promises for cancer prognosis. However, the major challenge of gastric cancer prognosis lies in the widely existing tumor heterogeneity, which leads to unexpected spectral variations within one type of samples. In this work, we have developed the Euclidean distance (ED)-based Raman spectroscopy (EDRS) method for the prognosis analysis of gastric cancer to eliminate the influence of tumor heterogeneity. Raman spectra were first collected on the slices of paraffin-preserved tumor tissues from gastric cancer patients. A standard spectrum to represent the 'worst prognostic tumor cells' was then established. The similarity between each spectrum of tissues and the standard spectrum was assessed by ED, to provide a direct assessment on the prognosis status. We have successfully classified the patients into poor and favorable prognosis groups, either based on the averaged regional ED values (sensitivity of 75 %, specificity of 96.8 %), or based on the minimal ED values at the patient level (sensitivity of 90 %, specificity of 100 %). EDRS was also investigated for survival analysis (AUC = 0.955), much better than the commonly applied post-neoadjuvant therapy (ypTNM) category (AUC = 0.718). Our work highlights EDRS as a rapid, accurate, low-cost and robust tool for heterogeneous cancer-related prognosis assessment and survival prediction, providing new insights for spectroscopic tumor analysis.
Collapse
Affiliation(s)
- Wenfang Wang
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Bowen Shi
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Chang He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Siyi Wu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lan Zhu
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Jiang Jiang
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Lingyun Wang
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Li Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China.
| | - Jian Ye
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, PR China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Huan Zhang
- Department of Radiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China.
| |
Collapse
|
32
|
Jia H, Liu J, Fang T, Zhou Z, Li R, Yin W, Qian Y, Wang Q, Zhou W, Liu C, Sun D, Chen X, Ouyang Z, Dong J, Wang Y, Yue S. The role of altered lipid composition and distribution in liver fibrosis revealed by multimodal nonlinear optical microscopy. SCIENCE ADVANCES 2023; 9:eabq2937. [PMID: 36638165 PMCID: PMC9839333 DOI: 10.1126/sciadv.abq2937] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Intracellular lipid accumulation is commonly seen in fibrotic livers, but its exact role in liver fibrosis remains elusive. Here, we established a multimodal nonlinear optical microscopy to quantitatively map distribution of biomolecules in fibrotic livers. Our data revealed that unsaturated triglycerides were predominantly accumulated in central vein area during liver fibrosis but not in portal vein area. Moreover, the lipid homeostasis was remarkably dysregulated in the late-stage compared to the early-stage fibrosis, including increased unsaturated triglycerides with decreased lipid unsaturation degree and decreased membrane fluidity. Such alterations were likely due to up-regulated lipogenesis, desaturation, and peroxidation, which consequently led to endoplasmic reticulum stress and cell death. Inspiringly, injured hepatocyte could be rescued by remodeling lipid homeostasis via either supply of unsaturated fatty acids or enhancement of membrane fluidity. Collectively, our study improves current understanding of the role of lipid homeostasis in fibrosis and open opportunities for treatment.
Collapse
Affiliation(s)
- Hao Jia
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Juan Liu
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing, 102218, China
| | - Tinghe Fang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Zhen Zhou
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Ruihong Li
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing, 102218, China
| | - Wenzhen Yin
- Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
| | - Yao Qian
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Qi Wang
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing, 102218, China
| | - Wanhui Zhou
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chang Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Dingcheng Sun
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xun Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Jiahong Dong
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing, 102218, China
| | - Yunfang Wang
- Hepato-Pancreato-Biliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
- Research Unit of Precision Hepatobiliary Surgery Paradigm, Chinese Academy of Medical Sciences, Beijing, 102218, China
- Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 102218, China
| | - Shuhua Yue
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| |
Collapse
|
33
|
Kavuru V, Senger RS, Robertson JL, Choudhury D. Analysis of urine Raman spectra differences from patients with diabetes mellitus and renal pathologies. PeerJ 2023; 11:e14879. [PMID: 36874959 PMCID: PMC9979830 DOI: 10.7717/peerj.14879] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/20/2023] [Indexed: 03/03/2023] Open
Abstract
Background Chronic kidney disease (CKD) poses a major public health burden. Diabetes mellitus (DM) is one of the major causes of CKD. In patients with DM, it can be difficult to differentiate diabetic kidney disease (DKD) from other causes of glomerular damage; it should not be assumed that all DM patients with decreased eGFR and/or proteinuria have DKD. Renal biopsy is the standard for definitive diagnosis, but other less invasive methods may provide clinical benefit. As previously reported, Raman spectroscopy of CKD patient urine with statistical and chemometric modeling may provide a novel, non-invasive methodology for discriminating between renal pathologies. Methods Urine samples were collected from renal biopsied and non-biopsied patients presenting with CKD secondary to DM and non-diabetic kidney disease. Samples were analyzed by Raman spectroscopy, baselined with the ISREA algorithm, and subjected to chemometric modeling. Leave-one-out cross-validation was used to assess the predictive capabilities of the model. Results This proof-of-concept study consisted of 263 samples, including renal biopsied, non-biopsied diabetic and non-diabetic CKD patients, healthy volunteers, and the Surine™ urinalysis control. Urine samples of DKD patients and those with immune-mediated nephropathy (IMN) were distinguished from one another with 82% sensitivity, specificity, positive-predictive value (PPV), and negative-predictive value (NPV). Among urine samples from all biopsied CKD patients, renal neoplasia was identified in urine with 100% sensitivity, specificity, PPV, and NPV, and membranous nephropathy was identified with 66.7% sensitivity, 96.4% specificity, 80.0% PPV, and 93.1% NPV. Finally, DKD was identified among a population of 150 patient urine samples containing biopsy-confirmed DKD, other biopsy-confirmed glomerular pathologies, un-biopsied non-diabetic CKD patients (no DKD), healthy volunteers, and Surine™ with 36.4% sensitivity, 97.8% specificity, 57.1% PPV, and 95.1% NPV. The model was used to screen un-biopsied diabetic CKD patients and identified DKD in more than 8% of this population. IMN in diabetic patients was identified among a similarly sized and diverse population with 83.3% sensitivity, 97.7% specificity, 62.5% PPV, and 99.2% NPV. Finally, IMN in non-diabetic patients was identified with 50.0% sensitivity, 99.4% specificity, 75.0% PPV, and 98.3% NPV. Conclusions Raman spectroscopy of urine with chemometric analysis may be able to differentiate between DKD, IMN, and other glomerular diseases. Future work will further characterize CKD stages and glomerular pathology, while assessing and controlling for differences in factors such as comorbidities, disease severity, and other lab parameters.
Collapse
Affiliation(s)
- Varun Kavuru
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,University Hospital at University of Virginia Medical Center, Charlottesville, VA, United States
| | - Ryan S Senger
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States.,DialySensors, Inc., Blacksburg, VA, United States
| | - John L Robertson
- DialySensors, Inc., Blacksburg, VA, United States.,Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States
| | - Devasmita Choudhury
- Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,Salem Veteran Affairs Health Care System, Salem, VA, United States
| |
Collapse
|
34
|
Zhao J, Matlock A, Zhu H, Song Z, Zhu J, Wang B, Chen F, Zhan Y, Chen Z, Xu Y, Lin X, Tian L, Cheng JX. Bond-selective intensity diffraction tomography. Nat Commun 2022; 13:7767. [PMID: 36522316 PMCID: PMC9755124 DOI: 10.1038/s41467-022-35329-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Recovering molecular information remains a grand challenge in the widely used holographic and computational imaging technologies. To address this challenge, we developed a computational mid-infrared photothermal microscope, termed Bond-selective Intensity Diffraction Tomography (BS-IDT). Based on a low-cost brightfield microscope with an add-on pulsed light source, BS-IDT recovers both infrared spectra and bond-selective 3D refractive index maps from intensity-only measurements. High-fidelity infrared fingerprint spectra extraction is validated. Volumetric chemical imaging of biological cells is demonstrated at a speed of ~20 s per volume, with a lateral and axial resolution of ~350 nm and ~1.1 µm, respectively. BS-IDT's application potential is investigated by chemically quantifying lipids stored in cancer cells and volumetric chemical imaging on Caenorhabditis elegans with a large field of view (~100 µm x 100 µm).
Collapse
Affiliation(s)
- Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Alex Matlock
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Hongbo Zhu
- State Key Laboratory of Luminescence and Applications, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.
| | - Ziqi Song
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiabei Zhu
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Biao Wang
- State Key Laboratory of Luminescence and Applications, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Fukai Chen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Yuewei Zhan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Zhicong Chen
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA
| | - Yihong Xu
- Department of Physics, Boston University, Boston, MA, 02215, USA
| | - Xingchen Lin
- State Key Laboratory of Luminescence and Applications, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Physics, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
35
|
Liu YJ, Kyne M, Wang S, Wang S, Yu XY, Wang C. A User-Friendly Platform for Single-Cell Raman Spectroscopy Analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 282:121686. [PMID: 35921751 DOI: 10.1016/j.saa.2022.121686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The optimization of Raman instruments greatly expands our understanding of single-cell Raman spectroscopy. The improvement in the speed and sensitivity of the instrument and the implementation of advanced data mining methods help to reveal the complex chemical and biological information within the Raman spectral data. Here we introduce a new Matlab Graphical User-Friendly Interface (GUI), named "CELL IMAGE" for the analysis of cellular Raman spectroscopy data. The three main steps of data analysis embedded in the GUI include spectral processing, pattern recognition and model validation. Various well-known methods are available to the user of the GUI at each step of the analysis. Herein, a new subsampling optimization method is integrated into the GUI to estimate the minimum number of spectral collection points. The introduction of the signal-to-noise ratio (SNR) of the analyte in the binomial statistical model means the new subsampling model is more sophisticated and suitable for complicated Raman cell data. These embedded methods allow "CELL IMAGE" to transform spectral information into biological information, including single-cell visualization, cell classification and biomolecular/ drug quantification.
Collapse
Affiliation(s)
- Ya-Juan Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology, and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Michelle Kyne
- School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland
| | - Shuang Wang
- Institute of Photonics and Photon-Technology, Northwest University, North Taibai Road, Xi'an 710069, Shaanxi, China
| | - Sheng Wang
- Key Laboratory of Molecular Target & Clinical Pharmacology, and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology, and the NMPA & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China.
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| |
Collapse
|
36
|
Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
Collapse
Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
| |
Collapse
|
37
|
Robertson JL, Senger RS, Talty J, Du P, Sayed-Issa A, Avellar ML, Ngo LT, Gomez De La Espriella M, Fazili TN, Jackson-Akers JY, Guruli G, Orlando G. Alterations in the molecular composition of COVID-19 patient urine, detected using Raman spectroscopic/computational analysis. PLoS One 2022; 17:e0270914. [PMID: 35849572 PMCID: PMC9292080 DOI: 10.1371/journal.pone.0270914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
We developed and tested a method to detect COVID-19 disease, using urine specimens. The technology is based on Raman spectroscopy and computational analysis. It does not detect SARS-CoV-2 virus or viral components, but rather a urine ‘molecular fingerprint’, representing systemic metabolic, inflammatory, and immunologic reactions to infection. We analyzed voided urine specimens from 46 symptomatic COVID-19 patients with positive real time-polymerase chain reaction (RT-PCR) tests for infection or household contact with test-positive patients. We compared their urine Raman spectra with urine Raman spectra from healthy individuals (n = 185), peritoneal dialysis patients (n = 20), and patients with active bladder cancer (n = 17), collected between 2016–2018 (i.e., pre-COVID-19). We also compared all urine Raman spectra with urine specimens collected from healthy, fully vaccinated volunteers (n = 19) from July to September 2021. Disease severity (primarily respiratory) ranged among mild (n = 25), moderate (n = 14), and severe (n = 7). Seventy percent of patients sought evaluation within 14 days of onset. One severely affected patient was hospitalized, the remainder being managed with home/ambulatory care. Twenty patients had clinical pathology profiling. Seven of 20 patients had mildly elevated serum creatinine values (>0.9 mg/dl; range 0.9–1.34 mg/dl) and 6/7 of these patients also had estimated glomerular filtration rates (eGFR) <90 mL/min/1.73m2 (range 59–84 mL/min/1.73m2). We could not determine if any of these patients had antecedent clinical pathology abnormalities. Our technology (Raman Chemometric Urinalysis—Rametrix®) had an overall prediction accuracy of 97.6% for detecting complex, multimolecular fingerprints in urine associated with COVID-19 disease. The sensitivity of this model for detecting COVID-19 was 90.9%. The specificity was 98.8%, the positive predictive value was 93.0%, and the negative predictive value was 98.4%. In assessing severity, the method showed to be accurate in identifying symptoms as mild, moderate, or severe (random chance = 33%) based on the urine multimolecular fingerprint. Finally, a fingerprint of ‘Long COVID-19’ symptoms (defined as lasting longer than 30 days) was located in urine. Our methods were able to locate the presence of this fingerprint with 70.0% sensitivity and 98.7% specificity in leave-one-out cross-validation analysis. Further validation testing will include sampling more patients, examining correlations of disease severity and/or duration, and employing metabolomic analysis (Gas Chromatography–Mass Spectrometry [GC-MS], High Performance Liquid Chromatography [HPLC]) to identify individual components contributing to COVID-19 molecular fingerprints.
Collapse
Affiliation(s)
- John L. Robertson
- Department of Biomedical Engineering and Mechanics, College of Engineering, Virginia Tech, Blacksburg, Virginia, United States of America
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
- * E-mail:
| | - Ryan S. Senger
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
- Department of Biological Systems Engineering, College of Life Sciences and Agriculture, Virginia Tech, Blacksburg, Virginia, United States of America
- Department of Chemical Engineering, College of Engineering, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Janine Talty
- Clinical Biomechanics and Orthopedic Medicine, Roanoke, Virginia, United States of America
| | - Pang Du
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
- Department of Statistics, College of Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Amr Sayed-Issa
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
| | - Maggie L. Avellar
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
- Department of Biological Systems Engineering, College of Life Sciences and Agriculture, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Lacey T. Ngo
- DialySensors Incorporated, Blacksburg, Virginia, United States of America
| | | | - Tasaduq N. Fazili
- Internal Medicine/Infectious Disease, Carilion Clinic, Roanoke, Virginia, United States of America
| | - Jasmine Y. Jackson-Akers
- Internal Medicine/Infectious Disease, Carilion Clinic, Roanoke, Virginia, United States of America
| | - Georgi Guruli
- Division of Surgical Urology/Urologic Oncology, Department of Surgery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Giuseppe Orlando
- Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| |
Collapse
|
38
|
Krishna R, Colak I. Advances in Biomedical Applications of Raman Microscopy and Data Processing: A Mini Review. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2094391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Ram Krishna
- Department of Mechanical Engineering, Madanapalle Institute of Technology & Science, Madanapalle, Andhra Pradesh, India
- Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
- Ohm Janki Biotech Research Private Limited, India
| | - Ilhami Colak
- Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
| |
Collapse
|
39
|
Steven CF, Lee M, Nichol GS, Davey PRJ, Chiarparin E, Brunton VG, Hulme AN. Design, Synthesis, and Analytical Evaluation of Fsp3‐Inspired Raman Probes for Cellular Imaging. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Craig F. Steven
- The University of Edinburgh School of Chemistry Joseph Black BuildingDavid Brewster Road EH9 3FJ Edinburgh UNITED KINGDOM
| | - Martin Lee
- The University of Edinburgh Edinburgh Cancer Research Centre Institute of Genetics and CancerCrewe Road South EH4 2XR Edinburgh UNITED KINGDOM
| | - Gary S. Nichol
- The University of Edinburgh School of Chemistry Joseph Black BuildingDavid Brewster Road EH9 3FJ Edinburgh UNITED KINGDOM
| | - Paul R. J. Davey
- AstraZeneca plc Oncology R&D AstraZeneca CB4 0WG Cambridge UNITED KINGDOM
| | | | - Valerie G. Brunton
- The University of Edinburgh Edinburgh Cancer Research Centre Institute of Genetics and CancerCrewe Road South EH4 2XR Edinburgh UNITED KINGDOM
| | - Alison Nicola Hulme
- The University of Edinburgh College of Medicine and Veterinary Medicine EaStCHEM School of Chemistry Joseph Black BuildingDavid Brewster Road EH9 3FJ Edinburgh UNITED KINGDOM
| |
Collapse
|
40
|
Manifold B, Fu D. Quantitative Stimulated Raman Scattering Microscopy: Promises and Pitfalls. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:269-289. [PMID: 35300525 PMCID: PMC10083020 DOI: 10.1146/annurev-anchem-061020-015110] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Since its first demonstration, stimulated Raman scattering (SRS) microscopy has become a powerful chemical imaging tool that shows promise in numerous biological and biomedical applications. The spectroscopic capability of SRS enables identification and tracking of specific molecules or classes of molecules, often without labeling. SRS microscopy also has the hallmark advantage of signal strength that is directly proportional to molecular concentration, allowing for in situ quantitative analysis of chemical composition of heterogeneous samples with submicron spatial resolution and subminute temporal resolution. However, it is important to recognize that quantification through SRS microscopy requires assumptions regarding both system and sample. Such assumptions are often taken axiomatically, which may lead to erroneous conclusions without proper validation. In this review, we focus on the tacitly accepted, yet complex, quantitative aspect of SRS microscopy. We discuss the various approaches to quantitative analysis, examples of such approaches, challenges in different systems, and potential solutions. Through our examination of published literature, we conclude that a scrupulous approach to experimental design can further expand the powerful and incisive quantitative capabilities of SRS microscopy.
Collapse
Affiliation(s)
- Bryce Manifold
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, Washington, USA;
| |
Collapse
|
41
|
Bi X, Miao K, Wei L. Alkyne-Tagged Raman Probes for Local Environmental Sensing by Hydrogen-Deuterium Exchange. J Am Chem Soc 2022; 144:8504-8514. [PMID: 35508077 DOI: 10.1021/jacs.2c01991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne-tagged Raman probes have shown high promise for noninvasive and sensitive visualization of small biomolecules to understand their functional roles in live cells. However, the potential for alkynes to sense cellular environments that goes beyond imaging remains to be further explored. Here, we report a general strategy for Raman imaging-based local environment sensing by hydrogen-deuterium exchange (HDX) of terminal alkynes (termed alkyne-HDX). We first demonstrate, in multiple Raman probes, that deuterations of the alkynyl hydrogens lead to remarkable shifts of alkyne Raman peaks for about 130 cm-1, providing resolvable signals suited for imaging-based analysis with high specificity. Both our analytical derivation and experimental characterizations subsequently establish that HDX kinetics are linearly proportional to both alkyne pKas and environmental pDs. After validating the quantitative nature of this strategy, we apply alkyne-HDX to sensing local chemical and cellular environments. We establish that alkyne-HDX exhibits high sensitivity to various DNA structures and demonstrates the capacity to detect DNA structural changes in situ from UV-induced damage. We further show that this strategy is also applicable to resolve subtle pD variations in live cells. Altogether, our work lays the foundation for utilizing alkyne-HDX strategy to quantitatively sense the local environments for a broad spectrum of applications in complex biological systems.
Collapse
Affiliation(s)
- Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
42
|
Zheng P, Wu L, Raj P, Mizutani T, Szabo M, Hanson WA, Barman I. A Dual-Modal Single-Antibody Plasmonic Spectro-Immunoassay for Detection of Small Molecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200090. [PMID: 35373504 PMCID: PMC9302383 DOI: 10.1002/smll.202200090] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/15/2022] [Indexed: 05/03/2023]
Abstract
Small molecules play a pivotal role in regulating physiological processes and serve as biomarkers to uncover pathological conditions and the effects of therapeutic treatments. However, it remains a significant challenge to detect small molecules given the size as compared to macromolecules. Recently, the newly emerging plasmonic immunoassays based on surface-enhanced Raman scattering (SERS) offer great promise to deliver extraordinary sensitivity. Nevertheless, they are limited by the intrinsic SERS intensity fluctuations associated with the SERS uncertainty principle. The single transducer that relies on the intensity change is also prone to false signals. Additionally, the prevailing sandwich immunoassay format proves less effective towards detecting small molecules. To circumvent these critical issues, a dual-modal single-antibody approach that synergizes both the intensity and shift of the peak-based immunoassay with Raman enhancement, coined as the INSPIRE assay, is developed for small molecules detection. With two independent transduction mechanisms, it allows better prediction of analyte concentration and attenuation of signal artifacts, providing a new and robust strategy for molecular analysis. With a proof-of-concept demonstration for detection of free T4 and testosterone in serum matrix, the authors envision that the INSPIRE assay could be expanded for a wide spectrum of applications in biomedical diagnosis, discovery of new biopharmaceuticals, food safety, and environmental monitoring.
Collapse
Affiliation(s)
- Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Takayuki Mizutani
- Beckman Coulter Diagnostics – Immunoassay Business Unit, 1000 Lake Hazeltine Dr, Chaska, MN 55318
| | - Miklos Szabo
- Beckman Coulter Diagnostics – Immunoassay Business Unit, 1000 Lake Hazeltine Dr, Chaska, MN 55318
| | - William A. Hanson
- Beckman Coulter Diagnostics – Immunoassay Business Unit, 1000 Lake Hazeltine Dr, Chaska, MN 55318
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
- To whom the correspondence should be addressed.
| |
Collapse
|
43
|
Zhao Y, Zhang J, Gouda M, Zhang C, Lin L, Nie P, Ye H, Huang W, Ye Y, Zhou C, He Y. Structure analysis and non-invasive detection of cadmium-phytochelatin2 complexes in plant by deep learning Raman spectrum. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128152. [PMID: 35033726 DOI: 10.1016/j.jhazmat.2021.128152] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Plants synthesize phytochelatins to chelate in vivo toxic heavy metal ions and produce nontoxic complexes for tolerating the stress. Detection of the complexes would simplify the identification of high phytoremediation cultivars, as well as assessment of plant food for safe consumption. Thus, a confocal Raman spectroscopy combined with density functional theory and deep learning was used for characterizing phytochelatin2 (PC2), and Cd-PC2 mixtures. Results showed the PC2 chelate Cd2+ in a 2:1 ratio to produce Cd(PC2)2; Cd-S bonds of the Cd(PC2)2 have signature Raman vibrations at 305 and 610 cm-1 which are the most distinctive spectral signatures for varieties of Cd-PCs complexes. The PC2 was used as a natural probe to stabilize the chemical status of Cd, and to enrich and magnify Raman signature of the trace Cd for deep learning models which enabled condition of the Cd(PC2)2 in pak choi leaf to be visualized, quantified, and classified by directly using raw spectra of the leaf. This study provides a general protocol by using Raman information for structure analysis and non-invasive detection of heavy metal-PCs complexes in plants and provides a novel idea for simplifying identification of high phytoremediation cultivars, as well as assessment of heavy metal related food safeties.
Collapse
Affiliation(s)
- Yinglei Zhao
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, 310000 Hangzhou, China; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou 310058, China
| | - Jinnuo Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Mostafa Gouda
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; Department of Nutrition & Food Science, National Research Centre, Dokki, 12622 Giza, Egypt
| | - Chenghao Zhang
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, 310000 Hangzhou, China
| | - Lei Lin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Pengcheng Nie
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou 310058, China
| | - Hongbao Ye
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, 310000 Hangzhou, China
| | - Wei Huang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yunxiang Ye
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, 310000 Hangzhou, China
| | - Chengquan Zhou
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences, 310000 Hangzhou, China
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture, Hangzhou 310058, China.
| |
Collapse
|
44
|
Qian N, Min W. Super-multiplexed vibrational probes: Being colorful makes a difference. Curr Opin Chem Biol 2022; 67:102115. [PMID: 35077919 PMCID: PMC8940683 DOI: 10.1016/j.cbpa.2021.102115] [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: 10/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/03/2022]
Abstract
Biological systems with intrinsic complexity require multiplexing techniques to comprehensively describe the phenotype, interaction, and heterogeneity. Recent years have witnessed the development of super-multiplexed vibrational microscopy, overcoming the 'color barrier' of fluorescence-based optical techniques. Here, we will review the recent progress in the design and applications of super-multiplexed vibrational probes. We hope to illustrate how rainbow-like vibrational colors can be generated from systematic studies on structure-spectroscopy relationships and how being colorful makes a difference to various biomedical applications.
Collapse
Affiliation(s)
- Naixin Qian
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
| |
Collapse
|
45
|
Wang H, Xie Q, Xu XG. Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope. Adv Drug Deliv Rev 2022; 180:114080. [PMID: 34906646 DOI: 10.1016/j.addr.2021.114080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 11/19/2022]
Abstract
Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.
Collapse
Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Xie
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA.
| |
Collapse
|
46
|
Du J, Wei L. Multicolor Photoactivatable Raman Probes for Subcellular Imaging and Tracking by Cyclopropenone Caging. J Am Chem Soc 2021; 144:777-786. [PMID: 34913693 DOI: 10.1021/jacs.1c09689] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photoactivatable probes, with high-precision spatial and temporal control, have largely advanced bioimaging applications, particularly for fluorescence microscopy. While emerging Raman probes have recently pushed the frontiers of Raman microscopy for noninvasive small-molecule imaging and supermultiplex optical imaging with superb sensitivity and specificity, photoactivatable Raman probes remain less explored. Here, we report the first general design of multicolor photoactivatable alkyne Raman probes based on cyclopropenone caging for live-cell imaging and tracking. The fast photochemically generated alkynes from cyclopropenones enable background-free Raman imaging with desired photocontrollable features. We first synthesized and spectroscopically characterized a series of model cyclopropenones and identified the suitable light-activating scaffold. We further engineered the scaffold for enhanced chemical stability in a live-cell environment and improved Raman sensitivity. Organelle-targeting probes were then generated to achieve targeted imaging of mitochondria, lipid droplets, endoplasmic reticulum, and lysosomes. Multiplexed photoactivated imaging and tracking at both subcellular and single-cell levels was next demonstrated to monitor the dynamic migration and interactions of the cellular contents. We envision that this general design of multicolor photoactivatable Raman probes would open up new ways for spatial-temporal controlled profiling and interrogations in complex biological systems with high information throughput.
Collapse
Affiliation(s)
- Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
47
|
Mandal A, Ziegler LD. Vibrational line shape effects in plasmon-enhanced stimulated Raman spectroscopies. J Chem Phys 2021; 155:194701. [PMID: 34800946 DOI: 10.1063/5.0067301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A density matrix treatment of plasmon-enhanced (PE) stimulated Raman spectroscopies is developed. Specifically, PE stimulated Raman Gain/Loss (PE-SRG/L) and coherent anti-Stokes Raman scattering (PE-CARS) due to monochromatic excitation and PE femtosecond stimulated Raman spectroscopy (PE-FSRS) are considered. A Lorentz oscillator model is used to explicitly describe the time dependence of plasmon-enhanced optical fields. These temporal characteristics are required for a density matrix based description of all plasmon-enhanced nonlinear molecular spectroscopies. Dispersive vibrational line shapes in PE-SRG/L and PE-FSRS spectra are shown to result primarily from terms proportional to the square of the complex optical field enhancement factor. The dependence on the plasmon resonance, picosecond and femtosecond pulse characteristics, and molecular vibrational properties are evident in the density matrix derived PE-FSRS intensity expression. The difference in signal detection mechanisms accounts for the lack of dispersive line shapes in PE spontaneous Raman spectroscopy. This density matrix treatment of PE-FSRS line shapes is compared with prior coupled wave results.
Collapse
Affiliation(s)
- Aritra Mandal
- Intel Corporation, 2501 NW 229th Ave., Hillsboro, Oregon 97124, USA
| | - L D Ziegler
- Department of Chemistry, Photonics Center Boston University, Boston, Massachusetts 02215, USA
| |
Collapse
|
48
|
Raman microscopy-based quantification of the physical properties of intracellular lipids. Commun Biol 2021; 4:1176. [PMID: 34625633 PMCID: PMC8501034 DOI: 10.1038/s42003-021-02679-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023] Open
Abstract
The physical properties of lipids, such as viscosity, are homeostatically maintained in cells and are intimately involved in physiological roles. Measurement of the physical properties of plasma membranes has been achieved primarily through chemical or genetically encoded fluorescent probes. However, since most probes target plasma membranes, physical properties of lipids in intracellular organelles, including lipid droplets (LDs) are yet to be analyzed. Here, we present a novel Raman microscopy-based approach for quantifying the physical properties of intracellular lipids under deuterium-labeled fatty acid treatment conditions. Focusing on the fact that Raman spectra of carbon-deuterium vibration are altered depending on the surrounding lipid species, we quantitatively represented the physical properties of lipids as the gauche/trans conformational ratio of the introduced labeled fatty acids, which can be used as an indicator of viscosity. Intracellular Raman imaging revealed that the gauche/trans ratio of cytosolic regions was robustly preserved against perturbations attempting to alter the lipid composition. This was likely due to LDs functioning as a buffer against excess gauche/trans ratio, beyond its traditional role as an energy storage organelle. Our novel approach enables the observation of the physical properties of organelle lipids, which is difficult to perform with conventional probes, and is useful for quantitative assessment of the subcellular lipid environment.
Collapse
|
49
|
Multiwell Raman plate reader for high-throughput biochemical screening. Sci Rep 2021; 11:15742. [PMID: 34344945 PMCID: PMC8333358 DOI: 10.1038/s41598-021-95139-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 11/08/2022] Open
Abstract
Although Raman spectroscopy has been used for the quantitative analysis of samples in many fields, including material science, biomedical, and pharmaceutical research, its low sensitivity hindered the application of the analytical capability for high-throughput screening. Here, we developed a high-throughput Raman screening system that can analyze hundreds of specimens in a multiwell plate simultaneously. Multiple high numerical aperture (NA) lenses are assembled under each well in the multiwell plate to detect Raman scattering simultaneously with high sensitivity. The Raman spectrum of 192 samples loaded on a standard 384-well plate can be analyzed simultaneously. With the developed system, the throughput of Raman measurement was significantly improved (about 100 times) compared to conventional Raman instruments based on a single-point measurement. By using the developed system, we demonstrated high-throughput Raman screening to investigate drug polymorphism and identify a small-molecule binding site in a protein. Furthermore, the same system was used to demonstrate high-speed chemical mapping of a centimeter-sized pork slice.
Collapse
|
50
|
Lima C, Muhamadali H, Goodacre R. The Role of Raman Spectroscopy Within Quantitative Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:323-345. [PMID: 33826853 DOI: 10.1146/annurev-anchem-091420-092323] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ninety-four years have passed since the discovery of the Raman effect, and there are currently more than 25 different types of Raman-based techniques. The past two decades have witnessed the blossoming of Raman spectroscopy as a powerful physicochemical technique with broad applications within the life sciences. In this review, we critique the use of Raman spectroscopy as a tool for quantitative metabolomics. We overview recent developments of Raman spectroscopy for identification and quantification of disease biomarkers in liquid biopsies, with a focus on the recent advances within surface-enhanced Raman scattering-based methods. Ultimately, we discuss the applications of imaging modalities based on Raman scattering as label-free methods to study the abundance and distribution of biomolecules in cells and tissues, including mammalian, algal, and bacterial cells.
Collapse
Affiliation(s)
- Cassio Lima
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
| |
Collapse
|