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Bui TT, Jang E, Shin JH, Kim TH, Kim H, Choi D, Vu TD, Chung H. Feasibility of Raman spectroscopic identification of gall bladder cancer using extracellular vesicles extracted from bile. Analyst 2023; 148:4156-4165. [PMID: 37501647 DOI: 10.1039/d3an00806a] [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: 07/29/2023]
Abstract
Extracellular vesicles (EVs), which are heterogeneous membrane-based vesicles with bilayer cell membrane structures, could be versatile biomarkers for the identification of diverse diseases including cancers. With this potential, this study has attempted the Raman spectroscopic identification of gall bladder (GB) cancer by directly measuring the EV solution extracted from human bile without further sample drying. For this purpose, bile samples were obtained from four normal individuals and 21 GB polyp, eight hepatocellular carcinoma (HCC), and five GB cancer patients, and EVs were extracted from each of the bile samples. The Raman peak shapes of the EVs extracted from the GB cancer samples, especially the relative intensities of peaks in the 1560-1340 cm-1 range, were dissimilar to those of the samples from the normal, GB polyp, and HCC groups. The intensity ratios of peaks at 1537 and 1453 cm-1 and at 1395 and 1359 cm-1 of the GB cancer samples were lower and higher, respectively, than those of the samples of the remaining three groups. The differences of peak intensity ratios were statistically significant based on the Mann-Whitney U test. DNA/RNA bases, amino acids, and bile salts contributed to the spectra of EVs, and their relative abundances seemed to vary according to the occurrence of GB cancer. The varied metabolite compositions and/or structures of EVs were successfully demonstrated by the dissimilar peak intensity ratios in the Raman spectra, thereby enabling the discrimination of GB cancer.
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Affiliation(s)
- Thu Thuy Bui
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
| | - Eunjin Jang
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
| | - Ji Hyun Shin
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Tae Hun Kim
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Hayoon Kim
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Dongho Choi
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Tung Duy Vu
- Faculty of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Hoeil Chung
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
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2
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Pavillon N, Smith NI. Non-invasive monitoring of T cell differentiation through Raman spectroscopy. Sci Rep 2023; 13:3129. [PMID: 36813799 PMCID: PMC9947172 DOI: 10.1038/s41598-023-29259-8] [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: 12/17/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
The monitoring of dynamic cellular behaviors remains a technical challenge for most established techniques used nowadays for single-cell analysis, as most of them are either destructive, or rely on labels that can affect the long-term functions of cells. We employ here label-free optical techniques to non-invasively monitor the changes that occur in murine naive T cells upon activation and subsequent differentiation into effector cells. Based on spontaneous Raman single-cell spectra, we develop statistical models that allow the detection of activation, and employ non-linear projection methods to delineate the changes occurring over a several day period spanning early differentiation. We show that these label-free results have very high correlation with known surface markers of activation and differentiation, while also providing spectral models that allow the identification of the underlying molecular species that are representative of the biological process under study.
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Affiliation(s)
- Nicolas Pavillon
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka, 565-0871, Japan.
| | - Nicholas I. Smith
- grid.136593.b0000 0004 0373 3971Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Open and Transdisciplinary Research Institute (OTRI), Osaka University, Yamadaoka 3-1, Suita, Osaka 565-0871 Japan
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3
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Ma Y, Li H, Gong Z, Yang S, Wang P, Tang C. Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate. J Am Chem Soc 2022; 144:4716-4720. [PMID: 35179357 DOI: 10.1021/jacs.1c12085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, which could lead to neurodegenerative diseases. Here, we report that, in the presence of Mg2+, RNA molecules containing 20× CAG repeats self-assemble into three morphologically distinct droplets. Using hyperspectral stimulated Raman microscopy, we show that RNA phase separation is accompanied by the clustering of nucleobases while forfeiting the canonical base-paired structure. As the RNA/Mg2+ ratio increases, the RNA droplets first expand and then shrink to adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like RNA droplets, the nucleobase-clustered structure is more prominent at the rim, suggesting a continuously hardening process. This mechanism may be implicated in the general aging processes of RNA-containing membrane-less organelles.
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Affiliation(s)
- Yingxue Ma
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Haozheng Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ping Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Center for Computational Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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4
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Robert C, Tsiampali J, Fraser-Miller SJ, Neumann S, Maciaczyk D, Young SL, Maciaczyk J, Gordon KC. Molecular monitoring of glioblastoma's immunogenicity using a combination of Raman spectroscopy and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119534. [PMID: 33588367 DOI: 10.1016/j.saa.2021.119534] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Raman spectroscopy (RS) has been used as a powerful diagnostic and non-invasive tool in cancer diagnosis as well as in discrimination of cancer and immune cells. In this study RS in combination with chemometrics was applied to cellular Raman spectral data to distinguish the phenotype of T-cells and monocytes after incubation with media conditioned by glioblastoma stem-cells (GSCs) showing different molecular background. For this purpose, genetic modulations of epithelial-to-mesenchymal transition (EMT) process and expression of immunomodulator CD73 were introduced. Principal component analysis of the Raman spectral data showed that T-cells and monocytes incubated with tumour-conditioned media (TCMs) of GSCs with inhibited EMT activator ZEB1 or CD73 formed distinct clusters compared to controls highlighting their differences. Further discriminatory analysis performed using linear discriminant analysis (LDA) and support vector machine classification (SVM), yielded sensitivities and specificities of over 70 and 67% respectively upon validation against an independent test set. Supporting those results, flow cytometric analysis was performed to test the influence of TCMs on cytokine profile of T-cells and monocytes. We found that ZEB1 and CD73 influence T-cell and monocyte phenotype and promote monocyte differentiation into a population of mixed pro- and anti-tumorigenic macrophages (MΦs) and dendritic cells (DCs) respectively. In conclusion, Raman spectroscopy in combination with chemometrics enabled tracking T-cells and monocytes.
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Affiliation(s)
- Chima Robert
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Julia Tsiampali
- Neurosurgery Department, University Hospital Duesseldorf, 40225 Duesseldorf, Germany
| | - Sara J Fraser-Miller
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Silke Neumann
- Department of Pathology, University of Otago, Dunedin, New Zealand
| | - Donata Maciaczyk
- Department of Pathology, University of Otago, Dunedin, New Zealand
| | - Sarah L Young
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Jaroslaw Maciaczyk
- Department of Neurosurgery, University Hospital Bonn, 53179 Bonn, Germany; Department of Surgical Sciences, University of Otago, Dunedin, New Zealand.
| | - Keith C Gordon
- Dodd-Walls Centre for Photonics and Quantum Technologies, Department of Chemistry, University of Otago, Dunedin, New Zealand.
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Cui X, Song M, Liu Y, Yuan Y, Huang Q, Cao Y, Lu F. Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study. Talanta 2020; 217:121073. [PMID: 32498900 DOI: 10.1016/j.talanta.2020.121073] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/20/2022]
Abstract
Theophylline is a potent bronchodilator for the treatment of asthma, bronchitis, and emphysema. Its narrow therapeutic window (20-100 μM) demands that the blood concentration of theophylline be monitored carefully, which can be achieved by aptamer capture. Thus, an understanding of what occurs when aptamers bind to theophylline is critical for identifying a high-affinity and high-specificity aptamer, which improve the sensitivity and selectivity of theophylline detection. Consequently, there is an urgent need to develop a simple, convenient, and nondestructive method to monitor conformational changes during the binding process. Here, we report the determination of the affinity of a selected aptamer and theophylline via biolayer interferometry (BLI) experiments. Additionally, using surface-enhanced Raman spectroscopy (SERS), the conformational changes on theophylline-aptamer binding were identified from differences in the SER spectra. Finally, molecular dynamics (MD) simulations were used to identify the specific conformational changes of the aptamer during the binding process. Such a combined BLI-SERS-MD method provides an in-depth understanding of the theophylline-aptamer binding processes and a comprehensive explanation for conformational changes, which helps to select, design, and modify an aptamer with high affinity and specificity. It can also be used as a scheme for the study of other aptamer-ligand interactions, which can be applied to the detection, sensing, clinical diagnosis, and treatment of diseases.
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Affiliation(s)
- Xiaolin Cui
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Liu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yifan Yuan
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yongbing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Feng Lu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China.
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6
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Cai W, Feng H, Yin L, Wang M, Jiang X, Qin Z, Liu W, Li C, Jiang H, Weizmann Y, Wang X. Bio responsive self-assembly of Au-miRNAs for targeted cancer theranostics. EBioMedicine 2020; 54:102740. [PMID: 32276223 PMCID: PMC7139156 DOI: 10.1016/j.ebiom.2020.102740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNA (miRNA) therapeutics are a promising approach to cancer treatment. However, this method faces considerable challenges to achieve tissue-specific, efficient, and safe delivery of miRNAs in vivo. Methods Herein, we developed a miRNA delivery system based on the in situ self-assembly of Au-miRNA nanocomplexes (Au-miRNA NCs). Within the cancer microenvironment, we constructed in situ self-assembled Au-miRNA NCs by coincubating gold salt and tumor suppressor mimics, such as let-7a, miRNA-34a, and miRNA-200a. Findings The in vitro experiments demonstrated that characteristic in situ self-assembled Au-miRNA NCs were present in cancer cells and can be taken up to inhibit the proliferation of cancer cells effectively. Most importantly, as proven in subcutaneous tumor treatment models, Au-miRNA NCs were especially useful for accurate target imaging and tumor suppression, with significantly enhanced antitumor effects for combination therapy. Interpretation These observations highlight that a new strategy for the in situ biosynthesis of Au-let-7a NCs, Au-miR-34a NCs, and Au-miR-200a NCs is feasible, and this may assist in the delivery of more miRNA to tumor cells for cancer treatment. This work opens up new opportunities for the development of miRNA tumor therapy strategies. Funding National Natural Science Foundation of China (91753106); Primary Research & Development Plan of Jiangsu Province (BE2019716); National Key Research and Development Program of China (2017YFA0205300).
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Affiliation(s)
- Weijuan Cai
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Shunde Hospital of Southern Medical University, Shunde 528300, China
| | - Huan Feng
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liang Yin
- Shunde Hospital of Southern Medical University, Shunde 528300, China
| | - Maonan Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuerui Jiang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhaojian Qin
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Weiwei Liu
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Chunmei Li
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hui Jiang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yossi Weizmann
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics (Chien-Shiung Wu Lab), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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7
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Noninvasive detection of macrophage activation with single-cell resolution through machine learning. Proc Natl Acad Sci U S A 2018; 115:E2676-E2685. [PMID: 29511099 DOI: 10.1073/pnas.1711872115] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We present a method enabling the noninvasive study of minute cellular changes in response to stimuli, based on the acquisition of multiple parameters through label-free microscopy. The retrieved parameters are related to different attributes of the cell. Morphological variables are extracted from quantitative phase microscopy and autofluorescence images, while molecular indicators are retrieved via Raman spectroscopy. We show that these independent parameters can be used to build a multivariate statistical model based on logistic regression, which we apply to the detection at the single-cell level of macrophage activation induced by lipopolysaccharide (LPS) exposure and compare their respective performance in assessing the individual cellular state. The models generated from either morphology or Raman can reliably and independently detect the activation state of macrophage cells, which is validated by comparison with their cytokine secretion and intracellular expression of molecules related to the immune response. The independent models agree on the degree of activation, showing that the features provide insight into the cellular response heterogeneity. We found that morphological indicators are linked to the phenotype, which is mostly related to downstream effects, making the results obtained with these variables dose-dependent. On the other hand, Raman indicators are representative of upstream intracellular molecular changes related to specific activation pathways. By partially inhibiting the LPS-induced activation using progesterone, we could identify several subpopulations, showing the ability of our approach to identify the effect of LPS activation, specific inhibition of LPS, and also the effect of progesterone alone on macrophage cells.
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8
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9
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Morla-Folch J, Gisbert-Quilis P, Masetti M, Garcia-Rico E, Alvarez-Puebla RA, Guerrini L. Conformational SERS Classification of K-Ras
Point Mutations for Cancer Diagnostics. Angew Chem Int Ed Engl 2017; 56:2381-2385. [DOI: 10.1002/anie.201611243] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/12/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Judit Morla-Folch
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- Medcom Advance S.A.; Av. Roma 08840 Barcelona Spain
| | - Patricia Gisbert-Quilis
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- Medcom Advance S.A.; Av. Roma 08840 Barcelona Spain
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum-Università di Bologna; via Belmeloro 6 40126 Bologna Italy
| | - Eduardo Garcia-Rico
- Department of Clinical Oncology; Hospital Univesitario; HM Torrelodones 28250 Madrid Spain
| | - Ramon A. Alvarez-Puebla
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- ICREA; Passeig Lluís Companys 23 08010 Barcelona Spain
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10
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Morla-Folch J, Gisbert-Quilis P, Masetti M, Garcia-Rico E, Alvarez-Puebla RA, Guerrini L. Conformational SERS Classification of K-Ras
Point Mutations for Cancer Diagnostics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Judit Morla-Folch
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- Medcom Advance S.A.; Av. Roma 08840 Barcelona Spain
| | - Patricia Gisbert-Quilis
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- Medcom Advance S.A.; Av. Roma 08840 Barcelona Spain
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology; Alma Mater Studiorum-Università di Bologna; via Belmeloro 6 40126 Bologna Italy
| | - Eduardo Garcia-Rico
- Department of Clinical Oncology; Hospital Univesitario; HM Torrelodones 28250 Madrid Spain
| | - Ramon A. Alvarez-Puebla
- Deapartment of Physical Chemistry; Universitat Rovira i Virgili; Carrer de Marcellí Domingo s/n 43007 Tarragona Spain
- ICREA; Passeig Lluís Companys 23 08010 Barcelona Spain
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11
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Spain E, Adamson K, Elshahawy M, Bray I, Keyes TE, Stallings RL, Forster RJ. Hemispherical platinum : silver core : shell nanoparticles for miRNA detection. Analyst 2017; 142:752-762. [DOI: 10.1039/c6an02609e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel electrochemical detection based on regioselective functionalised electrocatalytic nanoparticles suitable for the detection of low-abundance molecular biomarkers, miR-132 of neuroblastoma.
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Affiliation(s)
- Elaine Spain
- School of Chemical Sciences
- National Centre for Sensor Research
- Dublin City University
- Dublin 9
- Ireland
| | - Kellie Adamson
- School of Chemical Sciences
- National Centre for Sensor Research
- Dublin City University
- Dublin 9
- Ireland
| | - Mohammad Elshahawy
- School of Chemical Sciences
- National Centre for Sensor Research
- Dublin City University
- Dublin 9
- Ireland
| | - Isabella Bray
- Department of Molecular and Cellular Therapeutics
- Royal College of Surgeons in Ireland
- Dublin
- Ireland
| | - Tia E. Keyes
- School of Chemical Sciences
- National Centre for Sensor Research
- Dublin City University
- Dublin 9
- Ireland
| | - Raymond L. Stallings
- Department of Molecular and Cellular Therapeutics
- Royal College of Surgeons in Ireland
- Dublin
- Ireland
| | - Robert J. Forster
- School of Chemical Sciences
- National Centre for Sensor Research
- Dublin City University
- Dublin 9
- Ireland
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12
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Lebedev N, Griva I, Dressick WJ, Phelps J, Johnson JE, Meshcheriakova Y, Lomonossoff GP, Soto CM. A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor. Biosens Bioelectron 2016; 77:306-14. [DOI: 10.1016/j.bios.2015.09.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/10/2015] [Accepted: 09/13/2015] [Indexed: 02/05/2023]
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13
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Morla-Folch J, Xie HN, Alvarez-Puebla RA, Guerrini L. Fast Optical Chemical and Structural Classification of RNA. ACS NANO 2016; 10:2834-2842. [PMID: 26831953 DOI: 10.1021/acsnano.5b07966] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs.
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Affiliation(s)
- Judit Morla-Folch
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
- Universitat Rovira i Virgili and Centro Tecnológico de la Química de Catalunya , Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Hai-nan Xie
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
| | - Ramon A Alvarez-Puebla
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
- Universitat Rovira i Virgili and Centro Tecnológico de la Química de Catalunya , Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain
- ICREA , Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Luca Guerrini
- Medcom Advance , Viladecans Business Park, Edificio Brasil, Bertran i Musitu 83-85, 08840 Viladecans, Barcelona, Spain
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14
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Hobro AJ, Kumagai Y, Akira S, Smith NI. Raman spectroscopy as a tool for label-free lymphocyte cell line discrimination. Analyst 2016; 141:3756-64. [DOI: 10.1039/c6an00181e] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Raman spectroscopy can be used to discriminate between morphologically similar lymphocyte cell classes and cell lines.
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Affiliation(s)
- Alison J. Hobro
- Biophotonics Laboratory
- Immunology Frontier Research Center
- Osaka University
- Osaka
- Japan
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit
- Immunology Frontier Research Center
- Osaka University
- Osaka
- Japan
| | - Shizuo Akira
- Host Defense Laboratory
- Immunology Frontier Research Center
- Osaka University
- Osaka
- Japan
| | - Nicholas I. Smith
- Biophotonics Laboratory
- Immunology Frontier Research Center
- Osaka University
- Osaka
- Japan
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15
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Hobro AJ, Pavillon N, Fujita K, Ozkan M, Coban C, Smith NI. Label-free Raman imaging of the macrophage response to the malaria pigment hemozoin. Analyst 2015; 140:2350-9. [PMID: 25646175 DOI: 10.1039/c4an01850h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hemozoin, the 'malaria pigment', is engulfed by phagocytic cells, such as macrophages, during malaria infection. This biocrystalline substance is difficult to degrade and often accumulates in phagocytes. The macrophage response to hemozoin relates to the severity of the disease and the potential for malaria-related disease complications. In this study we have used Raman spectroscopy as a label-free method to investigate the biochemical changes occurring in macrophages during the first few hours of hemozoin uptake. We found a number of distinct spectral groups, spectrally or spatially related to the presence of the hemozoin inside the cell. Intracellular hemozoin was spectrally identical to extracellular hemozoin, regardless of the location in the cell. A small proportion of hemozoin was found to be associated with lipid-based components, consistent with the uptake of hemozoin into vesicles such as phagosomes and lysosomes. The spatial distribution of the hemozoin was observed to be inhomogeneous, and its presence largely excluded that of proteins and lipids, demonstrating that cells were not able to break down the biocrystals on the time scales studied here. These results show that Raman imaging can be used to answer some of the open questions regarding the role of hemozoin in the immune response. How different combinations of hemozoin and other molecules are treated by macrophages, whether hemozoin can be broken down by the cell, and more importantly, which co-factors or products are involved in the subsequent cell reaction are the expected issues to be elucidated by this technique.
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Affiliation(s)
- Alison J Hobro
- Biophotonics Laboratory, Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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Kuzmin AN, Pliss A, Prasad PN. Changes in Biomolecular Profile in a Single Nucleolus during Cell Fixation. Anal Chem 2014; 86:10909-16. [DOI: 10.1021/ac503172b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andrey N. Kuzmin
- Institute for Lasers, Photonics and Biophotonics, Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Paras N. Prasad
- Institute for Lasers, Photonics and Biophotonics, Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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Abstract
UNLABELLED In recent decades, Raman spectroscopy has entered the biological and medical fields. It enables nondestructive analysis of structural details at the molecular level and has been used to study viruses and their constituents. Here, we used Raman spectroscopy to study echovirus 1 (EV1), a small, nonenveloped human pathogen, in two different uncoating states induced by heat treatments. Raman signals of capsid proteins and RNA genome were observed from the intact virus, the uncoating intermediate, and disrupted virions. Transmission electron microscopy data revealed general structural changes between the studied particles. Compared to spectral characteristics of proteins in the intact virion, those of the proteins of the heat-treated particles indicated reduced α-helix content with respect to β-sheets and coil structures. Changes observed in tryptophan and tyrosine signals suggest an increasingly hydrophilic environment around these residues. RNA signals revealed a change in the environment of the genome and in its conformation. The ionized-carbonyl vibrations showed small changes between the intact virion and the uncoating intermediate, which points to cleavage of salt bridges in the protein structure during the uncoating process. In conclusion, our data reveal distinguishable Raman signatures of the intact, intermediate, and disrupted EV1 particles. These changes indicate structural, chemical, and solute-solvent alterations in the genome and in the capsid proteins and lay the essential groundwork for investigating the uncoating of EV1 and related viruses in real time. IMPORTANCE In order to combat virus infection, we need to know the details of virus uncoating. We present here the novel Raman signatures for opened and intact echovirus 1. This gives hope that the signatures may be used in the near future to evaluate the ambient conditions in endosomes leading to virus uncoating using, e.g., coherent anti-Stokes Raman spectroscopy (CARS) imaging. These studies will complement structural studies on virus uncoating. In addition, Raman/CARS imaging offers the possibility of making dynamic live measurements in vitro and in cells which are impossible to measure by, for example, cryo-electron tomography. Furthermore, as viral Raman spectra can be overwhelmed with various contaminants, our study is highly relevant in demonstrating the importance of sample preparation for Raman spectroscopy in the field of virology.
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