Raman tweezers microspectroscopy of circa 100 nm extracellular vesicles.

The technique of Raman tweezers microspectroscopy (RTM) for the global biomolecular content characterization of a single extracellular vesicle (EV) or a small number of EVs or other nanoscale bioparticles in an aqueous dispersion in the difficult-to-access size range of near 100 nm is described in detail. The particularities and potential of RTM are demonstrated using the examples of DOPC liposomes, exosomes from human urine and rat hepatocytes, and a mixed sample of the transfection reagent FuGENE in diluted DNA solution. The approach of biomolecular component analysis for the estimation of the main biomolecular contributions (proteins, lipids, nucleic acids, carotenoids, etc.) is proposed and discussed. Direct Raman evidence for strong intra-sample biomolecular heterogeneity of individual optically trapped EVs, due to variable contributions from nucleic acids and carotenoids in some preparations, is reported. On the basis of the results obtained, we are making an attempt to convince the scientific community that RTM is a promising method of single-EV research; to our knowledge, it is the only technique available at the moment that provides unique information about the global biomolecular composition of a single vesicle or a small number of vesicles, thus being capable of unravelling the high diversity of EV subpopulations, which is one of the most significant urgent challenges to overcome. Possible RTM applications include, among others, searching for DNA biomarkers, cancer diagnosis, and discrimination between different subpopulations of EVs, lipid bodies, protein aggregates and viruses.

[1]  P. Prasad,et al.  Nonlinear optical imaging and Raman microspectrometry of the cell nucleus throughout the cell cycle. , 2010, Biophysical journal.

[2]  Kamila Kochan,et al.  Raman spectroscopy of lipids: a review , 2015 .

[3]  C. Théry,et al.  Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes , 2016, Proceedings of the National Academy of Sciences.

[4]  Chen Chen,et al.  Facile detection of tumor-derived exosomes using magnetic nanobeads and SERS nanoprobes , 2016 .

[5]  C. Thomsen,et al.  Resonance Raman spectra of beta-carotene in solution and in photosystems revisited: an experimental and theoretical study. , 2009, Physical chemistry chemical physics : PCCP.

[6]  Pierre-Yves Turpin,et al.  Fast characterisation of cell-derived extracellular vesicles by nanoparticles tracking analysis, cryo-electron microscopy, and Raman tweezers microspectroscopy , 2012, Journal of extracellular vesicles.

[7]  K. Neuman,et al.  Optical trapping. , 2004, The Review of scientific instruments.

[8]  John M Sanderson,et al.  Analysis of liposomal membrane composition using Raman tweezers. , 2004, Chemical communications.

[9]  Guiwen Wang,et al.  NIR Raman spectroscopic investigation of single mitochondria trapped by optical tweezers. , 2007, Optics express.

[10]  J. Chan,et al.  A nanotweezer system for evanescent wave excited surface enhanced Raman spectroscopy (SERS) of single nanoparticles. , 2015, Optics express.

[11]  H. Hamaguchi,et al.  Casting new physicochemical light on the fundamental biological processes in single living cells by using Raman microspectroscopy. , 2012, Chemical record.

[12]  O. Maragò,et al.  SERS detection of Biomolecules at Physiological pH via aggregation of Gold Nanorods mediated by Optical Forces and Plasmonic Heating , 2016, Scientific Reports.

[13]  Peter Gardner,et al.  Raman tweezers and their application to the study of singly trapped eukaryotic cells. , 2009, Integrative biology : quantitative biosciences from nano to macro.

[14]  J. Falcón-Pérez,et al.  Abundance of Cytochromes in Hepatic Extracellular Vesicles Is Altered by Drugs Related With Drug‐Induced Liver Injury , 2018, Hepatology communications.

[15]  S. Muraishi,et al.  Raman Spectrum of a Transfer RNA , 1971, Science.

[16]  A. Pliss,et al.  Biomolecular component analysis of cultured cell nucleoli by Raman microspectrometry , 2013 .

[17]  A. Ashkin,et al.  Optical trapping and manipulation of single cells using infrared laser beams , 1987, Nature.

[18]  J. Rak,et al.  Microvesicles: Messengers and mediators of tumor progression , 2009, Cell cycle.

[19]  Zachary J. Smith,et al.  3D plasmonic nanobowl platform for the study of exosomes in solution. , 2015, Nanoscale.

[20]  Laurence Zitvogel,et al.  Exosomes: composition, biogenesis and function , 2002, Nature Reviews Immunology.

[21]  James W. Clancy,et al.  Tumor-derived microvesicles: shedding light on novel microenvironment modulators and prospective cancer biomarkers. , 2012, Genes & development.

[22]  J. Greve,et al.  Axial resolution of confocal Raman microscopes: Gaussian beam theory and practice , 1997 .

[23]  Y. Zimmels Diffusive buoyancy force and concentration‐dependent diffusivities , 1994 .

[24]  James W. Chan,et al.  SERS analysis of selectively captured exosomes using an integrin‐specific peptide ligand , 2017 .

[25]  L. Oddershede,et al.  Expanding the optical trapping range of lipid vesicles to the nanoscale. , 2011, Nano letters.

[26]  A. Seifalian,et al.  Exosomes as nano-theranostic delivery platforms for gene therapy. , 2013, Advanced drug delivery reviews.

[27]  S. Krol,et al.  Asymmetrical flow field-flow fractionation with multi-angle light scattering detection for the analysis of structured nanoparticles. , 2009, Journal of chromatography. A.

[28]  T. Alempijevic,et al.  Drug-induced liver injury: Do we know everything? , 2017, World journal of hepatology.

[29]  B P Gaber,et al.  On the quantitative interpretation of biomembrane structure by Raman spectroscopy. , 1977, Biochimica et biophysica acta.

[30]  J. Popp,et al.  SERS-based detection of biomolecules , 2014 .

[31]  L. Moreno,et al.  Hepatocyte-secreted extracellular vesicles modify blood metabolome and endothelial function by an arginase-dependent mechanism , 2017, Scientific Reports.

[32]  K. Torimitsu,et al.  Single Nanoparticle Trapping Using a Raman Tweezers Microscope , 2002 .

[33]  I. R. Lewis,et al.  Handbook of Raman Spectroscopy: From the Research Laboratory to the Process Line , 2001 .

[34]  B. Hernández,et al.  Vibrational analysis of amino acids and short peptides in hydrated media. VIII. Amino acids with aromatic side chains: L-phenylalanine, L-tyrosine, and L-tryptophan. , 2010, The journal of physical chemistry. B.

[35]  G. A. Myers,et al.  Confocal Raman microscopy of pH-gradient-based 10 000-fold preconcentration of compounds within individual, optically trapped phospholipid vesicles. , 2011, Analytical chemistry.

[36]  A. Ashkin Acceleration and trapping of particles by radiation pressure , 1970 .

[37]  H. Byrne,et al.  Spectral pre and post processing for infrared and Raman spectroscopy of biological tissues and cells. , 2016, Chemical Society reviews.

[38]  S. Raimondo,et al.  Exosomes as Intercellular Signaling Organelles Involved in Health and Disease: Basic Science and Clinical Applications , 2013, International journal of molecular sciences.

[39]  Ji-Ho Park,et al.  Exosome Classification by Pattern Analysis of Surface-Enhanced Raman Spectroscopy Data for Lung Cancer Diagnosis. , 2017, Analytical chemistry.

[40]  Cees Otto,et al.  Label-Free Prostate Cancer Detection by Characterization of Extracellular Vesicles Using Raman Spectroscopy , 2018, Analytical chemistry.

[41]  S. Kristensen,et al.  Extracellular Vesicle (EV) Array: microarray capturing of exosomes and other extracellular vesicles for multiplexed phenotyping , 2013, Journal of extracellular vesicles.

[42]  J. Inal,et al.  The role of microvesicles in cancer progression and drug resistance. , 2013, Biochemical Society transactions.

[43]  Belén Hernández,et al.  Characteristic Raman lines of phenylalanine analyzed by a multiconformational approach , 2013 .

[44]  A. Ashkin,et al.  Optical trapping and manipulation of viruses and bacteria. , 1987, Science.

[45]  H. Makse,et al.  A phase diagram for jammed matter , 2008, Nature.

[46]  Jürgen Popp,et al.  The many facets of Raman spectroscopy for biomedical analysis , 2014, Analytical and Bioanalytical Chemistry.

[47]  J. Popp,et al.  Raman Based Molecular Imaging and Analytics: A Magic Bullet for Biomedical Applications!? , 2016, Analytical chemistry.

[48]  M. Heyde,et al.  Vibrational spectra of some carotenoids and related linear polyenes. A Raman spectroscopic study. , 1973, Journal of the American Chemical Society.

[49]  M. Procházka,et al.  Drop coating deposition Raman spectroscopy of liposomes: role of cholesterol. , 2013, Chemistry and physics of lipids.

[50]  R. Dasari,et al.  Diagnosing breast cancer by using Raman spectroscopy. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  S. Mathivanan,et al.  Exosomes: extracellular organelles important in intercellular communication. , 2010, Journal of proteomics.

[52]  Brandon Redding,et al.  Raman Spectroscopy of Optically Trapped Single Biological Micro-Particles , 2015, Sensors.

[53]  R. Simpson,et al.  Proteomic insights into extracellular vesicle biology – defining exosomes and shed microvesicles , 2017, Expert review of proteomics.

[54]  Lynne T. Bemis,et al.  Standardization of sample collection, isolation and analysis methods in extracellular vesicle research , 2013, Journal of extracellular vesicles.

[55]  M Fitzmaurice,et al.  Raman microspectroscopy of human coronary atherosclerosis: biochemical assessment of cellular and extracellular morphologic structures in situ. , 2001, Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology.

[56]  C. Théry,et al.  Membrane vesicles as conveyors of immune responses , 2009, Nature Reviews Immunology.

[57]  C. Otto,et al.  The intensity of the 1602 cm-1 band in human cells is related to mitochondrial activity , 2009 .

[58]  M. Maurel,et al.  Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage , 2014, BMC biophysics.

[59]  J. Lötvall,et al.  Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells , 2007, Nature Cell Biology.

[60]  N. Maiti,et al.  Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein. , 2004, Journal of the American Chemical Society.

[61]  Kishan Dholakia,et al.  Optical micromanipulation. , 2008, Chemical Society reviews.

[62]  B. Hernández,et al.  All characteristic Raman markers of tyrosine and tyrosinate originate from phenol ring fundamental vibrations , 2016 .

[63]  B. Giebel On the function and heterogeneity of extracellular vesicles. , 2017, Annals of translational medicine.

[64]  Gema Moreno-Bueno,et al.  Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET , 2012, Nature Medicine.

[65]  Jun Li,et al.  Integration of a nanostructured dielectrophoretic device and a surface-enhanced Raman probe for highly sensitive rapid bacteria detection. , 2015, Nanoscale.

[66]  I. Tatischeff Cell-derived microvesicles and antitumoral multidrug resistance. , 2012, Comptes rendus biologies.

[67]  D. Gill,et al.  Resonance Raman Scattering of Laser Radiation by Vibrational Modes of Carotenoid Pigment Molecules in Intact Plant Tissues , 1970, Nature.

[68]  M Fitzmaurice,et al.  Diagnosis of human coronary atherosclerosis by morphology-based Raman spectroscopy. , 2001, Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology.

[69]  Ron Milo,et al.  Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans , 2016, Cell.

[70]  Raman-Microsampling Technique Applying Optical Levitation by Radiation Pressure , 1984 .

[71]  Alex Sabelnikov,et al.  Single-cell research: what determines its feasibility? , 2008, Analytical biochemistry.

[72]  A. Aransay,et al.  Transcriptome of Extracellular Vesicles Released by Hepatocytes , 2013, PloS one.

[73]  Keiichi Torimitsu,et al.  Laser trapping and Raman spectroscopy of single cellular organelles in the nanometer range. , 2002, Lab on a chip.

[74]  T. Huser,et al.  Raman spectroscopic analysis of biochemical changes in individual triglyceride-rich lipoproteins in the pre- and postprandial state. , 2005, Analytical chemistry.

[75]  Keiichi Torimitsu,et al.  Near-infrared Raman spectroscopy of single particles , 2001 .

[76]  Zachary J Smith,et al.  Single particle analysis: Methods for detection of platelet extracellular vesicles in suspension (excluding flow cytometry) , 2017, Platelets.

[77]  J. Conboy,et al.  Optical-trapping Raman microscopy detection of single unilamellar lipid vesicles. , 2003, Analytical chemistry.

[78]  Graça Raposo,et al.  Extracellular vesicles: Exosomes, microvesicles, and friends , 2013, The Journal of cell biology.

[79]  J. Guigner,et al.  4-Sulfonatocalix[6]arene-induced aggregation of ionic liquids. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[80]  Yong-qing Li,et al.  Near-infrared Raman spectroscopy of single optically trapped biological cells. , 2002, Optics letters.

[81]  André M. N. Silva,et al.  Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation , 2018, Nature Cell Biology.

[82]  R. Dasari,et al.  Raman microspectroscopic model of human breast tissue: implications for breast cancer diagnosis in vivo , 2002 .

[83]  J. Rak,et al.  Extracellular Vesicles – Biomarkers and Effectors of the Cellular Interactome in Cancer , 2013, Front. Pharmacol..

[84]  D. Armstrong,et al.  Extracellular Vesicles and the Promise of Continuous Liquid Biopsies , 2018, Journal of pathology and translational medicine.

[85]  Daniel P. Cherney,et al.  Optical trapping of unilamellar phospholipid vesicles: investigation of the effect of optical forces on the lipid membrane shape by confocal-Raman microscopy. , 2004, Analytical chemistry.

[86]  Silvia Picciolini,et al.  Raman spectroscopy uncovers biochemical tissue-related features of extracellular vesicles from mesenchymal stromal cells , 2017, Scientific Reports.

[87]  P. Robbins,et al.  Regulation of immune responses by extracellular vesicles , 2014, Nature Reviews Immunology.

[88]  Kit Lam,et al.  Single exosome study reveals subpopulations distributed among cell lines with variability related to membrane content , 2015, Journal of extracellular vesicles.

[89]  G. Thomas,et al.  Raman spectral studies of nucleic acids and related molecules—I Ribonucleic acid derivatives , 1967 .

[90]  Wolfgang Kiefer,et al.  Raman-Microsampling Technique Applying Optical Levitation by Radiation Pressure , 1984 .

[91]  Joel M. Harris,et al.  Confocal Raman microscopy of optical-trapped particles in liquids. , 2010, Annual review of analytical chemistry.

[92]  Hajime Torii,et al.  On the origin of the 1602 cm–1 Raman band of yeasts; contribution of ergosterol , 2012, Journal of biophotonics.

[93]  J. Brunberg,et al.  Characterisation of FXTAS related isolated intranuclear protein inclusions using laser tweezers Raman spectroscopy , 2010 .

[94]  G. Yousef,et al.  Liquid biopsy: a step forward towards precision medicine in urologic malignancies , 2017, Molecular Cancer.

[95]  Seema Singh,et al.  In vivo lipidomics using single-cell Raman spectroscopy , 2011, Proceedings of the National Academy of Sciences.

[96]  Henrik J Johansson,et al.  Cells release subpopulations of exosomes with distinct molecular and biological properties , 2016, Scientific Reports.

[97]  A. Kaczor,et al.  Raman spectroscopy of proteins: a review , 2013 .

[98]  I. Tatischeff Cell-derived Extracellular Vesicles Open New Perspectives for Cancer Research , 2015 .

[99]  S. Lane,et al.  Reagentless identification of single bacterial spores in aqueous solution by confocal laser tweezers Raman spectroscopy. , 2004, Analytical chemistry.

[100]  Aled Clayton,et al.  Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids , 2006, Current protocols in cell biology.

[101]  A. Falus,et al.  The role of membrane vesicles in tumorigenesis. , 2011, Critical reviews in oncology/hematology.

[102]  Kit S Lam,et al.  Multispectral Optical Tweezers for Biochemical Fingerprinting of CD9-Positive Exosome Subpopulations. , 2017, Analytical chemistry.

[103]  J. Lötvall,et al.  Exosomes purified from a single cell type have diverse morphology , 2016, bioRxiv.

[104]  Shelly C. Lu,et al.  Candidate biomarkers in exosome‐like vesicles purified from rat and mouse urine samples , 2010, Proteomics. Clinical applications.

[105]  Francesco Borghi,et al.  Flow field-flow fractionation for the analysis of nanoparticles used in drug delivery. , 2014, Journal of pharmaceutical and biomedical analysis.

[106]  T. Huser,et al.  Methods and Applications of Raman Microspectroscopy to Single-Cell Analysis , 2013, Applied spectroscopy.

[107]  E. Larquet,et al.  Nanovesicles released by Dictyostelium cells: a potential carrier for drug delivery. , 2009, International journal of pharmaceutics.

[108]  Max Diem,et al.  Spectral unmixing and clustering algorithms for assessment of single cells by Raman microscopic imaging , 2011 .

[109]  G. Thomas,et al.  Characterization of DNA structures by laser Raman spectroscopy , 1984, Biopolymers.

[110]  C. Théry,et al.  Why the need and how to approach the functional diversity of extracellular vesicles , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

[111]  Hiro-o Hamaguchi,et al.  Molecular‐level pursuit of yeast mitosis by time‐ and space‐resolved Raman spectroscopy , 2003 .

[112]  J Greve,et al.  Nonresonant confocal Raman imaging of DNA and protein distribution in apoptotic cells. , 2003, Biophysical journal.

[113]  J. Sturm,et al.  Continuous Particle Separation Through Deterministic Lateral Displacement , 2004, Science.

[114]  W. Peticolas,et al.  Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[115]  An Hendrix,et al.  Identification of Individual Exosome-Like Vesicles by Surface Enhanced Raman Spectroscopy. , 2016, Small.

[116]  Hiro-o Hamaguchi,et al.  Raman spectroscopic signature of life in a living yeast cell , 2004 .

[117]  R. Tuma Raman spectroscopy of proteins: from peptides to large assemblies , 2005 .

[118]  Koen Raemdonck,et al.  Therapeutic and diagnostic applications of extracellular vesicles. , 2016, Journal of controlled release : official journal of the Controlled Release Society.

[119]  György Nagy,et al.  Cellular and Molecular Life Sciences REVIEW Membrane vesicles, current state-of-the-art: emerging role of extracellular vesicles , 2022 .

[120]  K. Somasundaram,et al.  Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis. , 2016, Chemical Society reviews.

[121]  D V Petrov,et al.  Raman spectroscopy of optically trapped particles , 2007 .

[122]  F. Szoka,et al.  Preparation of liposomes of defined size distribution by extrusion through polycarbonate membranes. , 1979, Biochimica et biophysica acta.

[123]  J. Chan,et al.  Recent advances in laser tweezers Raman spectroscopy (LTRS) for label‐free analysis of single cells , 2013, Journal of biophotonics.