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Research Articles

Fourier-transform Infrared (FT-IR) spectroscopy fingerprints subpopulations of extracellular vesicles of different sizes and cellular origin

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Article: 1741174 | Received 30 May 2019, Accepted 28 Feb 2020, Published online: 30 Mar 2020

References

  • Van Niel G, D’Angelo G, Raposo G. Shedding light on the cell biology of extracellular vesicles. Nat Rev Mol Cell Biol. 2018;19(4):213–11.
  • Tkach M, Kowal J, Théry C. Why the need and how to approach the functional diversity of extracellular vesicles. Philos Trans R Soc B Biol Sci. 2018;373(1737). DOI:10.1098/rstb.2016.0479
  • Minimal Information for Studies of Extracellular Vesicles 2018 (MISEV2018), Théry C, Witwer KW, Aikawa E, et al. A position statement of the international society for extracellular vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles. 2019;8(1):1535750.
  • Lässer C, Jang SC, Lötvall J. Subpopulations of extracellular vesicles and their therapeutic potential. Mol Aspects Med. 2018;60:1–14.
  • Salvi A, Vezzoli M, Busatto S, et al. Analysis of a nanoparticle‑enriched fraction of plasma reveals MiRNA candidates for down syndrome pathogenesis. Int J Mol Med. 2019;43(6):2303–2318.
  • Zlotogorski-Hurvitz A, Dekel BZ, Malonek D, et al. FTIR-based spectrum of salivary exosomes coupled with computational-aided discriminating analysis in the diagnosis of oral cancer. J Cancer Res Clin Oncol. 2019;145(3):685–694.
  • Griffiths PR, De Haseth JA, Winefordner JD. Fourier transform infrared spectrometry. Wiley: Chemical Analysis: A Series of Monographs on Analytical Chemistry and Its Applications; 2007.
  • Parker F. Applications of infrared spectroscopy in biochemistry, biology, and medicine. Springer: US; 2012.
  • Baker MJ, Trevisan J, Bassan P, et al. Using Fourier transform IR spectroscopy to analyze biological materials. Nat Protoc. 2014;9(8). doi:10.1038/nprot.2014.110
  • Martin FL, Kelly JG, Llabjani V, et al. Distinguishing cell types or populations based on the computational analysis of their infrared spectra. Nat Protoc. 2010;5(11):1748–1760.
  • Mihály J, Deák R, Szigyártó IC, et al. Characterization of extracellular vesicles by IR spectroscopy: fast and simple classification based on amide and C[Sbnd]H stretching vibrations. Biochim Biophys Acta - Biomembr. 2017;1859(3):459–466.
  • Gualerzi A, Alexander S, Kooijmans A, et al. Journal of extracellular vesicles Raman spectroscopy as a quick tool to assess purity of extracellular vesicle preparations and predict their functionality. J Extracell Vesicles. 2019;8(1). doi:10.1080/20013078.2019.1568780
  • Lee W, Nanou A, Rikkert L, et al. Label-free prostate cancer detection by characterization of extracellular vesicles using Raman spectroscopy. Anal Chem. 2018;90(19):11290–11296.
  • Gualerzi A, Niada S, Giannasi C, et al. Raman spectroscopy uncovers biochemical tissue-related features of extracellular vesicles from mesenchymal stromal cells. Sci Rep. 2017;7(1):1–11. .
  • Kwizera EA, O’Connor R, Vinduska V, et al. Molecular and analysis of exosomes using surface-enhanced Raman scattering gold nanorods and a miniaturized device. Theranostics. 2018;8(10):2722–2738.
  • Tian YF, Ning CF, He F, et al. Highly sensitive detection of exosomes by SERS using gold nanostar@Raman reporter@nanoshell structures modified with a bivalent cholesterol-labeled DNA anchor. Analyst. 2018;143(20):4915–4922.
  • Merdalimova A, Chernyshev V, Nozdriukhin D, et al. Analysis of exosomes by surface-enhanced Raman spectroscopy. Appl Sci. 2019;9(6):1135.
  • Rojalin T, Phong B, Koster HJ, et al. Nanoplasmonic approaches for sensitive detection and molecular characterization of extracellular vesicles. Front Chem. 2019;7(279):0–24.
  • Shin H, Jeong H, Park J, et al. Correlation between cancerous exosomes and protein markers based on Surface-Enhanced Raman Spectroscopy (SERS) and Principal Component Analysis (PCA). ACS Sens. 2018;3(12):2637–2643.
  • Kruglik SG, Royo F, Guigner JM, et al. Raman Tweezers microspectroscopy of: circa 100 Nm extracellular vesicles. Nanoscale. 2019;11(4):1661–1679.
  • Kim SY, Khanal D, Kalionis B, et al. High-fidelity probing of the structure and heterogeneity of extracellular vesicles by resonance-enhanced atomic force microscopy infrared spectroscopy. Nat Protoc. 2019;14(2):576–593.
  • Chiang CY, Chen C. Toward characterizing extracellular vesicles at a single-particle level Tse-Hua Tan. J Biomed Sci. 2019;26(1):1–10.
  • Alessandri I, Depero LE. All-oxide Raman-active traps for light and matter: probing redox homeostasis model reactions in aqueous environment. Small. 2014;10(7):1294–1298.
  • Alessandri I, Lombardi JR. Enhanced Raman scattering with dielectrics. Chem Rev. 2016;116(24):14921–14981.
  • Kowal J, Arras G, Colombo M, et al. Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Proc Natl Acad Sci U S A. 2016;113(8):E968–77.
  • Livshts MA, Khomyakova E, Evtushenko EG, et al. Isolation of exosomes by differential centrifugation: theoretical analysis of a commonly used protocol. Sci Rep. 2015;5(October):1–14.
  • Faria M, Björnmalm M, Thurecht KJ, et al. Minimum information reporting in bio–nano experimental literature. Nat Nanotechnol. 2018;13(9):777–785. .
  • Van Deun J, Mestdagh P, Agostinis P, et al. EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nat Methods. 2017;14(3):228–232. .
  • Busatto S, Giacomini A, Montis C, et al. Uptake profiles of human serum exosomes by murine and human tumor cells through combined use of colloidal nanoplasmonics and flow cytofluorimetric analysis. Anal Chem. 2018;90(13):7855–7861.
  • Montis C, Zendrini A, Valle F, et al. Size distribution of extracellular vesicles by optical correlation techniques. Colloids Surf B Biointerfaces. 2017;158:331–338.
  • Shelke GV, Lässer C, Gho YS, et al. Importance of exosome depletion protocols to eliminate functional and RNA-containing extracellular vesicles from fetal bovine serum. J Extracell Vesicles. 2014;3(1):1–8.
  • Paolini L, Orizio F, Busatto S, et al. Exosomes secreted by hela cells shuttle on their surface the plasma membrane-associated sialidase NEU3. Biochemistry. 2017;56(48):6401–6408.
  • Vescovi R, Monti M, Moratto D, et al. Collapse of the plasmacytoid dendritic cells compartment in advanced cutaneous melanomas by components of the tumor cell secretome. Cancer Immunol Res. 2019;7(1): 12–28.
  • Radeghieri A, Savio G, Zendrini A, et al. Cultured human amniocytes express HTERT, which is distributed between nucleus and cytoplasm and is secreted in extracellular vesicles. Biochem Biophys Res Commun. 2017;483(1):706–711.
  • Berardocco M, Radeghieri A, Busatto S, et al. RNA-seq reveals distinctive RNA profiles of small extracellular vesicles from different human liver cancer cell lines. Oncotarget. 2017;8(47):82920–82939.
  • Horcas I, Fernández R, Gómez-Rodríguez JM, et al. WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev Sci Instrum. 2007;78(1):013705.
  • Montis C, Gerelli Y, Fragneto G, et al. Nucleolipid bilayers: a quartz crystal microbalance and neutron reflectometry study. Colloids Surf B Biointerfaces. 2016;137:203–213.
  • Zendrini A, Paolini L, Busatto S, et al. Augmented COlorimetric NANoplasmonic (CONAN) method for grading purity and determine concentration of EV microliter volume solutions. Front Bioeng Biotechnol. 2020;7(452):1–10. .
  • Paolini L, Radeghieri A, Civini S, et al. The Epsilon Hinge-Ear region regulates membrane localization of the AP-4 complex. Traffic. 2011;12(11):1604–1619.
  • Alvisi G, Paolini L, Contarini A, et al. Intersectin goes nuclear: secret life of an endocytic protein. Biochem J. 2018;475(8):1455–1472. .
  • Robasky K, Lewis N, Church G. The role of replicates for error mitigation in NGS. Nat Rev Genet. 2014;15(1):56–62.
  • Maiolo D, Paolini L, Di Noto G, et al. Colorimetric nanoplasmonic assay to determine purity and titrate extracellular vesicles. Anal Chem. 2015;87(8):4168–4176.
  • Jeppesen DK, Fenix AM, Franklin JL, et al. Reassessment of exosome composition. Cell. 2019;177(2):428–445.e18.
  • Meister M, Tikkanen R. Endocytic trafficking of membrane-bound Cargo: a flotillin point of view. Membranes (Basel). 2014;4(3):356–371.
  • Gutwein P, Mechtersheimer S, Riedle S, et al. ADAM10-mediated cleavage of L1 adhesion molecule at the cell surface and in released membrane vesicles. Faseb J. 2003;17(2):292–294.
  • Wei J-H, Zhang ZC, Wynn RM, et al. GM130 regulates golgi-derived spindle assembly by activating TPX2 and capturing microtubules. Cell. 2015;162(2):287–299.
  • Ollesch J, Drees SL, Heise HM, et al. FTIR spectroscopy of biofluids revisited: an automated approach to spectral biomarker identification. Analyst. 2013;138(14):4092–4102.
  • Barth A. Infrared spectroscopy of proteins. Biochim Biophys Acta - Bioenergy. 2007;1767(9):1073–1101.
  • Casal HL, Mantsch HH. Polymorphic phase behaviour of phospholipid membranes studied by infrared spectroscopy. BBA - Rev Biomembr. 1984;779(4):381–401.
  • Wold S, Esbensen K, Geladi P. Principal component analysis. Chemom Intellignet Lab Syst. 1987;2(1–3):37–52. June 2001. .
  • Thalib L, Kitching RL, Bhatti MI. Principal component analysis for grouped data—a case study. Environmetrics. 1999;10(5):565–574.
  • Paolini L, Zendrini A, Radeghieri A. Biophysical properties of extracellular vesicles in diagnostics. Biomark Med. 2018;12(4):383–391.
  • Tkach M, Kowal J, The C. Why the need and how to approach the functional diversity of extracellular vesicles. Philos. Trans. R. Soc. B Biol. Sci. 2017;373(1737):20160479.
  • Shen B, Wu N, Yang M, et al. Protein targeting to exosomes/microvesicles by plasma membrane anchors. J Biol Chem. 2011;286(16):14383–14395.
  • Minciacchi VR, Freeman MR, Di Vizio D. Extracellular vesicles in cancer: exosomes, microvesicles and the emerging role of large oncosomes. Semin Cell Dev Biol. 2015;40(41–51). DOI:10.1016/j.semcdb.2015.02.010
  • Brzozowski JS, Jankowski H, Bond DR, et al. Lipidomic profiling of extracellular vesicles derived from prostate and prostate cancer cell lines. Lipids Health Dis. 2018;17(1):1–12.
  • Crescitelli R, Lässer C, Szabó TG, et al. Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes. J Extracell Vesicles. 2013;2(1):20677.
  • Conley A, Minciacchi VR, Lee DH, et al. High-throughput sequencing of two populations of extracellular vesicles provides an MRNA signature that can be detected in the circulation of breast cancer patients. RNA Biol. 2017;14(3):305–316. .
  • Vagner T, Spinelli C, Minciacchi VR, et al. Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma. J Extracell Vesicles. 2018;7(1):1505403.
  • Vella LJ, Scicluna BJ, Cheng L, et al. A rigorous method to enrich for exosomes from brain tissue. J Extracell Vesicles. 2017;6(1):1348885.
  • Fernandez-Trillo F, Grover LM, Stephenson-Brown A, et al. Vesicles in nature and the laboratory: elucidation of their biological properties and synthesis of increasingly complex synthetic vesicles. Angew Chemie Int Ed. 2017;56(12):3142–3160.
  • Lee W, Lenferink ATM, Otto C, Offerhaus HL. Classifying Raman spectra of extracellular vesicles based on convolutional neural networks for prostate cancer detection. J Raman Spectrosc. 2020; 51: 293–300.
  • Picciolini S, Gualerzi A, Vanna R, et al. Characterization of different brain-derived subpopulations of plasma exosomes by surface plasmon resonance imaging. Anal Chem. 2018;90(15):8873–8880.
  • Di Noto G, Bugatti A, Zendrini A, et al. Merging colloidal nanoplasmonics and surface plasmon resonance spectroscopy for enhanced profiling of multiple myeloma-derived exosomes. Biosens Bioelectron. 2016;77:518–524.
  • Daaboul GG, Gagni P, Benussi L, et al. Digital detection of exosomes by interferometric imaging. Sci Rep. 2016;6(1):1–10. .
  • Hartjes TA, Mytnyk S, Jenster GW, et al. Extracellular vesicle quantification and characterization: common methods and emerging approaches. Bioengineering. 2019;6(1):7.