Extracellular Vesicle Metabolomics Holds Promise for Adult Axon Regeneration
Abstract
1. Introduction
2. Axon Regeneration
3. Isolation
Isolation Kits | |||
---|---|---|---|
Company | Type of Isolation | Catalog # | Reference |
ThermoFisher (Waltham, MA, USA) | Total Isolation from cell culture | 4478359 | [39] |
Total Isolation from plasma | 4484450 | [40,41] | |
Total Isolation from serum | 4478360 | [39] | |
Total Isolation from urine | 4484452 | [39] | |
Total Exosome RNA and Protein Isolation | 4478545 | [39] | |
QIAGEN (Hilden, Germany) | exoEasy Maxi Kit | 76064 | [42] |
miRCURY Exosome Serum/Plasma Kit | 76603 | [42] | |
System bioscience (Palo Alto, CA, USA) | ExoQuick-TC® ULTRA for Tissue Culture Media | EQULTRA-20TC-1 | [43,44] |
The Original ExoQuick | EXOQ5A-1 | [44] | |
ExoQuick® Exosome Isolation and RNA Purification Kit (for Tissue Culture Media) | EQ806TC-1 | [43] | |
ExoQuick® Exosome Isolation and RNA Purification Kit (for Serum and Plasma) | EQ806A-1 | [41] | |
IZON (Christchurch, New Zealand) | qEVoriginal Columns | ICO-35 | [42,44] |
Fujifilm (Tokyo, Japan) | MagCapture ™ Exosome Isolation Kit PS Ver.2 | 294-84101 | [45,46] |
4. Characterization
4.1. Morphometric Characterization
4.2. Compositional Characterization
4.3. Data Processing and Analysis in MS-Based Exosome Research
Data Analysis and Processing Resources | |||
---|---|---|---|
Omics Type | Data Analysis and Processing | Use(s) | |
Proteomics | Proteome Discoverer™ | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html?erpType=undefined (accessed on 9 April 2025) | Raw Data Processing, Data Normalization, Statistical Analysis, Identification of PTMs |
MaxQuant | https://www.maxquant.org/ (accessed on 9 April 2025) | Raw Data Processing | |
Express Analyst | https://www.expressanalyst.ca/ (accessed on 9 April 2025) | Statistical Analysis, Data Visualization | |
Uniprot | https://www.uniprot.org/ (accessed on 9 April 2025) | Protein and Peptide Description | |
KEGG | https://www.genome.jp/kegg/ (accessed on 9 April 2025) | Pathway Analysis | |
ProteomeXchange | https://www.proteomexchange.org/ (accessed on 9 April 2025) | Data Repository | |
Lipidomics | Lipid Search™ | https://www.thermofisher.com/order/catalog/product/OPTON-30880 (accessed on 9 April 2025) | Raw Data Processing |
MS-DIAL | https://systemsomicslab.github.io/compms/msdial/main.html (accessed on 9 April 2025) | Raw Data Processing | |
mzMine | https://mzio.io/mzmine-news/ (accessed on 9 April 2025) | Raw Data Processing | |
Compound Discoverer™ | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/compound-discoverer-software.html (accessed on 9 April 2025) | Raw Data Processing, Spectral Identification | |
MetaboAnalyst 6.0 | https://www.metaboanalyst.ca/ (accessed on 9 April 2025) | Statistical Analysis, Data Visualization | |
LipidOne | https://lipidone.eu/ (accessed on 9 April 2025) | Statistical Analysis, Data Visualization | |
LIPEA | https://hyperlipea.org/home (accessed on 9 April 2025) | Pathway Analysis | |
KEGG | https://www.genome.jp/kegg/ (accessed on 9 April 2025) | Pathway Analysis | |
Metabolomics Workbench | https://www.metabolomicsworkbench.org/ (accessed on 9 April 2025) | Data Repository | |
Metabolomics | Compound Discoverer™ | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/compound-discoverer-software.html (accessed on 9 April 2025) | Raw Data Processing, Spectral Identification |
MS-DIAL | https://systemsomicslab.github.io/compms/msdial/main.html (accessed on 9 April 2025) | Raw Data Processing | |
mzMine | https://mzio.io/mzmine-news/ (accessed on 9 April 2025) | Raw Data Processing | |
MetaboAnalyst 6.0 | https://www.metaboanalyst.ca/ (accessed on 9 April 2025) | Statistical Analysis, Data Visualization | |
KEGG | https://www.genome.jp/kegg/ (accessed on 9 April 2025) | Pathway Analysis | |
Metabolomics Workbench | https://www.metabolomicsworkbench.org/ (accessed on 9 April 2025) | Data Repository | |
Integromics | OmicsNet 2.0 | https://www.omicsnet.ca/ (accessed on 9 April 2025) | Data Processing, Data Visualization |
OmicsAnalyst 2.0 | https://www.omicsanalyst.ca/ (accessed on 9 April 2025) | Data Processing, Data Visualization |
5. Discussion
Microvesicles | ||
---|---|---|
Metabolites | Axon Regeneration | Reference (PMIDs) |
N-acetylglycosamine | CNS, PNS | [116,117] |
Allantoin | PNS | [118,136] |
Histidine | CNS, PNS | [119] |
Lysophosphatidylcholine (LPC) | CNS | [120,121] |
Lysophosphatidylethanolamine (LPE) | CNS | [122,123] |
Taurine | CNS | [124,125,126,127] |
Gangliosides | CNS, PNS | [38] |
Exosomes | ||
Metabolites | Axon regeneration | Reference |
Acetyl-L-Carnitine (ALCAR) | CNS, PNS | [128,129] |
Carnosine | CNS | [130,131] |
Dimethylglycine | CNS | [132] |
Histidine | CNS, PNS | [119] |
Lysophosphatidylcholine (LPC) | CNS | [120,133] |
Lysophosphatidylethanolamine (LPE) | CNS | [122,123] |
Taurine | CNS | [124,125,126,127] |
Gangliosides | CNS, PNS | [38] |
Lysophosphatidic acid (LPA) | CNS, PNS | [134] |
Modified vesicles/exosomes | ||
Metabolites | Axon regeneration | Reference |
Sphingolipids | CNS | [92,135] |
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
EVs | Extracellular Vesicles |
CNS | Central Nervous System |
PNS | Peripheral Nervous System |
RGCs | Retinal ganglion cells |
MGCs | Microglial cells |
PEG | polyethylene glycol |
IA | Immunoaffinity |
SEC | Size exclusion chromatography |
A4F | Asymmetric flow field-flow fractionation |
TEM | Transmission Electron Microscopy |
AFM | Atomic Force Microscopy |
Cryo-EM | Cryo-electron microscopy |
NTA | Nanoparticle Tracking Analysis |
DLS | Dynamic Light Scattering |
MS | Mass Spectrometry |
LC-MS/MS | Liquid Chromatography-Tandem Mass Spectrometry |
ESI-MS | Electrospray Ionization |
HRMS | High-Resolution Mass Spectrometry |
DDA | Data-Dependent Acquisition |
DIA | Data-Independent Acquisition |
MALDI- TOF MS | Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry |
PCs | phosphatidylcholines |
SMs | sphingomyelins |
PEs | phosphatidylethanolamines |
TMT | Tandem Mass Tag |
FVEPs | Flash visual-evoked potential |
UMSCs | Umbilical cord mesenchymal stem cells |
BMSCs | Bone marrow mesenchymal stem cells |
LPC | Lysophosphatidylcholine |
LPE | Lysophosphatidylethanolamine |
LPA | Lysophosphatidic acid |
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Cabrera Gonzalez, M.D.; Watson, J.; Leal, L.; Moceri, I.; Plummer, C.; Mahato, B.; Fouda, A.Y.; Bhattacharya, S.K. Extracellular Vesicle Metabolomics Holds Promise for Adult Axon Regeneration. Metabolites 2025, 15, 454. https://doi.org/10.3390/metabo15070454
Cabrera Gonzalez MD, Watson J, Leal L, Moceri I, Plummer C, Mahato B, Fouda AY, Bhattacharya SK. Extracellular Vesicle Metabolomics Holds Promise for Adult Axon Regeneration. Metabolites. 2025; 15(7):454. https://doi.org/10.3390/metabo15070454
Chicago/Turabian StyleCabrera Gonzalez, Maria D., Jackson Watson, Laura Leal, Isabella Moceri, Camille Plummer, Biraj Mahato, Abdelrahman Y. Fouda, and Sanjoy K. Bhattacharya. 2025. "Extracellular Vesicle Metabolomics Holds Promise for Adult Axon Regeneration" Metabolites 15, no. 7: 454. https://doi.org/10.3390/metabo15070454
APA StyleCabrera Gonzalez, M. D., Watson, J., Leal, L., Moceri, I., Plummer, C., Mahato, B., Fouda, A. Y., & Bhattacharya, S. K. (2025). Extracellular Vesicle Metabolomics Holds Promise for Adult Axon Regeneration. Metabolites, 15(7), 454. https://doi.org/10.3390/metabo15070454