# Comparative Analysis of Methodological Aspects of the Study of Extracellular Vesicles and Extracellular Mitochondria: From Isolation to Internalization

**Authors:** Natalia Yunusova, Dmitry Svarovsky, Evgenya Kaigorodova, Alexey Dobrodeev, Virab Sisakian, Svetlana Tamkovich

PMC · DOI: 10.3390/cimb48020217 · 2026-02-16

## TL;DR

This paper reviews methods for isolating and studying mitochondria-rich extracellular vesicles and their internalization mechanisms.

## Contribution

The paper provides a comparative analysis of methodologies for studying extracellular mitochondria and mitochondria-rich EVs.

## Key findings

- MitoEVs and extracellular mitochondria contain a characteristic set of mitochondrial nucleic acids, primarily mtDNA.
- EV internalization mechanisms include clathrin-dependent endocytosis, caveolin-dependent endocytosis, raft-mediated endocytosis, and macropinocytosis.
- Stem cells, platelet concentrate, and peripheral blood mononuclear cells are main sources for mitochondria-rich EVs for therapeutic use.

## Abstract

Mitochondrial transfer in mammals has been proven to occur both under physiological conditions and during pathological conditions. It has been shown that neighboring cells can exchange mitochondria via nanotunnel tubes. However, there is evidence that free mitochondria, as well as whole mitochondria and individual mitochondrial fragments, can be transported between cells within extracellular vesicles (EVs). This review discusses the methodological aspects of isolation and a minimal set of methods for characterizing mitochondria-rich EVs (mitoEVs), as well as methodological approaches for studying the nucleic acid, protein, and lipid composition. It has been shown that mitoEVs, as well as extracellular mitochondria, contain a characteristic set of nucleic acids of mitochondrial origin. First and foremost, the dominant fraction of mitochondrial nucleic acids is mitochondrial DNA (mtDNA), a circular double-stranded molecule approximately 16.6 thousand base pairs in length. The mechanisms involved in EV internalization include clathrin-dependent endocytosis, caveolin-dependent endocytosis, raft-mediated endocytosis, and macropinocytosis. Mitochondrial-enriched autologous and xenogeneic EVs are thought to be internalized by similar mechanisms. The review also presents the main sources (stem cells, platelet concentrate, peripheral blood mononuclear cells) for obtaining mitochondria-rich EVs for therapeutic purposes.

## Full-text entities

- **Genes:** FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, PDCD6IP (programmed cell death 6 interacting protein) [NCBI Gene 10015] {aka AIP1, ALIX, DRIP4, HP95, MCPH29}, GFAP (glial fibrillary acidic protein) [NCBI Gene 2670] {aka ALXDRD}, COX4I1 (cytochrome c oxidase subunit 4I1) [NCBI Gene 1327] {aka COX IV-1, COX4, COX4-1, COXIV, COXIV-1, MC4DN16}, COX1 (cytochrome c oxidase subunit I) [NCBI Gene 4512] {aka COI, MTCO1}, MIR146A (microRNA 146a) [NCBI Gene 406938] {aka MIRN146, MIRN146A, miR-146a, miRNA146A}, TIMM23 (translocase of inner mitochondrial membrane 23) [NCBI Gene 100287932] {aka TIM23}, MTSS1 (MTSS I-BAR domain containing 1) [NCBI Gene 9788] {aka MIM, MIMA, MIMB}, ATP6 (ATP synthase F0 subunit 6) [NCBI Gene 4508] {aka ATPase6, MTATP6}, CD9 (CD9 molecule) [NCBI Gene 928] {aka BTCC-1, DRAP-27, MIC3, MRP-1, TSPAN-29, TSPAN29}, CD63 (CD63 molecule) [NCBI Gene 967] {aka AD1, HOP-26, ME491, MLA1, OMA81H, Pltgp40}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, ARF6 (ARF GTPase 6) [NCBI Gene 382], MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, FGB (fibrinogen beta chain) [NCBI Gene 2244] {aka HEL-S-78p}, NT5E (5'-nucleotidase ecto) [NCBI Gene 4907] {aka CALJA, CD73, E5NT, NT, NT5, NTE}, CD81 (CD81 molecule) [NCBI Gene 975] {aka CVID6, S5.7, TAPA1, TSPAN28}, DNM1L (dynamin 1 like) [NCBI Gene 10059] {aka DLP1, DRP1, DVLP, DYMPLE, EMPF, EMPF1}, COX2 (cytochrome c oxidase subunit II) [NCBI Gene 4513] {aka COII, MTCO2}, KLF4 (KLF transcription factor 4) [NCBI Gene 9314] {aka EZF, GKLF}, MYLK (myosin light chain kinase) [NCBI Gene 4638] {aka AAT7, KRP, MLCK, MLCK1, MLCK108, MLCK210}, LAMB2 (laminin subunit beta 2) [NCBI Gene 3913] {aka LAMS, NPHS5, PIERS}, RNR1 (s-rRNA) [NCBI Gene 4549] {aka MTRNR1}, MUL1 (mitochondrial E3 ubiquitin protein ligase 1) [NCBI Gene 79594] {aka C1orf166, GIDE, MAPL, MULAN, RNF218}, ICAM1 (intercellular adhesion molecule 1) [NCBI Gene 3383] {aka BB2, CD54, P3.58}, TOMM22 (translocase of outer mitochondrial membrane 22) [NCBI Gene 56993] {aka 1C9-2, MST065, MSTP065, TOM22}, POU5F1 (POU class 5 homeobox 1) [NCBI Gene 5460] {aka OCT3, OCT4, OCT4Borf1, OTF-3, OTF3, OTF4}, ICAM2 (intercellular adhesion molecule 2) [NCBI Gene 3384] {aka CD102}, ND1 (NADH dehydrogenase subunit 1) [NCBI Gene 4535] {aka MTND1}, MFN1 (mitofusin 1) [NCBI Gene 55669] {aka hfzo1, hfzo2}, THY1 (Thy-1 cell surface antigen) [NCBI Gene 7070] {aka CD90, CDw90}, TOMM20 (translocase of outer mitochondrial membrane 20) [NCBI Gene 9804] {aka MAS20, MOM19, TOM20}
- **Diseases:** colorectal cancer (MESH:D015179), metastases (MESH:D009362), blood borne infections (MESH:D000086982), heart attack (MESH:D009203), EV (MESH:D004819), breast cancer (MESH:D001943), MMSCs (MESH:D002292), mitochondrial (MESH:D028361), inflammatory (MESH:D007249), injury to (MESH:D014947), neurodegenerative diseases (MESH:D019636), melanoma (MESH:D008545), chronic kidney disease (MESH:D051436), Alzheimer's disease (MESH:D000544), cancer (MESH:D009369), ischemic myocardium (MESH:D017682), stroke (MESH:D020521), hypoxic (MESH:D002534), obese (MESH:D009765)
- **Chemicals:** proton (MESH:D011522), Mito Tracker Green (-), cytochalasin D (MESH:D015638), nocodazole (MESH:D015739), amino acid (MESH:D000596), heme (MESH:D006418), Lipid (MESH:D008055), sodium carbonate (MESH:C005686), nystatin (MESH:D009761), ATP (MESH:D000255), chlorpromazine (MESH:D002746), steroid hormone (MESH:D013256), LY294002 (MESH:C085911), KCl (MESH:D011189), carbocyanine (MESH:D002232), simvastatin (MESH:D019821), salt (MESH:D012492), ezetimibe (MESH:D000069438), iodixanol (MESH:C044834), lalistat 2 (MESH:C576036), tricarboxylic acid (MESH:D014233), methyl-beta-cyclodextrin (MESH:C108732), EIPA (MESH:C039614), polyethylene glycol (MESH:D011092), TMRE (MESH:C110932), filipin (MESH:D005372), cholesterol (MESH:D002784)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090]
- **Cell lines:** TF1 — Homo sapiens (Human), Erythroleukemia, Cancer cell line (CVCL_3608), HMC1 — Homo sapiens (Human), Mast cell leukemia, Cancer cell line (CVCL_0003), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063)

## Figures

1 figure with captions in the complete paper: https://tomesphere.com/paper/PMC12939610/full.md

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Source: https://tomesphere.com/paper/PMC12939610