Proteomic signature of circulating extracellular vesicles in dilated cardiomyopathy

Abstract

Dilated cardiomyopathy (DCM) remains a major cause of heart failure and carries a poor prognosis despite important advances in recent years. Better disease characterization using novel molecular techniques is needed to refine its progression. This study explored the proteomic signature of plasma-derived extracellular vesicles (EVs) obtained from DCM patients and healthy controls using size-exclusion chromatography (SEC). EV-enriched fractions were analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Raw data obtained from LC-MS/MS were analyzed against the Uniprot human database using MaxQuant software. Additional analyses using Perseus software were based on the Intensity-Based Absolute Quantification (iBAQ) values from MaxQuant analyses. A total of 90.07 ± 21 proteins (227 different proteins) in the DCM group and 96.52 ± 17.91 proteins (183 different proteins) in the control group were identified. A total of 176 proteins (74.6%) were shared by controls and DCM patients, whereas 51 proteins were exclusive for the DCM group and 7 proteins were exclusive for the control group. Fibrinogen (α, β and γ chain), serotransferrin, α-1-antitrypsin, and a variety of apolipoprotein family members (C-I, C-III, D, H or β-2-glycoprotein, and J or clusterin) were clustered in SEC-EVs derived from DCM patients relative to controls (p< 0.05). Regarding Gene Ontology analysis, response to stress and protein activation-related proteins were enriched in DCM-EVs compared with controls. Thus, the present study reports the distinct proteomic signature of circulating DCM-EVs compared with control-EVs. Furthermore, we confirm that SEC obtains highly purified EV fractions from peripheral blood samples for subsequent use in determining disease-specific proteomic signatures.

Application of Extracellular Vesicles Proteomics to Cardiovascular Disease: Guidelines, Data Analysis, and Future Perspectives

“…In a recent study, the group of Roura and collaborators explored the proteomic profile of plasma-derived EVs obtained from DCM patients and healthy controls using size-exclusion chromatography. [141] They found 227 and 183 unique proteins in DCM patients and controls, respectively. Indeed, a total of 176 proteins (74.6%) were shared by controls and DCM patients, whereas 51 proteins were exclusive for the DCM group and 7 proteins were exclusive for the control group.…”

“…In a recent study, the group of Roura and collaborators explored the proteomic profile of plasma‐derived EVs obtained from DCM patients and healthy controls using size‐exclusion chromatography . They found 227 and 183 unique proteins in DCM patients and controls, respectively.…”

“…A detailed systems biology analysis showed that most proteins enriched in EVs from DCM patients are involved in stress response and protein activation‐related proteins. Nevertheless, further research is needed to better understand the precise role of these proteins in DCM progression …”

Proteomic Signature of Mesenchymal Stromal Cell‐Derived Small Extracellular Vesicles

“…Proteomic profiles of MSC‐EV isolated by SEC are likely to differ from those of MSC‐EV isolated by ultracentrifugation, HPLC, tangential flow filtration, or precipitation, as SEC is likely to better remove overabundant soluble proteins compared to other techniques, resulting in relatively more pure EV preparations. Thus, comparative studies on SEC‐isolated MSC‐EV, with a strong focus on EV purity and potential contaminations will be required to verify our conclusions on MSC‐EV cargo and their potential functional implications …”

“…Thus, comparative studies on SEC-isolated MSC-EV, with a strong focus on EV purity and potential contaminations will be required to verify our conclusions on MSC-EV cargo and their potential functional implications. [65,66] Furthermore, besides the mentioned variability in cell source, the harvesting time of the EV-containing conditioned medium shows great variability between studies, ranging from 24 h to 7 days. The optimal harvesting time may vary per EV-producing cell, and depends on a balance between high yield while preventing accumulation of unwanted substances such as apoptotic bodies, as nicely determined by Lee et al, who determined an optimal harvesting time of 48 h for their adipose tissue-derived MSC-EV.…”