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Extracellular vesicle-associated proteomic changes from autism patients before and after metabolic stimulation with long-term L-serine treatment

ABSTRACT: The oral medication of L-serine decreased clinical global impression-severity (CGI-S) and clinical global impression-improvement (CGI-I). Behavioral scores, including communication, daily living skills, socialization, and adaptive behavior composite standardized scores, were estimated by distribution based MCID (Minimal clinically important difference) and all scores showed a trend of improvement. Since L-serine naturally cannot bypass the blood-brain barrier, we assumed L-serine could alter systemic molecular profiles, including protein expression in immune cells. In this study, we conducted plasma extracellular vesicle (EV) proteomic analysis to gain insight about immune changes in L-serine treated ASD patients. In order to study proteomic changes of EVs in plasma after oral medication for the ASD patients, we extracted EVs from the ASD patient’s plasma. In a study of nine ASD patients, we used LC-MS/MS to analyze changes in the proteome profile of plasma EVs before and after oral L-serine treatment. In each analysis, EVs were isolated, treated with trypsin for LC-MS/MS analysis, and processed through the PD software and several R packages.

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ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

DISEASE(S): Autism Spectrum Disorder

SUBMITTER: Jaemyung Jang

LAB HEAD: Youngshik Choe

PROVIDER: PXD042314 | Pride | 2025-10-23

REPOSITORIES: Pride

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Project description:Background: Acute coronary syndromes (ACS) are associated with aberrant gene expression and epigenetic mechanisms. In particular, de novo DNA methylation is typically linked to gene silencing, but its role in heart disease remains not fully understood. Extracellular vesicles (EVs) are active components in cellular communication for their ability to carry a plethora of signalling biomolecules, thus representing a promising new diagnostic/therapeutic approach in cardiovascular diseases (CVDs). Indeed, there is the need of novel biomarkers for ACS prediction and timely detection. Purpose: We hypothesized that specific epigenetic signals can be carried by EVs. In this regard, we isolated and characterized circulating EVs from ACS patients and evaluated their potential role to influence DNA methylation in target cells. Methods: Circulating EVs were recovered, by ultracentrifugation, from plasma samples of 19 ACS patients and 50 healthy subjects (HS). Nanoparticle tracking analysis (NTA) and western blot (WB) were used to confirm the EVs integrity and purity. Peripheral blood mononuclear cells (PBMCs) of volunteer donors were treated with both ACS and HS derived EVs and genomic DNA was extracted to perform epigenome wide analysis through Reduced Representation Bisulfite Sequencing. ShinyGO, PANTHER, and STRING tools were interrogated to perform GO and PPI network analyses. Flow Cytometry, qRT-PCR, and WB analysis were also performed to evaluate and validate both intra-vesicular and intra-cellular signals. Results: Plasma ACS-derived EVs showed a significant up-regulation of DNA methyltransferases (DNMTs) gene expression levels as compared to HS (P<0.001). Specifically, de novo methylation transcripts, as DNMT3A and DNMT3B were significantly increased in plasma ACS-EVs. DNA methylation analysis of PBMCs from volunteer donors treated with HS- and ACS-derived EVs showed that RNF166 and CCND3 genes resulted the most hyper- and hypo-methylated, respectively, after by ACS-EV treatment. In addition, PPI network analysis specifically evidenced the subnetwork with SRC, as a hub gene, connecting it to NOTCH1, FOXO3, CDC42, IKBKG, RXRA, DGKG, known as important genes already involved in the onset of CVDs. Surprising, other novel genes, BAIAP2, SYP, CHL1, and SHB, which were hypomethylated, were found significantly overexpressed in PBMCs (P<0.005), underlying the fundamental modulating properties of EV cargo in atherosclerosis. Conclusions: These findings support the significant role of ACS plasma-derived EVs, inducing de novo DNA methylation signals, and modulating specific signaling pathways in target cells.

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Extracellular vesicle-associated proteomic changes from autism patients before and after metabolic stimulation with long-term L-serine treatment

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