Related Experiment Video
Updated: May 28, 2026
Isolation, Characterization, and Proteomic Analysis of Plasma-Derived Extracellular Vesicles for Cardiovascular Biomarker Discovery
Published on: January 31, 2025
Comprehensive High-Depth Proteomic Analysis of Plasma Extracellular Vesicle-Containing Preparations in CDKL5
Tadashi Shiohama1,2, Satoru Takahashi3, Ryo Takeguchi3
1Department of Pediatrics, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba-shi 260-0856, Chiba, Japan.
Insights
Researchers identified altered proteins in blood extracellular vesicles (EVs) of patients with CDKL5 deficiency disorder (CDD). This plasma EV proteome analysis offers potential biomarkers for this rare neurodevelopmental disorder.
Area of Science:
- Neuroscience
- Proteomics
- Biochemistry
Background:
- CDKL5 deficiency disorder (CDD) is a severe X-linked epileptic encephalopathy with limited objective biomarkers.
- Extracellular vesicles (EVs) in blood may harbor CNS-derived disease indicators.
Purpose of the Study:
- To characterize the plasma EV proteome in CDD patients.
- To identify molecular pathways associated with CDD using a hypothesis-generating approach.
Main Methods:
- Plasma samples from CDD patients and controls were analyzed.
- EVs were isolated using immunoprecipitation (CD9, CD63, CD81).
- Proteomic profiling was performed using data-independent mass spectrometry.
Main Results:
- Over 3500 proteins were quantified; 2108 were upregulated and 158 downregulated in CDD.
- Enrichment analysis indicated altered vesicle transport, cytoskeletal organization, and immune pathways.
- Protein expression correlated with CDKL5 Clinical Severity Assessment scores.
Conclusions:
- Plasma EV proteomics revealed significant molecular alterations in CDD.
- This approach may aid in biomarker discovery and understanding CDD mechanisms.
Abstract:
Background/Objectives: CDKL5 deficiency disorder (CDD) is a rare X-linked developmental and epileptic encephalopathy characterized by early onset refractory epilepsy and severe neurodevelopmental impairment with autistic features. Despite advances in genetic diagnosis, objective biomarkers reflecting disease mechanisms remain limited. Extracellular vesicles (EVs) circulating in the blood may contain disease-related proteins derived from the central nervous system. This study aimed to characterize the plasma EV proteome in CDD in a hypothesis-generating exploratory framework and identify the candidate molecular pathways associated with this disorder. Methods: Plasma samples from seven patients with genetically confirmed CDD and seven neurotypical developmental controls were analyzed. Extracellular vesicle-containing preparations (EVs-cp) were isolated via immunoprecipitation using antibodies against CD9, CD63, and CD81. Proteomic profiling was performed using data-independent mass spectrometry. Differentially expressed proteins were identified using Welch's t-test with a false discovery rate correction. Functional enrichment, protein interaction network, and correlation analyses were performed using CDKL5 Clinical Severity Assessment (CCSA) scores. Results: In total, 5617 proteins were identified, of which 3510 were used for quantitative analysis. Compared to the controls, 2108 proteins were upregulated and 158 were downregulated in the CDD samples. Enrichment analysis revealed alterations in vesicle-mediated transport, cytoskeletal organization, and immune-related pathways. Several proteins were also correlated with clinical severity scores. Conclusions: Plasma EV proteomics revealed molecular alterations associated with CDD and provided a potential approach for biomarker discovery and mechanistic investigation.
