Integrated proteomic and metabolomic analyses of the mitochondrial neurodegenerative disease MELAS
Haorong Li1, Martine Uittenbogaard2, Ryan Navarro1
1Department of Chemistry, The George Washington University, Science and Engineering Hall, 800 22nd St., NW, Washington, DC 20052, USA. linghao@gwu.edu.
Abstract:
MELAS (mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes) is a progressive neurodegenerative disease caused by pathogenic mitochondrial DNA variants. The pathogenic mechanism of MELAS remains enigmatic due to the exceptional clinical heterogeneity and the obscure genotype-phenotype correlation among MELAS patients. To gain insights into the pathogenic signature of MELAS, we designed a comprehensive strategy integrating proteomics and metabolomics in patient-derived dermal fibroblasts harboring the ultra-rare MELAS pathogenic variant m.14453G>A, specifically affecting the mitochondrial respiratory complex I. Global proteomics was achieved by data-dependent acquisition (DDA) and verified by data-independent acquisition (DIA) using both Spectronaut and the recently launched MaxDIA platforms. Comprehensive metabolite coverage was achieved for both polar and nonpolar metabolites in both reverse phase and HILIC LC-MS/MS analyses. Our proof-of-principle MELAS study with multi-omics integration revealed OXPHOS dysregulation with a predominant deficiency of complex I subunits, as well as alterations in key bioenergetic pathways, glycolysis, tricarboxylic acid cycle, and fatty acid β-oxidation. The most clinically relevant discovery is the downregulation of the arginine biosynthesis pathway, likely due to blocked argininosuccinate synthase, which is congruent with the MELAS cardinal symptom of stroke-like episodes and its current treatment by arginine infusion. In conclusion, we demonstrated an integrated proteomic and metabolomic strategy for patient-derived fibroblasts, which has great clinical potential to discover therapeutic targets and design personalized interventions after validation with a larger patient cohort in the future.
Insights
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) involves complex I deficiency. Multi-omics revealed arginine pathway downregulation, linking to stroke-like episodes and arginine treatment in MELAS patients.
Area of Science:
- Biochemistry
- Genetics
- Neuroscience
Background:
- Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is a progressive neurodegenerative disorder.
- Pathogenic mitochondrial DNA variants cause MELAS, but mechanisms are unclear due to clinical heterogeneity.
- Understanding the genotype-phenotype correlation is crucial for MELAS patient management.
Purpose of the Study:
- To investigate the pathogenic mechanisms of MELAS using multi-omics.
- To identify molecular signatures in patient-derived fibroblasts with the m.14453G>A variant.
- To explore genotype-phenotype correlations and potential therapeutic targets.
Main Methods:
- Integrated proteomics (DDA and DIA) and metabolomics on patient-derived fibroblasts.
- Utilized Spectronaut and MaxDIA platforms for proteomic analysis.
- Comprehensive LC-MS/MS analysis for polar and nonpolar metabolites.
Main Results:
- Demonstrated OXPHOS dysregulation with Complex I deficiency.
- Identified alterations in glycolysis, TCA cycle, and fatty acid beta-oxidation.
- Discovered downregulation of the arginine biosynthesis pathway, linked to stroke-like episodes.
Conclusions:
- Integrated multi-omics provides insights into MELAS pathogenesis.
- Arginine pathway dysregulation is a key finding, potentially explaining stroke-like episodes.
- This approach can identify therapeutic targets for personalized MELAS interventions.
