Integrated Proteomic, Lipidomic, and Metabolomic Characterization of Neuronal Molecular Responses to Particulate Matter–Induced Neurotoxicity

Abstract

Ambient particulate matter （PM） is a complex environmental pollutant whose pathological effects extend beyond the respiratory and cardiovascular systems to include the central nervous system, where the underlying molecular mechanisms remain poorly understood. Because the blood-brain barrier largely excludes intact particles from the brain parenchyma, neurons are primarily exposed to the soluble leachate components released from PM surfaces and to the protein corona that adsorbs onto particles upon contact with biological fluids. Whether these two physiologically distinct exposure forms are biologically equivalent at the molecular level has not been established. This dissertation characterizes the responses of SH-SY5Y human neuroblastoma cells to PM-protein corona, PM-leachate, and metal-depleted PM-leachate across three molecular layers—the proteome, lipidome, and metabolome—to determine whether each exposure form carries a distinct molecular fingerprint and to identify convergent pathways through which PM exerts neurotoxic effects. iTRAQ-based quantitative proteomics identified 4,967 proteins. Corona-treated cells exhibited broad protein downregulation （122 of 127 differentially regulated features）, accompanied by the positive enrichment of lysosomal, endoplasmic reticulum protein processing, and oxidative phosphorylation pathways. Conversely, leachate-treated cells displayed a more targeted response, characterized by the enrichment of Parkinson's disease-associated pathways, proteasome function, and arginine and proline metabolism. Notably, strong cation exchange- 20182094 based metal removal effectively abolished leachate cytotoxicity, confirming leached transition metals as the primary cytotoxic drivers. Untargeted lipidomics revealed a widespread accumulation of phosphatidylinositols （most prominently PI 40:4） and ceramides, alongside the depletion of cardiolipins （e.g., CL 72:4） across all PM-exposed groups. Furthermore, corona exposure specifically depleted plasmalogen PC O-38:5, a signature observed at a concentration 35-fold lower than the leachate cytotoxic dose. Untargeted metabolomics demonstrated reduced acylcarnitine levels indicative of impaired β-oxidation flux, a finding that stands in apparent contradiction to the protein-level upregulation of oxidative phosphorylation. Additional findings included treatment-specific lysophosphatidylcholine pool dynamics consistent with differential PLA₂ engagement, and corona-specific elevation of free aromatic amino acids consistent with the proteomic activation of lysosomal protein degradation pathways. Integrated across the three molecular layers, four principal findings emerge. First, PM exposure converges on three coordinated biological axes: mitochondrial impairment, membrane phospholipid remodeling, and protein degradation coupled to amino acid metabolism. Second, the protein corona functions as an independent toxicological entity rather than a higher-potency form of leachate. Third, while leached metals are sufficient to drive cytotoxicity, they do not account for the full biological footprint of PM exposure; metal-depleted leachate continues to drive lipid and metabolite alterations at sub-cytotoxic concentrations. Fourth, the molecular signatures identified across all exposure forms converge on Parkinson's disease–relevant pathology. Ultimately, these findings demonstrate that viability-based risk assessment substantially underestimates PM bioactivity, and that the protein corona warrants explicit mechanistic consideration in environmental neurotoxicology.