Plasma Proteomic Signatures in Alkaptonuria

Alkaptonuria (AKU) is a rare metabolic disorder caused by homogentisic acid accumulation and characterised by ochronosis, oxidative stress, chronic inflammation, and progressive connective tissue damage. This study aimed to define the circulating proteomic alterations associated with AKU and assess their relationship with nitisinone treatment. Plasma samples from 11 patients with AKU and 6 age- and sex-matched healthy controls were analysed by liquid chromatography coupled to tandem mass spectrometry using label-free quantification. Differentially abundant proteins were identified using thresholds of |log2FC| ≥ 1 and Benjamini–Hochberg false discovery rate ≤ 0.01, followed by functional enrichment and treatment-stratified analyses. Twenty-two proteins were differentially abundant between AKU patients and controls. Complement components (C1R, C1S, C9, C4BPA, CPN2), fibronectin, clusterin, PGLYRP2, and haemoglobin subunits showed increased abundance, whereas most immunoglobulin chains, kallikrein, apolipoprotein A2, and alpha-1-antitrypsin showed decreased abundance. Functional enrichment highlighted complement activation, B-cell-mediated and humoral immune responses, immunoglobulin-related functions, platelet activation, and erythrocyte gas-exchange pathways. Correlation analysis linked several proteins, particularly CPN2, APOA2, C1R and C1S, to core biochemical parameters of disease activity. Treatment-stratified analysis identified fourteen proteins that remained significantly altered in both treated and untreated patients, forming a treatment-resistant core of the signature, while several complement-, coagulation-, and lipid-related proteins were significant only in one treatment subgroup. These findings define an AKU plasma proteomic signature dominated by complement activation and humoral immune alterations, together with extracellular matrix, erythrocyte-, and coagulation-associated changes. The persistence of most alterations across treatment groups suggests that residual systemic proteomic dysregulation remains despite nitisinone treatment.