Metabolomic profiling in phenylketonuria: a systematic review of human studies

BACKGROUND: Phenylketonuria (PKU) is a rare metabolic disorder caused by a deficiency in the enzyme phenylalanine hydroxylase, leading to the accumulation of phenylalanine (Phe). Raised Phe levels can result in neurocognitive deficits, intellectual disabilities, and behavioral or psychiatric disorders. AIM OF REVIEW: To conduct a systematic review of human studies on metabolites identified through metabolomics in individuals with PKU, compared to healthy controls, and to provide insights into their biological significance. KEY SCIENTIFIC CONCEPTS OF REVIEW: A total of 26 human studies analyzing metabolites in urine and blood met the inclusion criteria. In total, 544 metabolites that differed between patients with PKU and healthy controls were identified through different metabolomic techniques (LC-MS, GC-MS, NMR). Differences were primarily observed in blood samples, which accounted for 95% of the total metabolites, with only 5% detected in urine samples, reflecting the limited use of this body fluid in only five studies. We found 60% of blood metabolites upregulated in patients with PKU, including Phe, Phe-related metabolites, lipids, and other amino acids, while tryptophan and kynurenine, among others, were downregulated (40%). Additionally, 35 metabolites (6% of the total) exhibited inconsistent directions of change (both up- and downregulated), including amino acids, carnitine derivatives, and lipids. These findings may be attributed to clinical factors (dietary adherence, supplementation, and treatment) and methodological differences in blood-derived matrices. Consequently, the high heterogeneity across studies, biological matrices and analytical platforms represents limitations for establishing a unique metabolomic signature. Overall, these results emphasize the metabolic complexity of PKU and highlight the potential of metabolomics to advance disease monitoring and management.