Metabolic signatures and a diagnostic model for citrin deficiency based on urinary organic acids

Abstract

Purpose: This study aimed to characterise urinary organic acid profiles in Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD) and develop a diagnosis model to distinguish NICCD patients from those in the non-specific metabolic abnormalities group (NAG), both of which exhibit elevated urinary 4-hydroxyphenyllactic acid (4-HPLA) and 4-hydroxyphenylpyruvic acid (4-HPPA), potentially leading to misdiagnosis.

Methods: A retrospective study was conducted from February 2021 to February 2025, enrolling 105 NICCD patients, 144 healthy controls (HC), and 298 individuals from NAG. Urine organic acids were measured using gas chromatography-mass spectrometry. Data from NICCD and NAG collected before October 2024 were used for model training and internal testing, with later data serving as an external validation. A three-step feature selection strategy identified biomarkers. Five machine learning (ML) methods were used to construct the model. Performance was compared using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, F1 score, etc.

Results: Compared to HC, NICCD patients exhibited 39 differential metabolites, enriched in tyrosine, aspartate, pyruvate, lipoic acid, and TCA cycle pathways. 4-HPLA, 4-HPPA, galactitol, 4-hydroxyphenylacetic acid, pyruvic acid, quinolinic acid, homovanillic acid, 4-hydroxybenzoic acid, and malic acid showed high diagnostic performance (AUC > .8). Nine robust markers were identified between NICCD and NAG. The random forest model demonstrated superior classification performance, with high AUC, accuracy, F1 score, and low Brier score. An online calculator was developed for clinical use.

Conclusion: Our findings highlight NICCD metabolic enrichment in energy and amino acid pathways and present an interpretable ML model for distinguishing NICCD from those of NAG.

Keywords

citrin deficiency / diagnostic model / machine learning / metabolomics / urine organic acids

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2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.