Proteo‐Metabolomic Profiling of PMM2‐CDG Reveals Dysregulation of Retinoic Acid Synthesis, Myo‐Inositol, and the Hexosamine Pathway

Abstract

Phosphomannomutase deficiency (PMM2‐CDG), the most common congenital disorder of glycosylation (CDG), is characterized by multisystem involvement and a lack of disease‐modifying therapies. While previous transcriptomic studies have uncovered disrupted cellular pathways, the functional consequences of these alterations remain poorly understood. To further investigate PMM2‐CDG pathophysiology, we integrated proteomic and metabolomic profiling of patient‐derived fibroblasts with previously published transcriptomic data. Proteomic analysis was performed using Tandem Mass Tag‐based mass spectrometry, while metabolomics was conducted via Nuclear Magnetic Resonance spectroscopy. Multi‐omics integration was performed using principal component analysis–based dimensionality reduction, incorporating clinical metadata as supplementary variables. Proteomic analysis identified 43 significantly altered proteins, with enrichment in the retinoic acid synthesis pathway, wound healing, and cytoskeletal organization. Metabolomic profiling revealed altered amino acid levels and elevated concentrations of UDP‐GlcNAc, consistent with perturbation of the hexosamine biosynthesis pathway, and increased levels of myo‐inositol. Notably, myo‐inositol levels showed a strong association with disease severity in the integrated analysis. RT‐qPCR confirmed the upregulation of GFPT2. This integrative multi‐omics study identifies consistent alterations in the retinoic acid synthesis pathway and hexosamine biosynthesis in PMM2‐CDG patient‐derived fibroblasts and reveals an association between intracellular myo‐inositol levels and disease severity. These findings provide new insights into PMM2‐CDG–associated molecular alterations and illustrate the value of multi‐omics integration for hypothesis generation in rare diseases.