Congenital disorders of glycosylation are
genetic disorders that occur due to defects in
protein and
lipid glycosylation pathways. A deficiency of
N-glycanase 1, encoded by the NGLY1 gene, results in a
congenital disorder of deglycosylation. The NGLY1
enzyme is mainly involved in cleaving N-
glycans from misfolded, retro-translocated
glycoproteins in the cytosol from the endoplasmic reticulum before their proteasomal degradation or activation. Despite the essential role of NGLY1 in deglycosylation pathways, the exact consequences of
NGLY1 deficiency on global cellular protein glycosylation have not yet been investigated. We undertook a multiplexed tandem mass tags-labeling-based quantitative glycoproteomics and proteomics analysis of fibroblasts from NGLY1-deficient individuals carrying different biallelic pathogenic variants in NGLY1. This quantitative mass spectrometric analysis detected 8041
proteins and defined a proteomic signature of differential expression across affected individuals and controls.
Proteins that showed significant differential expression included
phospholipid phosphatase 3,
stromal cell-derived factor 1,
collagen alpha-1 (IV) chain,
hyaluronan and
proteoglycan link protein 1, and thrombospondin-1. We further detected a total of 3255 N-
glycopeptides derived from 550 glycosylation sites of 407
glycoproteins by multiplexed N-glycoproteomics. Several extracellular matrix
glycoproteins and adhesion molecules showed altered abundance of N-
glycopeptides. Overall, we observed distinct alterations in specific
glycoproteins, but our data revealed no global accumulation of
glycopeptides in the patient-derived fibroblasts, despite the genetic defect in NGLY1. Our findings highlight new molecular and system-level insights for understanding NGLY1-CDDG.