LC-MS/MS-Based Proteomics Approach for the Identification of Candidate Serum Biomarkers in Patients with Narcolepsy Type 1

Abstract

Narcolepsy type 1 (NT1) is the most common type of narcolepsy known to be caused by the loss of specific neurons responsible for producing peptide neurotransmitters (orexins/hypocretins), resulting in a sleep-wake cycle disorder. It is characterized by its association with cataplexy and abnormalities in rapid eye movement. To date, no cure has been established for this life-threatening condition. Misdiagnosis of NT1 is also quite common, although it is not exceedingly rare. Therefore, successfully identifying candidate serum biomarkers for NT1 would be a head start for accurate diagnosis and development of therapeutics for this disorder. This study aims to identify such potential serum biomarkers. A depletion protocol was employed for 27 human serum samples (16 NT1 and 11 healthy controls), followed by applying LC-MS/MS bottom-up proteomics analysis, then LC-PRM-MS for validation. The comparison of the proteome profiles of the low-abundant proteins in the samples was then investigated based on age, sex, sample groups, and the presence of the Human Leukocyte Antigen (HLA) DQB1*0602 allele. The results were tracked to gene expression studies as well as system biology to identify key proteins and understand their relationship in the pathogenesis of NT1. Our results revealed 36 proteins significantly and differentially expressed. Among the impaired pathways and bioprocesses, the complement activation pathway is impaired by six of the differentially expressed proteins (DEPs). They are coded by the genes C2, CFB, C5, C1R, C1S, and MASP1, while 11 DEPs are involved in Acute Phase Response Signaling (APRS), which are coded by the genes FN1, AMBP, APOH, CFB, CP, ITIH2, C5, C2, F2, C1, and ITIH4. The combined AUCs of the downregulated and upregulated DEPs are 0.95 and 0.76, respectively. Overall, this study reveals potential serum-protein biomarkers of NT1 and explains the possible correlation between the biomarkers and pathophysiological effects, as well as important biochemical pathways involved in NT1.

LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1

“…The proteomic analysis of narcolepsy type 1 samples was published in our previous work [43]. This analysis identified several significant proteins, such as inter-alpha-trypsin inhibitor H4, complement factor B, ceruloplasmin, fibronectin, and prothrombin.…”

“…This analysis identified several significant proteins, such as inter-alpha-trypsin inhibitor H4, complement factor B, ceruloplasmin, fibronectin, and prothrombin. These proteins were found to play important roles in biochemical pathways that are correlated with narcolepsy type 1 [43]. Hence, it was logical to conduct a focused investigation on NT1 glycoproteomics and examine the expression of noteworthy glycopeptides inside two distinct cohorts: the control group and the NT1 group.…”

Metabolomic Changes in Rat Serum after Chronic Exposure to Glyphosate-Based Herbicide

“…Omics is an emerging field that holds promise to shine light on the molecular mechanisms causing diseases [ 10 ]. Most recently, proteomics, glycomics, glycoproteomics, and metabolomics changes have been implicated in several diseases [ 11 , 12 , 13 , 14 , 15 , 16 ]. To facilitate better understanding of diseases, many omics fields have advanced methods for better identification of glycans, glycopeptides, and their isomers [ 17 , 18 , 19 , 20 ], and have developed several bioinformatic tools [ 21 ] that improve interpretations of omics data.…”

Cross-platform Clinical Proteomics using the Charité Open Standard for Plasma Proteomics (OSPP)

“…Liquid chromatography-mass spectrometry (LC-MS) based plasma proteomics has gained significant attention in both the identification and analysis of individual biomarkers but is especially attractive for the discovery and measurement of marker panels 14,16,[18][19][20][21][22][23] . LC-MS enables simultaneous evaluation of large numbers of proteins, elucidating the functional implications of specific biomarkers and unveiling changes within pertinent pathways while maintaining relatively low operational costs 3,12,24,25 . However, their routine application still encounters obstacles originating from discrepancies in analytical platforms, data acquisition methods, and processing pipelines.…”