Glycoproteins as diagnostic and prognostic biomarkers for neurodegenerative diseases: A glycoproteomic approach

Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords

Introduction

ALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs).

Methods

This study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified.

Results

The analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < -0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037).

Conclusion

This study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.

Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics

Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named 'OxoScan-MS', identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples.

The neuroprotective effect of quercetin nanoparticles in the therapy of neuronal damage stimulated by acrolein

A gradual loss of neuronal function or structure causes neurodegenerative disorders such as Parkinson's and Alzheimer's. Neurological damage might cause cell death. Acrolein is a high-risk air and water contaminant that causes neurodegenerative disorders. Quercetin has several strategies for treating neurodegenerative disorders but has limited bioavailability inside the body. One of the hypotheses offered to improve quercetin's bioavailability is to convert it into quercetin nanoparticles. This study aims to comprehend the immunohistochemical devastation that might arise in the cerebellum because of acrolein treatment. Furthermore, the protective and ameliorative roles of quercetin nanoparticles against oxidative stress and neurotoxicity induced in mice by acrolein were assessed. Ninety male albino rats weighing 120 to 200 g were used in the present investigation. The animals were split up into the following six groups: the control group, the acrolein-treated group: animals were given acrolein (3 mg/kg) for 30 days, quercetin nanoparticles treated group: animals were given quercetin nanoparticles (30 mg/kg) for 30 days. The administration of acrolein was found to be connected to immunohistochemical abnormalities in the cerebellum. Marked differences were observed in Bax, Bcl-2, TNF-α, and GFAP expressions in the cerebellum. Treatment of rats with quercetin nanoparticles either before or after treatment with acrolein has been found to preserve the cerebellum tissues from the toxic impacts and oxidative stress induced by acrolein. This may open the door to more nanomedicine studies and a new avenue for employing nanoparticles as a therapeutic intervention in neurodegenerative illnesses.

Detection of N‑glycoprotein associated with IgA nephropathy in urine as a potential diagnostic biomarker using glycosylated proteomic analysis

The aim of the present study was to elucidate the potential diagnostic value of urinary N-glycoprotein in patients with IgA nephropathy (IgAN) using mass spectrometry (MS). All procedures were performed between June 2021 and June 2023 at Guangan People's Hospital (Guangan, China). Fresh mid-morning fasting midstream urine samples were collected from a total of 30 patients with IgAN and 30 sex- and age-matched healthy volunteers. Data acquired from 6 participants are available through ProteomeXchange with the identifier PXD041151. By comparison between the IgAN group (n=3) and healthy controls (n=3) and selection criteria of P<0.05 and |log fold-change|>2, a total of 11 upregulated and 22 downregulated glycoproteins in patients with IgAN were identified. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that glycoproteins are involved in various functions, such as the regulation of cell growth, cell adhesion, cellular component organization and protein binding, as well as multiple pathways, including p53, Notch and mTOR signaling pathways. The urine levels of afamin were further measured by ELISA in a validation cohort to assess the diagnostic performance of the single indicator model. In conclusion, MS-based proteomics of urinary glycoproteins may be an alternative option for diagnosing patients with IgAN. Biomarkers of IgAN may include, but are not limited to, CCL25, PD-L1, HLA-DRB1, IL7RD and WDR82. In addition, the levels of urinary AFM indicators are of diagnostic value for IgAN.

Mass Spectrometric Analysis of Urinary N-Glycosylation Changes in Patients with Parkinson's Disease

Urine is thought to provide earlier and more sensitive molecular changes for biomarker discovery than blood. Numerous glycoproteins, peptides, and free glycans are present in urine through glomerular filtration of plasma, cell shedding, apoptosis, proteolytic cleavage, and exosome secretion. Urine biomarkers have enormous diagnostic potential, and the use of these biomarkers is a long-standing practice. The discovery of non-urological disease biomarkers from urine is also gaining attention due to its non-invasive sample collection and ease of analysis. Abnormal protein glycosylation in plasma or cerebrospinal fluid has been associated with Parkinson's disease, however, whether urine with Parkinson's disease has characteristic glycosylation remains to be explored. Here, we use mass spectrometry-based glycomics and glycoproteomics approaches to analyze urine samples for glycans, glycosites, and intact glycopeptides of urine samples. Reduced abundance of N-glycans was detected at the level of total glycans as well as specific glycosites of glycopeptides. The most abundant N-glycan in urine is S(6)1H5N4F1; S(6)2H5N4 and N4H4F1 are highly present in serum and urine, and 10 biantennary galactosylated N-glycans in the urine of PD patients were significantly decreased. The downregulation of sialylation may be due to the reduction of ST3GAL2. Site-specific N-glycosylation analysis revealed that AMBP, UMOD, and RNase1 have PD-specific N-glycosylation sites. GO and KEGG analysis revealed that N-glycosylation changes may provide clues to identify disease-specific glycosylation biomarkers in Parkinson's disease.

Protein glycosylation in urine as a biomarker of diseases

Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.

Semi-Automated Lectin Magnetic Bead Array (LeMBA) for Translational Serum Glycoprotein Biomarker Discovery and Validation

Aberrant protein glycosylation is a characteristic of diverse diseases which has been explored as biomarkers. To support translational serum glycoprotein biomarker discovery and validation, we developed a semi-automated workflow using individual lectin-coupled magnetic beads to conduct lectin pulldowns in a high-throughput format. Lectins are naturally occurring glycoprotein binding proteins widely used in glycobiology. While lectin-affinity isolation has been coupled to mass spectrometry-based proteomics, the lectin magnetic bead array (LeMBA) platform allows technically robust screening and measurement of clinical cohorts. This chapter describes detailed lectin-magnetic bead coupling, serum denaturation, lectin magnetic bead pulldown, and on-bead trypsin digest. The resulting tryptic peptides are analyzed by untargeted or targeted liquid chromatography-mass spectrometry (LC-MS), for biomarker discovery, or qualification/validation, respectively. LeMBA-MS generates quantitative data for glycoforms based on lectin affinity of the glycoprotein coupled with MS measurement of one or more prototypic peptides and has successfully been used to discover and validate novel serum cancer glycoprotein biomarkers. This chapter includes detailed protocols for two different liquid handlers, along with recommendations on quality control measures for clinical biomarker studies.

Electrochemical Quantitation of the Glycosylation Level of Serum Neurofilament Light Chain for the Diagnosis of Neurodegeneration: An Interface-Solution Dual-Path Amplification Strategy

Serum neurofilament light chain (NFL), a potential general biomarker for neurodegenerative diseases, is not specific enough to differentiate neurodegenerative diseases from other brain diseases such as cerebral thrombosis (CT). According to the importance of glycosylation in neurodegenerative pathogenesis, the NFL glycosylation level (oNFL/tNFL), defined as the ratio of glycosylated NFL (oNFL) to total NFL (tNFL), may be a more effective index. The major challenge in serum oNFL/tNFL detection is the ultra-low abundance of both NFL forms. In this paper, we achieved a convenient one-step electrochemical quantitation of oNFL/tNFL based on an interface-solution dual-path amplification strategy. Two amplified electrochemical signals─the reduction of Cu²⁺ from adsorbed porous nanoparticles on the sensor interface and the reduction of O₂ from horseradish peroxidase-catalyzed H₂O₂ disproportionation in solution─were adopted to quantify tNFL and oNFL, respectively. The electrochemical sensor displayed good sensitivity, selectivity, and reproducibility. The dynamic range is 1-25 pg mL^-1 for tNFL and 0.25-25 pg mL^-1 for oNFL, respectively. By analyzing the clinic serum samples, for the first time, our work provided the abundance of oNFL in human serum and revealed that the oNFL/tNFL is effective not only in differentiating three kinds of brain damage patients from healthy people but also in differentiating neurodegeneration from non-neurodegeneration CT patients. As a general biomarker, the oNFL/tNFL is more specific than NFL, which is hoped to be a new and valid indicator for the diagnosis, progression, prediction, and treatment evaluation of neurodegenerative diseases.

Association between Galectin Levels and Neurodegenerative Diseases: Systematic Review and Meta-Analysis

Galectins are a family of proteins with an affinity for β-galactosides that have roles in neuroprotection and neuroinflammation. Several studies indicate that patients with neurodegenerative diseases have alterations in the concentration of galectins in their blood and brain. However, the results of the studies are contradictory; hence, a meta-analysis is performed to clarify whether patients with neurodegenerative diseases have elevated galectin levels compared to healthy individuals. Related publications are obtained from the databases: PubMed, Central-Conchrane, Web of Science database, OVID-EMBASE, Scope, and EBSCO host until February 2022. A pooled standard mean difference (SMD) with a 95% confidence interval (CI) is calculated by fixed-effect or random-effect model analysis. In total, 17 articles are included in the meta-analysis with a total of 905 patients. Patients with neurodegenerative diseases present a higher level of galectin expression compared to healthy individuals (MDS = 0.70, 95% CI 0.28–1.13, p = 0.001). In the subgroup analysis by galectin type, a higher galectin-3 expression is observed in patients with neurodegenerative diseases. Patients with Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALD), and Parkinson’s disease (PD) expressed higher levels of galectin-3. Patients with multiple sclerosis (MS) have higher levels of galectin-9. In conclusion, our meta-analysis shows that patients with neurovegetative diseases have higher galectin levels compared to healthy individuals. Galectin levels are associated with the type of disease, sample, detection technique, and region of origin of the patients.

Mass Spectrometry-Based Analysis of Serum N-Glycosylation Changes in Patients with Parkinson's Disease

It is urgently needed to find reliable biofluid biomarkers for early diagnosis of Parkinson's disease in order to achieve better treatment. Promising biomarkers can be found in Parkinson's disease-related glycoproteins as aberrant protein glycosylation plays an important role in disease progression. However, current information on serum N-glycoproteomic changes in Parkinson's disease is still limited. Here, we used glycoproteomics methods, which combine the solid-phase chemoenzymatic method, lectin affinity chromatography, and hydrophilic interaction chromatography with high-resolution mass spectrometry, to analyze the glycans, glycosites, and intact glycopeptides of serum. Increased abundance of glycans containing core fucose, sialic acid, and bisecting N-acetyl glucosamine was detected at the overall glycan level and also at specific glycosites of glycopeptides. Five Parkinson's disease-associated proteins with this type of N-glycosylation changes were also identified. We propose that the revealed site-specific N-glycosylation changes in serum can be potential biomarkers for Parkinson's disease.

Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity

Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.

Abnormal sialylation and fucosylation of saliva glycoproteins: Characteristics of lung cancer-specific biomarkers

Dysregulated surface glycoproteins play an important role in tumor cell proliferation and progression. Abnormal glycosylation of these glycoproteins may activate tumor signal transduction and lead to tumor development. The tumor microenvironment alters its molecular composition, some of which regulate protein glycosylation biosynthesis. The glycosylation of saliva proteins in lung cancer patients is different from healthy controls, in which the glycans of cancer patients are highly sialylated and hyperfucosylated. Most studies have shown that O-glycans from cancer are truncated O-glycans, while N-glycans contain fucoses and sialic acids. Because glycosylation analysis is challenging, there are few reports on how glycosylation of saliva proteins is related to the occurrence or progression of lung cancer. In this review, we discussed glycoenzymes involved in protein glycosylation, their changes in tumor microenvironment, potential tumor biomarkers present in body fluids, and abnormal glycosylation of saliva or lung glycoproteins. We further explored the effect of glycosylation changes on tumor signal transduction, and emphasized the role of receptor tyrosine kinases in tumorigenesis and metastasis.

Platelet total PLA2 activity, serum oxidative level and plasma Cu/Zn ratio: a vicious cycle with a potential role to monitor MCI and Alzheimer's disease progression

Alzheimer's disease (AD) has no cure, mainly because of late diagnosis. Early diagnostic biomarkers are crucial. Phospholipases A2 (PLA2) are hydrolases with several functions in the brain, nevertheless their deregulation contributes to neurodegeneration. We evaluated platelet total PLA2 activity (ptotPLA2) in healthy elderly subjects (HE, n = 102), patients suffering from Mild Cognitive Impairment (MCI, n = 90) and AD (n = 91). Platelets are considered "circulating neurons" and ptotPLA2 seems to mirror the cerebral activity. ptotPLA2 of the three cohorts was similar, but in MCI the higher ptotPLA2 the worse the global cognitive status (Mini Mental State Examination score, MMSE) and in AD the lower ptotPLA2 the more severe the pathology stage (Clinical Dementia Rating, CDR). Accordingly, MCI with MMSE ≥ 26 overlapped HE, in MCI with MMSE < 26 and in AD with CDR 1 ptotPLA2 increased, in AD with CDR 2 ptotPLA2 decreased. In MCI ptotPLA2 positively correlated with blood oxidation and inflammation, in AD it was the opposite. Finally, Discrimination Index (DI) - calculated multiplying ptotPLA2, oxidative level and Cu/Zn ratio (an inflammation parameter) - differentiated MCI patients who progressed to dementia in the following 24 months and AD patients with the worse pathology development. Summarizing, ptotPLA2 changes during MCI and AD progression, is linked, in opposite way, to oxidative/inflammatory status in MCI and AD and might help, when included in DI, to identify MCI converters to dementia and AD patients with the more severe prognosis. ptotPLA2 may have a diagnostic/prognostic value and be a potential therapeutic target.

Design and construction of a hydrophilic coating on macroporous adsorbent resins for enrichment of glycopeptides

Although macroporous adsorbent resins (MARs) have been commercialized and widely applied in industrial and life fields, it is still of necessity to develop simple approaches to functionalize MARs. One of the most widely used methods to realize excellent fouling resistance performance is surface modification of hydrophilic polymers on substrates to fabricate an anti-biofouling coating. Herein, three kinds of hydrophilic poly(glycidyl methacrylate-co-ethylene glycol dimethacrylate) MAR were designed and facilely prepared by coating a layer of porous organic polymers (POPs) via either an epoxy-amine ring-opening polymerization or amine-aldehyde condensation reaction using isophthalaldehyde (IPA), 1,4,7,10-tetraazacyclododecane (cyclen), melamine and 1,3,5-triglycidyl isocyanurate (TGIC) as precursors. By taking advantage of their merits, such as large surface area, excellent hydrophilicity and unbiased affinity toward all types of glycopeptide, three functionalized hydrophilic MARs were successfully applied to capture glycopeptides from complex samples as hydrophilic interaction liquid chromatography (HILIC) sorbents. A total of 694 N-glycopeptides and 372 N-glycosylation sites were identified from 2 μL of human serum digest with poly(TC)@MAR, which were not only more than those of poly(MT)@MAR (286 N-glycosylation sites and 547 N-glycopeptides) and poly(IM)@MAR (669 N-glycopeptides and 355 N-glycosylation sites), but also more than those of other reported HILIC materials. This work provided a new and simple way to synthesize enrichment materials for liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis of glycoproteomes.

What Can N-glycomics and N-glycoproteomics of Cerebrospinal Fluid Tell Us about Alzheimer Disease?

Proteomics-large-scale studies of proteins-has over the last decade gained an enormous interest for studies aimed at revealing proteins and pathways involved in disease. To fully understand biological and pathological processes it is crucial to also include post-translational modifications in the "omics". To this end, glycomics (identification and quantification of glycans enzymatically or chemically released from proteins) and glycoproteomics (identification and quantification of peptides/proteins with the glycans still attached) is gaining interest. The study of protein glycosylation requires a workflow that involves an array of sample preparation and analysis steps that needs to be carefully considered. Herein, we briefly touch upon important steps such as sample preparation and preconcentration, glycan release, glycan derivatization and quantification and advances in mass spectrometry that today are the work-horse for glycomics and glycoproteomics studies. Several proteins related to Alzheimer disease pathogenesis have altered protein glycosylation, and recent glycomics studies have shown differences in cerebrospinal fluid as well as in brain tissue in Alzheimer disease as compared to controls. In this review, we discuss these techniques and how they have been used to shed light on Alzheimer disease and to find glycan biomarkers in cerebrospinal fluid.