Machine Learning Reveals Serum Glycopatterns as Potential Biomarkers for the Diagnosis of Nonalcoholic Fatty Liver Disease (NAFLD).

Nonalcoholic fatty liver disease (NAFLD) has emerged as the predominant chronic liver condition globally, and underdiagnosis is common, particularly in mild cases, attributed to the asymptomatic nature and traditional ultrasonography's limited sensitivity to detect early-stage steatosis. Consequently, patients may experience progressive liver pathology. The objective of this research is to ascertain the efficacy of serum glycan glycopatterns as a potential diagnostic biomarker, with a particular focus on the disease's early stages. We collected a total of 170 serum samples from volunteers with mild-NAFLD (Mild), severe-NAFLD (Severe), and non-NAFLD (None). Examination via lectin microarrays has uncovered pronounced disparities in serum glycopatterns identified by 19 distinct lectins. Following this, we employed four distinct machine learning algorithms to categorize the None, Mild, and Severe groups, drawing on the alterations observed in serum glycopatterns. The gradient boosting decision tree (GBDT) algorithm outperformed other models in diagnostic accuracy within the validation set, achieving an accuracy rate of 95% in differentiating the None group from the Mild group. Our research indicates that employing lectin microarrays to identify alterations in serum glycopatterns, when integrated with advanced machine learning algorithms, could constitute a promising approach for the diagnosis of NAFLD, with a special emphasis on its early detection.

Discovery of Novel N-(Anthracen-9-ylmethyl) Benzamide Derivatives as ZNF207 Inhibitors Promising in Treating Glioma.

Targeting tumor stemness is an innovative approach to cancer treatment. Zinc Finger Protein 207 (ZNF207) is a promising target for weakening the stemness of glioma cells. Here, a series of novel N-(anthracen-9-ylmethyl) benzamide derivatives against ZNF207 were rationally designed and synthesized. The inhibitory activity was evaluated, and their structure-activity relationships were summarized. Among them, C16 exhibited the most potent inhibitory activity, as evidenced by its IC50 values ranging from 0.5-2.5 µM for inhibiting sphere formation and 0.5-15 µM for cytotoxicity. Furthermore, we found that C16 could hinder tumorigenesis and migration and promote apoptosis in vitro. These effects were attributed to the downregulation of stem-related genes. The in vivo evaluation demonstrated that C16 exhibited efficient permeability across the blood-brain barrier and potent efficacy in both subcutaneous and orthotopic glioma tumor models. Hence, C16 may serve as a potential lead compound targeting ZNF207 and has promising therapeutic potential for glioma.

Beneficial or detrimental: Recruiting more types of benign cases for cancer diagnosis based on salivary glycopatterns.

With the advantages of convenient, painless and non-invasive collection, saliva holds great promise as a valuable biomarker source for cancer detection, pathological assessment and therapeutic monitoring. Salivary glycopatterns have shown significant potential for cancer screening in recent years. However, the understanding of benign lesions at non-cancerous sites in cancer diagnosis has been overlooked. Clarifying the influence of benign lesions on salivary glycopatterns and cancer screening is crucial for advancing the development of salivary glycopattern-based diagnostics. In this study, 2885 samples were analyzed using lectin microarrays to identify variations in salivary glycopatterns according to the number, location, and type of lesions. By utilizing our previously published data of tumor-associated salivary glycopatterns, the performance of machine learning algorithm for cancer screening was investigated to evaluate the effect of adding benign disease cases to the control group. The results demonstrated that both the location and number of lesions had discernible effects on salivary glycopatterns. And it was also revealed that incorporating a broad range of benign diseases into the controls improved the classifier's performance in distinguishing cancer cases from controls. This finding holds guiding significance for enhancing salivary glycopattern-based cancer screening and facilitates their practical implementation in clinical settings.

Characterization of aberrant glycosylation associated with osteoarthritis based on integrated glycomics methods.

BACKGROUND: Osteoarthritis (OA) is the most common form of arthritis, affecting millions of aging people. Investigation of abnormal glycosylation is essential for the understanding of pathological mechanisms of OA. METHODS: The total protein was isolated from OA (n = 13) and control (n = 11) cartilages. Subsequently, glycosylation alterations of glycoproteins in OA cartilage were investigated by lectin microarrays and intact glycopeptides analysis. Finally, the expression of glycosyltransferases involved in the synthesis of altered glycosylation was assessed by qPCR and GEO database. RESULTS: Our findings revealed that several glycopatterns, such as α-1,3/6 fucosylation and high-mannose type of N-glycans were altered in OA cartilages. Notably, over 27% of identified glycopeptides (109 glycopeptides derived from 47 glycoproteins mainly located in the extracellular region) disappeared or decreased in OA cartilages, which is related to the cartilage matrix degradation. Interestingly, the microheterogeneity of N-glycans on fibronectin and aggrecan core protein was observed in OA cartilage. Our results combined with GEO data indicated that the pro-inflammatory cytokines altered the expression of glycosyltransferases (ALG3, ALG5, MGAT4C, and MGAT5) which may contribute to the alterations in glycosylation. CONCLUSION: Our study revealed the abnormal glycopatterns and heterogeneities of site-specific glycosylation associated with OA. To our knowledge, it is the first time that the heterogeneity of site-specific N-glycans was reported in OA cartilage. The results of gene expression analysis suggested that the expression of glycosyltransferases was impacted by pro-inflammatory cytokines, which may facilitate the degradation of protein and accelerate the process of OA. Our findings provide valuable information for the understanding of molecular mechanisms in the pathogenesis of OA.

Machine learning reveals salivary glycopatterns as potential biomarkers for the diagnosis and prognosis of papillary thyroid cancer.

The diagnosis of thyroid cancer, especially papillary thyroid cancer (PTC), is increasing rapidly worldwide. In this study, we aimed to study the glycosylation of salivary proteins associated with PTC and assess the likelihood that salivary glycopatterns may be a potential biomarker of PTC diagnosis. Firstly, 22 benign thyroid nodule (BTN) samples, 27 PTC samples, and 30 healthy volunteers (HV) samples were collected to probe the difference of salivary glycopatterns associated with PTC using lectin microarrays. Then, five machine learning models including K-Nearest Neighbor (KNN), Multilayer Perceptron (MLP), Logistic Regression (LR), Random Forest (RF), and Support Vector Machine (SVM) were established to distinguish HV, BTN and PTC based on the changes of salivary glycopatterns. As a result, SVM had the best diagnostic effect with an accuracy rate of 92 % in testing set. Besides, lectin microarrays were used to explore the differences in salivary glycopatterns of 26 paired salivary samples of PTC patients before and after operation in order to probe into salivary glycopatterns as potential biomarkers for prognosis of PTC patients. The results showed that the levels of salivary glycopatterns recognized by 6 different lectins in patients after the operation almost convergenced with HVs. This study could help to screen and assess patients with PTC and their prognosis based on precise changes of salivary glycopatterns.

Elevation of α-1,3 fucosylation promotes the binding ability of TNFR1 to TNF-α and contributes to osteoarthritic cartilage destruction and apoptosis.

BACKGROUND: Osteoarthritis (OA) is the most common form of arthritis and is characterized by the degradation of articular cartilage and inflammation of the synovial membrane. Fucosylation is an important feature of protein N/O-glycosylation and is involved in a variety of pathological processes, including inflammation and cancer. However, whether fucosylation impacts the OA pathological process is unknown. METHODS: Total proteins were extracted from cartilage samples obtained from patients with OA (n = 11) and OA rabbit models at different time points (n = 12). OA-associated abnormal glycopatterns were evaluated by lectin microarrays and lectin blots. The expression of fucosyltransferases involved in the synthesis of α-1,3 fucosylation was assessed by semi-qPCR. The synthesis of α-1,3 fucosylation mediated by FUT10 was interrupted by the transfection of siRNA, and the effect of α-1,3 fucosylation on OA-associated events was assessed. Then, immunoprecipitation and lectin blotting were used to investigate the relationship between the α-1,3 fucosylation level of tumor necrosis factor receptor superfamily member 1A (TNFR1) and OA. Finally, a TNFR1 antibody microarray was fabricated to evaluate the effect of α-1,3 fucosylation on the ability of TNFR1 to bind to tumor necrosis factor-α (TNF-α). RESULTS: Elevated α-1,3 fucosylation was observed in cartilage from OA patients, rabbit models, and chondrocytes induced by TNF-α (fold change> 2, p< 0.01). Our results and the GEO database indicated that the overexpression of FUT10 contributed to this alteration. Silencing the expression of FUT10 impaired the ability of TNFR1 to bind to TNF-α, impeded activation of the NF-κB and P38/JNK-MAPK pathways, and eventually retarded extracellular matrix (ECM) degradation, senescence, and apoptosis in chondrocytes exposed to TNF-α. CONCLUSION: The elevation of α-1,3 fucosylation is not only a characteristic of OA but also impacts the OA pathological process. Our work provides a new positive feedback loop of "inflammation conditions/TNF-α/FUT10/α-1,3 fucosylation of TNFR1/NF-κB and P38/JNK-MAPK pathways/proinflammatory processes" that contributes to ECM degradation and chondrocyte apoptosis.

Role of salivary glycopatterns for oral microbiota associated with gastric cancer.

Microbiota in the oral cavity plays an important role in maintaining human health. Our previous studies have revealed significant alterations of salivary glycopatterns in gastric cancer (GC) patients, but it is unclear whether these altered salivary glycopatterns can cause the dysbiosis of oral microbiota. In this study, the oral microbiome of healthy volunteers (HVs) and GC patients were detected. The neoglycoproteins were then synthesized according to the altered glycopatterns in GC patients and used to explore the effects of specific salivary glycopattern against oral microbiota. The results showed that five species were significantly increased (p < 0.05) while two species were significantly decreased (p < 0.01) in the saliva of GC patients compared with that of HVs. And the fucose-neoglycoproteins (30-100 µg/mL) could reduce the adhesion and toxicity of Aggregatibacter segnis (A. segnis) to oral cells (HOEC and CAL-27), change the glycan structures of lipopolysaccharide on the surface of A. segnis, and enhance the capacity of A. segnis to trigger innate immune responses. This study revealed that the changes of salivary protein glycopatterns in GC patients might contribute to the dysbiosis of oral microbiota, and had important implications in developing new carbohydrate drugs to maintain a balanced microbiota in the oral.

Characterization of glucose-binding proteins isolated from health volunteers and human type 2 diabetes mellitus patients.

Glucose is one of the most important monosaccharides. Although hyperglycemia in type 2 diabetes mellitus (T2DM) lead to a series of changes; however, little is known about the alterations of serum proteins in T2DM, especially those proteins with glucose affinity. In this study, the glucose-binding proteins (GlcBPs) of serum were isolated from 30 health volunteer (HV) and 30 T2DM patients by glucose-magnetic particle conjugates (GMPC) and identified by mass spectrum analysis. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated the main gene annotations and pathways of this GlcBPs, while Motif-X webtool provided the potential glucose-binding domains. Further docking analysis and glycan microarray were used to understand the interaction between the glucose and glucose-binding domains. A total of 149 and 119 GlcBPs were identified from HV and T2DM cases. Four hundred and sixty-eight GO annotations in 165 identified GlcBPs were available, while the majority involved in cellular processes and binding function. A short peptide, EGDEEITCLNGFWLE, which was derived from the Motif-X analysis, presented a high-binding ability to the glucose from both docking analysis and glycan analysis. GMPC provides a powerful tool for GlcBPs isolation and indicates the alteration of GlcBPs in T2DM.

The Abnormal Glycopatterns of Salivary Glycoproteins in Esophageal Squamous Cell Carcinoma Patients.

Glycosylation is one of the most crucial posttranslational modifications of proteins, containing a remarkable amount of biological information. The alteration of glycosylation is closely associated with certain diseases. Exploring glyco-code in the development of diseases is a hot topic in recent years. Esophageal squamous cell carcinoma (ESCC) is the primary pathological histology in developing countries and a severe threat to human health. Although the glycan profiles in the blood samples of ESCC patients were analyzed using glycomic and glycoproteomic methods, the difference of salivary glycopatterns between healthy subjects and ESCC patients is not explicit yet. In the present study, ESCC patients (n = 16) and healthy volunteers (HVs, n = 25) were enrolled. The glycomic strategy combining lectin microarray and lectin blotting was employed to investigate and confirm the altered salivary glycopatterns. Datura stramonium (DSA) was selected to isolate the GlcNAc or Galß1-4GlcNA-containing glycoproteins due to the distinct difference between ESCC patients and HVs. The N-glycans from DSA-enriched glycoproteins were released by PNGase F and further identified by MALDI-TOF/TOF-MS to obtain the precise structural information of the altered glycans. As a result, the glycopatterns recognized by 13 lectins (e.g., ECA, RCA120, and DSA) showed significant alterations in ESCC patients' saliva. The ESCC patients showed higher levels of GalNAc and Gal, sialic acid, and GlcNAc expression profiles and lower levels of mannose and fucose expression profiles. The MALDI-TOF/TOF-MS results indicated that the proportion of the GlcNAc or Galß1-4GlcNAc-containing N-glycans was increased in ESCC patients (79.04%) compared with HV (63.20%), which was consistent with the results of lectin microarrays. Our findings provide comprehensive information to understand the complex physiological changes in ESCC patients. And the altered salivary glycopatterns such as GlcNAc or Galß1-4GlcNAc-containing N-glycans recognized by DSA might serve as potential biomarkers for the diagnosis of ESCC patients.

Anti-Obesity and Gut Microbiota Modulation Effect of Secoiridoid-Enriched Extract from Fraxinus mandshurica Seeds on High-Fat Diet-Fed Mice.

Previously we conducted a phytochemical study on the seeds of Fraxinus excelsior and isolated nine secoiridoid compounds with adipocyte differentiation inhibitory activity and peroxisome proliferator activated receptor alpha (PPARα) activation effects. However, the bioactive constituents and functions of Fraxinus mandshurica seeds have not been studied. In the present study, we investigated the secoiridoid compounds in F. mandshurica seed extract (FM) using column chromatography, 1H-NMR, 13C-NMR and HPLC-DAD methods. The pancreatic lipase inhibitory activities of isolated compounds were evaluated in vitro. Additionally, the anti-obesity and gut microbiota modulation effect of FM on high-fat diet-induced obesity in C57BL/6 mice were also studied in vivo. The results showed that 19 secoiridoids were isolated from FM and identified. The total content of secoiridoids in FM reached 181.35 mg/g and the highest content was nuzhenide (88.21 mg/g). All these secoiridoid compounds exhibited good pancreatic lipase inhibitory activity with inhibition rate ranged from 33.77% to 70.25% at the concentration of 100 µM. After obese mice were administrated with FM at 400 mg/kg.bw for 8 weeks, body weight was decreased by 15.81%. Moreover, FM could attenuate the lipid accumulation in serum and liver, relieve the damage in liver and kidney, and extenuate oxidative stress injury and inflammation caused by obesity in mice. FM could also modulate the structural alteration of gut microbiota in obese mice, increasing the proportion of anti-obesity gut microbiota (Bacteroidetes, Bacteroidia, S24-7 and Allobaculum), and reducing the proportion of obesogenic gut microbiota (Firmicutes and Dorea). This study suggests that F. mandshurica seeds or their secoiridoids may have potential for use as a dietary supplement for obesity management.

Simultaneous characterization and quantification of flavonoids in Morus australis root as potential hepatoprotective nutraceutical.

Morus australis distributed widely in China has high value in food and agriculture. Twelve phenolic compounds were isolated and identified as major constituents of M. australis root from Shaanxi province, China, while the protective effect of M. australis root on liver injury has never been determined in detail. In this study, the hepatoprotective ability of M. australis root was investigated in vivo and in vitro. The ethanol-water extract prepared from M. australis root showed protection on alcohol-induced liver damage in mice by decreasing the levels of serum alanine aminotransferase, aspartate transaminase, triacylglycerol and malondialdehyde, and by increasing glutathione contents. Furthermore, among 12 major constituents of M. australis root, 10 flavonoids (especially 1) showed protection against carbon tetrachloride (CCl4 )-intoxicated HepG2 cell lines by decreased lactic dehydrogenase levels. In addition a validated HPLC-DAD method was established for the quantitative analysis of 10 flavonoids in the bioactive extract. PRACTICAL APPLICATIONS: Our results showed that M. australis root extract significantly alleviated the liver damage in mice. Ten flavonoids from the root of this plant exhibited protection on CCl4 -intoxicated HepG2 cell lines. This study suggests that Morus australis root has hepatoprotective potential as a promising supplement for the prevention and treatment of liver diseases.

The anti-diabetic effect of eight Lagerstroemia speciosa leaf extracts based on the contents of ellagitannins and ellagic acid derivatives.

Previously, we have reported the opposite effects of compounds isolated from Lagerstroemia speciosa leaves on a glucose transport (GLUT4) assay. Ellagitannins from L. speciosa activated GLUT4, while ellagic acid derivatives showed an inhibitory effect. As part of our continuing research on anti-diabetic nutritional supplements, we herein compared the anti-diabetic effects of several extracts (LE1-8) from leaves of L. speciosa using different manufacturing processes based on the contents of ellagitannins and ellagic acid derivatives. Their anti-diabetic effects were evaluated through glucose uptake and adipocyte differentiation in 3T3-L1 cells in vitro as well as alloxan induced diabetic mice in vivo. These extracts were given to mice by gavage at doses of 0.25, 1.0, and 4.0 g per kg body weight once a day for 21 consecutive days. Results showed that LE1 (1.0 g kg-1), LE3 (1.0 or 4.0 g kg-1), LE4 (1.0 or 4.0 g kg-1), LE5 (0.25 or 1.0 or 4.0 g kg-1) and LE7 (1.0 or 4.0 g kg-1) showed significant anti-diabetic effects in alloxan-induced diabetic mice as indicated by the decreased levels of fasting blood glucose, body weight, serum biomarkers, tissue weight and body fat, and increased final insulin levels. LE8 (1.0 g kg-1) showed a moderate anti-diabetic effect as illustrated by the reduced fasting blood glucose level while LE2 and LE6 showed slight effects in alloxan-induced diabetic mice. The potential correlation of the content of ellagitannins, ellagic acid derivatives, and corosolic acid with the anti-diabetic activity was discussed.