N-glycan Biosynthesis Research Articles

Processing of N-glycans in the ER and Golgi influences the production of surface sialylated glycoRNA.

Glycoconjugates, including glycans on proteins and lipids, have obtained significant attention due to their critical roles in both intracellular and intercellular biological functions and processes. Notably, recent discoveries have revealed the presence of glycosylated RNAs (glycoRNAs) on cell surfaces. Despite the well-characterized roles of RNA modifications, RNA glycosylation remains relatively unexplored. In this study, we investigate the relationship between N-glycosylation and RNA glycosylation. Using a recombinant Siglec11-Fc as a probe, we detected surface sialylated glycoRNAs in human cell lines and identified their dependency on the catalytic isoforms of the oligosaccharyltransferase (OST) complex, implicating STT3A-dependent protein glycosylation as a predominant contributor for affecting indirect generation of glycoRNAs. Additionally, perturbations in N-glycan biosynthesis pathways or changes in N-glycan structure impact surface sialylated glycoRNA levels, indicating a regulatory role of glycan metabolic pathways in RNA glycosylation. Together, our results underscore the intricate relationship between protein N-glycosylation and processing and RNA biology.

Abstract 4121970: Early to Mid-Gestational Testosterone Excess Sex-specifically Reprograms Cardiac Transcriptome and Metabolome Profiles of Sheep Fetuses

Exposure of sheep to excess testosterone (T) from days 30-90 of gestation (term 147 days) perturbs maternal systemic lipidome in late gestation, induces fetal growth restriction and sexually dimorphic perturbation in the cardiac left ventricular (LV) transcriptome in gestational (GD) day 90 fetuses culminating in cardiometabolic dysfunction in adult female offspring. We hypothesized that the detrimental impact of prenatal T excess on fetal cardiac transcriptome is a programmed event that will persist even after cessation of excess T exposure and will be accompanied by changes in fetal metabolome. Pregnant ewes were injected with 100 mg intramuscular T propionate or vehicle (C), twice weekly from GD 30-90. On GD120±5, 30 days after cessation of T treatment fetal weights were recorded, left ventricle (LV) tissue and fetal plasma processed for transcriptomics by RNA sequencing and metabolomics analysis (Female C (FC) n=6, T (FT) n=7; Male C (MC) n=6, T (MT) n=7). LV transcriptome-based pathways enrichment analysis revealed 1) downregulation of pathways associated with oxidative phosphorylation, citric acid cycle, pyruvate metabolism; 2) upregulation of TGF-β signaling pathway in T fetuses compared to C (p<0.05, FDR<0.1); 3) selective downregulation of the glycolytic pathway in MT relative to MC as opposed to downregulation of mitochondria-related pathways in FT vs FC (p<0.05, FDR<0.1). LV lipidomics analyses found glycerophospholipids and sphingolipids as main class lipid metabolites to be enriched in FT relative to FC fetuses (p<0.05, ER>1). Fetal systemic lipidome main class metabolites enriched (p<0.05, ER>2) in T vs C fetuses included 1) sphingomyelins in both sexes 2) fatty acyls metabolites only in MT vs MC as opposed to glycerophospholipids only in FT vs FC. LV polar metabolites enriched (p<0.05, ER>2) included 1) arginine&proline metabolism pathways in T vs C in both sexes 2) nicotinate and nicotinamide metabolism only in MT vs MC (p<0.05, ER>3), and porphyrin, riboflavin metabolism and N-glycan biosynthesis pathways only in FT vs FC. Systemic polar metabolites enriched (p<0.05, ER>2) included 1) D-amino acid metabolism pathways in T vs. C, 2) valine, leucine, and isoleucine pathways only in FT vs FC and glycerophospholipid and sphingolipid metabolism only in MT vs MC. These results suggest persistence of sex-specific perturbation in fetal transcriptome and systemic and cardiac metabolome in late gestational fetuses exposed to prenatal T excess.

Effect of time series on the degradation of lignin by Trametes gibbosa: Products and pathways

Lignin is the third most abundant organic resource in nature. The utilization of white-rot fungi for wood degradation effectively circumvents environmental pollution associated with chemical treatments, facilitating the benign decomposition of lignin. Trametes gibbosa is a typical white-rot fungus with rapid growth and strong wood decomposition ability. The lignin content decreased from 23.62 mg/mL to 17.05 mg/mL, which decreased by 27 % in 30 days. The activity of manganese peroxidase increased steadily by 9.44 times. The activities of laccase and lignin peroxidase had the same trend of change and reached peaks of 49.88 U/L and 10.43 U/L on the 25th day, respectively. The change in H2O2 content in vivo was opposite to its trend. For FTIR and GC–MS analysis, the fungi attacked the side chain structure of lignin phenyl propane polymer and benzene ring to crack into low molecular weight aromatic compounds. The side chains of low molecular weight aromatic compounds are oxidized, and long-chain carboxylic acids are formed. Additionally, the absorption peak in the vibration region of the benzene ring skeleton became complex, and the structure of the benzene rings changed. In the beginning, fungal growth was inhibited. Fungal autophagy was aggravated. The metal cation binding proteins of fungi were active, and the genes related to detoxification metabolism were upregulated. The newly produced compounds are related to xenobiotic metabolism. The degradation peak focused on the redox process, and the biological function was enriched in the regulation of macromolecular metabolism, lignin metabolism, and oxidoreductase activity acting on diphenols and related substances as donors. Notably, genes encoding key degradation enzymes, including lcc3, lcc4, phenol-2-monooxygenase, 3-hydroxybenzoate-6-hydroxylase, oxalate decarboxylase, and acetyl-CoA oxidase were significantly upregulated. On the 30th day, the N-glycan biosynthesis pathway was significantly enriched in glycan biosynthesis and metabolism. Weighted correlation network analysis was performed. A total of 1452 genes were clustered in the coral1 module, which were most related to lignin degradation. The genes were significantly enriched in oxidoreductase activity, peptidase activity, cell response to stimulation, signal transduction, lignin metabolism, and phenylpropane metabolism, while the rest were concentrated in glucose metabolism. In this study, the lignin degradation process and products were revealed by T. gibbosa. The molecular mechanism of lignin degradation in different stages was explored. The selection of an efficient utilization time of lignin will help to increase the degradation rate of lignin. This study provides a theoretical basis for the biofuel and biochemical production of lignin. SynopsisTrametes gibbosa degrades lignin in a pollution-free way, improving the utilization of carbon resources in an environmentally friendly spontaneous cycle. The products are the new way towards sustainable development and low-carbon technology.

N-glycan Core Tri-fucosylation Requires Golgi α-mannosidase III Activity that Impacts Nematode Growth and Behaviour

N-glycans with complex core chitobiose modifications (CCMs) are observed in various free-living and parasitic nematodes but are absent in mammals. Using Caenorhabditis elegans as a model, we demonstrated that the core N-acetylglucosamine (GlcNAc) residues are modified by three fucosyltransferases, namely FUT-1, FUT-6 and FUT-8. Interestingly, FUT-6 can only fucosylate N-glycans lacking the α1,6-mannose upper arm, indicating that a specific α-mannosidase is required to generate substrates for subsequent FUT-6 activity. By analysing the N-glycomes of aman-3 knockouts using offline HPLC-MALDI-TOF MS/MS, we observed that the absence of aman-3 abolishes α1,3-fucosylation of the distal GlcNAc of N-glycans, which suggests that AMAN-3 is the relevant mannosidase on whose action FUT-6 depends. Enzymatic characterisation of recombinant AMAN-3 and confocal microscopy studies using a knock-in strain (aman-3::eGFP) demonstrated a Golgi localisation. In contrast to the classical Golgi α-mannosidase II (AMAN-2), AMAN-3 displayed a cobalt-dependent α1,6-mannosidase activity towards N-glycans. Using AMAN-3 and other C. elegans glycoenzymes, we were able to mimic nematode N-glycan biosynthesis in vitro by remodelling a fluorescein conjugated-glycan and generate a tri-fucosylated structure. In addition, using a high-content computer-assisted C. elegans analysis platform, we observed that aman-3 deficient worms display significant developmental delays, morphological and behavioural alterations in comparison to the wild type. Our data demonstrated that AMAN-3 is a Golgi α-mannosidase required for core fucosylation of the distal GlcNAc of N-glycans. This enzyme is essential for the formation of the unusual tri-fucosylated CCMs in nematodes, which may play important roles in nematode development and behaviour.

Targeted metabolomics of muscle amino acid profles and hepatic transcriptomics analyses in grass carp (Ctenopharyngodon idellus) fed with broad beans

While tissue amino acid compositions reflect that of the dietary protein source, and the liver orchestrates amino acid metabolism. In this study, we investigated the muscle amino acid profiles in ordinary and crisp grass carp. The 22 amino acids were measured, and seventeen showed significant concentration differences. To understand the molecular mechanisms behind changes, we analyzed the liver transcriptome, and the 2519 differentially expressed genes (DEGs) were identified, with 1156 up-regulated and 1363 down-regulated genes. DEGs were enriched in ribosome-related biological processes. KEGG pathway analysis showed enrichment in tryptophan metabolism, lysine degradation, valine, leucine and isoleucine degradation, galactose metabolism, and glutathione metabolism with up-regulated genes, arginine and proline metabolism, arginine biosynthesis and alanine, aspartate, amino sugar and nucleotide sugar metabolism, N-Glycan biosynthesis and glutamate metabolism with down-regulated genes. A protein-protein interaction network with 260 nodes and 249 edges was constructed, and 3 modules were extracted. The top 10 hub genes with close connections to other nodes were ITM1, STT3B, SEL1L, UGGT1, MLEC, IL1B, ALG5, KRTCAP2, NFKB2, and IRAK3. In summary, this study identified candidate genes and focused on amino acid and glycan metabolism pathways, providing a reference for further investigation into liver amino acid metabolism in grass carp fed with broad beans.

A Bioorthogonal Precision Tool for Human N-Acetylglucosaminyltransferase V.

Correct elaboration of N-linked glycans in the secretory pathway of human cells is essential in physiology. Early N-glycan biosynthesis follows an assembly line principle before undergoing crucial elaboration points that feature the sequential incorporation of the sugar N-acetylglucosamine (GlcNAc). The activity of GlcNAc transferase V (MGAT5) primes the biosynthesis of an N-glycan antenna that is heavily upregulated in cancer. Still, the functional relevance and substrate choice of MGAT5 are ill-defined. Here, we employ protein engineering to develop a bioorthogonal substrate analog for the activity of MGAT5. Chemoenzymatic synthesis is used to produce a collection of nucleotide-sugar analogs with bulky, bioorthogonal acylamide side chains. We find that WT-MGAT5 displays considerable activity toward such substrate analogues. Protein engineering yields an MGAT5 variant that loses activity against the native nucleotide sugar and increases activity toward a 4-azidobutyramide-containing substrate analogue. By such restriction of substrate specificity, we show that the orthogonal enzyme-substrate pair is suitable to bioorthogonally tag glycoproteins. Through X-ray crystallography and molecular dynamics simulations, we establish the structural basis of MGAT5 engineering, informing the design rules for bioorthogonal precision chemical tools.

Exploring protein N-glycosylation in the green microalga Dunaliella salina

N-glycosylation is a major post-translational modification of proteins that has a crucial influence on cell targeting, activity, and half-life. This process starts in the endoplasmic reticulum where an oligosaccharide precursor is added to the newly synthesized protein and continues in the Golgi apparatus where the N-linked carbohydrate sequences are processed. Importantly, the most approved recombinant pharmaceutical proteins (so-called biologics) are glycoproteins mainly currently produced in mammalian cells which is a lengthy, costly, and complex process. Today, several microalgae such as the diatom Phaeodactylum tricornutum, and the green microalgae Chlamydomonas reinhardtii, Chlorella vulgaris, and Dunaliella salina are considered as efficient and eco-friendly alternative platforms for the production of biologics. However, unlike for C. reinhardtii, C. vulgaris, and P. tricornutum, there is to date no data reported regarding the protein N-glycosylation pathway in D. salina. Here, we first investigated the protein N-glycosylation in this green microalga by MALDI-TOF mass spectrometry. These analyses showed that proteins from D. salina are N-glycosylated with Man5GlcNAc2 oligomannoside. Using genome mining approaches, we then identified genes encoding proteins involved in the N-glycosylation pathways in D. salina. Genetic similarities and phylogenetic relationships of the putative sequences with homologues from C. reinhardtii, P. tricornutum, and humans were investigated. These data revealed that in D. salina the biosynthesis of nucleotide sugars and N-glycan biosynthesis share mainly similarities with the GnT I-independent pathway of C. reinhardtii that gives rise to the synthesis of a non-canonical oligomannoside Man5GlcNAc2. Although an α(1,3)-fucosyltransferase is identified in the D. salina genome, impairment of the cytosolic GDP-Fuc biosynthesis prevents the Golgi fucosylation of N-glycans. Taken together, these data demonstrated that proteins from D. salina are homogeneously N-glycosylated with a non-canonical Man5GlcNAc2.

Developing diagnostic biomarkers for Alzheimer's disease based on histone lactylation-related gene

BackgroundResearch underscores the significant influence of histone lactylation pathways in the progression of Alzheimer's disease (AD), though the molecular mechanisms associated with histone lactylation-related genes (HLRGs) in AD are still insufficiently investigated. MethodsThis study employed datasets GSE85426 and GSE97760 to identify candidate genes by intersecting weighted gene co-expression network analysis (WGCNA) module genes with AD-control differentially expressed genes (DEGs). Subsequently, machine learning refined key genes, validated by receiver operating characteristic (ROC) curve performance. Gene-set enrichment analysis (GSEA) explored the molecular mechanisms of these diagnostic markers. Concurrently, the association between the diagnostic genes and both differential immune cells and immune responses was examined. Furthermore, a ceRNA and gene-drug network was developed. Finally, the expression of the selected genes was validated using brain tissues from AD model mice. ResultsThis study identified five genes (ARID5B, NSMCE4A, SESN1, THADA, and XPA) with significant diagnostic utility, primarily enriched in olfactory transduction and N-glycan biosynthesis pathways. Correlation analysis demonstrated a strong positive association between all diagnostic genes and naive B cells. The ceRNA regulatory network comprised 7 miRNAs, 2 mRNAs, and 25 lncRNAs. Additionally, 33 drugs targeting the diagnostic genes were predicted. Following expression validation through training and validation sets, three genes (ARID5B, SESN1, XPA) were ultimately confirmed as biomarkers for this study. RT-qPCR and Western blot analyses revealed upregulated expression of ARID5B, SESN1, and XPA in the cerebral tissue of AD model mice. ConclusionThree histone lactylation-linked genes (ARID5B, SESN1, XPA) were identified as potential AD biomarkers, indicating a strong association with disease progression.

An untargeted comparative metabolomics analysis of infants with and without late-onset breast milk jaundice.

Late-onset breast milk jaundice (LBMJ) is a common form of hyperbilirubinemia, which can result in serious complications for newborns with persistently high bilirubin levels. The aim of this study was to investigate the differences in fecal metabolites between breastfed infants with and without LBMJ in order to elucidate potential biological mechanisms. Biological samples were collected from 12 infants with LBMJ and 12 healthy individuals. Ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF/MS) was utilized for non-targeted determination of fecal metabolites. Principal components analysis (PCA), cluster analysis, and differential metabolite analysis were performed in both positive ion mode and negative ion mode for the two groups. Additionally, the KEGG database was employed to comprehensively analyze the pathways of differential metabolites. There were no significant differences in maternal and neonatal demographic characteristics between the two groups (p > 0.05). The results of PCA and cluster heat map analysis in both modes showed that there were significant differences in metabolites between the two groups. Among 751 differential metabolites (DMs) detected in positive ion mode, 720 were up-regulated in the case group while 31 were down-regulated. In negative ion mode, 1891 DMs were detected, including 817 up-regulated metabolites and 1074 down-regulated metabolites in the case group. Analysis of differential metabolic pathways showed that the DMs of the two groups were mainly annotated and enriched in Biotin metabolism, N-Glycan biosynthesis, Taurine and hypotaurine metabolism, Pyrimidine metabolism, and Pentose and glucuronate interconversions. Significant differences exist in fecal metabolites between LBMJ infants and healthy controls. The study of differential metabolic pathways provides insights into the mechanism of LBMJ.

Comprehensive analysis of flavor compounds and metabolites of vinasse hairtail fermentation based on GC-IMS and untargeted-based metabolomics

This study focused on investigating the degradation of proteins, metabolites, and flavors during the fermentation of vinasse hairtail, a local specialty fermented food in Zhoushan, China. The whole-protein SDS-PAGE results showed significant degradation of proteins, particularly actin and myosin. Total free amino acid content significantly increased, glutamate, leucine, alanine, and lysine were identified as the primary flavor amino acids conducive to the flavor, with umami, sweet, and bitter amino acids being predominant. The volatile constituents of the vinasse hairtail samples collected before fermentation (0 days) and after fermentation (8 days) were examined using gas chromatography-ion mobility spectrometry (GC-IMS). It revealed a total of 83 volatile flavor compounds, with the relative content of esters increasing and alcohols decreasing during fermentation. The untargeted metabolomics analysis identified 395 unique metabolites; the top 100 metabolites exhibited significant differences, including 52 oligopeptides, 18 organic acids and their derivatives, and 12 lipids and lipid molecules. The metabolic pathways involved in N-glycan biosynthesis, taurine and hypotaurine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, alanine, aspartic acid, and glutamic acid metabolism, tricarboxylic acid cycle, and histidine metabolism. These pathways contribute to the generation of amino acids, sugars, organic acids, and other flavor compounds, ultimately influencing the evolution of the flavor of vinasse hairtail.

Insights into the microscopic heterogeneity of whey proteins between yak colostrum and mature milk based on 4D lable-free quantitative phosphoproteomics

This study aimed to reveal the change patterns of the phosphorylation modification status of yak whey phosphoproteins during lactation and their physiological effects. Herein, we comprehensively characterized whey phosphoproteome in yak colostrum and mature milk using an ultra-high throughput phosphoproteomics approach incorporating trapped ion mobility technology. A total of 344 phosphorylation sites from 206 phosphoproteins were identified, with individual site modification predominating. Notably, 117 significantly different phosphorylation sites were distributed on 89 whey phosphoproteins. Gene ontology analysis indicated that these significantly different whey phosphoproteins (SDWPPs) were mainly annotated to carbohydrate metabolic process, membrane, extracellular region and calcium ion binding. Metabolic pathway enrichment analysis demonstrated that SDWPPs were critically involved in protein processing in endoplasmic reticulum, NOD-like receptor signaling pathway and N-glycan biosynthesis. Our results elucidate the phosphorylation profiles of yak whey phosphoproteins at different lactations and their adaptive regulatory role in meeting the nutritional requirements of yak calves during development.

Add-On Bifidobacterium Bifidum Supplement in Children with Attention-Deficit/Hyperactivity Disorder: A 12-Week Randomized Double-Blind Placebo-Controlled Clinical Trial.

We conducted a 12-week randomized double-blind placebo-controlled clinical trial to investigate the potential impact of Bifidobacterium bifidum (Bf-688) supplementation on attention-deficit/hyperactivity disorder (ADHD). Children with ADHD who were already receiving a stable dose of methylphenidate (MPH) treatment were enrolled and were randomly assigned to two groups: one receiving add-on Bf-688 (daily bacterial count of 5 × 109 CFUs) (n = 51) and the other receiving a placebo (n = 51). All participants underwent assessments using Conners' Continuous Performance Test (CPT) and Conners' Continuous Auditory Test of Attention (CATA). Additionally, fecal samples were collected at the beginning of the trial (week 0) and at the endpoint (week 12). Remarkably, the group receiving Bf-688 supplementation, but not the placebo group, exhibited significant improvements in omission errors in CPT as well as Hit reaction time in both CPT and CATA. Gut microbiome analysis revealed a significant increase in the Firmicutes to Bacteroidetes ratio (F/B ratio) only in the Bf-688 group. Furthermore, we identified significant negative correlations between N-Glycan biosynthesis and Hit reaction time in both CPT and CATA. Our results demonstrate that the probiotic Bf-688 supplement can enhance neuropsychological performance in children with ADHD, possibly by altering the composition of the gut microbiota, ultimately leading to reduced N-Glycan biosynthesis.

Machine learning-based integration of omics and clinical data reveals an N-glycan biosynthesis signature predictive of the outcome in low-grade glioma: an in silico study

Machine learning-based integration of omics and clinical data reveals an N-glycan biosynthesis signature predictive of the outcome in low-grade glioma: an <i>in silico</i> study

Disintegrin Accutin inhibits A549 cell migration though suppression of EMT and FAK/AKT signaling pathway

Integrins are heterodimers composed of two subunits, α(120-185kD) and β (90-110kD), which mediate the connection between cells and their external environment, such as extracellular matrix (ECM), and play an important role in the regulation of cell shape, proliferation and migration. Herein, we identified a potent anti-tumor migration peptide Accutin from crude venom of Agkistrodon acutus using an A549 3D tumor sphere model, and simulation tools and RNA sequencing were performed to reveal the mechanism of Accutin. Accutin is a disintegrin and docking, molecular dynamics simulations and ITC assay indicate that the RGD motif in the Accutin sequence can stably bind to integrins α5β1. 9.22 nM Accutin can significantly inhibit the migration and invasion of lung cancer cell lines. Transcriptome analysis indicated that many genes are involved in tumor cell adhesion-related biological processes. Several pathways, like the “mTOR signaling pathway”, “TGF-β signaling pathway”, and “Focal adhesion” were enriched. Interestingly, pathways involved in “N-Glycan biosynthesis” etc. were significantly inhibited. These transcriptomics data suggested that the molecular basis of Accutin-mediated inhibition of cancer cell migration may be by inhibiting N-glycosylation of integrin, then inhibiting signaling pathways such as PI3K/AKT/mTOR and TGFβ/smad. Western blotting analysis further confirmed that Accutin could suppress migration via down-regulating the phosphorylation of FAK and AKT and inhibiting EMT (epithelial-mesenchymal transition). Taken together, as a disintegrin with high efficiency, Accutin may be a potential precursor of a therapeutic agent for the treatment of lung cancer migration.

Characteristics of phosgene aspiration lung injury analyzed based on transcriptomics and proteomics.

Phosgene is a chemical material widely used worldwide. No effective method has been developed to reverse its pathological injuries. Some studies have shown that neuronal inflammation in lung tissue is involved, but the specific mechanism has not been reported. To analyze the expression alterations of whole transcriptome gene sequencing bioinformatics and protein expression profile in lung tissue after phosgene aspiration lung injury (P-ALI) and find the main factors and pathways affecting the prognosis of P-ALI. Rat models of P-ALI were made by phosgene. Rats were divided into a P-ALI group and a blank group. Hematoxylin-eosin (HE) staining and lung wet/dry ratio measurement were used to evaluate the lung injury. The levels of inflammatory factors were measured by ELISA. High-throughput sequencing was used to measure the expression profile of each gene. Protein expression profiles were determined by label-free relative quantification of the differential proteome. Lung injury such as the disordered structure of alveolar wall and inflammatory factors (IL-1β, IL-18, and IL-33) were significantly increased in the P-ALI group (p < 0.05). There were 225 differentially expressed lncRNAs, including 85 upregulated and 140 downregulated genes. They were also the genomes with the most significant changes in transcriptome gene expression, mainly constituting cytoplasmic, synaptic structures and transporters, and involved in amino acid and carbon metabolism. There were 42 differentially expressed circRNAs, including 25 upregulated genes and 17 downregulated genes, mainly involved in cell composition, growth, differentiation, and division. There were only 10 differentially expressed miRNAs genes, all upregulated and mainly involved in the inflammatory response pathway. Proteome identification showed 79 differentially expressed proteins. KEGG enrichment analysis showed that it was mainly involved in the N-glycan biosynthesis pathway. We discovered that differentially regulated genes (lncRNAs, circRNAs, and miRNAs) were primarily associated with neuronal reflexes and synaptic signaling, including neurotransmitter transmission, ion signaling pathway conduction, neuronal projection, and synaptic vesicle circulation. They affected inflammatory factors and other metabolic pathways. This finding could be explored in future studies.

Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata.

To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.

Estrogen Signaling Modulation Prevents and Even Reverses Skeletal Muscle Fibrosis

Background: Skeletal muscle fibrosis represents accumulation of extracellular matrix (ECM), often leading to muscle weakness and atrophy. Notably, lower abdominal muscle (LAM) fibrosis and atrophy cause inguinal herniation—a prevalent condition lacking pharmacological treatment. We developed a herniation mouse model, Aromhum, characterized by spontaneous scrotal hernias due to local estradiol (E2) production within LAM as well as hernia-associated fibroblasts (HAFs) that express platelet-derived growth factor alpha (PDGFRA) and estrogen receptor alpha (ESR1). Objectives &amp; Hypothesis: Our objective was to investigate the mechanism of ESR1 signaling on LAM HAFs and subsequent development of hernias. Methods: We manipulated estrogen signaling in two ways: first, we generated fibroblast-specific estrogen receptor alpha knockout mice (fEsr1−/−-Aromhum) capable of local E2 production but incapable of signaling through ESR1 (n = 5-10 mice/group). Second, we blocked E2 signaling pharmacologically using the potent ESR1 antagonist fulvestrant (0.15mg/kg, 90 days, n=10-15 mice/group). We conducted in vitro experiments on primary LAM HAFs exposed to 10nM E2 ± 100nM Fulvestrant (24-48h). These cells underwent analysis via ESR1 ChIP, ATAC, and RNA-seq in 3 technical replicates (3-5 mice each). Additionally, to demonstrate clinical relevance, we probed human herniated LAM tissues from patients (n=25 samples, 21-76 years). Results: All Aromhum mice develop scrotal hernias by 6 weeks. However, fEsr1−/−-Aromhum mice did not develop hernias, while littermate controls exhibited hernias. Thus, HAF ESR1 depletion mitigated LAM fibrosis and atrophy. Similarly, administering fulvestrant prior to hernia onset prevented hernia development. Remarkably, fulvestrant treatment in mice that had developed large scrotal hernias (&gt;200mm2) led to complete hernia regression with reversed muscle fibrosis and fiber atrophy (collagen levels comparable to wild-type mice). In vitro HAF culturing and subsequent multiomic analyses unveiled a core set of 58 genes directly influenced by E2/ESR1, including crucial ECM genes like fibulins ( Fbln5, Fbln7), metalloproteases ( Adamts3, Adamts6), and signaling molecules ( Ltbp1, Ncam1, Piezo2). Pathways such as TGFβ, WNT, and N-Glycan biosynthesis were significantly upregulated by E2. Human herniated LAM tissues exhibited substantial fibrosis, along with stromal HAF markers PDGFRA and ESR1. We also validated expression of the core E2-modulated genes in human LAM tissues ( NCAM1, LTBP1, ADAMTS6, PIEZO2). Collectively, these findings provide compelling evidence of ESR1 pathway activation and downstream gene involvement in both Aromhum scrotal hernias and human inguinal hernias. Conclusion: Our research underscores the central role of E2 in skeletal muscle fibrosis. Notably, we demonstrated that fibrosis can be entirely reversed by modulation of ESR1 signaling. Our study offers valuable insights into downstream genes and pathways that may serve as therapeutic targets for inguinal hernias and other fibrotic disorders. Funding: NIH: R01DK121529, Department of Veterans Affairs Research Career Scientist Award: IK6 RX003351. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

The proteomic analysis uncovers the cellular responses to the African swine fever virus membrane proteins p54, p17, and pB117L

African swine fever virus (ASFV) infection causes African swine fever (ASF), a highly contagious and fatal disease that poses severe threat to swine production. To gain insights into the host responses to ASFV, we generated recombinant adenovirus Ad5 expressing viral membrane proteins p54, p17, and pB117L individually and infected an alveolar cell line, 3D4/21, with these recombinant viruses. Then, the cell lysates were analyzed using label-free quantification proteomic analysis method. A total of 2158 differentially expressed proteins (DEPs) were identified, of which 817, 466, and 875 proteins were from Ad5-p54-, Ad5-p17-, Ad5-pB117L-infected 3D4/21 cells, respectively. Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed distinct yet interconnecting patterns of protein interaction networks. Specifically, the Ad5-p54 virus infection enriched the DEPs primarily involved in the metabolic pathways, endocytosis, adherens junction, and SNARE interactions in vesicular transport. The Ad5-p17 virus infection enriched the DEPs in endocytosis, ubiquitin-mediated proteolysis, N-Glycan biosynthesis, and apoptosis, while the Ad5-pB117L virus infection enriched the DEPs in metabolic pathways, endocytosis, oxidative phosphorylation, and focal adhesion. In summary, these results provide a comprehensive proteinomics analysis of the cellular responses to three ASFV membrane proteins, thus facilitating our understanding of ASFV pathogenesis.

Lymphoblast transcriptome analysis in 22q11.2 deletion syndrome individuals with schizophrenia-spectrum disorder

Objectives 22q11.2 deletion is the most prominent risk factor for schizophrenia (SZ). The aim of the present study was to identify unique transcriptome profile for 22q11.2 deletion syndrome (DS)-related SZ-spectrum disorder (SZ-SD). Methods We performed RNA-Seq screening in lymphoblasts collected from 20 individuals with 22q11.2DS (10 men and 10 women, four of each sex with SZ-SD and six with no psychotic disorders (Np)). Results Sex effect in RNA-Seq descriptive analysis led to separating the analyses between men and women. In women, only one differentially expressed gene (DEG), HLA-DQA2, was associated with SZ-SD. In men, 48 DEGs (adjp < 0.05) were found to be associated with SZ-SD. Ingenuity pathway analysis of top 85 DEGs (p < 4.66E − 04) indicated significant enrichment for immune-inflammatory response (IIR) and neuro-inflammatory signalling pathways. Additionally, NFATC2, IFNG, IFN-alpha, STAT1 and IL-4 were identified as upstream regulators. Co-expression network analysis revealed the contribution of endoplasmic reticulum protein processing and N-Glycan biosynthesis. These findings indicate dysregulation of IIR and post-translational protein modification processes in individuals with 22q11.2DS-related SZ-SD. Conclusions Candidate pathways and upstream regulators may serve as novel biomarkers and treatment targets for SZ. Future transcriptome studies, including larger samples and proteomic analysis, are needed to substantiate our findings.

Determination, expression and characterization of an UDP-N-acetylglucosamine:α-1,3-D-mannoside β-1,2-N-acetylglucosaminyltransferase I (GnT-I) from the Pacific oyster, Crassostrea gigas

Molluscs are intermediate hosts for several parasites. The recognition processes, required to evade the host’s immune response, depend on carbohydrates. Therefore, the investigation of mollusc glycosylation capacities is of high relevance to understand the interaction of parasites with their host. UDP-N-acetylglucosamine:α-1,3-D-mannoside β-1,2-N-acetylglucosaminyltransferase I (GnT-I) is the key enzyme for the biosynthesis of hybrid and complex type N-glycans catalysing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to the α-1,3 Man antenna of Man5GlcNAc2. Thereby, the enzyme produces a suitable substrate for further enzymes, such as α-mannosidase II, GlcNAc-transferase II, galactosyltransferases or fucosyltransferases. The sequence of GnT- I from the Pacific oyster, Crassostrea gigas, was obtained by homology search using the corresponding human enzyme as the template. The obtained gene codes for a 445 amino acids long type II transmembrane glycoprotein and shared typical structural elements with enzymes from other species. The enzyme was expressed in insect cells and purified by immunoprecipitation using protein A/G-plus agarose beads linked to monoclonal His-tag antibodies. GnT-I activity was determined towards the substrates Man5-PA, MM-PA and GnM-PA. The enzyme displayed highest activity at pH 7.0 and 30 °C, using Man5-PA as the substrate. Divalent cations were indispensable for the enzyme, with highest activity at 40 mM Mn2+, while the addition of EDTA or Cu2+ abolished the activity completely. The activity was also reduced by the addition of UDP, UTP or galactose. In this study we present the identification, expression and biochemical characterization of the first molluscan UDP-N-acetylglucosamine:α-1,3-D-mannoside β-1,2-N-acetylglucosaminyltransferase I, GnT-I, from the Pacific oyster Crassostrea gigas.Graphical abstractIllustration of GnT-I activity. (a) Transfer of GlcNAc to Man5-PA, creating Man5GlcNAc3-PA. (b) Transfer of GlcNAc to MM-PA, creating MGn-PA. (c) Transfer of GlcNAc to GnM-PA, creating GnGn-PA. Blue squares represent N-acetylglucosamine, green cycles depict mannose. Graphic illustration of N-glycans were created using bioRENDER.