Engineering最新文献

{"title":"The Serum-Derived Extracellular Vesicle N-Glycome as a New Biosignature for Childhood Epilepsy","authors":"Yuanyuan Liu ,&nbsp;Yanbin Guo ,&nbsp;Changzhen Li ,&nbsp;Zhiwen Huang ,&nbsp;Xiang Liu ,&nbsp;Han Xie ,&nbsp;Wenhui Wang ,&nbsp;Lili Guan ,&nbsp;Bi-Feng Liu ,&nbsp;Si Liu ,&nbsp;Guoping Wang ,&nbsp;Xin Liu","doi":"10.1016/j.eng.2025.12.009","DOIUrl":"10.1016/j.eng.2025.12.009","url":null,"abstract":"<div><div>Childhood epilepsy poses a serious threat to patients’ growth, development, and life safety, creating an urgent need for precise, non-invasive, and longitudinally monitorable biomarkers. Previous studies have confirmed that extracellular vesicles (EVs) with abnormal N-glycosylation modifications regulate various neurological disorders, where characteristic <em>N</em>-glycans serve as potential diagnostic markers. In this study, we systematically compared the properties of EVs isolated via three different methods. The results demonstrated that an exosome purification filter column (EPF) combined with ultrafiltration emerged as the optimal approach for isolating EVs from large-scale clinical samples. Subsequent matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based glycomic profiling of EVs and serum revealed distinct <em>N</em>-glycan signatures. Utilizing a novel two-step machine learning model, we identified 47 characteristic <em>N</em>-glycans in EVs as biomarkers for epilepsy diagnosis and classification. These biomarkers effectively distinguished between normal, focal, and generalized epilepsy subtypes while also exhibiting superior diagnostic performance compared to serum <em>N</em>-glycan profiles. Furthermore, we constructed a correlation network map of glycans, which highlighted dynamic alterations in the expression patterns of EV glycans during epileptogenesis. Taken together, the <em>N</em>-glycans of EVs exhibit promising potential as biomarkers for epilepsy detection, offering new insights into non-invasive diagnosis and disease monitoring.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 126-137"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145785551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep Reinforcement Learning-Driven Multi-Omics Integration for Constructing gtAge: A Novel Aging Clock from the IgG N-Glycome and Blood Transcriptome","authors":"Yao Xia ,&nbsp;Syed Mohammed Shamsul Islam ,&nbsp;Xingang Li ,&nbsp;Abdul Baten ,&nbsp;Xuerui Tan ,&nbsp;Wei Wang","doi":"10.1016/j.eng.2025.08.016","DOIUrl":"10.1016/j.eng.2025.08.016","url":null,"abstract":"<div><div>Previous studies have demonstrated that the immunoglobulin G (IgG) N-glycome and transcriptome are potential biochemical signatures of chronological and biological ages, and several aging clocks have been developed. By integrating the IgG N-glycome and transcriptome, we propose a novel aging clock, gtAge. We developed a deep reinforcement learning-based multiomics integration method called AlphaSnake. The results showed that AlphaSnake achieved a predicted coefficient of determination (<em>R²</em>) value of 0.853, outperforming the concatenation-based integration method (<em>R²</em> = 0.820)<span><math><mrow><mo>.</mo></mrow></math></span> The gtAge estimated by AlphaSnake explained up to 85.3% of the variance in chronological age, which was higher than that in age predicted from IgG N-glycome solely (gAge; <em>R²</em> = 0.290) and age predicted from transcriptome solely (tAge; <em>R²</em> = 0.812). We also found that the delta age—the difference between the predicted age and chronological age—was associated with several age-related phenotypes. Both delta gtAge and tAge were negatively associated with high-density lipoprotein (<em>p</em> = 0.02 and <em>p</em> = 0.022, respectively), whereas delta gAge was positively correlated with cholesterol (<em>p</em> = 0.006), triglyceride (<em>p</em> = 0.002), fasting plasma glucose (<em>p</em> = 0.014), low-density lipoprotein (<em>p</em> = 0.006), and glycated hemoglobin (<em>p</em> = 0.039). These findings suggest that gtAge, tAge, and gAge are potential biomarkers for biological age.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 100-112"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotype–Target Coupled Drug Screening: A High-Efficiency Framework for Innovative Drug Discovery from CHMs","authors":"Wei Zhou,&nbsp;Yue Gao","doi":"10.1016/j.eng.2025.11.019","DOIUrl":"10.1016/j.eng.2025.11.019","url":null,"abstract":"","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 10-13"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomics and Metabolomics Reveal Intrinsic Drivers of Pyrite-Based Mixotrophic Denitrifying Biofilters: Microbial Spatial Stratification, Nitrogen Removal Pathways, and Key Metabolites","authors":"Qi Zhou ,&nbsp;Weizhong Wu ,&nbsp;Jianlong Wang","doi":"10.1016/j.eng.2025.05.006","DOIUrl":"10.1016/j.eng.2025.05.006","url":null,"abstract":"<div><div>Microbial functions and metabolism are intrinsic drivers of pollutant removal in mixotrophic denitrification systems. Four pyrite-based mixotrophic denitrifying biofilters were constructed and monitored for 304 days. Variations in pollutant characteristics indicated that the hot zones of heterotrophic denitrification, autotrophic denitrification, and sulfate reduction were located in the bottom, middle-lower, and upper parts of biofilters, respectively. These hot zones corresponded to preferential enrichment of heterotrophic denitrifying, S-based mixotrophic denitrifying, and sulfate-reducing bacteria, respectively, highlighting microbial spatial stratification. Differential functional gene analysis for S reduction revealed that only a dissimilated sulfate reduction process could consistently provide biogenic S⁰ as a new electron donor via the flavocytochrome c sulfide dehydrogenase (Fcc) enzyme and extracellular polymeric substance protection systems, enhancing the denitrification process. X-ray photoelectron spectroscopy confirmed the accumulation of biogenic S⁰. Untargeted metabolomic analysis suggested that vitamin B₁₂ and tryptophan might be the key metabolites for realizing synergistic promotion of autotrophic and heterotrophic denitrification. The microbe–metabolite network indicated that dominant bacteria (e.g., <em>Thiothrix</em> and <em>unclassified_f_Rhodocyclaceae</em>) were specialists with less cross-feeding metabolism, while rare species (e.g., <em>Thiobacillus</em> and <em>Desulfobacter</em>) were generalists with complex cross-feeding metabolism in the constructed mixotrophic denitrification systems. The electron transfer pattern indicated that most of the electrons released from S, C, and Fe oxidation were utilized in denitrification processes as the dominant nitrogen removal pathway, including S²⁻/S⁰-based autotrophic, fermentation acetic acid production-heterotrophic, and Fe(II)-based autotrophic denitrification. Some electrons were utilized for coupling dissimilatory nitrate reduction to ammonia (DNRA) and anammox processes as an auxiliary pathway for systemic nitrogen removal. The findings of this study advance our understanding of the deeper intrinsic drivers of nitrogen removal by pyrite-based mixotrophic denitrifying biofilters, facilitating their optimization.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 236-249"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Is the Brain Drain Reversing?","authors":"","doi":"10.1016/j.eng.2025.11.011","DOIUrl":"10.1016/j.eng.2025.11.011","url":null,"abstract":"","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 3-5"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fucosylated IgG Contributes to Adipose Tissue Dysfunction During Aging","authors":"Jingyu Wang ,&nbsp;Wei Su ,&nbsp;Haotian Wang ,&nbsp;Licui Liu ,&nbsp;Jinlong Li ,&nbsp;Youxin Wang","doi":"10.1016/j.eng.2025.10.008","DOIUrl":"10.1016/j.eng.2025.10.008","url":null,"abstract":"<div><div>Immunoglobulin G (IgG) is recognized as a key regulator of metabolic dysfunction and fibrosis in adipose tissue, and its functional properties are tightly regulated by its glycosylation profile. However, the role of IgG glycosylation in adipose aging remains unclear. Here, we performed transcriptomic and glycoproteomic analyses of epididymal white adipose tissue (eWAT) from young and aged mice. RNA sequencing (RNA-seq) analysis revealed a significant downregulation of adipogenic genes in aged eWAT, accompanied by elevated expression levels of inflammatory and fibrotic markers, which were further validated by quantitative polymerase chain reaction (qPCR). N- and O-glycoproteomic analyses revealed widespread changes in glycosylation. Differentially glycosylated proteins are primarily localized to the extracellular space and participate in innate immune responses, transport and signal transduction, extracellular matrix (ECM)–receptor interaction pathways, and so on. Notably, IgG glycosylation levels were significantly increased in aged mice. Specifically, the N-fucosylation of IgG1, IgG2a, and IgG3 was elevated by 3.1-, 10.4-, and 3.2-fold, respectively, while only IgG2a showed increased O-fucosylation. These findings suggest that N-fucosylation is a common age-related modification across IgG subtypes. Using <em>in vivo</em> models, we further demonstrated that B-cell depletion-induced IgG reduction increased adipogenic and inflammatory gene expression, while the expression of fibrotic markers was suppressed. These effects were reversed upon repletion with either fucosylated or nonfucosylated IgG. Importantly, compared with nonfucosylated IgG, fucosylated IgG exacerbated inflammation and fibrosis but inhibited adipogenesis more strongly. Taken together, our results identify fucosylated IgG as a key mediator of adipose dysfunction during aging and suggest that modulating IgG fucosylation may offer therapeutic potential for age-related metabolic disorders.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 149-158"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GlycoPro: A High-Throughput Sample-Processing Platform for Multi-Glycosylation-Omics Analysis","authors":"Xuejiao Liu ,&nbsp;Yue Meng ,&nbsp;Bin Fu ,&nbsp;Haoru Song ,&nbsp;Bing Gu ,&nbsp;Ying Zhang ,&nbsp;Haojie Lu","doi":"10.1016/j.eng.2025.01.011","DOIUrl":"10.1016/j.eng.2025.01.011","url":null,"abstract":"<div><div>Glycosylation-omics has emerged as a prominent field for early detection and diagnosis by identifying alterations in glycosylation patterns linked to cancer. In the realm of clinical multi-glycosylation-omics applications, there is a critical need for robust, efficient, and cost-effective preprocessing methodologies capable of handling large sample cohorts. To bridge this gap, we introduce the GlycoPro platform, an innovative solution designed to overcome the limitations of existing analysis methods. Tailored for multi-glycosylation-omics sample preprocessing, GlycoPro refines existing workflows by seamlessly integrating steps including protein extraction, desalting, digestion, derivatization, and enrichment. The GlycoPro platform employs a 96-well plate format, enabling the efficient enrichment or desalting of up to 384 samples in a single day. This capability represents a significant increase in throughput, meeting the demands of large-scale clinical sample preprocessing for mass spectrometry analysis. The GlycoPro platform was used to successfully enrich serum <em>N</em>-glycans from breast cancer patients, revealing unique glycomic signatures that distinguish malignant from benign conditions. We have developed a robust <em>N</em>-glycan biomarker panel, demonstrating a sensitivity of 88.24% and a specificity of 78.95% in diagnostics.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 43-57"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New Avenues for Human Blood Plasma Biomarker Discovery via Improved In-Depth Analysis of the Low-Abundant N-Glycoproteome","authors":"Frania J. Zuniga-Banuelos ,&nbsp;Marcus Hoffmann ,&nbsp;Udo Reichl ,&nbsp;Erdmann Rapp","doi":"10.1016/j.eng.2024.11.039","DOIUrl":"10.1016/j.eng.2024.11.039","url":null,"abstract":"<div><div>To understand the implications of protein glycosylation for clinical diagnostics and biopharmaceuticals, innovative glycoproteomic technologies are required. Recently, significant advances have been made in such technologies, particularly in the area of structure-focused <em>N-</em>glyco-proteomic analyses. Mass spectrometric analysis of intact <em>N-</em>glycopeptides using stepped collision fragmentation along with glycan oxonium ion profiling now makes it possible to reliably discriminate between different <em>N-</em>glycan structures. Still, current <em>N-</em>glycoproteomic approaches have weaknesses that must be overcome, namely ① the handling of incorrect identifications, ② the identification of rare and modified <em>N-</em>glycans, and ③ insufficient glycoproteomic coverage, especially in complex samples. To address these shortcomings, we have established an innovative <em>N-</em>glycoproteomic workflow that aims to provide comprehensive site-specific and structural <em>N-</em>glycoproteomic data on human blood plasma (HBP) glycoproteins. The workflow features protein depletion plus a fractionation strategy and the use of high-resolution mass spectrometry with stepped collision fragmentation. Furthermore, by including a new decision tree procedure developed for data validation, we can significantly improve the description of <em>N-</em>glycan micro-heterogeneity. Our advanced data analysis workflow allows the reliable differentiation of ambiguous <em>N-</em>glycan structures such as antenna versus core fucosylation, as well as modified and rare <em>N-</em>glycans such as sulfated and glucuronidated ones. With this workflow, we were able to achieve the detection of HBP glycoproteins with reported concentrations within the ng·mL⁻¹ level. A total of 1929 <em>N-</em>glycopeptides and 942 <em>N-</em>glycosites derived from 805 human middle- to low-abundant glycoproteins were identified. Overall, the presented workflow holds great potential to improve our understanding of protein glycosylation and to foster the discovery of blood plasma biomarkers.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 23-42"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rational Modulation of Pt d Electrons to Significantly Enhance the Catalytic Dehydrogenation Performance of Liquid Organic Hydrogen Carriers","authors":"Chao Sun ,&nbsp;Tianzuo Wang ,&nbsp;Ruijie Gao ,&nbsp;Xiaoyang Liu ,&nbsp;Kang Xue ,&nbsp;Chengxiang Shi ,&nbsp;Xiangwen Zhang ,&nbsp;Lun Pan ,&nbsp;Ji-Jun Zou","doi":"10.1016/j.eng.2025.07.045","DOIUrl":"10.1016/j.eng.2025.07.045","url":null,"abstract":"<div><div>Understanding the intrinsic features of dehydrogenation reactions of liquid organic hydrogen carriers (LOHCs) is a formidable challenge due to the combined impact of electronic and geometric effects. Herein, we constructed a series of Pt/MO<em>_x</em> catalysts (CeO₂, MgO, ZrO₂, TiO₂, Al₂O₃, or SiO₂) with similar sizes of Pt (∼1.7 nm) to investigate the effects of Pt electron structures (tuned by electronic metal–support interactions) on the catalytic dehydrogenation of LOHCs. The results revealed a volcano-shaped correlation between Pt d electrons on different supports and the turnover frequency of catalytic dehydrogenation. Importantly, the Pt/MgO catalyst exhibited the highest dehydrogenation activity. With decreasing d electron content, Pt/MgO increases the bonding orbital dominance of Pt–C bonds and leads to stable adsorption of H6-monobenzyltoluene (MBT), which facilitates subsequent C–H bond scission. This study offers insight for the strategic development of high-efficiency dehydrogenation catalysts via d electron density modulation of Pt sites.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 217-226"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145383742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of Sleep and Circadian Rhythms by S-Adenosylmethionine-Producing Probiotics","authors":"Peijun Tian ,&nbsp;Yuming Lan ,&nbsp;Zhiying Jin ,&nbsp;Feng Hang ,&nbsp;Xuhua Mao ,&nbsp;Xing Jin ,&nbsp;Gang Wang ,&nbsp;Wei Chen","doi":"10.1016/j.eng.2024.12.025","DOIUrl":"10.1016/j.eng.2024.12.025","url":null,"abstract":"<div><div>Current first-line medications for sleep disorders often overlap with antidepressants, yet their effectiveness remains suboptimal, highlighting the urgent need for novel therapeutic strategies based on new mechanisms. Our study initially identified a significant reduction in serum <em>S</em>-adenosylmethionine (SAM) levels in insomnia patients through a cross-sectional analysis, suggesting SAM as a potential biomarker and therapeutic target for sleep disorders. We then screened 60 gut strains across seven species and identified a high-SAM-producing probiotic, <em>Lactobacillus helveticus</em> CCFM1320, which improved cognitive and memory impairments caused by sleep deprivation in mice. Mechanistically, CCFM1320 enhances the methylation of <em>N</em>-acetylserotonin, a precursor of melatonin synthesis, normalizing the expression of downstream circadian rhythm genes. A subsequent four-week placebo-controlled clinical trial demonstrated that CCFM1320 significantly improved sleep quality in patients with sleep disorders, as evidenced by reduced Pittsburgh sleep quality index (PSQI) scores, lower serum cortisol levels, and decreased prevalence of pathogenic species in the gut. Probiotic treatment also elevated the abundance of SAM synthesis and metabolism-related enzyme genes in the gut microbiome, likely due to the introduction of high-SAM-producing probiotics and subsequent SAM accumulation. This study presents a promising probiotic-based strategy for managing sleep disorders, offering a potential non-pharmacological treatment alternative.</div></div>","PeriodicalId":11783,"journal":{"name":"Engineering","volume":"57 ","pages":"Pages 250-261"},"PeriodicalIF":11.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}