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21 pages, 34775 KB  
Article
Etiology, Pathogenicity, and Fungicide Management of Pigeonpea Shoot Dieback Caused by Lasiodiplodia theobromae in China
by Feiyun Huang, Xi Xu and Yanzhong Li
J. Fungi 2026, 12(7), 474; https://doi.org/10.3390/jof12070474 - 28 Jun 2026
Viewed by 406
Abstract
Pigeonpea (Cajanus cajan) shoot tip dieback was recently observed in Danzhou, Hainan Province, China, with disease incidence of 30–100% in affected fields, but its causal agent and management options remained unclear. This study aimed to isolate and identify the fungal agent [...] Read more.
Pigeonpea (Cajanus cajan) shoot tip dieback was recently observed in Danzhou, Hainan Province, China, with disease incidence of 30–100% in affected fields, but its causal agent and management options remained unclear. This study aimed to isolate and identify the fungal agent associated with the disease, verify its pathogenicity, characterize its biological traits and effects on host growth, and screen candidate fungicides. Fungal isolates were obtained from symptomatic shoot margins and purified by hyphal-tip and single-spore isolation. Representative isolates LYZ0717, LYZ0718, and LYZ0719 were characterized by colony morphology, pycnidial and conidial traits, and combined phylogenetic analysis of ITS and TEF1-α sequences. These analyses identified the isolates as Lasiodiplodia theobromae. Spray inoculation of 20-day-old pigeonpea seedlings reproduced typical shoot tip dieback symptoms within 6 days, and the inoculated fungus was reisolated from symptomatic tissues, fulfilling Koch’s postulates. The pathogen grew over a pH range of 3–11 and at temperatures of 5–35 °C, with optimal mycelial growth at 25–30 °C and maximum sporulation under acidic conditions. At 20 days after inoculation, infection reduced plant height, dry weight, and total flavonoid content by 45.21%, 75.88%, and 42.19%, respectively. Among the seven fungicides tested, trifloxystrobin–tebuconazole and thiophanate-methyl showed the strongest in vitro inhibition, with EC50 values of 0.0270 and 0.0614 ppm, respectively. In greenhouse pot experiments, thiophanate-methyl achieved the highest disease control efficacy, reaching 64.35% after the second application. These findings demonstrate that L. theobromae is the causal agent of pigeonpea shoot tip dieback in China and provide a basis for disease diagnosis, biological understanding, and fungicide-based management. Full article
(This article belongs to the Special Issue Plant Pathogenic Fungal Infections, Biocontrol and Novel Fungicides)
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26 pages, 4551 KB  
Article
Development and Optimization of Ionic Strength-Responsive Lipid–Polymer Hybrid Nanoparticles for Buccal Protein Delivery
by Eslam Ramadan, Nooh Mdrmah, Martin Deák, Norbert Varga, Edit Csapó, Tamás Sovány and Katalin Kristó
Pharmaceutics 2026, 18(6), 719; https://doi.org/10.3390/pharmaceutics18060719 - 11 Jun 2026
Viewed by 412
Abstract
Background: Oral protein delivery is a major challenge in the field of pharmaceutical technology due to poor stability and limited permeability through intestinal barriers. Buccal delivery is a promising alternative with less restricting physiological conditions; however, low protein permeability is still a limiting [...] Read more.
Background: Oral protein delivery is a major challenge in the field of pharmaceutical technology due to poor stability and limited permeability through intestinal barriers. Buccal delivery is a promising alternative with less restricting physiological conditions; however, low protein permeability is still a limiting factor. Multiple nanocarriers have been proposed to improve buccal protein delivery with lipid–polymer hybrid nanoparticles (LPHNs) combining the advantages of both polymeric and lipid-based systems. However, these conventional carriers rely on passive protein protection and lack adaptive release mechanisms. Objectives: This work aimed to develop and systematically optimize an ionic strength-responsive LPHN system that can minimize protein release in buccal ionic conditions while offering a triggered release in plasma after absorption. Methods: LPHNs were prepared by a two-step approach where polymeric cores of Eudragit-L100 were prepared by electrostatic complexation with Lysozyme (LYZ) followed by lipid shell formation by the ethanol injection method. Systematic optimization was performed using two-level factorial and central composite designs. Moreover, the ionic strength responsiveness and in vitro LYZ release were investigated in different ionic strength media. Results: The final optimized formulations, LPHNs and sodium deoxycholate-containing LPHNs (NaDC-LPHNs), exhibited a particle size of 257.2 ± 1.5 nm and 246 ± 5.7 nm, encapsulation efficiency of 69.89 ± 0.22% and 68.14 ± 0.16%, and high drug loading efficiency of 24.11 ± 0.06% and 23.65 ± 0.04%, respectively. Moreover, both formulations showed minimal protein release at low ionic strength (buccal-like) conditions while demonstrating a triggered release at higher ionic strength (plasma-like) conditions. Conclusions: The developed system may provide a promising smart strategy to improve buccal protein delivery by enhancing buccal protection and improving systemic delivery. Full article
(This article belongs to the Special Issue Emerging Stimuli-Responsive Nanoparticles for Bioactive Delivery)
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25 pages, 3712 KB  
Article
An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia
by Santoshi Borra, Da Yan, Robert S. Welner and Zongliang Yue
Biology 2026, 15(7), 588; https://doi.org/10.3390/biology15070588 - 6 Apr 2026
Cited by 1 | Viewed by 1532
Abstract
Background: A major technical challenge in single-cell transcriptomics is the absence of an integrative analytic pipeline that can simultaneously leverage gene regulatory network (GRN) architecture, AI-assisted gene panel discovery, and functional relevance analyses to generate coherent biological insights. Existing approaches often treat these [...] Read more.
Background: A major technical challenge in single-cell transcriptomics is the absence of an integrative analytic pipeline that can simultaneously leverage gene regulatory network (GRN) architecture, AI-assisted gene panel discovery, and functional relevance analyses to generate coherent biological insights. Existing approaches often treat these components independently, focusing on clusters, marker genes, or predictive features without integrating them into a mechanistically grounded framework. Consequently, comprehensive screening that links regulatory association, gene signature screening, and functional interpretation within single-cell datasets remains limited, underscoring the need for an integrated strategy. Methods: We developed an integrative bioinformatics pipeline based on Gene regulatory network–AI–Functional Analysis (GAFA), combining latent-space integration, unsupervised clustering, diffusion pseudotime analysis, lineage-resolved generalized additive modeling, GRN inference, and machine learning-based gene panel discovery. This framework enables systematic mapping of cell-state structure, reconstruction of differentiation and effector trajectories, and identification of transcriptional and regulatory features strongly associated with clinical outcomes. As a case study, we applied the pipeline to NK cell transcriptomes from six CML patients (two early relapse, two late relapse, two durable treatment-free remission—TFR; 15 samples) collected at TKI discontinuation and 6–12 months after therapy cessation. Results: We reanalyzed publicly available scRNA-seq data from a previously published CML cohort to evaluate NK-cell transcriptional programs associated with treatment-free remission and relapse. We resolved six transcriptionally distinct NK cell states spanning CD56bright-like cytokine-responsive, early activated, terminally mature, cytotoxic, lymphoid trafficking, and HLA-DR+ immunoregulatory populations, each exhibiting outcome-specific compositional differences. Pseudotime analysis revealed two major NK cell lineages—a maturation trajectory and a cytotoxic effector trajectory. TFR samples displayed balanced occupancy of both lineages, whereas early relapse samples showed marked depletion of the maturation branch and preferential accumulation in cytotoxic end states. AI-guided feature selection and random forest modeling identified an 18-gene panel that distinguished NK cells from TFR and relapse samples in an exploratory manner. Among them, CST7, FCER1G, GNLY, GZMA, and HLA-C were conventional NK-associated genes, whereas ACTB, CYBA, IFITM2, IFITM3, LYZ, MALAT1, MT2A, MYOM2, NFKBIA, PIM1, S100A8, S100B, and TSC22D3 were novel. The GRN inference further uncovered outcome-specific regulatory modules, with RUNX3, EOMES, ELK4, and REL regulons enriched in TFR, whereas FOSL2 and MAF regulons were enriched in relapse, and their downstream targets linked to IFN-γ signaling, metabolic reprogramming, and immunoregulatory feedback circuits. Conclusions: This AI-enabled single-cell analysis demonstrates how NK cell state composition, differentiation trajectories, and regulatory network rewiring collectively shape TFR versus relapse following TKI discontinuation in CML. The integrative pipeline provides a modular framework that could be extended to additional datasets for data-driven biomarker discovery and mechanistic stratification, and highlights candidate transcriptional regulators and NK cell programs that may be leveraged to improve remission durability, pending validation in larger patient cohorts. Full article
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17 pages, 1381 KB  
Article
Effects of Dietary Supplementation with α-Mangostin on Oviduct Inflammation and Eggshell Quality in Aging Laying Hens
by Lu Huang, Ruixin Qin, Qianqian Yu, Qili Yan and Desheng Qi
Animals 2026, 16(7), 1118; https://doi.org/10.3390/ani16071118 - 5 Apr 2026
Viewed by 830
Abstract
This study investigated the effects of dietary supplementation with α-mangostin (α-Ma), a bioactive xanthone derived from mangosteen pericarp, on production performance and egg quality in late-phase laying hens. The experiment was conducted using a completely randomized design. In total, 576 healthy 51-week-old Beinong [...] Read more.
This study investigated the effects of dietary supplementation with α-mangostin (α-Ma), a bioactive xanthone derived from mangosteen pericarp, on production performance and egg quality in late-phase laying hens. The experiment was conducted using a completely randomized design. In total, 576 healthy 51-week-old Beinong No. 2 laying hens were randomly assigned to 4 dietary treatments (n = 12): a basal diet (CON) or the basal diet supplemented with 80, 120, or 160 mg/kg α-Ma. The experiment lasted for 4 weeks, after which production performance, egg quality, serum biochemical and antioxidant parameters, inflammatory markers, and uterine gene expression were evaluated. Dietary supplementation with α-mangostin, particularly at 120 mg/kg, significantly improved feed efficiency (p < 0.05), as evidenced by a reduced feed-to-egg ratio from week 2 onward, without affecting average daily feed intake or egg production rate. After 4 weeks, hens receiving 120 mg/kg α-Ma exhibited significantly greater egg weight and eggshell strength (p < 0.05). Serum and hepatic antioxidant capacities were significantly enhanced, with increased glutathione peroxidase and catalase activities, elevated total antioxidant capacity, and decreased malondialdehyde levels (p < 0.05). Moreover, α-Ma at 120 mg/kg specifically lowered the concentration of the pro-inflammatory cytokine interleukin-1β in both serum and uterine tissue (p < 0.05). At the molecular level, this dosage significantly upregulated uterine genes essential for eggshell formation (p < 0.05), including calcium transporters (TRPV6, ATP2B2), the matrix protein gene OC-116, and other key genes (LYZ, CA2, SLC4A9, and ATP6V0D2). In conclusion, dietary supplementation with 120 mg/kg α-Ma effectively enhances feed efficiency, strengthens antioxidant and anti-inflammatory defenses, and upregulates uterine genes involved in biomineralization, thereby improving eggshell quality in aging laying hens. These findings support α-Ma as a promising plant-based feed additive for maintaining productivity and egg quality in antibiotic-free layer production systems. Full article
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22 pages, 2116 KB  
Article
Optimizing Self-Emulsifying Drug Delivery Systems for the Oral Delivery of a Hydrophobic Ion-Paired Lysozyme Complex
by Martin Deák, Nur Aslan, Eslam Ramadan, Katalin Kristó, Gábor Katona and Tamás Sovány
Pharmaceutics 2026, 18(2), 275; https://doi.org/10.3390/pharmaceutics18020275 - 23 Feb 2026
Cited by 1 | Viewed by 1224
Abstract
Background: The oral delivery of biopharmaceuticals remains a major challenge for researchers and the pharmaceutical industry. Therefore, extensive research is ongoing to develop a viable delivery method, hence self-emulsifying drug delivery systems (SEDDSs) are being investigated because of their ability to protect [...] Read more.
Background: The oral delivery of biopharmaceuticals remains a major challenge for researchers and the pharmaceutical industry. Therefore, extensive research is ongoing to develop a viable delivery method, hence self-emulsifying drug delivery systems (SEDDSs) are being investigated because of their ability to protect the carried macromolecules in the gastrointestinal environment and facilitate absorption through the intestinal barrier. Objectives: To systematically investigate this promising method for the oral delivery of lysozyme (LYZ) and to model oral peptide/protein administration. Methods: LYZ/sodium dodecyl sulfate (SDS) hydrophobic ion pairs (HIPs) were prepared to enhance protein solubility and stability in SEDDSs. Different surfactants (Tween® 20 and 80) and as co-surfactants (Span® 20 and 80) were combined for the preparation of liquid SEDDSs according to a 22 full factorial design and samples of each combination were formulated based on a three-factor-constrained mixture design. The critical quality attributes (CQAs), droplet size, polydispersity index (PDI), and zeta potential were measured by dynamic light scattering (DLS). The process design space was determined by response surface methodology (RSM) and two-dimensional ternary contour plots. An in vitro release test was performed using the sample-and-separate approach. Results: Emulsions of SEDDSs with the optimal properties of droplet size < 200 nm, PDI < 0.4 and zeta potential < −10 mV were prepared. Consequently, a HIP load of 10 mg/g was achievable, exhibiting apparent first-order kinetics, with approximately 80% of the loaded LYZ released within 6 h. Conclusions: This study may contribute to better understanding of the effects and interactions of formulating materials for SEDDSs and their possible role in the oral delivery of biopharmaceuticals. Full article
(This article belongs to the Section Drug Delivery and Controlled Release)
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14 pages, 9918 KB  
Article
Iron Deficiency Inhibits the Proliferation of Intestinal Stem Cells and Induces Their Differentiation to Enterocytes
by Yecheng Xu, Jing Zhao, Shouchuan Jiang, Yu Han, Yi Zheng, Xi Qiao, Xin Wen, Yuanyuan Zhang, Yunqin Li, Jingxia Kong and Huahua Du
Nutrients 2026, 18(3), 392; https://doi.org/10.3390/nu18030392 - 24 Jan 2026
Cited by 1 | Viewed by 742
Abstract
Objectives: Iron deficiency impairs intestinal mucosal structure and function, yet its impact on intestinal stem cells (ISCs) remains unclear. This study was therefore designed to examine how iron deficiency affects the proliferation and differentiation of ISCs. Methods: Iron-deficient mouse and enteroid [...] Read more.
Objectives: Iron deficiency impairs intestinal mucosal structure and function, yet its impact on intestinal stem cells (ISCs) remains unclear. This study was therefore designed to examine how iron deficiency affects the proliferation and differentiation of ISCs. Methods: Iron-deficient mouse and enteroid models were established. Expression of key cell markers was analyzed using Western blot, qPCR, and immunofluorescence. Results: Iron deficiency led to structural impairment of the intestinal mucosa, characterized by decreased small intestinal villus height. In iron-deficient mice, expression of ChrA (enteroendocrine cell marker), Lyz (Paneth cell marker), and Muc2 (goblet cell marker) was significantly downregulated across duodenum, jejunum and ileum, whereas Vil1 (enterocyte marker) expression increased. Moreover, both Lgr5 (an ISC marker) expression and the number of Ki67-positive proliferating cells were significantly reduced, along with a decrease in Ki67 transcriptional levels under iron-deficient conditions. Similarly, deferoxamine (DFO)-treated enteroids showed fewer Lgr5-positive ISCs, downregulation of Lgr5, Lyz and Muc2, and upregulation of Vil1. RNA-seq further confirmed that iron deficiency skews ISC differentiation toward absorptive lineage. This shift was associated with modulation of the Notch signaling pathway: upregulation of the ligand Dll1, receptors Notch2 and Notch3, and the protease ADAM10, alongside downregulation of the negative regulator Atoh1. These findings indicate that Notch pathway activation promotes enterocyte differentiation under iron deprivation. Conclusions: Iron deficiency suppressed the proliferation of ISCs and induced their differentiation toward enterocytes, which is associated with the modulation of the Notch signaling pathway, providing a mechanistic insights for impaired intestinal repair and the potential for nutrient-targeted therapies. Full article
(This article belongs to the Special Issue Iron Supplements and Intestinal Health)
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31 pages, 3950 KB  
Article
Effects of Red Kojic Rice Supplementation on Growth, Immunity, Antioxidant Capacity, and Intestinal Health of Litopenaeus vannamei Fed a Diet with Fish Meal Replacement by Soybean Meal
by Qianping Huang, Hongkai Ye, Zhanzhan Wang, Bo Liu, Min Yang, Xiaobin Chen, Shengli Liu and Chuanpeng Zhou
Fishes 2026, 11(1), 58; https://doi.org/10.3390/fishes11010058 - 16 Jan 2026
Viewed by 563
Abstract
This study aimed to investigate the effects of adding Red kojic rice (RKR) on the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of Litopenaeus vannamei fed a diet with fishmeal replacement by soybean meal. Shrimps (initial mean weight [...] Read more.
This study aimed to investigate the effects of adding Red kojic rice (RKR) on the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of Litopenaeus vannamei fed a diet with fishmeal replacement by soybean meal. Shrimps (initial mean weight = 1.88 ± 0.03 g) were fed six experimental diets for 8 weeks, including a normal fishmeal control group (FM), a soybean meal-replaced fishmeal group (H0), and four soybean meal-replaced fishmeal groups supplemented with 0.5%, 1%, 2%, and 4% RKR, respectively, which are designated as H1, H2, H3, and H4, respectively. Each group had three replicates, with 30 shrimp per replicate. The results showed that the final average weight (FWG), weight gain rate (WG), and specific growth rate (SGR) of H2 group were significantly higher than those of H0, H3, and H4 groups (p < 0.05). The feed conversion ratio (FCR) of H2 group was significantly lower than that of H0 and H4 groups (p < 0.05). In contrast to the H0 group, the blood ACP activity in the H2 group was significantly increased (p < 0.05). The blood lysozyme (LYZ) activity in H3 group was significantly higher than that in H1 group (p < 0.05), while the opposite was true for phenoloxidase (PO). The activities of trypsin and amylase in hepatopancreas of H3 group were significantly higher than those of H0 and H1 groups (p < 0.05). Compared with the FM group, the hepatopancreatic malondialdehyde (MDA) levels in H0, H3, and H4 groups were significantly increased (p < 0.05). Compared with the H0 group, the hepatopancreatic MDA levels in H1 and H2 groups were significantly decreased (p < 0.05). Analysis of gene expression levels in hepatopancreas revealed that antioxidant (gpx, sod, cat, gst, nrf2, trx, and ho-1), non-specific immune (tnf-α, il-1β, and ifn-γ), and digestive (trypsin and α-amylase) genes were suppressed in the H0 group but enhanced by RKR supplementation. Similar expression patterns of those genes were observed in the intestine. Microbial community analysis showed reduced diversity and altered composition in the H0 group, which were partially restored by RKR. Network analysis showed “small-world” property in microbial co-occurrence network. Metabolomic analysis revealed that among the differential metabolites, Bismurrayaquinone A and Harmol exhibit highly significant differences. Correlation analysis revealed that beneficial bacteria Rhodococcus_C and Oceanobacillus in H2 group exhibited higher richness and showed significant correlation. In conclusion, supplementation of 0.5–2% RKR promoted the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of shrimp fed a diet with fishmeal replacement by soybean meal. The optimal RKR supplementing content is 1%. Full article
(This article belongs to the Section Nutrition and Feeding)
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19 pages, 3075 KB  
Article
Multi-Omics Mechanism of Chronic Gout Arthritis and Discovery of the Thyroid Hormone–AMPK–Taurine Metabolic Axis
by Guizhen Zhu, Yuan Luo, Xiangyi Zheng, Zhusong Mei, Qiao Ye, Jie Peng, Fengsen Duan, Yueying Cui, Peiyu An, Yangqian Song, Hongxia Li, Haitao Zhang and Guangyun Wang
Cells 2026, 15(1), 41; https://doi.org/10.3390/cells15010041 - 25 Dec 2025
Cited by 1 | Viewed by 1665
Abstract
The acute gouty arthritis (AGA) to chronic gouty arthritis (CGA) transition is a critical phase leading to irreversible joint damage and systemic complications. However, current molecular mechanism investigations have remained limited to single-omics approaches that lack comprehensive multi-omics explorations. We integrate high-depth data-independent [...] Read more.
The acute gouty arthritis (AGA) to chronic gouty arthritis (CGA) transition is a critical phase leading to irreversible joint damage and systemic complications. However, current molecular mechanism investigations have remained limited to single-omics approaches that lack comprehensive multi-omics explorations. We integrate high-depth data-independent acquisition (DIA) proteomics and untargeted metabolomics to analyze serum samples from healthy controls (n =28), AGA (n = 31), and CGA (n = 14) patients to address this gap. Through differential expression analysis, we identified nine persistently dysregulated pivotal proteins with robust discriminative capacity, including the urate excretion regulator ZBTB20 and inflammation/immune-related proteins (GUCY1A2, CNDP1, LYZ, SERPINA5, GSN). Additionally, 11 consistently altered core metabolites with diagnostic potential were detected, indicating perturbations in sex hormones, thyroid hormones, gut microbiota-derived metabolites, environmental exposures, and nutritional factors. Multi-omics KEGG enrichment analysis highlighted thyroid hormone synthesis, AMPK signaling pathway, and taurine and hypotaurine metabolism as central pathways. Correlation network analysis further revealed significant immune dysregulation, illustrating an evolution from acute immune activation to chronic inflammation during AGA-to-CGA progression. Our study establishes that a coordinated disruption of the thyroid hormone–AMPK–taurine metabolic axis and concomitant immune microenvironment remodeling is associated with chronic gout development. These findings provide critical targets for developing early diagnostic indicators and targeted interventions for CGA. Full article
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18 pages, 5390 KB  
Article
LYZ Gene as a Novel Therapeutic Target and Diagnostic Biomarker in Glioblastoma: Insights from Multi-Omics Analysis and Functional Validation
by Nuoyan Zhu, Jiahui Wang and Liangliang Cai
Biology 2026, 15(1), 9; https://doi.org/10.3390/biology15010009 - 19 Dec 2025
Viewed by 850
Abstract
Immune checkpoint blockade is one of the current treatments for glioblastoma (GBM), which is still a very aggressive and treatment-resistant tumor of the central nervous system. This study focused on the LYZ gene to find new therapeutic targets. We performed a thorough screening [...] Read more.
Immune checkpoint blockade is one of the current treatments for glioblastoma (GBM), which is still a very aggressive and treatment-resistant tumor of the central nervous system. This study focused on the LYZ gene to find new therapeutic targets. We performed a thorough screening of differential gene expressions between GBM and normal samples using many databases (TCGA, GTEx, GEO, and CGGA). Because LYZ is significantly upregulated in GBM tissues and is associated with shorter patient survival periods, we identified it as a gene of interest. LYZ’s position on the exterior side of the plasma membrane and its participation in leukocyte-mediated immunity were identified by functional enrichment analysis, indicating a role in cell surface immune responses. Significant associations between LYZ expression and particular immune cell types were found using immune infiltration analysis, suggesting that LYZ may have an impact on the tumor microenvironment. Within GBM, single-cell research verified LYZ expression in macrophages and monocytes. LYZ was shown to express differently in GBM cell lines than in normal glial cells, according to cellular experimental verification. The LYZ gene’s functional importance in the pathophysiology of GBM was highlighted by the dramatic reduction in cell proliferation, motility, and invasion that resulted from its knockout. These results suggest that LYZ is a viable therapeutic target and possible GBM diagnostic biomarker, which calls for more research into its mechanisms of action and potential clinical use. Full article
(This article belongs to the Section Medical Biology)
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27 pages, 6972 KB  
Article
Integrated Multi-Omics and Independent Validation Reveal MPO and TREM2 as Secretory Biomarkers for Non-Healing Diabetic Foot Ulcers
by Boya Li, Tianbo Li, Jiangning Wang and Lei Gao
Genes 2025, 16(12), 1419; https://doi.org/10.3390/genes16121419 - 28 Nov 2025
Cited by 2 | Viewed by 1121
Abstract
Background: Diabetic foot ulcers (DFUs) are chronic wounds with high morbidity and mortality. Secretory proteins coordinate intercellular communication and may regulate inflammation, tissue repair and regeneration, but their contributions to DFU pathogenesis remain unclear. Aim: To discover and validate secretory protein–linked biomarkers [...] Read more.
Background: Diabetic foot ulcers (DFUs) are chronic wounds with high morbidity and mortality. Secretory proteins coordinate intercellular communication and may regulate inflammation, tissue repair and regeneration, but their contributions to DFU pathogenesis remain unclear. Aim: To discover and validate secretory protein–linked biomarkers that distinguish non-healing DFUs and to explore their potential utility for diagnosis and therapy. Methods: We integrated bulk RNA-sequencing datasets (GSE199939 training set; GSE80178 and GSE143735 validation sets) and a single-cell RNA-sequencing dataset (GSE223964). Differentially expressed genes, secretory protein lists, and weighted gene co-expression networks were intersected to select candidates. Functional enrichment, protein interaction networks and support vector machine–recursive feature elimination identified key markers. We visualized their cell-type distribution at single-cell resolution and validated their expression in external cohorts. Pathway enrichment, gene co-expression networks, ceRNA regulatory analysis and qRT-PCR in patient samples were used for further characterization. Results: Among 4803 differentially expressed genes, 743 overlapped with known secretory proteins. WGCNA highlighted modules strongly associated with DFUs, yielding 386 candidates. SVM-RFE combined with protein interaction analysis pinpointed four secretory proteins—LYZ, MPO, SLCO2B1 and TREM2—as putative biomarkers. Single-cell analyses showed that MPO, LYZ, SLCO2B1 and TREM2 transcripts are detectable in multiple skin-resident and immune cell populations, and that the DFU-associated upregulation of MPO and LYZ is most pronounced within keratinocyte clusters, while MPO and TREM2 remained consistently dysregulated in independent bulk cohorts. MPO-associated genes were enriched for immune and inflammatory pathways, whereas TREM2-linked genes implicated cell cycle and cytoskeletal regulation. GeneMANIA and ceRNA analyses revealed extensive interaction networks. qRT-PCR confirmed differential expression of MPO and TREM2 in clinical DFU tissues. Conclusions: Integrated multi-modal analysis identifies secretory proteins, particularly MPO and TREM2, as central determinants of impaired healing in DFUs. These molecules and their regulatory networks represent promising biomarkers and therapeutic targets for precision management of diabetic wounds. Full article
(This article belongs to the Section Bioinformatics)
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22 pages, 4209 KB  
Article
Physicochemical Properties Determination of Recombinant Human Lysozyme and Its Effects on Intestinal Development in Mice
by Ruwei Liu, Qin An, Yunxia Zou, Zhuoxing Zhang, Qinyong Meng, Wentian Yue, Wenwen Dong and Yali Zhang
Nutrients 2025, 17(23), 3730; https://doi.org/10.3390/nu17233730 - 28 Nov 2025
Viewed by 1041
Abstract
Background/Objectives: Breast milk lysozyme is crucial for infant intestinal health. The low breastfeeding rate has driven the investigation of alternatives like hen egg white lysozyme (HEWL) for infant formula supplementation. However, HEWL differs significantly from human lysozyme. This study aimed to systematically [...] Read more.
Background/Objectives: Breast milk lysozyme is crucial for infant intestinal health. The low breastfeeding rate has driven the investigation of alternatives like hen egg white lysozyme (HEWL) for infant formula supplementation. However, HEWL differs significantly from human lysozyme. This study aimed to systematically compare the functional efficacy of recombinant human lysozyme (rhLYZ) and HEWL to assess their suitability as formula supplements. Methods: The physicochemical properties (enzymatic activity, optimal pH, thermal stability) of rhLYZ and HEWL were analyzed. Biological functions were evaluated using HT-29 intestinal cells for proliferation, differentiation, and protection against lipopolysaccharide-induced damage. In vivo effects on growth, intestinal morphology, and gene expression were assessed in a mouse pup model via transcriptomic analysis. Gut microbiota composition was also examined. Results: rhLYZ exhibited twice the enzymatic activity of HEWL, with an optimal pH of 6.0. In cellular models, rhLYZ enhanced intestinal epithelial differentiation at low concentrations. In vivo, rhLYZ supplementation significantly improved pup body weight, intestinal maturity, and villus-to-crypt ratios, outperforming HEWL. Transcriptomics revealed rhLYZ upregulated broad-spectrum antimicrobial peptides (e.g., Defa, lactoferrin) and immune-related genes, whereas HEWL induced a narrower antibacterial response and downregulated key defensins. Furthermore, rhLYZ significantly increased gut microbiota diversity and enriched beneficial butyrate-producing bacteria. Conclusions: rhLYZ more effectively mimics human milk lysozyme by promoting intestinal development, broad-spectrum immunity, and a balanced microbiota. HEWL shows a narrower functional profile. These findings provide a scientific basis for optimizing lysozyme selection in infant formula, highlighting the superior potential of rhLYZ. Full article
(This article belongs to the Section Pediatric Nutrition)
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22 pages, 4445 KB  
Article
Downregulation of Enteroendocrine Genes Predicts Survival in Colon Cancer: A Bioinformatics-Based Analysis
by Eloisa Martins da Silva, Marcella Cipelli, Mariana Abrantes do Amaral, Alvaro Pacheco-Silva, Niels O. S. Câmara and Vinicius Andrade-Oliveira
Int. J. Mol. Sci. 2025, 26(22), 11127; https://doi.org/10.3390/ijms262211127 - 18 Nov 2025
Viewed by 1237
Abstract
Colorectal cancer (CRC) is the fourth most common and the third mostly deadly cancer globally. Even with alternative therapies, some patients do not respond to treatment. Identifying modulations in the tumor microenvironment (TME) of CRC is a significant challenge due to the complex [...] Read more.
Colorectal cancer (CRC) is the fourth most common and the third mostly deadly cancer globally. Even with alternative therapies, some patients do not respond to treatment. Identifying modulations in the tumor microenvironment (TME) of CRC is a significant challenge due to the complex and dynamic nature of the TME. The intestinal epithelium comprises different types of secretory lineage cells, including goblet, tuft, Paneth, and enteroendocrine cells (EECs). Yet the relevance of each subtype of secretory intestinal epithelial cell (IEC) within the TME is still debated. This study investigated the involvement of IECs in CRC development through an integrative bioinformatics analysis. We used publicly available datasets from the National Center for Biotechnology Information, the Cancer Genome Atlas Program, and the National Cancer Institute’s Proteomics Tumor Analysis Consortium, encompassing both human and mouse CRC samples. Our findings reveal a CRC microenvironment characterized by elevated expression levels of genes associated with WNT pathway activity. Remarkably, there was increased expression of Paneth cell-associated markers and transcription factors, such as WISP1, LYZ, SOX9, and DEFA1. Conversely, EEC-specific gene markers, such as GCG (encoding glucagon-like peptide-1) and CHGA exhibited significant downregulation in CRC tissue compared with healthy tissue, partially due to Paneth cell activity. Gene ontology analysis showed species-conserved downregulation in hormone/peptide secretion-related pathways in both mouse and human CRC. Of note, lower levels of GCG and CHGA correlated with reduced overall survival and demonstrated a correlation with the cell cycle, apoptosis, and proliferation. These results suggest that the disruption of enteroendocrine cell signaling is a hallmark of CRC development and may hold prognostic and therapeutic value in treating CRC patients. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Oncology in Brazil, 3rd Edition)
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21 pages, 1778 KB  
Article
Immune Protective Effect of Chitosan Oligosaccharide on Lipopolysaccharide-Stimulated Coelomocytes of Sea Cucumber Apostichopus japonicus In Vitro
by Rongyue Wang, Xiaoyu Nie, Xiaofan Li, Jinwei Tang, Chong Huang and Juan Liu
Polymers 2025, 17(20), 2752; https://doi.org/10.3390/polym17202752 - 14 Oct 2025
Viewed by 1422
Abstract
In recent years, chitosan oligosaccharide (COS) has demonstrated promising applications in enhancing the immune protective function of sea cucumbers. However, the immune-protective effect of COS on sea cucumber coelomocytes in vitro remains unclear. This study investigated the effect of COS on lipopolysaccharide (LPS)-stimulated [...] Read more.
In recent years, chitosan oligosaccharide (COS) has demonstrated promising applications in enhancing the immune protective function of sea cucumbers. However, the immune-protective effect of COS on sea cucumber coelomocytes in vitro remains unclear. This study investigated the effect of COS on lipopolysaccharide (LPS)-stimulated inflammation in sea cucumber coelomocytes. First, we measured the effects of COS and LPS on the viability of coelomocytes. COS exhibited no toxic effects on sea cucumber coelomocytes. Furthermore, pre-incubating the coelomocytes with COS significantly improved coelomocytes’ viability after LPS stimulation (p < 0.05). Secondly, the phagocytic activity and respiratory burst of the coelomocytes were assessed to evaluate their immune levels. COS alone significantly increased the respiratory burst and phagocytic activity of the coelomocytes (p < 0.05). However, with LPS stimulated, COS significantly increased both the respiratory burst and phagocytic activity of the coelomocytes. The activities of lysozyme (Lyz), total nitric oxide synthase (T-NOSs), and superoxide dismutase (SOD) in sea cucumber coelomocytes were measured to evaluate their response to LPS stimulation. The results indicated that LPS stimulation significantly increases the activities of Lyz, T-NOSs, and SOD in sea cucumber coelomocytes (p < 0.05). Additionally, it was found that COS could inhibit the LPS-mediated expression of Lyz, T-NOSs, and SOD activities in the coelomocytes (p < 0.05). Furthermore, the relative expression of six immune-related genes—Aj-IL-17, Aj-TNF-α, Aj-i-Lys, Aj-NOS, Aj-Rel, Aj-P105—were analyzed in the coelomocytes stimulated by LPS after being cultured with COS. Finally, through transcriptomic technology analysis, it was determined that COS primarily alleviates LPS-induced inflammation via the tumor necrosis factor signaling pathway and the phagosome signaling pathway. The findings demonstrated that COS inhibited the expression of immune genes in sea cucumber coelomocytes in a dose-dependent manner. In summary, pretreatment with chitosan oligosaccharides appears to confer an immune protective role in LPS-stimulated sea cucumber coelomocytes. Full article
(This article belongs to the Section Biobased and Biodegradable Polymers)
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22 pages, 3221 KB  
Article
Pharmacokinetic Profiling Using 3H-Labeled Eggshell Membrane and Effects of Eggshell Membrane and Lysozyme Oral Supplementation on DSS-Induced Colitis and Human Gut Microbiota
by Miho Shimizu, Wataru Sugai, Eri Ohto-Fujita, Aya Atomi, Norio Nogawa, Koichi Takamiya, Hisao Yoshinaga, Yoshihide Asano, Takashi Yamashita, Shinichi Sato, Atsushi Enomoto, Nozomi Hatakeyama, Shunsuke Yasuda, Kazuya Tanaka, Tomoaki Atomi, Kenji Harada, Yukio Hasebe, Toshiyuki Watanabe and Yoriko Atomi
Int. J. Mol. Sci. 2025, 26(18), 9102; https://doi.org/10.3390/ijms26189102 - 18 Sep 2025
Viewed by 2535
Abstract
Eggshell membrane (ESM) is composed of approximately 90% protein. Our previous studies in healthy adults demonstrated that two months of daily ESM intake improved respiratory function, zigzag walking speed, and skin elasticity. The present study aims to address the knowledge gap regarding the [...] Read more.
Eggshell membrane (ESM) is composed of approximately 90% protein. Our previous studies in healthy adults demonstrated that two months of daily ESM intake improved respiratory function, zigzag walking speed, and skin elasticity. The present study aims to address the knowledge gap regarding the in vivo effects of ESM in the context of inflammatory bowel disease (IBD). Proteomic analysis was performed on powdered ESM used as a dietary supplement. To investigate its pharmacokinetics in mice, tritium (3H)-labeled ESM was prepared using the 6Li(n,α)3H nuclear reaction. The therapeutic potential of ESM was further examined in a 2.0% dextran sulfate sodium (DSS)-induced murine model of IBD. In addition, fecal samples from both mice and healthy human subjects were analyzed using a modified terminal restriction fragment length polymorphism (T-RFLP) method. Lysozyme C (LYZ) was the most abundant protein (47%), followed by lysyl oxidase (12%) in ESM used in this study. 3H-ESM was mixed with MediGel, and orally administered to mice. Radioactivity levels were measured in blood, organs (duodenum, small intestine, large intestine, liver, kidney, lung, skin), and rectal feces at 0.5, 2, 5, 24, 48, and 72 h post-administration. Radioactivity in feces indicated excretion of undigested components, while systemic distribution suggested potential whole-body effects of ESM. Oral ESM and LYZ significantly alleviated body weight loss, diarrhea, and hematochezia in a DSS-induced murine model of IBD, leading to a significantly lower disease activity index on day 3 and showing a similar trend on day 5. Gut microbiota analysis showed increased Bacteroidales in the DSS group, while the ESM + DSS group maintained levels similar to the control. In humans, a double-blind, randomized controlled trial was conducted to evaluate the effects of ESM on gut microbiota in healthy adults. Participants received either ESM or placebo for 8 weeks. revealed a significant increase in alpha diversity at weeks 1 and 8 in the ESM group (p < 0.05), with between-group differences evident from week 1 (p < 0.01). ESM intake reduced Bacteroides and significantly increased Bifidobacterium and Lactobacillales at weeks 4 and 8. These findings suggest ESM supplementation promotes beneficial modulation of gut microbiota. These findings suggest that ESM, through its major protein components such as LYZ, may serve as a promising dietary intervention for maintaining intestinal health and mitigating inflammation in the context of IBD. Full article
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25 pages, 2451 KB  
Article
Complexation and Thermal Stabilization of Protein–Polyelectrolyte Systems via Experiments and Molecular Simulations: The Poly(acrylic acid)/Lysozyme Case
by Sokratis N. Tegopoulos, Sisem Ektirici, Vagelis Harmandaris, Apostolos Kyritsis, Anastassia N. Rissanou and Aristeidis Papagiannopoulos
Polymers 2025, 17(15), 2125; https://doi.org/10.3390/polym17152125 - 1 Aug 2025
Cited by 2 | Viewed by 1688
Abstract
Protein–polyelectrolyte nanostructures assembled via electrostatic interactions offer versatile applications in biomedicine, tissue engineering, and food science. However, several open questions remain regarding their intermolecular interactions and the influence of external conditions—such as temperature and pH—on their assembly, stability, and responsiveness. This study explores [...] Read more.
Protein–polyelectrolyte nanostructures assembled via electrostatic interactions offer versatile applications in biomedicine, tissue engineering, and food science. However, several open questions remain regarding their intermolecular interactions and the influence of external conditions—such as temperature and pH—on their assembly, stability, and responsiveness. This study explores the formation and stability of networks between poly(acrylic acid) (PAA) and lysozyme (LYZ) at the nanoscale upon thermal treatment, using a combination of experimental and simulation measures. Experimental techniques of static and dynamic light scattering (SLS and DLS), Fourier transform infrared spectroscopy (FTIR), and circular dichroism (CD) are combined with all-atom molecular dynamics simulations. Model systems consisting of multiple PAA and LYZ molecules explore collective assembly and complexation in aqueous solution. Experimental results indicate that electrostatic complexation occurs between PAA and LYZ at pH values below LYZ’s isoelectric point. This leads to the formation of nanoparticles (NPs) with radii ranging from 100 to 200 nm, most pronounced at a PAA/LYZ mass ratio of 0.1. These complexes disassemble at pH 12, where both LYZ and PAA are negatively charged. However, when complexes are thermally treated (TT), they remain stable, which is consistent with earlier findings. Atomistic simulations demonstrate that thermal treatment induces partially reversible structural changes, revealing key microscopic features involved in the stabilization of the formed network. Although electrostatic interactions dominate under all pH and temperature conditions, thermally induced conformational changes reorganize the binding pattern, resulting in an increased number of contacts between LYZ and PAA upon thermal treatment. The altered hydration associated with conformational rearrangements emerges as a key contributor to the stability of the thermally treated complexes, particularly under conditions of strong electrostatic repulsion at pH 12. Moreover, enhanced polymer chain associations within the network are observed, which play a crucial role in complex stabilization. These insights contribute to the rational design of protein–polyelectrolyte materials, revealing the origins of association under thermally induced structural rearrangements. Full article
(This article belongs to the Section Polymer Physics and Theory)
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