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19 pages, 7431 KB  
Article
Systems Pharmacology and Multi-Omics Elucidation of Irpex lacteus Polysaccharides in the Treatment of Lupus Nephritis Through PI3K/AKT/NF-κB Pathway Inhibition
by Guoxin Ji, Zhuangzhuang Yao, Yuetong Zhao, Cuicui Li, Bo Yang, Zhimeng Li, Mingfang Kuang, He Wang, Xian Wu, Huiyang Yuan, Yue Deng, Shumin Wang and Huan Wang
Pharmaceuticals 2025, 18(11), 1619; https://doi.org/10.3390/ph18111619 (registering DOI) - 27 Oct 2025
Abstract
Background: Lupus nephritis (LN), a severe complication of systemic lupus erythematosus (SLE), necessitates effective therapeutic strategies. Polysaccharides derived from Irpex lacteus have demonstrated beneficial biological activities in MRL/lpr mice; however, their precise mechanisms of intervention in LN require further elucidation. Methods: MRL/lpr mice [...] Read more.
Background: Lupus nephritis (LN), a severe complication of systemic lupus erythematosus (SLE), necessitates effective therapeutic strategies. Polysaccharides derived from Irpex lacteus have demonstrated beneficial biological activities in MRL/lpr mice; however, their precise mechanisms of intervention in LN require further elucidation. Methods: MRL/lpr mice were administered low-dose and high-dose Irpex lacteus polysaccharide (PCP) continuously for 8 weeks. The therapeutic efficacy of PCP was systematically assessed by measuring autoantibody levels, inflammatory cytokine expression, and renal function markers. The underlying pharmacological mechanisms were investigated through integrated transcriptomics and metabolomics analyses. Results: PCP treatment significantly improved renal function in MRL/lpr mice, normalizing serum levels of anti-nuclear antibodies (ANA), anti-double-stranded DNA antibodies (anti-dsDNA), anti-Sm antibody (Sm), creatinine (Cr), blood urea nitrogen (BUN), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and proteinuria. Integrated transcriptomic and metabolomic analyses revealed that the therapeutic action of PCP involves modulation of the PI3K/AKT/NF-κB pathway. This inhibition was further confirmed by Western blot analysis. Conclusions: PCP exerts renal protective effects in MRL/lpr mice by mitigating inflammation, modulating immune responses, and preserving renal function. The combined application of transcriptomics, metabolomics, and Western blotting elucidates that this protection is mediated through inhibition of the PI3K/AKT/NF-κB signaling pathway. Full article
(This article belongs to the Section Pharmacology)
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23 pages, 3235 KB  
Article
Green-Synthesized Silver Nanoparticles from Garlic Peel Target NF-κB and Redox Imbalance: A Novel Therapeutic Strategy Against Pyrogallol-Induced Hepatotoxicity in Rats
by Duaa A. Althumairy
Nanomaterials 2025, 15(21), 1610; https://doi.org/10.3390/nano15211610 - 22 Oct 2025
Viewed by 290
Abstract
Background/Objectives: Hepatotoxicity remains a major therapeutic challenge driven by oxidative stress and inflammation. This study investigated the hepatoprotective potential of green-synthesized silver nanoparticles derived from ethanolic garlic peel extract (GPE-Ag) against pyrogallol-induced liver injury. Methods: Adult rats were randomly assigned into four groups: [...] Read more.
Background/Objectives: Hepatotoxicity remains a major therapeutic challenge driven by oxidative stress and inflammation. This study investigated the hepatoprotective potential of green-synthesized silver nanoparticles derived from ethanolic garlic peel extract (GPE-Ag) against pyrogallol-induced liver injury. Methods: Adult rats were randomly assigned into four groups: a control group, a pyrogallol-treated group, a group receiving GPE-Ag nanoparticles (50 mg/kg, orally) for 28 days, and GPE-Ag + pyrogallol co-treated. Results: The garlic peel extract was analyzed by high-performance liquid chromatography (HPLC), revealing high levels of phenolic acids (66.83 µg/g) and flavonoids (59.81 µg/g), predominantly ellagic, gallic, and syringic acids, along with kaempferol, quercetin, and myricetin. The synthesized GPE-Ag nanoparticles were characterized using UV–Vis spectroscopy, transmission and scanning electron microscopy (TEM and SEM), zeta potential, dynamic light scattering (DLS), and energy-dispersive X-ray analysis (EDAX). GPE-Ag treatment markedly attenuated pyrogallol-induced hepatic injury by reducing serum liver enzyme levels, lipid peroxidation, and proinflammatory cytokines, including interleukin-1 (IL-1), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and nuclear factor-kappa B (NF-κB), while enhancing the activities of antioxidant enzymes, catalase (CAT) and glutathione peroxidase (GPx), as well as the anti-inflammatory cytokine interleukin-10 (IL-10). Histological examination further confirmed the restoration of normal hepatic architecture. Conclusion: This study provides the first evidence that garlic peel–derived silver nanoparticles exert potent hepatoprotective effects through redox homeostasis restoration and modulation of the NF-κB signaling pathway. These findings highlight GPE-Ag as a promising, sustainable nanotherapeutic candidate for managing chemically induced liver injury. Full article
(This article belongs to the Section Biology and Medicines)
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18 pages, 1534 KB  
Article
Monoterpenoids from the Roots of Liquidambar formosana (Formosan Sweet Gum) Exhibit Senomorphic Activity Against Cellular Senescence
by Minh Thi Tuyet Le, Quang Huy Vu, Van-Hieu Mai, Jorge Eduardo Ponce-Zea, Seri Choi, Jin-Pyo An and Won-Keun Oh
Nutrients 2025, 17(21), 3321; https://doi.org/10.3390/nu17213321 (registering DOI) - 22 Oct 2025
Viewed by 244
Abstract
Background/objectives: Cellular senescence is a hallmark of aging that contributes to tissue dysfunction and age-related diseases. This process is characterized by the activation of the cyclin-dependent kinase inhibitor p16INK4A and the secretion of pro-inflammatory factors collectively known as the senescence-associated secretory phenotype [...] Read more.
Background/objectives: Cellular senescence is a hallmark of aging that contributes to tissue dysfunction and age-related diseases. This process is characterized by the activation of the cyclin-dependent kinase inhibitor p16INK4A and the secretion of pro-inflammatory factors collectively known as the senescence-associated secretory phenotype (SASP). In this study, we used human lung-derived cells, including A549 and IMR90 fibroblasts, to identify bioactive compounds from the roots of Liquidambar formosana that suppress p16INK4A activity and attenuate SASP expression. Methods: Bioactivity-guided isolation was performed to obtain target compounds. The structures of the new compounds were elucidated using extensive 1D and 2D NMR spectroscopic analyses as well as high-resolution mass spectrometry. All isolated compounds were evaluated for their ability to inhibit p16INK4A, a key regulator of the cell cycle and an important tumor suppressor protein. Results: Two previously undescribed monoterpenoids (1 and 2), characterized as cinnamic acid esters with a monoterpene-derived core, were isolated from the roots of L. formosana, along with six known compounds (38). Notably, compound 3 exhibited promising inhibition of p16INK4A with an IC50 value of 3.9 μM. Furthermore, this compound attenuated the senescence phenotype, as demonstrated by β-galactosidase staining and RT-qPCR analysis. This represents the first report identifying bioactive monoterpenoids from L. formosana that inhibit aging-related biomarkers such as p16INK4A. Conclusions: These results suggest that cinnamic acid-conjugated monoterpenoids may serve as interesting lead structures for the development of agents targeting the p16INK4A pathway for the treatment of aging-associated diseases. Further studies will be required to clarify the mechanisms of action of this compound and to evaluate its in vivo efficacy. Full article
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13 pages, 265 KB  
Communication
Investigation of Metabolites in Feces and Plasma Associated with the Number of Piglets Weaned per Sow per Year
by Takamitsu Tsukahara, Hiroto Miura, Takahiro Kawase, Shu Yoshimura, Yoshihiro Mizukami, Yoshihiro Yahara, Kikuto Fukuta and Ryo Inoue
Metabolites 2025, 15(11), 683; https://doi.org/10.3390/metabo15110683 - 22 Oct 2025
Viewed by 244
Abstract
Background: Sow reproductive performance is a critical parameter for the productivity of commercial pig farms. Gut microbiota is associated with performance in sow reproduction. At least, under healthy conditions, microbial metabolites from the gut microbiota are considered major contributors to host physiological [...] Read more.
Background: Sow reproductive performance is a critical parameter for the productivity of commercial pig farms. Gut microbiota is associated with performance in sow reproduction. At least, under healthy conditions, microbial metabolites from the gut microbiota are considered major contributors to host physiological regulation and productivity. However, information on the differences in gut-derived metabolites related to the sow reproductive performance remain scarce. Our aim was to investigate the relationship between the reproductive performance and microbial metabolite levels in sow’s feces and plasma. Methods: We selected four commercial farms: two with high- (group H) and two with low-reproductive performance (group L). Sows had their feces and blood collected. Results: Except for the iso-butyrate concentration, fecal short-chain fatty acid concentrations remained unchanged between groups. Among intestinal putrefactive metabolites, the indole concentration was higher (p < 0.05) in group H. The concentrations of plasma metabolites p-cresyl sulfate, p-cresyl glucuronide and trimethylamine N-oxide (TMAO) were higher (p < 0.05) in group L than in group H, while the opposite was true for the acetate concentration (p < 0.05). Among plasma biochemicals, tumor necrosis factor (TNF)-alpha and potassium concentrations were higher (p < 0.05) in group L. Conclusions: Blood metabolites, especially gut microbiota-derived metabolites, seemed to be associated with the performance related to sow reproduction. Particularly, harmful metabolites such as p-cresyl glucuronide, p-cresyl sulfate and TMAO were of importance, because they are potentially inflammation factors. In fact, TNF-alpha was stimulated in group L. According to our results, we estimated that p-cresyl glucuronide, p-cresyl sulfate, TMAO and TNF-alpha could be useful physiological indicators to understand sow reproductive performance. Full article
28 pages, 8307 KB  
Article
Design, Synthesis and Biological Evaluation of Pyrazolopyrimidine Derivatives as Aryl Hydrocarbon Receptor Antagonists for Colorectal Cancer Immunotherapy
by Byeong Wook Choi, Jae-Eon Lee, Da Bin Jeon, Pyeongkeun Kim, Gwi Bin Lee, Saravanan Parameswaran, Ji Yun Jang, Gopalakrishnan Chandrasekaran, So Yeon Jeong, Geumi Park, Kyoung-jin Min, Heegyum Moon, Jihyeon Yoon, Yerim Heo, Donggun Kim, Se Hwan Ahn, You Jeong Choi, Seong Soon Kim, Jung Yoon Yang, Myung Ae Bae, Yong Hyun Jeon, Seok-Yong Choi and Jin Hee Ahnadd Show full author list remove Hide full author list
Pharmaceutics 2025, 17(10), 1359; https://doi.org/10.3390/pharmaceutics17101359 - 21 Oct 2025
Viewed by 318
Abstract
Background: Aryl hydrocarbon receptor (AhR) is a transcription factor that is involved in the regulation of immunity. AhR inhibits T cell activation in tumors, which induces immune suppression in the blood and solid tumors. We identified effective small-molecule AhR antagonists for cancer immunotherapy. [...] Read more.
Background: Aryl hydrocarbon receptor (AhR) is a transcription factor that is involved in the regulation of immunity. AhR inhibits T cell activation in tumors, which induces immune suppression in the blood and solid tumors. We identified effective small-molecule AhR antagonists for cancer immunotherapy. Methods: A new series of pyrazolopyrimidine derivatives was synthesized and evaluated for AhR antagonistic activity. Results: Compound 7k exhibited significant antagonistic activity against AhR in a transgenic zebrafish model. In addition, 7k exhibited good AhR antagonist activity, with a half-maximal inhibitory concentration (IC50) of 13.72 nM. Compound 7k showed a good pharmacokinetic profile with an oral bioavailability of 71.0% and a reasonable half-life of 3.77 h. Compound 7k selectively exerted anti-proliferative effects on colorectal cancer cells without affecting normal cells, concurrently suppressing the expression of AhR-related genes and the PD-1/PD-L1 signaling pathway. Compound 7k exhibited potent antitumor activity in syngeneic colorectal cancer models. Importantly, the combination of anti-PD1 and compound 7k enhanced antitumor immunity by augmenting cytotoxic T lymphocyte (CTL)-mediated activity. Conclusions: Collectively, a new pyrazolopyrimidine derivative, 7k, shows promise as a potential therapeutic agent for treating colorectal cancer. Full article
(This article belongs to the Special Issue Small-Molecule Inhibitors for Novel Therapeutics)
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19 pages, 4270 KB  
Article
CGF-Conditioned Medium Modulates Astrocytic Differentiation and Invasiveness in U87MG Glioblastoma Cells
by Laura Giannotti, Benedetta Di Chiara Stanca, Francesco Spedicato, Christian Demitri, Eleonora Stanca, Andrea Palermo, Franco Ferrante, Fabrizio Damiano, Maria Antonietta De Sangro, Luciano Abbruzzese and Luisa Siculella
Biology 2025, 14(10), 1461; https://doi.org/10.3390/biology14101461 - 21 Oct 2025
Viewed by 272
Abstract
Background: Glioblastoma (GBM) is a highly aggressive tumor characterized by elevated plasticity and poor differentiation. Platelet-derived preparations such as Concentrated Growth Factors (CGF) are rich in bioactive molecules, but their effects on tumor biology remain underexplored. Methods: U87MG glioblastoma cells were cultured with [...] Read more.
Background: Glioblastoma (GBM) is a highly aggressive tumor characterized by elevated plasticity and poor differentiation. Platelet-derived preparations such as Concentrated Growth Factors (CGF) are rich in bioactive molecules, but their effects on tumor biology remain underexplored. Methods: U87MG glioblastoma cells were cultured with a conditioned medium obtained from CGF over 14 days (CGF-CM). We analyzed cell viability, morphology, DNA integrity, migration, proliferation, and expression of astrocytic markers. Results: CGF-CM treatment induced early enhancement of cell viability, followed by decreased proliferation and reduced migration at later time points. Morphological analyses revealed astrocyte-like features. The expression of glial fibrillary acidic protein (GFAP), an astrocytic marker, and its α/δ isoform ratio increased over time, while GBM -GBM-associated markers, such as AQP-4 and S100B, were downregulated. Conclusions: Our findings demonstrate that CGF-CM modulates the phenotypic plasticity of U87MG cells and promotes differentiation toward an astroglial-like profile. These results provide a basis for future studies on the modulation of GBM aggressiveness using bioactive autologous derivatives. Full article
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13 pages, 2900 KB  
Article
Multiplexing Proteomic and Ingenuity Pathway Analysis of Attention/Working Memory in Virally Suppressed Women with HIV: A Feasibility Study
by Wei Li, Leah H. Rubin, Yanxun Xu, Yuezhe Wang, Raha Dastgheyb, Travis Ptacek, Ge Wang, Mirjam-Colette Kempf, Jodie A. Dionne, Deborah Konkle-Parker, Daniel Y. Li, Anandi Sheth, Igho Ofotokun and David E. Vance
Diagnostics 2025, 15(20), 2649; https://doi.org/10.3390/diagnostics15202649 - 21 Oct 2025
Viewed by 223
Abstract
Background/Objectives: Individual plasma protein biomarkers have been shown to correlate with cognitive performance in people with HIV (PWH). This study aimed to investigate the association between plasma proteomic signatures and attention/working memory in virologically well-controlled women with HIV (WWH). Methods: Seventy-seven WWH from [...] Read more.
Background/Objectives: Individual plasma protein biomarkers have been shown to correlate with cognitive performance in people with HIV (PWH). This study aimed to investigate the association between plasma proteomic signatures and attention/working memory in virologically well-controlled women with HIV (WWH). Methods: Seventy-seven WWH from three Women’s Interagency HIV Study (WIHS) sites completed neuropsychological (NP) testing and a blood draw. Selected protein biomarkers (200 total) were analyzed using a multiplexing method. Results: Random forest analysis was used to identify the top 10 biomarkers that were each positively or negatively associated with attention/working memory. Ingenuity pathway analysis (IPA) was used to facilitate data interpretation. Tumor necrosis factor receptor 1 (TNF RI), TNF RII, interleukin 1 receptor 1 (IL-1RI), and IL-6R were negatively associated with attention/working memory. Conclusions: Based on the IPA, two gene signaling networks were proposed for associating these plasma protein biomarkers with attention/working memory function. This novel methodology demonstrates how gene networks can be identified using blood draws in conjunction with cognitive assessment, and then used in random forest analysis, to derive value that can be put in IPA. Full article
(This article belongs to the Section Clinical Laboratory Medicine)
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15 pages, 18510 KB  
Article
Bovine β-Casein Peptide YPFPGPIH Regulates Inflammation and Macrophage Activity via TLR/NF-κB/MAPK Signaling
by Junpeng Zhang, Xinyu Zhang, Guangqing Mu, Xiaomeng Wu and Jianping Wu
Foods 2025, 14(20), 3572; https://doi.org/10.3390/foods14203572 - 20 Oct 2025
Viewed by 379
Abstract
Food-derived bioactive peptides are known to possess immunomodulatory properties, although their molecular mechanisms remain incompletely characterized. In this study, we investigated the immunoregulatory effects and underlying mechanisms of YPFPGPIH, a peptide derived from bovine β-casein, using the RAW264.7 macrophage model. Our results demonstrate [...] Read more.
Food-derived bioactive peptides are known to possess immunomodulatory properties, although their molecular mechanisms remain incompletely characterized. In this study, we investigated the immunoregulatory effects and underlying mechanisms of YPFPGPIH, a peptide derived from bovine β-casein, using the RAW264.7 macrophage model. Our results demonstrate that YPFPGPIH enhanced macrophage proliferation and phagocytosis in a dose-dependent manner and promoted chemotactic migration through the upregulation of monocyte chemoattractant proteins MCP-1 and MCP-3. Under lipopolysaccharide (LPS)-induced inflammatory conditions, YPFPGPIH significantly reduced the levels of pro-inflammatory mediators, including interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and nitric oxide (NO), while increasing the production of the anti-inflammatory cytokine interleukin-10 (IL-10), thereby reestablishing cytokine balance. Mechanistic studies revealed that YPFPGPIH inhibited LPS-induced activation of the NF-κB and MAPK pathways, as indicated by reduced nuclear translocation of p65 and decreased phosphorylation of ERK, JNK, and p38. Molecular docking analysis indicated strong binding affinities between YPFPGPIH and Toll-like receptors TLR2 and TLR4, suggesting the involvement of TLR-mediated signaling. Notably, YPFPGPIH downregulated inducible nitric oxide synthase (iNOS) expression and upregulated chemokine mRNA levels, reflecting its dual role in modulating inflammatory and migratory responses. These findings highlight YPFPGPIH as a multifunctional immunomodulatory peptide that fine-tunes macrophage activity through crosstalk between TLR, NF-κB, and MAPK signaling pathways. This study provides new insights for developing peptide-based therapeutics and functional foods aimed at managing inflammatory diseases. Full article
(This article belongs to the Special Issue Milk Bioactive Compounds and Gut Microbiota Modulation)
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13 pages, 1920 KB  
Article
Protaetia brevitarsis seulensis Larvae Extract Attenuates Inflammatory Osteoclast Differentiation and Bone Loss
by Hyun Yang, Dong Ryun Gu, Hye Jin Yang, Wei Li, Younghoon Go, Ra-Yeong Choi, In-Woo Kim and Hyunil Ha
Nutrients 2025, 17(20), 3273; https://doi.org/10.3390/nu17203273 - 17 Oct 2025
Viewed by 298
Abstract
Background/Objectives: The larvae of Protaetia brevitarsis seulensis (PB), an edible insect, exhibit diverse bioactivities, but their effects on inflammatory bone loss remain unclear. We investigated whether a 70% ethanol extract of PB larvae (PBE) suppresses osteoclast differentiation and bone loss under inflammatory conditions. [...] Read more.
Background/Objectives: The larvae of Protaetia brevitarsis seulensis (PB), an edible insect, exhibit diverse bioactivities, but their effects on inflammatory bone loss remain unclear. We investigated whether a 70% ethanol extract of PB larvae (PBE) suppresses osteoclast differentiation and bone loss under inflammatory conditions. Methods: Osteoclast differentiation was assessed in co-cultures of mouse bone marrow cells and osteocytic cells stimulated with interleukin-1 (IL-1). Direct effects on osteoclast precursors were tested in bone marrow–derived macrophages exposed to receptor activator of nuclear factor-κB ligand (RANKL) or tumor necrosis factor-α (TNF-α). Skeletal effects were evaluated in a mouse model of lipopolysaccharide (LPS)-induced bone loss. Results: PBE inhibited IL-1–induced osteoclast differentiation in co-culture, reduced osteocytic RANKL expression and prostaglandin E2 (PGE2) production, and dampened early IL-1 signaling. In osteoclast precursors, PBE directly suppressed osteoclastogenesis driven by RANKL or TNF-α. In vivo, PBE attenuated LPS-induced bone loss and blunted the associated increases in bone RANKL and PGE2. Conclusions: PBE limits inflammatory osteoclastogenesis by downregulating PGE2 and RANKL production in osteoclast-supporting cells and directly inhibiting osteoclast precursor differentiation, thereby attenuating LPS-induced bone loss. These findings identify PBE as a food-derived candidate for managing inflammation-associated bone loss and support further preclinical and nutritional intervention studies. Full article
(This article belongs to the Special Issue Bone-Health-Promoting Bioactive Nutrition)
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27 pages, 6290 KB  
Article
The Role of the Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 in Breast Cancer Pathophysiology
by Lena Habenicht, Nourhan Hassan, Nancy A. Espinoza-Sànchez, Jessica Oyie Sousa Onyeisi, Balázs Győrffy, Lars Hanker, Burkhard Greve and Martin Götte
Cells 2025, 14(20), 1612; https://doi.org/10.3390/cells14201612 - 17 Oct 2025
Viewed by 358
Abstract
The heparan sulfate proteoglycan syndecan-3 (SDC3) is a critical regulator of cell–matrix interactions. While other syndecan family members contribute to the progression of multiple cancers, SDC3’s functional contributions to tumor biology remain largely unexplored. This study investigates the potential role of SDC3 in [...] Read more.
The heparan sulfate proteoglycan syndecan-3 (SDC3) is a critical regulator of cell–matrix interactions. While other syndecan family members contribute to the progression of multiple cancers, SDC3’s functional contributions to tumor biology remain largely unexplored. This study investigates the potential role of SDC3 in the pathogenesis of breast cancer. By conducting an in-silico analysis of publicly available datasets, including TNM-plot, The Human Protein Atlas, and Kaplan–Meier Plotter, we observed that SDC3 is upregulated in breast cancer tissue. Notably, high SDC3 expression correlates with improved relapse-free survival in breast cancer patients. In vitro experiments revealed that SDC3 depletion significantly impairs cell viability, cell-cycle progression, cell migration, and 3D-spheroid-formation in MDA-MB-231 and MCF-7 breast cancer cells. Furthermore, SDC3 depletion results in upregulated gene expression of matrix metalloproteinases (MMP1, MMP9), downregulation of E-cadherin (CDH1), and altered levels of vascular endothelial growth factor A (VEGFA). Activation of proto-oncogene tyrosine-protein kinase Src was inhibited when SDC3 depletion was combined with tissue factor pathway inhibitor treatment. These findings demonstrate that breast cancer cell-derived SDC3 plays a pivotal role in tumor progression. Full article
(This article belongs to the Special Issue Role of Extracellular Matrix in Cancer and Disease)
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20 pages, 5947 KB  
Article
Integrative Single-Cell and Bulk Transcriptomic Analysis Identifies Macrophage-Related Gene Signatures Predictive of Hepatocellular Carcinoma in Cirrhosis 
by Zhongyuan Zhang, Chuisheng Zeng, Xuetong Yong, Wenping Zhou, Yongfang Xie and Jianzhong Shu
Genes 2025, 16(10), 1213; https://doi.org/10.3390/genes16101213 - 15 Oct 2025
Viewed by 510
Abstract
Background/Objectives: Liver cirrhosis is a major global health challenge and a key risk factor for hepatocellular carcinoma (HCC), a malignancy with high mortality due to late diagnosis. This study aimed to integrate single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) [...] Read more.
Background/Objectives: Liver cirrhosis is a major global health challenge and a key risk factor for hepatocellular carcinoma (HCC), a malignancy with high mortality due to late diagnosis. This study aimed to integrate single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) data, using single-cell data to identify macrophage-associated transcriptomic changes during the progression from cirrhosis to HCC, and using bulk data to validate these findings in independent cohorts, while developing predictive models for early risk assessment. Methods: We integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing datasets derived from liver tissues of cirrhosis and HCC patients. Single-cell data were used to identify macrophage subtypes and their dynamic transcriptional changes, while bulk data provided validation in independent cohorts. Gene expression and network analyses were performed, and candidate genes were used to construct diagnostic models with Lasso regression, Random Forest, and Extreme Gradient Boosting (XGBoost). Model performance was evaluated using receiver operating characteristic curves. Results: We identified eleven macrophage-associated genes, among which KLK11, MARCO, CFP, KRT19, GAS1, SOD3, and CYP2C8 were downregulated in HCC, indicating loss of tumor-suppressive and pro-apoptotic functions, while TOP2A, CENPF, MKI67, and NUPR1 were upregulated, reflecting enhanced cell cycle progression, proliferation, and M2 polarization. These are all associated with the progression from liver cirrhosis to HCC. Based on these findings, we established predictive models using Lasso, Random Forest, and XGBoost, which stratified cirrhotic patients into high- and low-risk groups according to cutoff values using liver tissue transcriptomic data. All three models demonstrated high diagnostic performance. Conclusions: This study highlights the critical role of macrophage-associated transcriptomic remodeling in liver disease progression. The machine learning–based predictive models offer a promising approach for early diagnosis and clinical decision-making in patients with cirrhosis. Full article
(This article belongs to the Section Bioinformatics)
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57 pages, 1386 KB  
Article
Bidirectional Endothelial Feedback Drives Turing-Vascular Patterning and Drug-Resistance Niches: A Hybrid PDE-Agent-Based Study
by Zonghao Liu, Louis Shuo Wang, Jiguang Yu, Jilin Zhang, Erica Martel and Shijia Li
Bioengineering 2025, 12(10), 1097; https://doi.org/10.3390/bioengineering12101097 - 12 Oct 2025
Viewed by 527
Abstract
We present a hybrid partial differential equation-agent-based model (PDE-ABM). In our framework, tumor cells secrete tumor angiogenic factor (TAF), while endothelial cells chemotactically migrate and branch in response. Reaction–diffusion PDEs for TAF, oxygen, and cytotoxic drug are coupled to discrete stochastic dynamics of [...] Read more.
We present a hybrid partial differential equation-agent-based model (PDE-ABM). In our framework, tumor cells secrete tumor angiogenic factor (TAF), while endothelial cells chemotactically migrate and branch in response. Reaction–diffusion PDEs for TAF, oxygen, and cytotoxic drug are coupled to discrete stochastic dynamics of tumor cells and endothelial tip cells, ensuring multiscale integration. Motivated by observed perfusion heterogeneity in tumors and its pharmacokinetic consequences, we conduct a linear stability analysis for a reduced endothelial–TAF reaction–diffusion subsystem and derive an explicit finite-domain threshold for Turing instability. We demonstrate that bidirectional coupling, where endothelial cells both chemotactically migrate along TAF gradients and secrete TAF, is necessary and sufficient to generate spatially periodic vascular clusters and inter-cluster hypoxic regions. These emergent patterns produce heterogeneous drug penetration and resistant niches. Our results identify TAF clearance, chemotactic sensitivity, and endothelial motility as effective levers to homogenize perfusion. The model is two-dimensional and employs simplified kinetics, and we outline necessary extensions to three dimensions and saturable kinetics required for quantitative calibration. The study links reaction–diffusion mechanisms with clinical principles and suggests actionable strategies to mitigate resistance by targeting endothelial–TAF feedback. Full article
(This article belongs to the Special Issue Applications of Partial Differential Equations in Bioengineering)
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13 pages, 1381 KB  
Article
Anti-Inflammatory Effects of L-Fucose in 3T3-L1 Adipocytes
by Tomoya Nakamura, Tomohiko Nakao, Kazuyuki Ohara, Yuri Kominami, Miho Ito, Kazuki Mochizuki, Teruki Aizawa, Yusuke Akahori, Tomoya Ueno and Hideki Ushio
Obesities 2025, 5(4), 74; https://doi.org/10.3390/obesities5040074 - 11 Oct 2025
Viewed by 301
Abstract
L-fucose is a monosaccharide derived from brown algae and has potential applications as a functional food ingredient. Previous studies have reported that L-fucose reduces lipid accumulation in murine adipose tissue. Adipose tissue not only regulates energy metabolism but also functions as an endocrine [...] Read more.
L-fucose is a monosaccharide derived from brown algae and has potential applications as a functional food ingredient. Previous studies have reported that L-fucose reduces lipid accumulation in murine adipose tissue. Adipose tissue not only regulates energy metabolism but also functions as an endocrine organ involved in inflammation through the production and secretion of various adipokines. L-fucose is expected to exert anti-inflammatory effects and modulate adipokine secretion in adipocytes. In the present study, we investigated the anti-inflammatory effects of L-fucose in adipocytes. L-fucose significantly suppressed the expression of pro-inflammatory mediators and reduced the production of reactive oxygen species induced by inflammatory stimulation with a combination of lipopolysaccharide (LPS), tumor necrosis factor-⍺ (TNF-⍺), and interferon-γ (IFN-γ). These effects are likely mediated through the inhibition of key signaling pathways, including mitogen-activated protein kinase (MAPK) and nuclear factor-kappa B (NF-κB) pathways. Additionally, we found that L-fucose promoted the multimerization and secretion of high molecular weight (HMW) adiponectin, even under inflammatory conditions. Our results suggest that although L-fucose downregulates adiponectin expression, it contributes to the formation and/or stabilization of HMW adiponectin, which is functionally more relevant in anti-inflammatory and metabolic regulation. L-fucose thus holds promise as a functional food ingredient for mitigating inflammation in adipocytes. Full article
(This article belongs to the Special Issue How to Prevent Obesity and Inflammatory Disease 2025)
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20 pages, 1203 KB  
Review
Central Roles of Glucosylceramide in Driving Cancer Pathogenesis
by Xueheng Zhao and Manoj Kumar Pandey
Int. J. Mol. Sci. 2025, 26(20), 9879; https://doi.org/10.3390/ijms26209879 - 10 Oct 2025
Viewed by 575
Abstract
Glucosylceramide (GlcCer), a central glycosphingolipid derived from ceramide, is increasingly recognized as a bioactive lipid that intersects with key metabolic, inflammatory, and oncogenic pathways. While its dysregulation has long been associated with lysosomal storage disorders such as Gaucher disease (GD), growing evidence implicates [...] Read more.
Glucosylceramide (GlcCer), a central glycosphingolipid derived from ceramide, is increasingly recognized as a bioactive lipid that intersects with key metabolic, inflammatory, and oncogenic pathways. While its dysregulation has long been associated with lysosomal storage disorders such as Gaucher disease (GD), growing evidence implicates GlcCer in cancer initiation and progression, particularly within tumor-predisposing conditions. GlcCer modulates membrane microdomains, intracellular trafficking, and cell signaling, counteracting ceramide-induced apoptosis and promoting cellular survival. In cancer, aberrant upregulation of UDP-glucose ceramide glucosyltransferase (UGCG), the enzyme responsible for GlcCer synthesis, drives tumor growth, metastasis, and multidrug resistance through activation of pathways such as phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), mitogen-activated protein kinase (MAPK), canonical Wnt pathway (Wnt/β-catenin), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways. Specific GlcCer species (e.g., C16:0, C18:0, C24:1) display tissue-dependent functions, adding structural specificity to their oncogenic potential. Moreover, emerging links between GlcCer metabolism and chronic inflammation, oxidative stress, and altered glucose utilization highlight its role as a metabolic node bridging inherited metabolic disorders and malignancy. This review integrates recent advances in GlcCer biology, emphasizing its roles in tumor-predisposing diseases and exploring its potential as a biomarker and therapeutic target in oncology. Full article
(This article belongs to the Section Molecular Oncology)
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Article
Cannabigerol Modulates Cannabinoid Receptor Type 2 Expression in the Spinal Dorsal Horn and Attenuates Neuropathic Pain Models
by Bismarck Rezende, Gabriel Gripp Fernandes, Vitória Macario de Simas Gonçalves, Gabriela Guedes Nascimento, Kethely Lima Marques, Barbara Conceição Costa Azeredo de Oliveira, Yure Bazilio dos Santos, Maria Eduarda Barros de Andrade, Karine Simões Calumbi, Eduardo Perdigão Maia, Luisa Menezes Trefilio, Fernanda Antunes, Fabrícia Lima Fontes-Dantas and Guilherme Carneiro Montes
Pharmaceuticals 2025, 18(10), 1508; https://doi.org/10.3390/ph18101508 - 8 Oct 2025
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Abstract
Background/Objectives: The expanding focus on novel therapeutic pathways for long-term pain relief has directed interest toward compounds obtained from Cannabis sativa. This study evaluated the antinociceptive potential of cannabigerol-enriched extract (CBG) in models of acute and chronic hypernociception, along with morphological outcomes. Methods: [...] Read more.
Background/Objectives: The expanding focus on novel therapeutic pathways for long-term pain relief has directed interest toward compounds obtained from Cannabis sativa. This study evaluated the antinociceptive potential of cannabigerol-enriched extract (CBG) in models of acute and chronic hypernociception, along with morphological outcomes. Methods: Formalin and hot plate tests were used on male Swiss mice to assess acute oral antinociception. To the chronic pain model, 8-week-old male Wistar rats underwent spinal nerve ligation (SNL), and CBG was administered orally by gavage once daily for 14 days. Results: CBG reduced nociceptive responses in the formalin test and hot plate tests, mainly at a dose of 30 mg/kg, showing antinociceptive activity. CBG attenuated SNL-induced thermal and mechanical hypersensitivity, accompanied by reduced microglial density and spinal morphological changes. Importantly, cannabinoid receptor type 2 (CB2R) signaling contributed to the antinociceptive effects of orally administered CBG, whereas cannabinoid receptor type 1 (CB1R), Brain-Derived Neurotrophic Factor (BDNF), and Tumor Necrosis Factor (TNF) did not appear to play major roles under our experimental conditions. Conclusions: Collectively, these findings support CBG as a promising alternative for chronic pain management. Full article
(This article belongs to the Topic Research on Natural Products of Medical Plants)
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