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19 pages, 3457 KiB  
Article
Transcriptome Analysis Revealed the Immune and Metabolic Responses of Grass Carp (Ctenopharyngodon idellus) Under Acute Salinity Stress
by Leshan Ruan, Baocan Wei, Yanlin Liu, Rongfei Mu, Huang Li and Shina Wei
Fishes 2025, 10(8), 380; https://doi.org/10.3390/fishes10080380 - 5 Aug 2025
Viewed by 135
Abstract
Freshwater salinization, an escalating global environmental stressor, poses a significant threat to freshwater biodiversity, including fish communities. This study investigates the grass carp (Ctenopharyngodon idellus), a species with the highest aquaculture output in China, to elucidate the molecular underpinnings of its [...] Read more.
Freshwater salinization, an escalating global environmental stressor, poses a significant threat to freshwater biodiversity, including fish communities. This study investigates the grass carp (Ctenopharyngodon idellus), a species with the highest aquaculture output in China, to elucidate the molecular underpinnings of its physiological adaptations to fluctuating salinity gradients. We used high-throughput mRNA sequencing and differential gene expression profiling to analyze transcriptional dynamics in intestinal and kidney tissues of grass carp exposed to heterogeneous salinity stressors. Concurrent serum biochemical analyses showed salinity stress significantly increased Na+, Cl, and osmolarity, while decreasing lactate and glucose. Salinity stress exerted a profound impact on the global transcriptomic landscape of grass carp. A substantial number of co-regulated differentially expressed genes (DEGs) in kidney and intestinal tissues were enriched in immune and metabolic pathways. Specifically, genes associated with antigen processing and presentation (e.g., cd4-1, calr3b) and apoptosis (e.g., caspase17, pik3ca) exhibited upregulated expression, whereas genes involved in gluconeogenesis/glycolysis (e.g., hk2, pck2) were downregulated. KEGG pathway enrichment analyses revealed that metabolic and cellular structural pathways were predominantly enriched in intestinal tissues, while kidney tissues showed preferential enrichment of immune and apoptotic pathways. Rigorous validation of RNA-seq data via qPCR confirmed the robustness and cross-platform consistency of the findings. This study investigated the core transcriptional and physiological mechanisms regulating grass carp’s response to salinity stress, providing a theoretical foundation for research into grass carp’s resistance to salinity stress and the development of salt-tolerant varieties. Full article
(This article belongs to the Special Issue Adaptation and Response of Fish to Environmental Changes)
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20 pages, 5322 KiB  
Article
Regulation of Tetraspanin CD63 in Chronic Myeloid Leukemia (CML): Single-Cell Analysis of Asymmetric Hematopoietic Stem Cell Division Genes
by Christophe Desterke, Annelise Bennaceur-Griscelli and Ali G. Turhan
Bioengineering 2025, 12(8), 830; https://doi.org/10.3390/bioengineering12080830 - 31 Jul 2025
Viewed by 295
Abstract
(1) Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder driven by the BCR::ABL oncoprotein. During the chronic phase, Philadelphia chromosome-positive hematopoietic stem cells generate proliferative myeloid cells with various stages of maturation. Despite this expansion, leukemic stem cells (LSCs) retain self-renewal capacity [...] Read more.
(1) Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder driven by the BCR::ABL oncoprotein. During the chronic phase, Philadelphia chromosome-positive hematopoietic stem cells generate proliferative myeloid cells with various stages of maturation. Despite this expansion, leukemic stem cells (LSCs) retain self-renewal capacity via asymmetric cell divisions, sustaining the stem cell pool. Quiescent LSCs are known to be resistant to tyrosine kinase inhibitors (TKIs), potentially through BCR::ABL-independent signaling pathways. We hypothesize that dysregulation of genes governing asymmetric division in LSCs contributes to disease progression, and that their expression pattern may serve as a prognostic marker during the chronic phase of CML. (2) Methods: Genes related to asymmetric cell division in the context of hematopoietic stem cells were extracted from the PubMed database with the keyword “asymmetric hematopoietic stem cell”. The collected relative gene set was tested on two independent bulk transcriptome cohorts and the results were confirmed by single-cell RNA sequencing. (3) Results: The expression of genes involved in asymmetric hematopoietic stem cell division was found to discriminate disease phases during CML progression in the two independent transcriptome cohorts. Concordance between cohorts was observed on asymmetric molecules downregulated during blast crisis (BC) as compared to the chronic phase (CP). This downregulation during the BC phase was confirmed at single-cell level for SELL, CD63, NUMB, HK2, and LAMP2 genes. Single-cell analysis during the CP found that CD63 is associated with a poor prognosis phenotype, with the opposite prediction revealed by HK2 and NUMB expression. The single-cell trajectory reconstitution analysis in CP samples showed CD63 regulation highlighting a trajectory cluster implicating HSPB1, PIM2, ANXA5, LAMTOR1, CFL1, CD52, RAD52, MEIS1, and PDIA3, known to be implicated in hematopoietic malignancies. (4) Conclusion: Regulation of CD63, a tetraspanin involved in the asymmetric division of hematopoietic stem cells, was found to be associated with poor prognosis during CML progression and could be a potential new therapeutic target. Full article
(This article belongs to the Special Issue Micro- and Nano-Technologies for Cell Analysis)
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18 pages, 14612 KiB  
Article
Integrated Proteomic and Transcriptomic Analysis Reveals the Mechanism of Selenium-Mediated Cell Wall Polysaccharide in Rice (Oryza sativa L.) Cadmium Detoxification
by Sixi Zhu, Xianwang Du, Wei Zhao, Xiuqin Yang, Luying Sheng, Huan Mao and Suxia Su
Toxics 2025, 13(8), 642; https://doi.org/10.3390/toxics13080642 - 30 Jul 2025
Viewed by 256
Abstract
Cadmium (Cd) toxicity destroys plant cells and affects plant growth and development. Due to its unique metallic properties, selenium (Se) has been shown to be effective in antioxidants, cellular immunity, and heavy metal detoxification. When Se and Cd are present together in plants, [...] Read more.
Cadmium (Cd) toxicity destroys plant cells and affects plant growth and development. Due to its unique metallic properties, selenium (Se) has been shown to be effective in antioxidants, cellular immunity, and heavy metal detoxification. When Se and Cd are present together in plants, they antagonize. However, the mechanism of action of the two in the rice cell wall remains to be clarified. In this study, we analyzed the mechanism of Cd detoxification by rice (Oryza sativa L.) cellular polysaccharides mediated by Se, using the cell wall as an entry point. Proteomic and transcriptomic analyses revealed that “Glycosyl hydrolases family 17”, “O-methyltransferase”, and “Polygalacturonase” protein pathways were significantly expressed in the cell wall. The most abundant enzymes involved in polysaccharide biosynthesis were found, including bglB, otsB, HK, PFP, ADH1, and ALDH, which resulted in the synthetic pathway of polysaccharide formation in the rice cell wall. Finally, the essential genes/proteins, such as protein Os03g0170500, were identified. The study showed that Se inhibits Cd uptake and transport when Se (1 mg/kg) is low relative to Cd (3 mg/kg), has little inhibitory effect, and even promotes Cd (3 mg/kg) uptake when Se (5 mg/kg) is relatively high. Full article
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18 pages, 2600 KiB  
Article
Nintedanib Induces Mesenchymal-to-Epithelial Transition and Reduces Subretinal Fibrosis Through Metabolic Reprogramming
by David Hughes, Jüergen Prestle, Nina Zippel, Sarah McFetridge, Manon Szczepan, Heike Neubauer, Heping Xu and Mei Chen
Int. J. Mol. Sci. 2025, 26(15), 7131; https://doi.org/10.3390/ijms26157131 - 24 Jul 2025
Viewed by 359
Abstract
This study aimed to investigate the tyrosine kinase inhibitor Nintedanib and its potential role in reversing epithelial–mesenchymal transition (EMT) induced by transforming growth factor beta 2 (TGF-β2) in retinal pigment epithelial (RPE) cells, along with its therapeutic potential using a mouse model of [...] Read more.
This study aimed to investigate the tyrosine kinase inhibitor Nintedanib and its potential role in reversing epithelial–mesenchymal transition (EMT) induced by transforming growth factor beta 2 (TGF-β2) in retinal pigment epithelial (RPE) cells, along with its therapeutic potential using a mouse model of subretinal fibrosis. We hypothesized that the blockade of angiogenesis promoting and fibrosis inducing signaling using the receptor tyrosine kinase inhibitor Nintedanib (OfevTM) can prevent or reverse EMT both in vitro and in our in vivo model of subretinal fibrosis. Primary human retinal pigment epithelial cells (phRPE) and adult retinal pigment epithelial cell line (ARPE-19) cells were treated with TGF-β210 ng/mL for two days followed by four days of Nintedanib (1 µM) incubation. Epithelial and mesenchymal phenotypes were assessed by morphological examination, quantitative real-time polymerase chain reaction(qPCR) (ZO-1, Acta2, FN, and Vim), and immunocytochemistry (ZO-1, vimentin, fibronectin, and αSMA). Metabolites were measured using luciferase-based assays. Extracellular acidification and oxygen consumption rates were measured using the Seahorse XF system. Metabolic-related genes (GLUT1, HK2, PFKFB3, CS, LDHA, LDHB) were evaluated by qPCR. A model of subretinal fibrosis using the two-stage laser-induced method in C57BL/6J mice assessed Nintedanib’s therapeutic potential. Fibro-vascular lesions were examined 10 days later via fluorescence angiography and immunohistochemistry. Both primary and ARPE-19 RPE stimulated with TGF-β2 upregulated expression of fibronectin, αSMA, and vimentin, and downregulation of ZO-1, consistent with morphological changes (i.e., elongation). Glucose consumption, lactate production, and glycolytic reserve were significantly increased in TGF-β2-treated cells, with upregulation of glycolysis-related genes (GLUT1, HK2, PFKFB3, CS). Nintedanib treatment reversed TGF-β2-induced EMT signatures, down-regulated glycolytic-related genes, and normalized glycolysis. Nintedanib intravitreal injection significantly reduced collagen-1+ fibrotic lesion size and Isolectin B4+ neovascularization and reduced vascular leakage in the two-stage laser-induced model of subretinal fibrosis. Nintedanib can induce Mesenchymal-to-Epithelial Transition (MET) in RPE cells and reduce subretinal fibrosis through metabolic reprogramming. Nintedanib can therefore potentially be repurposed to treat retinal fibrosis. Full article
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22 pages, 5242 KiB  
Article
Effects of Hypoxia and Reoxygenation on Hypoxia-Responsive Genes, Physiological and Biochemical Indices in Hybrid Catfish (Pelteobagrus vachelli ♀ × Leiocassis longirostris ♂)
by Jie Yan, Faling Zhang, Fenfei Liang, Cheng Zhao, Shaowu Yin and Guosong Zhang
Biology 2025, 14(8), 915; https://doi.org/10.3390/biology14080915 - 23 Jul 2025
Viewed by 291
Abstract
Hypoxia represents a critical environmental stressor in aquaculture, significantly disrupting aquatic organisms’ physiological homeostasis and thereby constraining the sustainable development of aquaculture industries. To elucidate the mechanisms underlying hypoxia-induced metabolic regulation in aquatic species, this study employed hybrid yellow catfish (Pelteobagrus vachelli [...] Read more.
Hypoxia represents a critical environmental stressor in aquaculture, significantly disrupting aquatic organisms’ physiological homeostasis and thereby constraining the sustainable development of aquaculture industries. To elucidate the mechanisms underlying hypoxia-induced metabolic regulation in aquatic species, this study employed hybrid yellow catfish (Pelteobagrus vachelli ♀ × Leiocassis longirostris ♂) as a model organism to systematically investigate the multidimensional physiological responses in brain, liver, and muscle tissues under hypoxia (0.7 mg/L) and reoxygenation (7.0 mg/L) conditions. Through qRT-PCR and enzymatic activity analyses, we comprehensively assessed molecular alterations associated with oxygen sensing (HIF-1α gene), respiratory metabolism (PFKL, HK1, PK, CS, and LDHA genes and corresponding enzyme activities), oxidative stress (SOD1, SOD2, GSH-PX, and CAT genes, along with LPO, MDA, PCO, T-SOD, GSH-PX, and CAT levels), apoptosis (Caspase-3, Bax/Bcl-2), inflammatory response (IL-1β, IKKβ), and mitochondrial function (COXIV, PGC-1α, ATP5A1). Key findings demonstrated pronounced HIF-1α activation across all examined tissues. Hepatic tissues exhibited adaptive metabolic reprogramming from aerobic to anaerobic metabolism, whereas cerebral tissues displayed suppressed anaerobic glycolysis during prolonged hypoxia, and muscular tissues manifested concurrent inhibition of both glycolytic and aerobic metabolic pathways. Notably, skeletal muscle exhibited marked oxidative stress accompanied by mitochondrial dysfunction, exacerbated inflammation, and apoptosis activation during hypoxia/reoxygenation cycles. This study delineates tissue-specific adaptive mechanisms to hypoxia in yellow catfish, providing theoretical foundations for both piscine hypoxia physiology research and aquaculture practices. Full article
(This article belongs to the Special Issue Nutrition, Environment, and Fish Physiology)
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19 pages, 6789 KiB  
Article
Metabolic Plasticity and Transcriptomic Reprogramming Orchestrate Hypoxia Adaptation in Yak
by Ci Huang, Yilie Liao, Wei Peng, Hai Xiang, Hui Wang, Jieqiong Ma, Zhixin Chai, Zhijuan Wu, Binglin Yue, Xin Cai, Jincheng Zhong and Jikun Wang
Animals 2025, 15(14), 2084; https://doi.org/10.3390/ani15142084 - 15 Jul 2025
Viewed by 291
Abstract
The yak (Bos grunniens) has exceptional hypoxia resilience, making it an ideal model for studying high-altitude adaptation. Here, we investigated the effects of oxygen concentration on yak cardiac fibroblast proliferation and the underlying molecular regulatory pathways using RNA sequencing (RNA-seq) and [...] Read more.
The yak (Bos grunniens) has exceptional hypoxia resilience, making it an ideal model for studying high-altitude adaptation. Here, we investigated the effects of oxygen concentration on yak cardiac fibroblast proliferation and the underlying molecular regulatory pathways using RNA sequencing (RNA-seq) and metabolic analyses. Decreased oxygen levels significantly inhibited cardiac fibroblast proliferation and activity. Intriguingly, while the mitochondrial DNA (mtDNA) content remained stable, we observed coordinated upregulation of mtDNA-encoded oxidative phosphorylation components. Live-cell metabolic assessment further demonstrated that hypoxia led to mitochondrial respiratory inhibition and enhanced glycolysis. RNA-seq analysis identified key hypoxia adaptation genes, including glycolysis regulators (e.g., HK2, TPI1), and hypoxia-inducible factor 1-alpha (HIF-1α), with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighting their involvement in metabolic regulation. The protein–protein interaction network identified three consensus hub genes across five topological algorithms (CCNA2, PLK1, and TP53) that may be involved in hypoxia adaptation. These findings highlight the importance of metabolic reprogramming underlying yak adaptation to hypoxia, providing valuable molecular insights into the mechanisms underlying high-altitude survival. Full article
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12 pages, 1668 KiB  
Article
The PAS-B Domain of BMAL1 Controls Proliferation, Cellular Energetics, and Inflammatory Response in Human Monocytic Cell Line THP-1
by Yoko Gozu, Junichi Hosoi, Hiroaki Nagatomo, Kayako Ishimaru and Atsuhito Nakao
Int. J. Mol. Sci. 2025, 26(14), 6737; https://doi.org/10.3390/ijms26146737 - 14 Jul 2025
Viewed by 283
Abstract
Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in [...] Read more.
Brain muscle ARNT-like1 (Bmal1) is a transcriptional factor, consisting of basic helix–loop–helix (bHLH) and PER-ARNT-SIM (PAS) domains, that plays a central role in circadian clock activity. However, the precise roles of the BMAL1-PAS domain, a circadian rhythm-regulating structure, remain unexplored in monocytes. Here, we highlight the BMAL1-PAS domain as a key structure in monocyte pleiotropic functions by using human monocytic cell line THP-1. THP-1 cells lacking the BMAL1-PAS-B domain (THP-1#207) abrogated the circadian expression of core clock genes. THP-1#207 cells exhibited less proliferation, glycolysis and oxidative phosphorylation activity, and LPS-induced IL-1β production, but exhibited more production of LPS-induced IL-10 than THP-1 cells. A quantitative proteomics analysis revealed significant expression changes in ~10% metabolic enzymes in THP-1#207 cells compared to THP-1 cells, including reduction in a rate-limiting enzyme hexokinase2 (HK2) in the glycolytic pathway. Importantly, treatment of THP-1 with 2-deoxy-D-glucose (2-DG), an HK2 inhibitor, largely recapitulated the phenotypes of THP-1#207 cells. These findings suggest that the BMAL1-PAS-B domain is an important structure for the regulation of proliferation, cellular energetics, and inflammatory response in THP-1 cells, at least in part, via the control of glycolytic activity. Thus, the BMAL1-PAS-B domain may become a promising pharmacological target to control inflammation. Full article
(This article belongs to the Special Issue The Importance of Molecular Circadian Rhythms in Health and Disease)
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18 pages, 2348 KiB  
Article
Glucomannan Accumulation Induced by Exogenous Lanthanum in Amorphophallus konjac: Insights from a Comparative Transcriptome Analysis
by Xiaoxian Li, Zhouting Zeng, Siyi Zhu, Xirui Yang, Xiaobo Xuan and Zhenming Yu
Biology 2025, 14(7), 849; https://doi.org/10.3390/biology14070849 - 11 Jul 2025
Viewed by 329
Abstract
Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. [...] Read more.
Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. In this study, 20~80 mg L−1 La significantly stimulated KGM accumulation compared with the control group. We performed a transcriptome analysis and found 21,047 differentially expressed genes (DEGs), predominantly enriched in carbohydrate and glycan metabolism pathways. A total of 48 DEGs were linked to KGM biosynthesis, with 20 genes (SuSy, INV1/3/5/6, HK1/2, FPK2, GPI3, PGM3, UGP2, GMPP1/4, CslA3~7, CslH2, and MSR1.2) showing significant positive correlations with KGM content. Interestingly, three key terminal pathway genes (UGP1, UGP3, and CslD3) exhibited strong upregulation (log2 fold change > 3). Seven DEGs were validated with qRT-PCR, aligning with the transcriptomic results. Furthermore, 12 hormone-responsive DEGs, including 4 ethylene-related genes (CTR1, EBF1/2, EIN3, and MPK6), 6 auxin-related genes (AUX/IAA1-3, SAUR1-2, and TIR1), and 2 gibberellin-related genes (DELLA1-2), were closely linked to KGM levels. Additionally, the transcription factors bHLH and AP2/ERF showed to be closely related to the biosynthesis of KGM. These results lay the foundation for a model wherein La (Ш) modulates KGM accumulation by coordinately regulating biosynthetic and hormonal pathways via specific transcription factors. Full article
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15 pages, 1870 KiB  
Article
Transcriptome Analyses Reveal the Molecular Response of Juvenile Greater Amberjack (Seriola dumerili) to Marine Heatwaves
by Yali Tian, Liancheng Li, Hongzhao Long, Dongying Zhang, Chen Wang, Ruijuan Hao, Hang Li, Xiaoying Ru, Qiuxia Deng, Qin Hu, Yang Huang and Chunhua Zhu
Animals 2025, 15(13), 1871; https://doi.org/10.3390/ani15131871 - 24 Jun 2025
Viewed by 430
Abstract
Marine heatwaves (MHWs) have recently become more frequent, intense, and prolonged, posing significant threats to marine life and fisheries. In this study, transcriptomic analysis was employed to investigate the genes and pathways in Seriola dumerili that respond to MHW-induced stress at 28 °C [...] Read more.
Marine heatwaves (MHWs) have recently become more frequent, intense, and prolonged, posing significant threats to marine life and fisheries. In this study, transcriptomic analysis was employed to investigate the genes and pathways in Seriola dumerili that respond to MHW-induced stress at 28 °C (T28) and 32 °C (T32), using 24 °C (T24) as the control. Transcriptome sequencing revealed that 17 differentially expressed genes (DEGs) belonging to the heat shock protein (HSP) families—HSP30, HSP40, HSP70, and HSP90—were significantly upregulated under short-lasting MHW stress in the T24-4d vs. T32-4d comparison. Additionally, genes related to oxidative stress (e.g., protein disulfide isomerase family A member 6 [pdia6]), immune responses (e.g., interferon regulatory factor 5 [irf5]), and energy metabolism (e.g., hexokinase-1 [hk1]) were also identified. Enrichment analysis of DEGs in the T24-4d vs. T32-4d group revealed that S. dumerili exhibited adaptive responses to MHWs through the upregulation of HSPs and the activation of antioxidant, energy metabolism, and immune response pathways. However, in the T24-13d vs. T32-13d group, DEGs associated with these pathways were either not significantly expressed or were downregulated. These findings indicate that S. dumerili is unable to sustain its adaptive responses under repeated, intense MHW exposure, resulting in the disorder of its antioxidant defense system, immune suppression, and metabolic dysfunction. This study provides valuable insights into the molecular responses of S. dumerili to MHWs and supports the selection for thermal resistance in this species. Full article
(This article belongs to the Special Issue Omics in Economic Aquatic Animals)
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11 pages, 1438 KiB  
Article
Purple Potato Extract Suppresses Hypoxia-Induced Metabolic Reprogramming and Inhibits HIF-1α Signaling in Caco-2 Cells
by Qiaorong Cui, Qi Sun, Alejandro Bravo Iniguez, Xinrui Li, Min Du and Mei-Jun Zhu
Nutrients 2025, 17(13), 2079; https://doi.org/10.3390/nu17132079 - 23 Jun 2025
Viewed by 495
Abstract
Background: The hypoxia-inducible factor 1α (HIF-1α) pathway plays a key role in promoting glycolysis and tumor progression under hypoxic conditions in cancer cells. Purple potato (PP) extract, which is a polyphenol-rich natural product, has previously been shown to enhance mitochondrial function and suppress [...] Read more.
Background: The hypoxia-inducible factor 1α (HIF-1α) pathway plays a key role in promoting glycolysis and tumor progression under hypoxic conditions in cancer cells. Purple potato (PP) extract, which is a polyphenol-rich natural product, has previously been shown to enhance mitochondrial function and suppress tumor growth in several cancer models. We hypothesized that PP extract could counteract hypoxia-induced glycolysis by targeting the HIF-1α pathway. Methods: Human colonic epithelial Caco-2 cells were treated with PP extract under hypoxic conditions, and its effects on glycolysis, oxidative phosphorylation, and HIF-1α signaling were evaluated. Results: Under hypoxia PP extract suppressed glycolysis, as evidenced by reduced lactate production and lower phosphorylated pyruvate dehydrogenase levels. In parallel, genes associated with oxidative phosphorylation were upregulated by PP extract, suggesting a metabolic shift under hypoxia. Additionally, PP extract reduced the protein accumulation of HIF-1α and its transcriptional activator XBP1 induced by hypoxia. Correspondingly, the expression of several HIF-1α downstream target genes, including Vegfa, Pdk1, Ldha, Hk1, and Glut1, was markedly reduced. Functionally, PP extract inhibited cell proliferation, migration, and drug resistance under hypoxic stress, indicating a broader inhibitory effect on hypoxia-driven malignant phenotypes. Conclusion: These findings suggest that PP extract disrupts cancer cell adaptation to hypoxia and supports its potential as a dietary approach against hypoxia-driven colorectal cancer, through further preclinical studies are warranted. Full article
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24 pages, 3424 KiB  
Article
Oxidative Stress, Energy Metabolism Disorder, Mitochondrial Damage, and miR-144 Participated in Molecular Mechanisms of 4-Octylphenol-Caused Cardiac Autophagic Damage in Common Carps (Cyprinus carpio L.)
by Minna Qiu, Chunyu Jiang, Jiatian Liang, Qin Zhou, Yuhao Liu, Zhiyu Hao, Yuhang Liu, Xiumei Liu, Xiaohua Teng, Wei Sun and You Tang
Metabolites 2025, 15(6), 391; https://doi.org/10.3390/metabo15060391 - 11 Jun 2025
Viewed by 594
Abstract
Background/Objectives: In 4-octylphenol (4-OP), a toxic environmental pollutant with endocrine disruptive effect, the use of 4-OP causes pollution in the freshwater environment and poses risks to aquatic organisms. Common carps (Cyprinus carpio L.) live in freshwater and are experimental animals for [...] Read more.
Background/Objectives: In 4-octylphenol (4-OP), a toxic environmental pollutant with endocrine disruptive effect, the use of 4-OP causes pollution in the freshwater environment and poses risks to aquatic organisms. Common carps (Cyprinus carpio L.) live in freshwater and are experimental animals for studying the toxic effects of environmental pollutants on fish. Its heart is susceptible to toxicants. However, whether 4-OP has a toxic effect on common carp heart remains unknown. Methods: Here, we conducted a common carp 4-OP exposure experiment (carp treated with 17 μg/L 4-OP for 45 days), aiming to investigate whether 4-OP has a toxic effect on common carp hearts. We observed the microstructure and ultrastructure of carp heart and detected autophagy genes, mitochondrial fission genes, mitochondrial fusion genes, glycolytic enzymes, AMPK, ATPase, and oxidative stress factors, to investigate the molecular mechanism of 4-OP induced damage in common carp hearts. Results: Our results showed that 4-OP exposure caused mitochondrial damage, autophagy, and damage in common carp hearts. 4-OP exposure increased the levels of miR-144, and eight autophagy factors (Beclin1, RB1CC1, ULK1, LC3-I, LC3-II, ATG5, ATG12, and ATG13), and decreased the levels of four autophagy factors (PI3K, AKT, mTOR, and SQSTM1). Furthermore, 4-OP exposure induced the imbalance between mitochondrial fission and fusion and mitochondrial dynamics imbalance, as demonstrated by the increase in three mitochondrial fission factors (Mff, Drp1, and Fis1) and the decrease in three mitochondrial fusion factors (Mfn1, Mfn2, and Opa1). Moreover, excess 4-OP treatment caused energy metabolism disorder, as demonstrated by the reduction in four ATPase (Na+K+-ATPase, Ca2+Mg2+-ATPase, Ca2+-ATPase, and Mg2+-ATPase), elevation in four glycolysis genes (HK1, HK2, LDHA, and PGK1), reduction in glycolysis gen (PGAM2), and the elevation in energy-sensing AMPK. Finally, 4-OP treatment induced the imbalance between antioxidant and oxidant and oxidative stress, as demonstrated by the increase in oxidant H2O2, and the decreases in five antioxidant factors (CAT, SOD, T-AOC, Nrf2, and HO-1). Conclusions: miR-144 mediated autophagy by targeting PI3K, mTOR, and SQSTM1, and the miR-144/PI3K-AKT-mTOR/ULK1 pathway was involved in 4-OP-induced autophagy. Mff-Drp1 axis took part in 4-OP-caused mitochondrial dynamics imbalance, and mitochondrial dynamics imbalance mediated autophagy via Mfn2-SQSTM1, Mfn2/Beclin1, and Mff-LC3-II axes. Energy metabolism disorder mediated mitochondrial dynamics imbalance through the AMPK-Mff-Drp1 pathway. Oxidative stress mediated energy metabolism disorder via the H2O2-AMPK axis. Taken together, oxidative stress triggered energy metabolism disorder, induced mitochondrial dynamics imbalance, and caused autophagy via the H2O2-AMPK-Mff-LC3-II pathway. Our study provided references for the toxic effects of endocrine disruptor on common carp hearts, and provided a basis for assessing environmental pollutant-induced damage in common carp heart. We only studied the toxic effects of 4-OP on common carp, and the toxic effects of 4-OP on other fish species need to be further studied. Full article
(This article belongs to the Section Cell Metabolism)
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24 pages, 7622 KiB  
Article
Hypoxia Promotes the In Vitro Proliferation of Buffalo Spermatogonial Cells by Increasing Lactate and H3K18la Lactylation Levels
by Mengqi Li, Yanyu Ma, Shenzhi Wang, Haiying Zheng, Chunyan Yang, Anqin Duan, Benliang Zhou, Jianghua Shang, Xingwei Liang and Xiaogan Yang
Cells 2025, 14(11), 832; https://doi.org/10.3390/cells14110832 - 3 Jun 2025
Viewed by 957
Abstract
Hypoxia benefits the proliferation and maintenance of animal spermatogonial cells; however, the underlying mechanism remains incompletely understood. This study aims to investigate the role and mechanism of the hypoxia–glycolysis–histone lactylation axis in the proliferation of buffalo spermatogonial cells (bSCs). bSCs were cultured under [...] Read more.
Hypoxia benefits the proliferation and maintenance of animal spermatogonial cells; however, the underlying mechanism remains incompletely understood. This study aims to investigate the role and mechanism of the hypoxia–glycolysis–histone lactylation axis in the proliferation of buffalo spermatogonial cells (bSCs). bSCs were cultured under different oxygen concentrations to observe changes in cell proliferation. RNA-seq was used to analyze gene expression and signaling pathways. Changes in lactylation were monitored, and CUT&Tag-seq was utilized to determine the regulatory effects of lactylation on gene expression. The glycolytic pathway was regulated to validate the results of the bioinformatic analysis. Oxygen concentrations between 2.5% and 10% support the proliferation of bSCs, with 5% having the most pronounced effect. An amount of 5% oxygen significantly increased the proliferation and pluripotency of bSCs while also promoting glycolysis and lactylation. Inhibition of glycolysis eliminated the proliferative effects of hypoxia. By analyzing genes associated with the key lactylation site H3K18la using CUT&Tag technology, we found that it is closely linked to genes involved in the regulation of proliferation. After inhibition of HK-2 expression, cell proliferation, H3K18la expression, and the expression of these target genes were all suppressed. Hypoxia promotes the proliferation of bSCs via activation of glycolysis, leading to an increase in H3K18la and altered expression of its target genes. Full article
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13 pages, 1598 KiB  
Article
Detection of Selection Signatures and Genome-Wide Association Analysis of Body Weight Traits in Xianan Cattle
by Huaini Zhu, Xiaofeng Li, Man Zhang, Siyu Liu, Yan Zhang, Ying Zheng, Zhitong Wei, Mingpeng Han, Hetian Huang, Tong Fu and Dong Liang
Genes 2025, 16(6), 682; https://doi.org/10.3390/genes16060682 - 30 May 2025
Viewed by 511
Abstract
Background: Xianan cattle, the first cross-bred beef cattle developed in China, are recognized for their rapid growth, tolerance to rough feed, and high meat yield. These characteristics make them a valuable model for studies aimed at improving beef production traits. Methods: In this [...] Read more.
Background: Xianan cattle, the first cross-bred beef cattle developed in China, are recognized for their rapid growth, tolerance to rough feed, and high meat yield. These characteristics make them a valuable model for studies aimed at improving beef production traits. Methods: In this study, two complementary gene mapping strategies, selection signature analysis and association analysis, were employed to identify candidate genes associated with body weight. The analyses utilized resequencing data comprising 16,250,950 high-quality single nucleotide polymorphisms (SNPs). Twenty independent variables showed significant correlations with body weight, with effect sizes ranging from 239 kg to 629.37 kg, while controlling for a false discovery rate (FDR) of less than 0.5. Results: The most prominent signal was identified in the 54.24–54.39 MB region on chromosome 9, which contains the MANEA gene. Furthermore, we investigated the functional role of the MANEA gene at the cellular level. siRNA-mediated knockdown of MANEA resulted in significant alterations in the expression of downstream genes, notably MGAT1, MGAT3, FUT8, and HK1. Among these, the expression of MGAT1 was markedly increased, showing an increase of up to 600-fold compared to the control. Conclusions: These results offer critical insights into the molecular mechanisms underlying body weight regulation and provide a foundation for developing strategies to enhance economically important production traits in beef cattle. Full article
(This article belongs to the Special Issue Research on Genetics and Breeding of Cattle)
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24 pages, 21945 KiB  
Article
Drug Pair of Astragali Radix–Ligustri Lucidi Fructus Alleviates Acute Kidney Injury in Mice Induced by Ischemia–Reperfusion Through Inhibiting Ferroptosis
by Xuanhe Liu, Dan Zhang, Yuting Xie, Mengdan Wang, Xiaochun Chen, Weijie Yu, Yuming Ma, Jia Zeng, Qixuan Long, Guangrui Huang, Jie Geng and Anlong Xu
Pharmaceuticals 2025, 18(6), 789; https://doi.org/10.3390/ph18060789 - 25 May 2025
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Abstract
Background: Acute kidney injury (AKI), characterized by high morbidity and mortality, is primarily caused by renal ischemia–reperfusion injury (RIRI). Ferroptosis plays a key role in RIRI, yet its underlying mechanisms remain unclear. The drug pair of Astragali Radix–Ligustri Lucidi Fructus (DAL) shows promise [...] Read more.
Background: Acute kidney injury (AKI), characterized by high morbidity and mortality, is primarily caused by renal ischemia–reperfusion injury (RIRI). Ferroptosis plays a key role in RIRI, yet its underlying mechanisms remain unclear. The drug pair of Astragali Radix–Ligustri Lucidi Fructus (DAL) shows promise in renal diseases, but its protective effects against RIRI and associated molecular pathways via ferroptosis inhibition are unknown. This study aimed to investigate DAL’s therapeutic effects on RIRI and its mechanisms. Methods: A mouse model of bilateral renal ischemia–reperfusion was established. Renal function (serum creatinine, Scr; blood urea nitrogen, BUN), inflammatory cytokines (TNF-α, IFN-γ, IL-6), ferroptosis markers (GPX4, MDA, GSH, tissue iron), and pathological damage were evaluated. Transcriptomic sequencing and electron microscopy analyzed gene pathways and mitochondrial structure. In HK-2 cells, oxygen–glucose deprivation/reoxygenation (OGD/R) and RSL3-induced ferroptosis models were used to assess DAL-containing serum effects via cell viability, GPX4 expression, and mitochondrial morphology. LC-MS analyzed DAL’s chemical components, and network pharmacology predicted ferroptosis-related targets. Results: DAL significantly reduced Scr/BUN levels, alleviated tubular injury, fibrosis, and apoptosis, and downregulated inflammatory cytokines and damage markers. It inhibited ferroptosis by upregulating GPX4, decreasing MDA/tissue iron, and increasing GSH. Transcriptomics revealed enrichment in lipid metabolism pathways. DAL restored the mitochondrial cristae structure; DAL-containing serum improved cell viability, blocked RSL3-induced GPX4 downregulation, and mitigated mitochondrial dysfunction. Network pharmacology identified DAL’s potential active components and targets. Molecular docking validated binding affinity and interaction patterns of active components with targets. Conclusions: DAL protects against RIRI by upregulating GPX4, preserving the mitochondrial structure, and inhibiting ferroptosis, highlighting its therapeutic potential for AKI prevention and treatment. Full article
(This article belongs to the Special Issue New Development in Pharmacotherapy of Kidney Diseases)
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20 pages, 6700 KiB  
Article
The Hypoglycemic Activity of Gracilaria lemaneiformis Polysaccharide Gels Based on IR/IRS-2/PI3k/Akt/Glut4 and Glycometabolism Signaling Pathways in HepG2 Cells
by Xiaoshan Long, Shucheng Liu, Xianqing Yang, Yongqiang Zhao, Shaoling Yang, Ya Wei, Chuang Pan, Shengjun Chen, Peihong Jiang, Bo Qi and Xiao Hu
Gels 2025, 11(5), 366; https://doi.org/10.3390/gels11050366 - 15 May 2025
Viewed by 542
Abstract
The aim of this study was to investigate the hypoglycemic activity and mechanism of G. lemaneiformis polysaccharide gels (GLP and GLP-HV) based on IR/IRS-2/PI3k/Akt/Glut4 and glycometabolism signaling pathways in HepG2 cells. After H2O2-Vc degradation, the molecular weight of G. [...] Read more.
The aim of this study was to investigate the hypoglycemic activity and mechanism of G. lemaneiformis polysaccharide gels (GLP and GLP-HV) based on IR/IRS-2/PI3k/Akt/Glut4 and glycometabolism signaling pathways in HepG2 cells. After H2O2-Vc degradation, the molecular weight of G. lemaneiformis polysaccharide gel declined from 1478 kDa to 16 kDa. Molecular weight chromatogram and distribution indicated that GLP-HV had a high molecular weight homogeneity compared to GLP. G. lemaneiformis polysaccharide gels significantly decreased the TC, TG, LDL-C, MDA, and LDH contents and enhanced the activities of HDL-C, T-AOC, CAT, GSH-PX, SOD, insulin, and glycogen in HepG2 cells. Fluorescent staining results showed that G. lemaneiformis polysaccharide gels reduced ROS and calcium ions levels in HepG2 cells. GLP and GLP-HV displayed excellent hypoglycemic activity, with GLP-HV performing better. Furthermore, qPCR and Western blot analysis revealed that G. lemaneiformis polysaccharide gels remarkably strengthened the levels of IR, IRS-2, PI3K, Akt, Glut4, HK, G6PD, PFK, PEPCK, GK, PK genes, and proteins. Spearman’s correlation analysis revealed that the IR/IRS-2/PI3k/Akt/Glut4 signaling pathway played a dominant role in regulating activity. These results show that G. lemaneiformis polysaccharide gels present a prominent hypoglycemic effect mediated by the IR/IRS-2/PI3k/Akt/Glut4 and glycometabolism signaling pathways, with the former playing a dominant role. Full article
(This article belongs to the Special Issue Food Gels: Gelling Process and New Applications)
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