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23 pages, 2309 KB  
Review
The Oncogenic Role of Long Non-Coding RNA NEAT1 in Head and Neck Squamous Cell Carcinoma: From Molecular Mechanisms to Clinical Implications
by Yuanxin Shi, Bin Chen and Guohui Bai
Biology 2026, 15(4), 307; https://doi.org/10.3390/biology15040307 - 10 Feb 2026
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with poor patient outcomes. The long non-coding RNA NEAT1 (lncRNA NEAT1) has emerged as a critical driver of HNSCC pathogenesis. This review synthesizes current knowledge on lncRNA NEAT1’s aberrant expression, [...] Read more.
Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with poor patient outcomes. The long non-coding RNA NEAT1 (lncRNA NEAT1) has emerged as a critical driver of HNSCC pathogenesis. This review synthesizes current knowledge on lncRNA NEAT1’s aberrant expression, molecular mechanisms, and functional roles in HNSCC. LncRNA NEAT1 is significantly upregulated in tumors and promotes progression by acting as a competing endogenous RNA (ceRNA) for multiple miRNAs, such as miR-125b-5p, miR-204, and miR-34a-5p, thereby regulating downstream targets including SLC1A5, ZEB1, and components of the Wnt/β-catenin pathway. These interactions drive key oncogenic processes, including proliferation, metastasis, epithelial–mesenchymal transition, therapy resistance, and cell death inhibition. Clinically, high lncRNA NEAT1 expression correlates with advanced T stage, lymph node metastasis, and reduced survival, underscoring its potential as a diagnostic and prognostic biomarker. Therapeutically, emerging approaches such as nanoparticle-mediated delivery of siRNA/shRNA offer a promising strategy to target lncRNA NEAT1, potentially synergizing with existing immunotherapies. Although clinical translation remains challenging, lncRNA NEAT1 represents a highly promising biological target for future precision oncology in HNSCC. Full article
(This article belongs to the Special Issue Head and Neck Cancer: Current Advances and Future Perspectives)
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37 pages, 617 KB  
Review
Genetic and Environmental Architecture of Ram Fertility Traits: A Review
by Kaiyue Zheng, Krishani Sinhalage, Guilherme Henrique Gebim Polizel and Ángela Cánovas
Genes 2026, 17(2), 210; https://doi.org/10.3390/genes17020210 - 9 Feb 2026
Viewed by 45
Abstract
Background/Objectives: Ram fertility is essential for sheep production, influenced by genetic, physiological, behavioral, and environmental factors. This narrative review synthesizes findings from over 190 peer-reviewed publications to evaluate the phenotypic indicators, genetic architecture, molecular candidates, and management conditions influencing testicular development, semen quality, [...] Read more.
Background/Objectives: Ram fertility is essential for sheep production, influenced by genetic, physiological, behavioral, and environmental factors. This narrative review synthesizes findings from over 190 peer-reviewed publications to evaluate the phenotypic indicators, genetic architecture, molecular candidates, and management conditions influencing testicular development, semen quality, and reproductive performance in rams. Methods: A narrative synthesis of peer-reviewed studies was conducted, integrating findings from quantitative genetics, genome-wide association studies, transcriptomics, and controlled environmental and management experiments. Emphasis was placed on studies evaluating fertility-related traits across breeds, ages, and production systems. Results: Recent genomic and transcriptomic studies have identified potential biomarkers (e.g., IGF1, IGFALS, FOXO1) and gene networks linked to ram fertility, including semen quality, scrotal circumference, and endocrine regulation. For instance, genome-wide association studies (GWASs) have identified candidate genes such as SLC2A8 and MAPK3, which are associated with spermatogenesis and semen quality. Additionally, Y-linked SNPs such as ZFY16: g.146 C > T have been linked to testicular development. Genetic potential is heavily modulated by environmental constraints. Heat stress emerges as a disruptor of testicular thermoregulation, with recent evidence highlighting the vulnerability of spermatogenesis even in adapted breeds. Management interventions, specifically nutritional supplementation and hormonal modulation via melatonin, are discussed as effective strategies to mitigate environmental impacts. Conclusion: Improving ram fertility will require an approach that prioritizes phenotypic traits supported by candidate genes identified through transcriptomic analyses and GWASs. Integrating these genetic tools together with cost-effective nutritional and hormonal management strategies can further improve semen quality, libido, and testicular traits, thereby enhancing fertility gains while maintaining sheep breed adaptability across production systems. Full article
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21 pages, 3284 KB  
Review
The SLC41 Family of Magnesium Transporters: Molecular Regulators of Magnesium Homeostasis and Their Multifaceted Roles in Human Diseases
by Yu Cao, Caijun Rao and Zhipeng Du
Int. J. Mol. Sci. 2026, 27(4), 1673; https://doi.org/10.3390/ijms27041673 - 9 Feb 2026
Viewed by 55
Abstract
Magnesium ion (Mg2+), particularly its free intracellular form, is indispensable for regulating diverse cellular functions. This critical role implies the existence of dedicated transporters and channels in the plasma membrane that coordinate Mg2+ uptake, intracellular storage, and efflux to maintain [...] Read more.
Magnesium ion (Mg2+), particularly its free intracellular form, is indispensable for regulating diverse cellular functions. This critical role implies the existence of dedicated transporters and channels in the plasma membrane that coordinate Mg2+ uptake, intracellular storage, and efflux to maintain homeostasis. Although numerous molecular entities responsible for such Mg2+ transport have been reported over the past decades, there is still limited knowledge of their precise functions and disease implications. This review focuses on the solute carrier family 41 (SLC41), which consists of three isoforms (A1, A2, and A3) that share homology with the prokaryotic magnesium transporter E (MgtE) Mg2+ transporter family. Accumulating evidence has established SLC41A1 as the Na+/Mg2+ exchanger—a predominant Mg2+-efflux system. By contrast, the subcellular site of SLC41A2-mediated Mg2+ flux remains undefined, with potential roles at either the plasma membrane or organellar membranes, and SLC41A3 facilitates Na+-dependent Mg2+ efflux from mitochondria. Additionally, several studies have reported the association between SLC41s and diseases, including Parkinson’s disease, hepatocellular carcinoma, and nephronophthisis-related ciliopathies. By synthesizing current knowledge, this review aims to enhance the understanding of SLC41 transporters in health and disease and to explore their potential as therapeutic targets for clinical intervention. Full article
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22 pages, 553 KB  
Article
Efficacy of Early Feeding with Probiotic-Fermented Feed in Promoting Growth Performance, Immunity, Antioxidant Activity, Gene Expression, and Gut Integrity in Ostrich Chicks (Struthio camelus)
by Haifa Ali Alqhtani, Hadeel A. Almamoory, Huda A. Alqahtani, Ahmed M. Elbaz, Ahmed Sabry Arafa, Eman Kamel M. Khalfallah, Fatmah A. Safhi, Ahmed Ateya, Ayman Abd El-Aziz, Rowa K. Zarah, Ahmed H. Ghonaim, AbdelRahman Y. Abdelhady and Mohamed Marzok
Vet. Sci. 2026, 13(2), 168; https://doi.org/10.3390/vetsci13020168 - 8 Feb 2026
Viewed by 94
Abstract
The purpose of this study was to evaluate the effect of early feeding with probiotic-fermented feed on growth performance, intestinal microbiota structure, immune responses, and gene expression. Two hundred and forty-one-day-old African ostrich chicks were randomly divided into three groups (eight replicates/group). The [...] Read more.
The purpose of this study was to evaluate the effect of early feeding with probiotic-fermented feed on growth performance, intestinal microbiota structure, immune responses, and gene expression. Two hundred and forty-one-day-old African ostrich chicks were randomly divided into three groups (eight replicates/group). The control group was fed a basal diet (CON), whereas the PELF3 and PELF6 groups were fed the probiotic-fermented feed for the first 3 or 6 days post-hatching, respectively, after which, all chicks were fed the basal diet for 56 days. The results showed that adding PELF3 or PELF6 significantly enhanced body weight gain and the feed conversion ratio. Chicks fed PELF had higher superoxide dismutase (SOD, p < 0.05), immunoglobulin A (IgA), and IL-10 levels and lower IL-6 and malondialdehyde (MDA, p < 0.05) levels than those fed CON. Plasma cholesterol, low-density lipoprotein (LDL), creatinine, uric acid, and alanine aminotransferase (ALT) levels decreased; however, high-density lipoprotein (HDL, p < 0.05) levels increased in the PELF groups. The addition of PELF reduced the pathogenic counts in the intestines of chicks (p < 0.05). Moreover, increased expression of IGF-1 and MUC-2 genes was observed in the PELF3 and PELF6 groups, whereas the expression of SLC15A1 increased in the PELF6 group. In conclusion, growth performance, immunity, gene expression, oxidative stability, and gut microbiota can all be significantly enhanced by early feeding with PELF. This study demonstrated an effective technique for applying early feeding of PELF in ostrich chicks. Full article
(This article belongs to the Special Issue Feed Fermentation and Animal Health: Nutrition and Metabolism)
13 pages, 1889 KB  
Article
Structural Characterization of Glycoprotein Glycans and Glycosaminoglycans of Brain Tissues in Slc35a3-Knockout Mice
by Ikumi Hirose, Hisatoshi Hanamatsu, Shuji Mizumoto, Rina Yamashita, Shuhei Yamada, Jun-ichi Furukawa, Tatsuya Furuichi and Hirokazu Yagi
Int. J. Mol. Sci. 2026, 27(4), 1643; https://doi.org/10.3390/ijms27041643 - 8 Feb 2026
Viewed by 122
Abstract
Glycosylation depends on luminal nucleotide sugars delivered by solute carrier 35 (SLC35) transporters. SLC35A3 is a uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) transporter. In humans, biallelic mutations in SLC35A3 cause arthrogryposis, mental retardation, and seizures (AMRS). To define how loss of SLC35A3 function reshapes [...] Read more.
Glycosylation depends on luminal nucleotide sugars delivered by solute carrier 35 (SLC35) transporters. SLC35A3 is a uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) transporter. In humans, biallelic mutations in SLC35A3 cause arthrogryposis, mental retardation, and seizures (AMRS). To define how loss of SLC35A3 function reshapes the neural glycome, we profiled N-, O-, and glycosaminoglycans (GAGs) in Slc35a3 knockout mouse brains. N- and O-glycans were analyzed by MALDI-TOF MS, and GAG disaccharides were quantified by anion-exchange HPLC. Knockout mouse brains exhibited attenuation of complex-type N-glycans with a reciprocal rise in high-mannose species, as revealed by MALDI-TOF MS profiling. In contrast, ConA lectin blotting showed no significant change, consistent with its preferential detection of mannose-rich glycans. Branching analysis revealed loss of tri- and tetra-antennary structures compared with biantennary species. O-glycan profiling showed core-2-type species (Hex2HexNAc2 backbone) decreased. The dominant disialyl core-1 remained stable. Total GAG output (chondroitin/dermatan sulfate, heparan sulfate, and hyaluronan) was preserved. These findings support a microdomain model in which SLC35A3 acts as a locally effective supplier of UDP-GlcNAc to MGAT4 (branching N-acetylglucosaminyltransferase that installs the β1,4-GlcNAc arm) in the brain, while alternative routes buffer UDP-GlcNAc delivery for GAG and mucin-type O-glycan biosynthesis. Accordingly, AMRS may be attributed to impaired higher-order N-glycan branching in the brain. Full article
(This article belongs to the Special Issue New Research Perspectives in Protein Glycosylation)
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26 pages, 7728 KB  
Article
Onconase Induces Apoptosis in Dabrafenib-Resistant Melanoma Cell Lines Through Dysregulation of ROS Homeostasis, Antioxidant Protein Expression, and Mitochondrial Dynamics
by Carlotta Passarini, Alessia Cardile, Filippo Zuanetti, Valentina Zanrè, Raffaella Pacchiana, Adriana Celesia, Federica Danzi, Alessandra Fiore, Giovanni Gotte and Marta Menegazzi
Int. J. Mol. Sci. 2026, 27(4), 1638; https://doi.org/10.3390/ijms27041638 - 7 Feb 2026
Viewed by 95
Abstract
Advanced melanoma remains difficult to treat due to its intrinsic resistance to conventional therapies and the frequent development of acquired resistance to targeted agents, such as BRAF inhibitors. Onconase (ONC), an amphibian ribonuclease with established antitumor activity, had been previously shown to have [...] Read more.
Advanced melanoma remains difficult to treat due to its intrinsic resistance to conventional therapies and the frequent development of acquired resistance to targeted agents, such as BRAF inhibitors. Onconase (ONC), an amphibian ribonuclease with established antitumor activity, had been previously shown to have selective cytotoxicity toward melanoma cells. In this study, we investigated the molecular mechanisms underlying ONC-induced cytotoxicity in BRAF-mutated melanoma cell lines that are either sensitive or resistant to the BRAF inhibitor dabrafenib. We focused on oxidative stress regulation, mitochondrial dynamics, and cell death-related signaling pathways. ONC treatment resulted in a marked increase in reactive oxygen species (ROS) levels, concomitant with a pronounced downregulation of NRF2 and multiple NRF2-dependent antioxidant proteins. These effects were particularly evident in dabrafenib-resistant melanoma cells. In parallel, ONC impaired mitochondrial plasticity by inhibiting mitochondrial biogenesis and fission, as evidenced by reduced PGC1α, DRP1, and FIS1 expression. Confocal analysis confirmed the presence of more enlarged mitochondria in ONC-treated cells. Mitophagy and autophagy are hindered by ONC due to the downregulation of PINK1, beclin1, ATG3 expression, as well as the lack of LC3B activation. These mitochondrial defects were associated with mitochondrial-dependent apoptosis, characterized by caspase-9 activation and strong downregulation of the antiapoptotic protein survivin. Lipid peroxidation was also induced by ONC, especially in the A375 cell line. Additionally, ONC inhibited key proliferation-related signaling pathways, including STAT3 and NF-κB, and reduced cyclin-dependent kinase 1, 2, and 4 activities. Collectively, these findings demonstrate that ONC disrupts redox homeostasis, mitochondrial function, and survival signaling in melanoma cells, exerting particularly potent effects in BRAF inhibitor-resistant populations. This study provides mechanistic insight into the anti-melanoma activity of ONC and supports its potential therapeutic application in drug-resistant melanoma. Full article
(This article belongs to the Special Issue Environmental Influences on Cellular Responses)
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18 pages, 2523 KB  
Article
Modulation of Ochratoxin A-Induced Oxidative Stress and Gene Expression by Bilberries (Vaccinium myrtillus L.) in an In Vitro Intestinal Model
by Denisia Pașca, Alessandra Cimbalo, Pilar Vila-Donat, Lorena Filip, Oana Mîrza, Doina Miere, Felicia Loghin and Lara Manyes
Pharmaceuticals 2026, 19(2), 272; https://doi.org/10.3390/ph19020272 - 5 Feb 2026
Viewed by 139
Abstract
Background/Objectives: Mycotoxin contamination in grain-derived foods is still a major food safety concern; thus, innovative mitigation approaches need to be continuously developed. This study investigated the influence of bilberry (Vaccinium myrtillus L.) incorporated into a food matrix on ochratoxin A (OTA)-induced [...] Read more.
Background/Objectives: Mycotoxin contamination in grain-derived foods is still a major food safety concern; thus, innovative mitigation approaches need to be continuously developed. This study investigated the influence of bilberry (Vaccinium myrtillus L.) incorporated into a food matrix on ochratoxin A (OTA)-induced cellular responses using a dietary-relevant in vitro intestinal model. Methods: Four bread types were prepared: control (C), OTA-contaminated (OTA), bilberry-enriched (VM), and OTA + VM (OTA-VM). Simulated intestinal digests of these breads were applied to differentiated Caco-2 cells for 24 h. Apoptotic and necrotic cell populations, as well as reactive oxygen species (ROS) levels, were quantified by flow cytometry, while RT-qPCR assessed the expression of 10 genes related to mitochondrial function, oxidative stress response, and intestinal barrier integrity. Results: Exposure to OTA resulted in increased cytotoxicity, reflected by a higher proportion of necrotic cells (5.11 ± 0.35%), and elevated ROS levels compared with control cells. Co-exposure to bilberry-enriched digests was associated with attenuation of apoptotic responses, a reduced proportion of necrotic cells (2.16 ± 0.61%) and a 16% decrease in ROS levels. Gene expression profiles in the VM group were comparable to control, whereas OTA exposure led to downregulation of several genes related to oxidative stress response and intestinal barrier integrity (e.g., CLDN2, OCLN, SLC7A11). In the OTA-VM group, a partial recovery of gene expression was observed. Conclusions: These findings suggest that bilberry incorporation into a food matrix may modulate OTA-induced cellular stress responses by attenuating oxidative imbalance and supporting the expression of genes associated with antioxidant defense and epithelial barrier integrity. Bilberries may therefore represent a promising functional ingredient for influencing intestinal cellular responses to dietary mycotoxin exposure. Full article
(This article belongs to the Section Natural Products)
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20 pages, 44649 KB  
Article
Multi-Omic and Spatial Profiling Identifies an Epithelial DKK1 Associated with Microenvironmental Remodeling in Pancreatic Ductal Adenocarcinoma
by Jiajia Xu, Kaiqiang Qian, Yanyu Ding, Jianghao Cheng, Xu Zhang, Yong Huang and Bo Liu
Curr. Issues Mol. Biol. 2026, 48(2), 182; https://doi.org/10.3390/cimb48020182 - 5 Feb 2026
Viewed by 121
Abstract
Objective: This study aimed to identify clinically relevant regulators of pancreatic ductal adenocarcinoma (PDAC), a disease characterized by stromal remodeling and immune suppression, and to define their links to malignant progression and microenvironmental reprogramming. Methods: We integrated multi-cohort bulk, single-cell, and spatial transcriptomic [...] Read more.
Objective: This study aimed to identify clinically relevant regulators of pancreatic ductal adenocarcinoma (PDAC), a disease characterized by stromal remodeling and immune suppression, and to define their links to malignant progression and microenvironmental reprogramming. Methods: We integrated multi-cohort bulk, single-cell, and spatial transcriptomic datasets and subsequently validated bulk differential expression and network analyses with machine learning-based prioritization in an independent combined cohort (TCGA-PAAD plus GSE62452). Single-cell mapping was used to assess cell-type specificity, positioning candidates along inferCNV- and pseudotime-defined malignant continua. In Visium sections, a DKK1-associated program score quantified intratumoral spatial heterogeneity and informed our analyses of ligand–receptor communication. Bulk immune deconvolution linked gene levels to immune infiltration patterns, and functional assays were used to test the impact of DKK1 knockdown on migration, proliferation, clonogenic growth, and apoptosis in PDAC cells. Results: Four reproducible tumor-associated genes—DKK1, COL10A1, SULF1, and SLC24A3—were prioritized and validated externally. DKK1 was predominantly expressed by epithelial tumor cells and tracked along a malignant progression continuum. Spatially, the DKK1 program localized to epithelial-dominant regions, revealed pronounced intratumoral heterogeneity, and highlighted epithelial–endothelial and endothelial–immune signaling in high-score areas. Immune deconvolution associated higher DKK1 expression with increased myeloid infiltration and reduced cytotoxic lymphocyte signatures. Functionally, DKK1 knockdown impaired migration, proliferation, and clonogenicity while increasing apoptosis. Conclusions: We demonstrate that DKK1 is an epithelial-derived regulator linked to malignant progression and tumor–stroma–immune remodeling, supporting its potential as a biomarker and therapeutic target in PDAC treatment, including rational combinations with stroma-modulating strategies and immunotherapy. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 3rd Edition)
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20 pages, 9472 KB  
Article
Single-Cell Analysis Reveals Epithelial Heterogeneity and Tumor Microenvironment Characteristics During the Malignant Progression of Colorectal Cancer
by Qianqian Chen, Yaoqian Yuan, Shuai Tian, Jiayan Zhou, Kunming Lv and Enqiang Linghu
Biomedicines 2026, 14(2), 371; https://doi.org/10.3390/biomedicines14020371 - 5 Feb 2026
Viewed by 236
Abstract
Background/Objectives: To mine single-cell sequencing data for colorectal cancer (CRC), identify CRC epithelial cell subtypes, and explore the heterogeneity of epithelial cells and their impact on the tumor microenvironment (TME). Methods: The GSE201348 dataset, including normal, colorectal adenoma, high-grade colorectal intraepithelial neoplasia, and [...] Read more.
Background/Objectives: To mine single-cell sequencing data for colorectal cancer (CRC), identify CRC epithelial cell subtypes, and explore the heterogeneity of epithelial cells and their impact on the tumor microenvironment (TME). Methods: The GSE201348 dataset, including normal, colorectal adenoma, high-grade colorectal intraepithelial neoplasia, and CRC tumor tissue samples, was downloaded from the Gene Expression Omnibus. The Seurat package of R software was used for data quality control, data integration, normalization, and clustering. The Feature Plot and the Recode function were executed to annotate and group the epithelial cells. Finally, genetic differences, copy number variant heterogeneity, pseudotime, cell–cell communication, and Gene Set Variation Analysis (GSVA) were further conducted. Results: In total, 26,335 gene matrices from 263,872 cells were obtained for subsequent analyses. Four cell clusters, including immune cells, fibroblasts, endothelial cells, and epithelial cells, were identified. Epithelial cells were further divided into 11 subgroups characterized by MKI67, SLC27A6, PLCE1, NKD1, KCNMA1, GDA, CLCA4, BEST4, LRMP, ACTG2, and ASPM. GSVA enrichment analysis suggested a role of the “P53 pathway,” “Wnt–β-catenin signaling,” and “MYC targets V1” pathways in epithelial cells during the malignant progression of tumors. Survival analysis indicated that downregulation of KCNMA1 and upregulation of MKI67 were associated with poor prognosis. Cell–cell communication analysis suggested a bidirectional regulatory role between epithelial and fibroblast subsets. Conclusions: This study analyzed the gene expression characteristics of 11 types of epithelial cells during the malignant progression of CRC. KCNMA1+ and MKI67+ epithelial subpopulations are important indicators for the malignant progression of CRC. Full article
(This article belongs to the Special Issue Advancements in the Treatment of Colorectal Cancer)
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21 pages, 858 KB  
Review
Fueling the Fire: How Glutamine Metabolism Sustains Leukemia Growth and Resistance
by Giovannino Silvestri
BioMed 2026, 6(1), 7; https://doi.org/10.3390/biomed6010007 - 4 Feb 2026
Viewed by 299
Abstract
Glutamine metabolism has emerged as one of the most critical bioenergetic and biosynthetic programs sustaining leukemic cell growth, survival, stemness and therapeutic resistance. In both acute and chronic leukemias, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), malignant cells display a [...] Read more.
Glutamine metabolism has emerged as one of the most critical bioenergetic and biosynthetic programs sustaining leukemic cell growth, survival, stemness and therapeutic resistance. In both acute and chronic leukemias, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), malignant cells display a strong dependency on extracellular glutamine to support mitochondrial respiration, anabolic biosynthesis and redox homeostasis. This dependency is reinforced by oncogenic signaling networks, post-transcriptional metabolic regulation and microenvironmental adaptation within the bone marrow niche. Therapeutic strategies targeting glutamine utilization, including glutaminase inhibition, transporter blockade and enzymatic glutamine depletion, have demonstrated robust antileukemic activity in preclinical models, and early clinical efforts have begun to explore glutamine-directed interventions in myeloid neoplasms. However, metabolic plasticity, microenvironment-derived nutrient buffering and systemic toxicity remain significant limitations to clinical translation. This review provides a detailed synthesis of the biochemical framework of glutamine metabolism in leukemia, the molecular mechanisms enforcing glutamine addiction, the downstream functional consequences on proliferation, redox balance and leukemic stem cell biology, the current landscape of therapeutic strategies and emerging directions aimed at overcoming resistance and improving clinical efficacy. Full article
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21 pages, 1994 KB  
Article
Vitamin D Reprograms Non-Coding RNA Networks to Block Zika Virus in Human Macrophages
by Julieta M Ramírez-Mejía, Geysson Javier Fernandez and Silvio Urcuqui-Inchima
Pathophysiology 2026, 33(1), 15; https://doi.org/10.3390/pathophysiology33010015 - 3 Feb 2026
Viewed by 189
Abstract
Background: Zika virus (ZIKV), a mosquito-borne flavivirus, is associated with congenital malformations and neuroinflammatory disorders, highlighting the need to identify host factors that shape infection outcomes. Macrophages, key targets and reservoirs of ZIKV, orchestrate both antiviral and inflammatory responses. Methods: Vitamin D (VitD) [...] Read more.
Background: Zika virus (ZIKV), a mosquito-borne flavivirus, is associated with congenital malformations and neuroinflammatory disorders, highlighting the need to identify host factors that shape infection outcomes. Macrophages, key targets and reservoirs of ZIKV, orchestrate both antiviral and inflammatory responses. Methods: Vitamin D (VitD) has emerged as a potent immunomodulator that enhances macrophage antimicrobial activity and regulates inflammation. To investigate how VitD shapes macrophage responses to ZIKV, we reanalyzed publicly available RNA-seq and miRNA-seq datasets from monocyte-derived macrophages (MDMs) of four donors, differentiated with or without VitD and subsequently infected with ZIKV. Results: Differential expression analysis identified long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs integrated into competing endogenous RNA (ceRNA) networks. In VitD-conditioned and ZIKV-infected MDMs, 65 lncRNAs and 23 miRNAs were significantly modulated. Notably, lncRNAs such as HSD11B1-AS1, Lnc-FOSL2, SPIRE-AS1, and PCAT7 were predicted to regulate immune and metabolic genes, including G0S2, FOSL2, PRELID3A, and FBP1. Among the miRNAs, let-7a and miR-494 were downregulated, while miR-146a, miR-708, and miR-378 were upregulated, all of which have been previously implicated in antiviral immunity. Functional enrichment analysis revealed pathways linked to metabolism, stress responses, and cell migration. ceRNA network analysis suggested that SOX2-OT and SLC9A3-AS1 may act as molecular sponges, modulating regulatory axes relevant to immune control and viral response. Conclusions: Despite limitations in sample size and experimental validation, this study provides an exploratory map of ncRNA–mRNA networks shaped by VitD during ZIKV infection, highlighting candidate molecules and pathways for further studies on host–virus interactions and VitD-mediated immune regulation. Full article
(This article belongs to the Section Cellular and Molecular Mechanisms)
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17 pages, 4912 KB  
Article
Transcriptomic Analysis of Gene Expression Patterns in the Cecal Tissue of Liangshan Yanying Chickens and Arbor Acres (AA) Chickens Before 28 Days of Age
by Zengwen Huang, Jing Wang, Chaoyun Yang and Runjin Wang
Animals 2026, 16(3), 474; https://doi.org/10.3390/ani16030474 - 3 Feb 2026
Viewed by 249
Abstract
To dissect the molecular mechanisms underlying chicken cecal development, this study used Liangshan Yanying chickens (a local slow-growing breed) and Arbor Acres (AA) chickens (a fast-growing breed) as experimental models. Cecal tissues were collected from healthy chickens at 1, 14, and 28 days [...] Read more.
To dissect the molecular mechanisms underlying chicken cecal development, this study used Liangshan Yanying chickens (a local slow-growing breed) and Arbor Acres (AA) chickens (a fast-growing breed) as experimental models. Cecal tissues were collected from healthy chickens at 1, 14, and 28 days of age (n = 10 per breed per day of age) to measure cecal length and perform transcriptome sequencing. Through the screening of differentially expressed genes (DEGs), functional enrichment analysis, construction of protein–protein interaction (PPI) networks, and qRT-PCR validation, temporal changes in cecal development between the two breeds were systematically compared. Results showed that cecal length of both breeds increased significantly with age (p < 0.05), with significant differences between breeds. A total of 18 high-quality samples were obtained from transcriptome analysis (Q30 ≥ 93%), with a mapping efficiency of 86.2–90.5%. The number of DEGs was highest between 1 and 28 days of age (1844 DEGs in Liangshan Yanying chickens and 1747 DEGs in AA chickens), and the number of inter-breed DEGs reached 2133 at 28 days of age. A total of 70 DEGs with consistent expression trends were identified (22 upregulated and 48 downregulated), which were enriched in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways such as “B cell activation”, “peptide transport”, and “bile acid metabolism”. qRT-PCR validation indicated that the expression trends of genes (e.g., CD79B, IRF4) were highly consistent with sequencing results (R2 = 0.91). PPI network analysis suggested that SLC15A1, ACE, and ENPEP were key hub genes, forming a “transport–metabolism” synergistic module. This study reveals the temporal dynamics of chicken cecal development and the molecular basis of inter-breed differences, providing a theoretical foundation for broiler genetic improvement. Full article
(This article belongs to the Section Poultry)
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36 pages, 2193 KB  
Article
Alcohol Consumption and DNA Methylation in a Mediterranean Cohort: A Focus on Oxidative Stress and Aging Biomarkers
by Oscar Coltell, Eva M. Asensio, José V. Sorlí, Rebeca Fernández-Carrión, Carolina Ortega-Azorín, Rocío Barragán, Alejandro Perez-Fidalgo, Olga Portolés, Jose M. Ordovas and Dolores Corella
Antioxidants 2026, 15(2), 197; https://doi.org/10.3390/antiox15020197 - 2 Feb 2026
Viewed by 265
Abstract
There is considerable interest in the connection between alcohol-induced oxidative stress, DNA methylation, antioxidants, and accelerated aging across diverse populations. Nevertheless, self-reported alcohol consumption is prone to bias, and objective biomarkers of alcohol intake are needed. Our aims were to investigate the performance [...] Read more.
There is considerable interest in the connection between alcohol-induced oxidative stress, DNA methylation, antioxidants, and accelerated aging across diverse populations. Nevertheless, self-reported alcohol consumption is prone to bias, and objective biomarkers of alcohol intake are needed. Our aims were to investigate the performance of an epigenomic biomarker of alcohol consumption in a Mediterranean population using self-reported data and the biomarker gamma-glutamyl transferase (GGT); to examine the effects of alcohol (self-reported and biomarker-assessed) on epigenome-wide methylation; to analyze the association between alcohol (self-reported and biomarker-assessed) and telomere length and other aging biomarkers; and to explore the modulating effect of the Mediterranean diet (MedDiet). We performed blood epigenome-wide methylation studies (EWAS) in a Mediterranean cohort (aged 55–75 years). Self-reported alcohol consumption and MedDiet were assessed by questionnaires. A replication cohort (cohort 2) from the same area was also analyzed. For both cohorts, the DNA methylation-based biomarker (450-CpGs) was computed alongside epigenetic clocks for the following biological age acceleration metrics: DNAm telomere length, GrimAgeAcceleration, PhenoAgeAcceleration, and CausalityAgeYing (cohort 1). The association between the epigenomic biomarker and self-reported alcohol consumption was significant (p < 0.001) in both cohorts, but modest. However, the association was stronger when predicting high alcohol intake (AUC: 0.76; 95%CI: 0.65–0.86; p < 0.0001). In the EWAS, the hit (cg06690548-SLC7A11, in a cystine transporter that enhances glutathione production for antioxidant defense) was shared among the self-reported alcohol consumption, GGT, and the epigenomic biomarker, with alcohol linked to hypomethylation. We detected differential methylation in pre-selected oxidative stress-related genes. Enrichment analysis revealed “Rap1 signaling pathway” as the hit (p < 0.00001). High self-reported alcohol consumption and the epigenomic biomarker were associated with shorter telomere length (p < 0.05) in cohort 1. Additionally, a modulation by Mediterranean diet adherence was hypothesized. No significant associations were found between self-reported alcohol intake and the other aging biomarkers; however, the epigenomic score was directly associated with GrimAge, PhenoAge and CausAgeYing biomarkers in cohort 1 (p < 0.001), and two were replicated in cohort 2. In conclusion, alcohol intake has an impact on DNA methylation at the epigenome-wide level in this Mediterranean population, replicating the main hits from other populations and validating the epigenomic biomarker for intake, although improvement is needed. Moreover, several associations with aging biomarkers were observed. Full article
(This article belongs to the Special Issue Alcohol-Induced Oxidative Stress in Health and Disease, 2nd Edition)
9 pages, 221 KB  
Article
Sex- and Exercise-Dependent Modulation of Hypertrophic Remodeling by the MCT1 rs1049434 Polymorphism
by Natalia Fernández-Suárez, María Teresa Viadero, Teresa Amigo, José Antonio Benitez-Muñoz, Rocío Cupeiro and Domingo González-Lamuño
Genes 2026, 17(2), 188; https://doi.org/10.3390/genes17020188 - 2 Feb 2026
Viewed by 252
Abstract
Background: The monocarboxylate transporter 1 (MCT1) plays a central role in myocardial lactate handling and metabolic adaptation. The functional rs1049434 polymorphism (T1470A; Asp490Glu) affects MCT1-mediated lactate transport and substrate utilization, but its clinical relevance in sarcomere-related hypertrophic cardiomyopathy (HCM) remains poorly defined. Methods: [...] Read more.
Background: The monocarboxylate transporter 1 (MCT1) plays a central role in myocardial lactate handling and metabolic adaptation. The functional rs1049434 polymorphism (T1470A; Asp490Glu) affects MCT1-mediated lactate transport and substrate utilization, but its clinical relevance in sarcomere-related hypertrophic cardiomyopathy (HCM) remains poorly defined. Methods: We studied 56 carriers of pathogenic or likely pathogenic sarcomeric variants examined in a familial HCM program. All participants underwent standardized clinical phenotyping, including electrocardiography, transthoracic echocardiography, and cardiac magnetic resonance imaging. Genotyping of MCT1 rs1049434 was performed on genomic DNA. Analyses focused on sex-stratified genotype distribution, phenotypic expression among the 26 individuals who fulfilled diagnostic criteria for HCM, and the influence of habitual vigorous exercise. Septal wall thickness was the primary structural endpoint. Results: Among the 26 patients with established HCM (10 women, 16 men), a marked sex-specific effect emerged. Female carriers of the T-allele (TT/TA) exhibited significantly greater interventricular septal thickness compared with AA homozygotes (23.2 vs. 14.2 mm; p = 0.037). In men, septal thickness did not differ by genotype. However, male patients engaged in vigorous physical activity showed a consistently milder structural phenotype, including lower septal thickness (18.3 vs. 19.9 mm; p = 0.585) and directionally favorable markers of mechanical severity. Phenotypic distribution was predominantly asymmetric septal hypertrophy in both sexes, without genotype-dependent differences. Conclusions: The phenotypic impact of MCT1 rs1049434 in sarcomere-positive HCM is context-dependent. In women, impaired monocarboxylate handling is associated with greater hypertrophic remodeling, whereas in men, exercise-related metabolic conditioning appears to attenuate disease severity. These findings support a genotype–sex–environment interaction relevant to precision medicine approaches in HCM. Full article
25 pages, 7448 KB  
Article
Pterostilbene Promotes Spinal Cord Injury Recovery by Inhibiting Ferroptosis via Keap1/Nrf2/SLC7A11/GPX4 Axis Activation
by Yadan Dong, Yichen Liu, Yixuan Ji, Wen Meng, Xiaoxin Cheng and Xu Zheng
Antioxidants 2026, 15(2), 188; https://doi.org/10.3390/antiox15020188 - 2 Feb 2026
Viewed by 332
Abstract
Background: Spinal cord injury (SCI) represents a form of traumatic damage to the central nervous system, and oligodendrocytes play a central role in SCI recovery. Ferroptosis is a major factor in the pathophysiological development of SCI symptoms. Pterostilbene (Pte) has antioxidant, anti-inflammatory, and [...] Read more.
Background: Spinal cord injury (SCI) represents a form of traumatic damage to the central nervous system, and oligodendrocytes play a central role in SCI recovery. Ferroptosis is a major factor in the pathophysiological development of SCI symptoms. Pterostilbene (Pte) has antioxidant, anti-inflammatory, and neuroprotective effects. This study aims to investigate the potential role of Pte in SCI. Methods: A SCI model of rats was constructed. The BBB score assessment, the footprint test, EC staining, immunofluorescence (IF), and Western blot (WB) were conducted to observe the neuroprotective effects of Pte. The factors of ferroptosis, such as Glutathione (GSH), Malondialdehyde (MDA), Fe2+, solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4), were assessed. Then, transcriptomic data, network pharmacology, molecular docking analysis, and the erastin-induced ferroptosis model of OLN-93 cell lines were used to investigate the mechanism of inhibiting ferroptosis by Pte. Results: Pte treatment restored motor function and spinal cord tissue in SCI rats. Furthermore, Pte dramatically decreased oligodendrocyte ferroptosis. Finally, we discovered that Pte can repair SCI by blocking ferroptosis via the Keap1/Nrf2/SLC7A11/GPX4 axis. Conclusions: Pte reduces lipid peroxidation via the Keap1/Nrf2/SLC7A11/GPX4 axis, which reduces the development of ferroptosis in oligodendrocytes and improves locomotor function in rats with SCI. Full article
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