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Keywords = tissue expression analysis

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21 pages, 1878 KB  
Article
Proanthocyanidins Inhibit Neuroinflammation in High-Fat-Induced Obese Mice by Modulating Intestinal Flora and Their Metabolites
by Min Yao, Xiaotong Pang, Hailiang Wang, Cunxi Nie, Ruolin Huang, Fang Wang, Heng Zhao, Wenna Tang, Yueran Hao and Yixin Ren
Nutrients 2026, 18(3), 431; https://doi.org/10.3390/nu18030431 (registering DOI) - 28 Jan 2026
Abstract
Background/Objectives: The effect of proanthocyanidins (PAs) on neuroinflammation through the modulation of colonic microflora and their metabolites was investigated in obese mice fed a high-fat diet (HFD). Methods: Thirty healthy male C57BL/6J mice of similar body weight were randomly divided into [...] Read more.
Background/Objectives: The effect of proanthocyanidins (PAs) on neuroinflammation through the modulation of colonic microflora and their metabolites was investigated in obese mice fed a high-fat diet (HFD). Methods: Thirty healthy male C57BL/6J mice of similar body weight were randomly divided into control (CON), high-fat diet (HFD), and proanthocyanidin (PA_HFD) groups. HFD and PA_HFD groups were fed an HFD, whereas the CON group was fed a basic diet for 8 weeks. Subsequently, the CON and HFD groups were administered equal doses of saline, and the PA_HFD group was administered PA (100 mg/kg/day) daily. We evaluated microbial changes through gut microbiota richness and probiotic relative abundance, analyzed metabolite variations via non-targeted metabolomics and pathway enrichment, assessed neuroinflammation via related gene expression, and measured cognitive function using platform crossing frequency and target quadrant time in the Morris water maze, where longer duration and more crossings indicate better cognition. Results: Body weight was significantly lower in the PA_HFD group than in the HFD group. In the PA_HFD group, fewer inflammatory and hepatic fat cells were observed, and hepatocellular edema was alleviated. PA significantly decreased total cholesterol, low-density lipoprotein, IL-1β, TNF-α, lipopolysaccharide, and Lc3 expression and increased Sirt1 and FGF21 expression in hippocampal tissue (p < 0.01). PA significantly altered the abundance of colonic microbiota (p < 0.01), including phyla Patescibacteria and Bacteroidota and genera Lactobacillus and Akkermansia. KEGG analysis revealed that differences in metabolite profiles between CON and HFD groups were reflected in glycerophospholipid metabolism, while those between HFD and PA_HFD groups were in steroid hormone biosynthesis and tryptophan metabolism. Metabolomic analysis demonstrated that changes in metabolites and microbiota were significantly correlated with neuroinflammation. Conclusions: In conclusion, PAs play a role in modulating neuroinflammation, colonic microflora, and colonic metabolites in mice and have a mitigating effect on cognitive decline in HFD-induced obese mice. Full article
(This article belongs to the Section Nutrition and Obesity)
17 pages, 4617 KB  
Article
Integrated mRNA-miRNA Analysis Reveals the Regulatory Network Under Salt–Alkali Stress in Alfalfa (Medicago sativa L.)
by Mengya Liu, Yanran Xu, Lijun Zhao, Haojie Yu, Lijun Shi, Wenxuan Zhu, Bai Du, Xiao Li and Ruicai Long
Agriculture 2026, 16(3), 323; https://doi.org/10.3390/agriculture16030323 (registering DOI) - 28 Jan 2026
Abstract
Soil salinization and alkalinization critically constrain alfalfa (Medicago sativa L.) productivity, yet the regulatory mechanisms underlying its responses to salt–alkali stress are not fully understood. In this study, the alfalfa variety “Zhongmu No. 1” was used as experimental material. The seeds were [...] Read more.
Soil salinization and alkalinization critically constrain alfalfa (Medicago sativa L.) productivity, yet the regulatory mechanisms underlying its responses to salt–alkali stress are not fully understood. In this study, the alfalfa variety “Zhongmu No. 1” was used as experimental material. The seeds were subjected to salt stress (75 mM NaCl), alkali stress (15 mM NaHCO3), and combined salt–alkali stress (50 mM NaCl + 5 mM NaHCO3) in dishes, with ddH2O serving as the control (CK). After 7 days of germination, the seedlings were transferred to a hydroponic system containing Hoagland nutrient solution supplemented with the corresponding treatments. Following 32 days of stress exposure, leaf and root tissue samples were collected for morphological and physiological measurements, as well as mRNA and miRNA sequencing analyses. Physiological assays revealed significant growth inhibition and increased electrolyte leakage under stress conditions. Transcriptome profiling identified over 5000 common differentially expressed genes (DEGs) in both leaves and roots under stress conditions, mainly enriched in pathways related to “iron ion binding”, “flavonoid biosynthesis”, “MAPK signaling”, and “alpha-Linolenic acid metabolism”. MiRNA sequencing detected 453 miRNAs, including 188 novel candidates, with several differentially expressed miRNAs (DEMs) exhibiting tissue- and stress-specific patterns. Integrated analysis revealed 147, 81, and 140 negatively correlated miRNA–mRNA pairs across three treatment groups, highlighting key regulatory modules in hormone signaling and metabolic pathways. Notably, in the ethylene and abscisic acid signaling pathways, ERF (XLOC_006645) and PP2C (MsG0180000476.01) were found to be regulated by miR5255 and miR172c, respectively, suggesting a post-transcriptional layer of hormonal control. DEM target genes enrichment pathway analyses also identified stress-specific regulation of “Fatty acid degradation”, “Galactose metabolism”, and “Fructose and mannose metabolism”. qRT-PCR validation confirmed the expression trends of selected DEGs and DEMs. Collectively, these findings reveal the complexity of miRNA–mRNA regulatory networks in alfalfa’s response to salt–alkali stress and provide candidate regulators for breeding stress-resilient cultivars. Full article
(This article belongs to the Special Issue Forage Breeding and Cultivation—2nd Edition)
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23 pages, 7598 KB  
Article
Molecular Remodeling of Peritumoral Tissue in Clear Cell Renal Cell Carcinoma: Insights into Inflammaging and Prognostic Markers
by Giuseppe Stefano Netti, Federica Spadaccino, Giuseppe Lucarelli, Valeria Catalano, Andrea Checchia, Alessandra Stasi, Federica De Luca, Valentina Camporeale, Giorgia Leccese, Roberto Cuttano, Dario Troise, Barbara Infante, Giuseppe Carrieri, Walter J. Storkus, Giovanni Stallone and Elena Ranieri
Cancers 2026, 18(3), 414; https://doi.org/10.3390/cancers18030414 (registering DOI) - 28 Jan 2026
Abstract
Background/Objectives: Renal cell carcinoma (RCC) is a common and often asymptomatic malignancy with limited treatment options for advanced stages. Chronic inflammation and cellular senescence—collectively termed “inflammaging”—are emerging as key contributors to tumor progression. This study aimed to investigate the expression of inflammaging-related [...] Read more.
Background/Objectives: Renal cell carcinoma (RCC) is a common and often asymptomatic malignancy with limited treatment options for advanced stages. Chronic inflammation and cellular senescence—collectively termed “inflammaging”—are emerging as key contributors to tumor progression. This study aimed to investigate the expression of inflammaging-related markers in RCC tissues, focusing on the role of PTX3, IL-6, and senescence-associated proteins in the tumor microenvironment. Methods: A retrospective cohort of 57 patients with clear cell RCC who underwent nephrectomy was analyzed. Formalin-fixed paraffin-embedded samples from tumor, peritumoral, and normal renal tissues were examined using confocal immunofluorescence microscopy to assess PTX3, IL-6, p21, and p16 expression. Senescence-associated β-galactosidase staining was performed to identify senescent cells. Serum IL-6 levels were measured by ELISA, and survival analysis was conducted using Kaplan–Meier curves and Cox regression analysis. Results: PTX3 and IL-6 were significantly upregulated in both peritumoral and tumor tissues compared to normal kidney samples (p < 0.001). Expression of senescence markers p21 and p16 were elevated in peritumoral areas (p < 0.001) as compared to normal renal tissues, but their expression was reduced or absent in the tumor core. High-grade and high-stage tumors exhibited stronger PTX3 and IL-6 expression and lower levels of cell cycle inhibitors (p < 0.001). Patients with elevated serum IL-6 levels had significantly lower 5-year cancer-specific survival (p < 0.005) and shorter progression-free survival (p < 0.001). Conclusions: Our findings suggest that peritumoral tissue in RCC exhibits a senescent and proinflammatory phenotype that may support tumor progression. PTX3 and IL-6 are potential biomarkers of disease severity and prognosis. Targeting inflammaging pathways could offer new therapeutic strategies for RCC, particularly in aggressive disease forms. Full article
(This article belongs to the Section Cancer Immunology and Immunotherapy)
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15 pages, 3084 KB  
Article
Widely Targeted Liver Metabolomics Reveals Potential Biomarkers in Mice with Drug-Induced Liver Injury
by Jiangning Peng, Tingting Zhao, Xuehong Zhang, Hong Wang, Hui Li and Yan Liang
Metabolites 2026, 16(2), 96; https://doi.org/10.3390/metabo16020096 - 28 Jan 2026
Abstract
Background: Drug-induced liver injury (DILI), a major type of adverse drug reaction, has become one of the leading causes of acute liver injury and liver failure worldwide. Its clinical significance lies not only in acute hepatocyte necrosis and functional failure but also in [...] Read more.
Background: Drug-induced liver injury (DILI), a major type of adverse drug reaction, has become one of the leading causes of acute liver injury and liver failure worldwide. Its clinical significance lies not only in acute hepatocyte necrosis and functional failure but also in its role as a key initiating factor for liver cancer progression. Therefore, early diagnosis of DILI is of great importance. Methods: This study employed ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) to perform widely targeted metabolomics analysis on acetaminophen (APAP)-induced liver injury mice and healthy mice. Results: UPLC-QTRAP-MS/MS identified 41 differentially expressed metabolites primarily involved in glycerophospholipid metabolism, arginine and proline metabolism, primary bile acid biosynthesis, and glutathione metabolism pathways. The significant elevation of serum and hepatic alanine aminotransferase (ALT) and aspartate aminotransferase (AST) confirmed the successful establishment of the drug-induced liver injury (DILI) model. ROC curve analysis indicated 11 metabolites with AUC values exceeding 0.90 as potential biomarkers, including (R)-2-Hydroxybutyric acid, Glu-Gln, γ-Glu-Gln, 2-Methyllactic acid, L-Serine, Hyodeoxycholic acid, 3-Epideoxycholic acid, and Glycochenodeoxycholic acid 7-sulfate. Conclusions: We propose that these differential metabolites may serve as candidate biomarkers for DILI. Our findings provide a novel metabolomic signature derived directly from the injured tissue and offer a theoretical foundation for further research into early diagnosis of drug-induced liver injury. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
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22 pages, 1738 KB  
Article
Tissue-Specific Multi-Omics Integration Demonstrates Molecular Signatures Connecting Obesity to Immune Vulnerability
by Ozge Onluturk Aydogan, Aytac Dursun Oksuzoglu and Beste Turanli
Metabolites 2026, 16(2), 95; https://doi.org/10.3390/metabo16020095 (registering DOI) - 27 Jan 2026
Abstract
Background: Adipose tissue surrounds organs and tissues in the body and can alter their function. It could secrete diverse biological molecules, including lipids, cytokines, hormones, and metabolites. In light of all this information, obesity can influence many tissues and organs in the body, [...] Read more.
Background: Adipose tissue surrounds organs and tissues in the body and can alter their function. It could secrete diverse biological molecules, including lipids, cytokines, hormones, and metabolites. In light of all this information, obesity can influence many tissues and organs in the body, and this situation makes obesity a central contributor to multiple disorders. It is very important to investigate the crosstalk between tissues and organs in the body to clarify the key mechanisms of obesity. Methods: In this study, we analyzed the gene expression profiles of the liver, skeletal muscle, blood, visceral, and subcutaneous adipose tissue. Differentially expressed genes (DEGs) were identified for each tissue, and functional enrichment and protein–protein interaction network analyses were performed on genes commonly identified across tissues. Priority candidate genes were identified using network-based centrality measures, and potential molecular intersection points were explored through host-pathogen interaction network analysis. This study provides an integrative framework for characterizing inter-tissue molecular patterns associated with obesity at the network level. Results: The muscle, subcutaneous adipose tissue, and blood have the highest number of DEGs. The subcutaneous adipose tissue and blood stand out due to the number of DEGs they possess, although liver and visceral adipose tissue have lower amounts. Cancer ranks first in terms of diseases associated with obesity, and this association is accompanied by leukemia, lymphoma, and gastric cancer. RPL15 and RBM39 are the top genes in both degree and betweenness metrics. The host–pathogen interaction network consists of 13 unique-host proteins, 54 unique-pathogen proteins, and 27 unique-pathogen organisms, and the Influenza A virus had the highest interaction. There were a small number of common metabolites in all tissues: 2-Oxoglutarate, Adenosine, Succinate, and D-mannose. Conclusions: In this study, we aimed to identify candidate molecules for obesity using an integrative approach, examining the gene profiles of different organs and tissues. The findings of this study suggest a possible link between obesity and immune-related biological processes. The network obtained from the host-pathogen interaction analysis, and especially the pathways associated with viral infections that stand out in the functional enrichment analysis, may overlap with molecular signatures linked to obesity. Furthermore, the co-occurrence of cytokine signaling, insulin, and glucose metabolism pathways in the enrichment results indicates that the response of cells to insulin may be affected in obese individuals, suggesting a potential interaction between immune and metabolic processes; however, further experimental validation is needed to reveal the direct functional effects of these relationships. Full article
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23 pages, 3163 KB  
Article
Cross-Species Upregulation of MAGED2 in Liver Cancer Suggests a Role in Obesity-Driven Tumor Progression
by Tara Bayat, Farzana Yeasmin Popy, Rebecca R. Florke Gee, Benjamin Barr, Yusuff Olayiwola, Juan Sebastian Solano Gutierrez, Denis Štepihar, Jorge Diaz-Riaño, Stephanie Myers, Kaja Blagotinšek Cokan, Damjana Rozman, Lauren Gollahon and Klementina Fon Tacer
Curr. Issues Mol. Biol. 2026, 48(2), 139; https://doi.org/10.3390/cimb48020139 - 27 Jan 2026
Abstract
Melanoma-associated antigens (MAGEs) are cancer-testis antigens (CTAs) aberrantly expressed in multiple cancer types, including hepatocellular carcinoma (HCC), and associated with aggressive phenotypes. Although MAGE proteins are widely studied as cancer immunotherapy targets, their roles in HCC and the regulation of their expression during [...] Read more.
Melanoma-associated antigens (MAGEs) are cancer-testis antigens (CTAs) aberrantly expressed in multiple cancer types, including hepatocellular carcinoma (HCC), and associated with aggressive phenotypes. Although MAGE proteins are widely studied as cancer immunotherapy targets, their roles in HCC and the regulation of their expression during liver pathogenesis in mouse models, including dietary effects, remain poorly understood. We analyzed Mage gene expression in liver tissues from 78 C3H/HeJ mice with chronic diet-induced obesity. While type I MAGE genes are frequently expressed in human HCC, we found no evidence of their expression in mouse liver tumors, suggesting species-specific regulation. In contrast, type II Maged2, previously reported to be upregulated in human HCC, was significantly increased in mouse liver tumors. Analysis of human HCC samples from The Cancer Genome Atlas (TCGA) database confirmed MAGED2 upregulation and its association with patient prognosis. Together, these findings identify MAGED2 as a conserved marker of liver cancer in both humans and mice and emphasize the importance of cross-species comparative approaches for selecting appropriate models and accurately interpreting results, particularly for CTAs, which often evolved recently and in a species-specific manner. Full article
(This article belongs to the Section Molecular Medicine)
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19 pages, 2360 KB  
Article
High Frequency Loss of 17q11.2 and Downregulation of the Cancer Metastasis Suppression microRNA miR-193a-3p in Prostate Cancer Bone Metastasis
by Elzbieta Stankiewicz, Sarah C. McCarley, Xueying Mao, Sakunthala Kudahetti, Tim Oliver, Jonathan Shamash, Trevor Graham, Daniel M. Berney and Yong-Jie Lu
Cancers 2026, 18(3), 403; https://doi.org/10.3390/cancers18030403 - 27 Jan 2026
Abstract
Background/Objectives: Although 90% of prostate cancer (PCa) metastasis occurs in the bone, there are limited studies and rarely available genome-wide profiles at individual sample level for genomic copy number changes in the literature. Methods: We performed Affymetrix SNP 6.0 high-density microarray analysis [...] Read more.
Background/Objectives: Although 90% of prostate cancer (PCa) metastasis occurs in the bone, there are limited studies and rarely available genome-wide profiles at individual sample level for genomic copy number changes in the literature. Methods: We performed Affymetrix SNP 6.0 high-density microarray analysis to generate the genome-wide copy number change profiles for six cases of PCa bone metastases. A common genomic loss was confirmed by fluorescence in situ hybridization (FISH) in paraffin-embedded PCa bone metastasis samples together with primary PCa and benign prostate hyperplasia samples. We overexpressed the candidate miRNA in PCa cell lines and knocked down its target genes by siRNA transfection and investigated the effect on protein expression and cell viability, migration, and invasion abilities, respectively. Protein expression in PCa tissues was analyzed by immunohistochemical staining. Results: We provided high-resolution PCa bone metastasis profiles of six cases and identified potential bone metastasis-specific common genomic alterations, including a 1.6 mb region on 17q11.2, as well as those shared by non-bone metastatic PCa. The common 17q11.2 loss was confirmed by FISH in further 14/21 PCa bone metastasis samples but was only found in 9/151 primary PCa samples. The well-established tumor-suppressing miRNA located within this small genomic region, miR-193a-3p, was downregulated in both bone metastasis and primary PCa cases, leading to overexpression of cyclin D1 and uPA to promote cancer cell migration and invasion. Cyclin D1 was highly expressed in both localized PCa and bone metastasis samples, and the expression was significantly higher in the latter group (p = 0.013). Conclusions: We generated high-resolution copy number change profiles for bone metastasis samples. This led to the identification of a common, small genomic loss and downregulation of miR-193a-3p, which suppresses PCa bone metastasis through inhibition of its target proteins, providing new insight into bone metastasis development. Full article
22 pages, 33045 KB  
Article
Pan-Genome Analysis and Expression Profiling of HIPP Gene Family in Cassava
by Zhanming Xia, Jiazheng Zhao, Changyi Wang, Shuwen Wu, Yuwei Zang, Dayong Wang, Shousong Zhu and Yi Min
Genes 2026, 17(2), 136; https://doi.org/10.3390/genes17020136 - 27 Jan 2026
Abstract
Background: Cassava (Manihot esculenta Crantz) ranks as the sixth largest food crop worldwide and serves as an important cash and energy crop. Heavy-metal-associated isoprenylated plant proteins (HIPPs) are metallochaperones involved in metal homeostasis and stress adaptation in vascular plants. However, research on [...] Read more.
Background: Cassava (Manihot esculenta Crantz) ranks as the sixth largest food crop worldwide and serves as an important cash and energy crop. Heavy-metal-associated isoprenylated plant proteins (HIPPs) are metallochaperones involved in metal homeostasis and stress adaptation in vascular plants. However, research on the identification and function of HIPPs in cassava has been poorly explored. Methods: This study conducted a pan-genome-wide investigation to identify and characterize MeHIPPs in 31 cassava accessions. Subsequent analyses examined their physicochemical properties, subcellular localization, phylogeny, Ka/Ks, chromosomal localization, synteny, gene structure, and cis-acting elements. Additionally, the expression profiles of MeHIPPs in different tissues and cell subsets and under different stress conditions were analyzed using transcriptome data and quantitative real-time polymerase chain reaction (qRT-PCR). Results: A total of 59 MeHIPP pan-genes were identified, including five core genes, 22 softcore genes, 17 dispensable genes, and 15 private genes, which were unevenly distributed on chromosomes. Based on phylogenetic analysis, these genes were classified into five major subgroups. Evolutionary analyses indicated that segmental duplication predominated in family expansion and that most members may be subjected to purifying selection. Cis-element analysis highlighted the importance of MeHIPPs in plant adaptation to environmental stress. The expression profiles suggested widespread involvement of MeHIPP genes in response to Xanthomonas phaseoli pv. manihotis (Xpm) infection and drought stress. Different MeHIPP genes exhibited varying transcript levels in different tissues and cell subsets. qRT-PCR analysis revealed that the selected MeHIPP genes had distinct expression patterns under Cd stress. Conclusions: This study provides valuable insights into the functional characteristics of MeHIPP genes and their evolutionary relationships, laying a theoretical foundation for further functional research on stress resistance. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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23 pages, 4189 KB  
Article
Comparative Effects of Cellulose- and Gelatin-Based Hemostatic Biomaterials on the Early Stage of Wound Healing—An In Vivo Study
by Helena Hae In Ströthoff, Polina Shabes, Katharina Henrika Beckamp, Markus Udo Wagenhäuser, Wiebke Ibing, Julian-Dario Rembe, Hubert Schelzig and Waseem Garabet
J. Funct. Biomater. 2026, 17(2), 64; https://doi.org/10.3390/jfb17020064 - 27 Jan 2026
Abstract
Hemostatic biomaterials are widely used in surgical and trauma settings, yet their influence on early wound healing remains incompletely understood. This in vivo study investigated the effects of cellulose- and gelatin-based hemostatic biomaterials on early wound healing using a murine skin wound model. [...] Read more.
Hemostatic biomaterials are widely used in surgical and trauma settings, yet their influence on early wound healing remains incompletely understood. This in vivo study investigated the effects of cellulose- and gelatin-based hemostatic biomaterials on early wound healing using a murine skin wound model. Oxidized non-regenerated cellulose (ONRC), oxidized regenerated cellulose (ORC), and a porcine gelatin-based matrix (GELA) were left in situ following standardized subcutaneous implantation and compared with sham-treated controls. Tissue responses were analyzed at postoperative days 3 and 7 using histology, immunohistochemistry, and quantitative real-time polymerase chain reaction (qPCR). Cellulose-based materials persisted as eosinophilic remnants, whereas fibrous matrix structures and enhanced extracellular matrix deposition were observed in the GELA group. Immunohistochemical analysis revealed increased cluster of differentiation 68 (CD68)–positive macrophage presence in the ORC group at day 3 and in the GELA group at day 7, indicating biomaterial-dependent modulation of macrophage involvement during early wound healing. Expression of Kiel 67 (Ki-67), a marker of cellular proliferation, was significantly elevated in the epidermis of the GELA group at day 7, suggesting enhanced proliferative activity during the reparative phase. In contrast, no significant differences were detected in the expression of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), or cluster of differentiation 14 (CD14) between groups. Overall, none of the investigated biomaterials impaired early wound healing, while the gelatin-based material demonstrated features consistent with enhanced reparative cellular responses without excessive inflammation. Full article
(This article belongs to the Special Issue Biomaterials for Hemostasis and Wound Healing Applications)
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16 pages, 3779 KB  
Article
The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits
by Die Tang, Shuangshuang Chen, Chuang Tang, Xiangyu Li, Mingzhou Li, Xuewei Li, Kai Zhang and Jideng Ma
Animals 2026, 16(3), 390; https://doi.org/10.3390/ani16030390 - 26 Jan 2026
Abstract
This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially [...] Read more.
This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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20 pages, 779 KB  
Review
Does the B7-H3 Immune Checkpoint Have High Potential as a Therapeutic Target?
by Marco Agostini, Pietro Traldi and Mahmoud Hamdan
Cells 2026, 15(3), 239; https://doi.org/10.3390/cells15030239 - 26 Jan 2026
Abstract
B7-H3 (CD276), a member of the B7 family of proteins, is known to play a key role in the progression of a number of cancers. This protein is selectively expressed in both tumor cells and immune cells within the tumor microenvironment. Various investigations, [...] Read more.
B7-H3 (CD276), a member of the B7 family of proteins, is known to play a key role in the progression of a number of cancers. This protein is selectively expressed in both tumor cells and immune cells within the tumor microenvironment. Various investigations, including a number of clinical trials, have reported high levels of expression of this protein in cancerous tissues compared to their healthy counterparts. This difference in expression attracted various research efforts to establish whether such a difference can be linked to the therapeutic potential of this molecule. It is worth noting that B7-H3 is not the only immune checkpoint expressed at different levels in cancerous and healthy cells. Therapeutic strategies, based on different levels of expression, have been tested with other checkpoints. To inhibit the expression of some checkpoints, immune checkpoint inhibitors (ICIs) were developed. The introduction of these inhibitors for the treatment of some forms of advanced-stage tumors has been justly described as an important milestone in the landscape of immune therapy. Years after the launch of these inhibitors, numerous clinical trials revealed that these inhibitors benefit a narrow subset of patients suffering from advanced-stage tumors, while the majority of patients treated with these inhibitors either did not respond positively or simply did not respond at all (refractory patients). Other clinical trials showed that this form of treatment can provoke serious immune-related adverse events (irAEs). It is fair to state that changes in the expression level of a given protein in diseased tissue is an important parameter to take into account in the assessment of such a protein as a therapeutic target. However, the last ten years have demonstrated that taking the level of expression of a given checkpoint within a cancerous tissue is not sufficient to consider such expression a reliable predictive biomarker for the investigated disease. On the other hand, to establish a solid base for a given therapeutic strategy, these varying levels of expression have to be combined with a deep understanding of the biology of the molecule under investigation, as well as the identification and thorough analysis of the relevant signaling pathways, particularly those communicating with both the investigated molecule and the immune system. Recently, a number of pharmaceutical and biotechnology firms have suggested that B7-H3 is a highly promising therapeutic target for the development of immune therapeutics. In this review, we ask why hopes of better therapeutic performance are attached to this immune checkpoint. A partial answer to this question is provided through the careful consideration of the available data generated by various clinical trials. The contribution of mass spectrometry-based proteomics to this area of research is highlighted. Full article
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24 pages, 10948 KB  
Article
Genome-Wide Characterization of the wnt Gene Family Reveals a wnt5b-Mediated Regulatory Mechanism of Testicular Development in Cynoglossus semilaevis
by Zhengjie Li, Junhao Wang, Chao Li and Ying Zhu
Animals 2026, 16(3), 387; https://doi.org/10.3390/ani16030387 - 26 Jan 2026
Abstract
The wnt gene family encodes a group of highly conserved secreted glycoproteins that play essential roles in vertebrate development, including tissue patterning, cell differentiation, and gonadal regulation. However, the genomic organization, evolutionary dynamics, and functional roles of Wnt signaling components in flatfish remain [...] Read more.
The wnt gene family encodes a group of highly conserved secreted glycoproteins that play essential roles in vertebrate development, including tissue patterning, cell differentiation, and gonadal regulation. However, the genomic organization, evolutionary dynamics, and functional roles of Wnt signaling components in flatfish remain poorly understood. In this study, we performed a comprehensive genome-wide identification, evolutionary characterization, expression profiling, and functional analysis of wnt genes in Cynoglossus semilaevis, a flatfish species exhibiting ZW/ZZ sex determination and temperature-induced sex reversal. A total of 20 wnt genes were identified and classified into 13 subfamilies, displaying conserved structural organization and phylogenetic relationships consistent with other teleosts. Chromosomal mapping revealed lineage-specific WNT clusters, including a unique wnt3–wnt7b–wnt5b–wnt16 block, as well as syntenic associations with reproduction-related genes (e.g., adipor2, sema3a, nape-pld, erc2, lamb2), suggesting coordinated genomic regulation. Tissue transcriptome analysis demonstrated strong sex- and tissue-biased expression patterns, with wnt5a predominantly expressed in ovaries and wnt5b specifically upregulated in pseudo-male testes. Functional assays revealed that knockdown of wnt5a or wnt5b induced testis-specific genes (sox9b, tesk1) and suppressed ovarian markers (foxl2, cyp19a1a), indicating antagonistic regulatory roles in gonadal fate determination. Promoter analysis identified yy1a as a selective repressor of wnt5b, but not wnt5a, providing a mechanistic basis for paralog divergence. Furthermore, pull-down combined with LC–MS/MS analysis showed that WNT5b interacts with proteins enriched in ribosome biogenesis and ubiquitin-mediated proteolysis, suggesting a role in translational regulation and protein turnover during spermatogenesis. Together, these findings establish WNT5 signaling—particularly wnt5b—as a key driver of testicular development in C. semilaevis and provide new insights into the molecular mechanisms underlying sex differentiation and sex reversal in flatfish. Full article
(This article belongs to the Special Issue Sustainable Aquaculture: A Functional Genomic Perspective)
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19 pages, 2602 KB  
Article
Laser-Enhanced Biomorphic Scaffolds Support Multipotent Stem Cell Differentiation and Angiogenesis for Vascularised Bone Regeneration
by Sandeep Kumar, Neelam Iqbal, Yahui Pan, Evangelos Daskalakis, Heather Elizabeth Owston, El Mostafa Raif, Payal Ganguly, Sarathkumar Loganathan, Peter V. Giannoudis and Animesh Jha
J. Funct. Biomater. 2026, 17(2), 62; https://doi.org/10.3390/jfb17020062 - 26 Jan 2026
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Abstract
Biomorphic hydroxyapatite scaffolds derived from rattan wood (GreenBone) show significant promise in bone tissue engineering due to their inherent structural similarity to natural bone. Laser-drilled GreenBone scaffolds were studied for enhanced porosity, nutrient diffusion, cellular infiltration, and vascularisation. Patient-derived bone marrow mesenchymal stromal/stem [...] Read more.
Biomorphic hydroxyapatite scaffolds derived from rattan wood (GreenBone) show significant promise in bone tissue engineering due to their inherent structural similarity to natural bone. Laser-drilled GreenBone scaffolds were studied for enhanced porosity, nutrient diffusion, cellular infiltration, and vascularisation. Patient-derived bone marrow mesenchymal stromal/stem cells (BMMSCs) and culture-expanded mesenchymal stem cells (cMSCs) demonstrated high cell viability (>90%), considerable adhesion, and extensive cytoskeletal organisation. Trilineage differentiation confirmed the multipotency of BMMSCs, with osteogenic, adipogenic, and chondrogenic markers being successfully expressed. BMMSCs and cMSCs exhibited enhanced differentiation and gene expression profiles. At week 4, key osteogenic and angiogenic genes such as BMP2, VEGFC, RUNX2, and COL1A1 showed elevated expression, indicating improved bone formation and vascularisation activity. Markers associated with extracellular matrix (ECM) remodelling, including MMP9 and TIMP1, were also upregulated, suggesting active tissue remodelling. ELISA analysis for VEGF further demonstrated increased VEGF secretion, highlighting the scaffold’s angiogenic potential. The improved cellular response and vascular signalling emphasise the translational relevance of laser-modified GreenBone scaffolds for bone tissue engineering, particularly for critical-sized defect repair requiring rapid vascularised bone regeneration. Full article
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23 pages, 1713 KB  
Article
Evaluation of Germplasm Resistance in Several Soybean Accessions Against Soybean Fusarium Root Rot in Harbin, Heilongjiang Province, China
by Xue Qu, Sobhi F. Lamlom, Guangqing Ren, Yuxin Sang, Honglei Ren, Yang Wang and Runnan Zhou
Plants 2026, 15(3), 379; https://doi.org/10.3390/plants15030379 - 26 Jan 2026
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Abstract
Soybean root rot, caused by diverse soil-borne pathogens, is a major constraint on production worldwide, with yield losses ranging from 10 to 60% under epidemic conditions. Symptomatic plants were collected from three locations in Harbin, Heilongjiang Province, China, and 23 fungal isolates were [...] Read more.
Soybean root rot, caused by diverse soil-borne pathogens, is a major constraint on production worldwide, with yield losses ranging from 10 to 60% under epidemic conditions. Symptomatic plants were collected from three locations in Harbin, Heilongjiang Province, China, and 23 fungal isolates were recovered using standard tissue isolation procedures. Integrated morphological characterization and rDNA-ITS sequencing identified these isolates as three Fusarium species: F. oxysporum (18 isolates, 78%), F. equiseti (3 isolates, 13%), and F. brachygibbosum (2 isolates, 9%). Pathogenicity assays following Koch’s postulates confirmed F. oxysporum as the predominant and most aggressive pathogen in this region. To identify resistance resources, 200 soybean germplasm accessions adapted to Northeast China were screened using an etiolated seedling hypocotyl inoculation method with Fusarium oxysporum isolate A3 (DSI = 68.5) as the test pathogen. Disease severity indices exhibited a continuous distribution (mean = 52.84, range = 0–100), suggesting quantitative inheritance. Accessions were classified as highly resistant (13, 6.5%), resistant (40, 20%), moderately susceptible (67, 33.5%), susceptible (43, 21.5%), or highly susceptible (37, 18.5%). To explore potential molecular mechanisms underlying resistance, RT-qPCR analysis was performed on two extreme genotypes—a highly resistant line (H9477F5, DSI = 15.3) and a highly susceptible line (HN91, DSI = 88.7) at 1, 3, and 5 days post-inoculation. The resistant line maintained consistently higher expression of positive regulators GmFER and GmSOD1, with GmFER reaching 15.89-fold induction at day 3. Conversely, expression of negative regulators GmJAZ1 and GmTAP1 remained lower in the resistant line, with susceptible plants showing 5.62-fold higher GmJAZ1 expression at day 3. These findings provide characterized pathogen isolates, resistant germplasm resources (53 accessions with HR or R classifications), and preliminary molecular insights that may inform breeding strategies for improving root rot resistance in Northeast China. Full article
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19 pages, 3252 KB  
Article
Lactiplantibacillus plantarum GUANKE Enhances Antiviral Defense Against Respiratory Syncytial Virus Through the STING-TBK1-IRF3-IFN Pathway
by Kun Yue, Simin Lu, Hanyu Ma, Jielan Mi, Qianjin Fan, Tao Yang, Yuanming Huang, Liqiong Song, Zhihong Ren, Lili Ren and Jianguo Xu
Nutrients 2026, 18(3), 399; https://doi.org/10.3390/nu18030399 - 26 Jan 2026
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Abstract
Background/Objectives: To investigate the antagonistic effect of probiotic Lactiplantibacillus plantarum GUANKE against respiratory syncytial virus (RSV) and its underlying molecular mechanisms. Methods: in vitro cell models (A549 and HEp2 cells) and an in vivo mouse model (BALB/c mice) were employed. RT-qPCR, TCID50 assay, [...] Read more.
Background/Objectives: To investigate the antagonistic effect of probiotic Lactiplantibacillus plantarum GUANKE against respiratory syncytial virus (RSV) and its underlying molecular mechanisms. Methods: in vitro cell models (A549 and HEp2 cells) and an in vivo mouse model (BALB/c mice) were employed. RT-qPCR, TCID50 assay, immunofluorescence, ELISA, Western blot, and histopathological analysis were used to investigate the effects of GUANKE on RSV replication, inflammatory responses, and the type I interferon pathway. Results: Oral administration of GUANKE effectively cleared RSV and alleviated RSV-induced pulmonary inflammatory responses. GUANKE inhibited viral replication. The GUANKE intervention group exhibited significantly reduced pathological damage to lung tissue and decreased the expression of inflammatory cytokines (IL-1β, IL-6, MCP-1, TNF-α). GUANKE augmented the early type I interferon response and activated the STING-TBK1-IRF3-IFN signaling pathway. Conclusions: GUANKE exerts anti-RSV effects by enhancing the early type I interferon response and activating the STING-TBK1-IRF3-IFN signaling pathway, thereby inhibiting RSV replication and alleviating pulmonary inflammatory responses. This suggests its potential value as an anti-RSV agent. Full article
(This article belongs to the Section Prebiotics, Probiotics and Postbiotics)
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